Information

What is an apomorphy? What is a plesiomorphy? Can someone confirm these definitions?

What is an apomorphy? What is a plesiomorphy? Can someone confirm these definitions?


We are searching data for your request:

Forums and discussions:
Manuals and reference books:
Data from registers:
Wait the end of the search in all databases.
Upon completion, a link will appear to access the found materials.

I want to know the correct definitions for the terms apomorphy and plesiomorphy. Unfortunately, there seems to be a variety of ways to define these terms depending on the language one uses. Thus, it has been hard to determine the correct definitions. I have settled on definitions that seem correct to me and also have examples. I would like confirmation from someone if I am understanding the definitions correctly.

  • Apomorphy -- any character state or trait novel to a species and its descendants. An apomorphy occurs when a taxon is selected to have a particular trait. Example: within the class reptilia, the suborder serpentes (snakes) has an apomorphy because its members have no legs.
  • Plesiomorphy -- an evolutionary trait or character state that is homologous within a particular taxon but is not unique to members of that group and therefore cannot be used as a diagnostic character for the group. Example: within the class reptilia, legs are a plesiomorphy for its members.

My Question:

Are these definitions and examples accurate?


That sounds pretty good. On this kind of things wikipaedia is very reliable. You can also look at this very synthetic page:

https://www.enotes.com/homework-help/distinguish-between-synapomorphy-apomorphy-304128


Apomorphy can simply be defined as derived trait or character state that is distinct to a particular species or group in a phylogenetic tree down to its descendants. The example you cited is fine.

Plesiomorphy is an ancestral or primitive traits that are homologous to a certain group of organisms but not unique to the other members of the group, hence cannot be used as a diagnostic character for the group.


Fifty shades of cladism

Quinn (Biol Philos 32:581–598, 2017) offered seven definitions of “cladist” and discussed the context in which they are used in relation to historical and current debates in systematics. As a member of her study taxon, I offer some contextual color commentary, clarifications on the views of “pattern cladists” regarding monophyly, ancestors, synapomorphy and other concepts, a definition of “syncretist”, and some thoughts on cladistics and philosophy in the twenty first century.

This is a preview of subscription content, access via your institution.


Biology Exam

2. Next step results in divergence in traits such as
mating system or habitat use, etc.

- Found patterns supportive of dispersal and colonization hypothesis

1. Allele frequencies in a population will not change generation after generation

Assume single isolated population with no gene flow

Avoided if population is infinitely large

Increases frequency of homozygotes
Decreases frequency of heterozygotes

Does not lead to adaptation

Not same as seasonal movement

Almost hunted in North America to extinction, few individuals left built population back up

Because of founder effect there is now limited genetic diversity

Less variation in diversity

Compression around the average

Decrease in heterozygotes (Aa)

Trims off top of the trait distribution increasing the variance

Shifts average phenotype value left or right

Fitness consistently increases or decreases with the value of a trait

2. Determine the order and polarity of the characters

3. Code the characters and construct a matrix

4. Group by synapomorphies (phylogenetic hypothesis)

5. Solve possible problems (parsimony)

2) Use of spices should be greatest in hot climates, where unrefrigerated foods spoil


What is an apomorphy? What is a plesiomorphy? Can someone confirm these definitions? - Biology

The goal of systematics : The diversity of living things presents us with a seemingly infinite variety. The science of systematics is dedicted to identifying and ordering the diversity of living things .

But first, where does the diversity come from?

Not from this!

  • It fails to reflect the prevalence of branching lineages as a source of evolutionary diversity.
  • It reflects Lamarck's early evolutionary hypothesis involving multiple asynchronous creations of lineages that evolve along a fixed trajectory (slime -> worms -> bugs -> fish -> reptiles -> mammals -> humans.)
  • It reflects the ancient concept of the Scala Naturae or Great Chain of Being, first proposed by Plato and embraced by scholars of classical antiquity and the Middle Ages which ranked matter from minerals to angels.

Fortunately real life is more interesting.
Lineages : Just what is a lineage: = an interbreeding group of sexually reproducing organisms projected through time .

  • By interbreeding I don't mean that everyone mates with everyone else, but that over the long term there is no barrier to gene flow throughout the population.
    • Other organisms that don't contribute genes to a lineage don't qualify as members. These may be organisms that simply never interbreed (E.g. Humans and gorillas), or organisms that interbreed but don't produce fertile offspring. Horses and donkeys can be deceived by humans and induced to interbreed, producing sterile mules.
    • Note that the boundaries of a lineage may be fuzzy:
      Mules usually they are sterile, however once in blue moon they are fertile. The amount of gene flow that occurrs between horses and donkeys in this manner is negligible, and we consider them separate lineages.
    • Some species' ranges may even meet at broad hybrid zones along which interbreeding occurs, producing relatively unfit hybrid offspring. Even so, the hybrid zone is typically a barrier to gene flow between the primary populations. (E.G. the hybrid zone of the black carrion crow and the hooded crow in Eurasia.

    The first tree of evolution from a notebook of Charles Darwin from victorianweb.org

    Speciation

    • If we placed a physical barrier between members of our lineage here, then:
      • the individuals on one side of the barrier would be deprived of the genetic material on the other side, thus any modifications that occurred in one group could not be passed on to the others
      • The populations on different sides of the barrier would begin to accumulate different sets of modifications.
      • Ultimate, they might diverge morphologically to the point that if they ever reestablished contact, the two groups would be sufficiently dissimilar that they could not or would not mate and produce fertile offspring. At this point, their separation would have been made permanent.
        Allopatric speciation : Members of a population are geographically separated by either a dispersal event or by the creation of a barrier between them.
          a. Example of former: Canada geese and Nene or Hawaiian geese.
          b. Example of the latter: Many North American song birds, e.g. blue jay (right) and Steller's jay.
          a. Acheta: In the east US there are two species of gray cricket that are thought to derive from a recent common ancestor. In both, juveniles are extremely vulnerable to cold. Their responses to this problem differ. One species mates in the fall, eggs are laid which overwinter and adults die. The other overwinters as adults and mates in the spring. By next fall, the juveniles are grown and overwinter as adults. Common ancestor lived in a warmer climate and mated year round.
          b. Busycon (right): Sudden appearance of sinistrality (right) in marine snails prevents mating between dextral and sinistral individuals.
        • Terminal taxa : the organisms A, B, and C at the ends of the branches.
        • evolving lineages : The line segments of the graphic.
        • Nodes: Branch points representing lineage splitting events or speciation events. These represent the latest common ancestor of the descendants depicted above it.

        Note that in a cladogram, it does not matter whether things apear on the left or right. What counts is the sequence of branching events (i.e. which ones appear on top or on the bottom). In the figure on the right, cladograms 1 and 2 depict exactly the same relationships, whereas cladogram 3 is different.

        Note: The taxa whose relationships are indicated above, A, B, and C may be individual species or they may, themselves, be taxonomic groups whose members' relationships could be shown with its own cladogram.

        • A heirarchy of internested groups
        • An organizational principle.

        For example, in our lives, we have all employed the taxonomic system in which animals are classified according to the organizational principle of their utility to humans . Generally, there is little ambiguity.


        Problem : The criteria that we use to classify animals according to this system are arbitrary and subjective . For example:

        A reptile enthusiast might classify a green tree python as a pet , where a person who was terrified of snakes would call it vermin , and an entrepeneur who raises reptiles for the pet trade would view it as livestock .

        Ideally, we would like to have some non-arbitrary, natural organizing principle for a taxonomic system that natural scientists can use. Such a principle is provided by the pattern of evolution . In order to understand it, you must first understand the conventions for graphically displaying the pattern of evolution.

        The phylogenetic taxonomic system : Taxonomic groups can be named and defined based on their descent from a common ancestor. The cladogram to the right shows the real relationships between several major vertebrate groups.

        Working from this cladogram, systematists have named the following taxonomic groups:

        In this drawing, we have drawn circles around the groups that could be defined by the relationships shown on this cladogram, and indicated their names. Ordinarily, one would simply write the group names next to the node of the last common ancestor:

        • A hierarchy of internested groups , with those descended from more recent common ancestors being nested within those descended from more distant ones. For instance, "Tetrapoda", the common ancestor of land vertebrates and its descendants, is nested within "Choanata", the common ancestor of vertebrates with choanae and all of its descendants.
        • An organizing principle , the branching pattern of evolution itself.

          * Memorize * this definition: A monophyletic group is an ancestor and ALL of its descendants .

        Note: You may be familiar with two types of non-monophyletic groups:

        Note carefully : Only monophyletic groups are based exclusively on natural, non-arbitrary criteria. When we define a paraphyletic group, we must arbitrarily decide which descendants to exclude. In the case of polyphyletic groups, we must decide which ancestors to leave out.

        The Phylogenetic System of Taxonomy: The organizing principle of modern biology is evolution (descent with modification). Ultimately, evolution implies that all living things descend from single common ancestor. The history of these lineages is their phylogeny. (We already know how to draw it). This supplies the organizational principle used by modern systematists. It is hierarchical because groups that are descended from very recent common ancestors may be nested within groups descended from distant common ancestors.

        Character analysis

        One obvious utility of cladograms is that we can map evolutionary changes onto them. As lineages evolve, the characters of their members change. I.e. they go from ancestral to derived states.

        • Plesiomorphy: The ancestral character state - inherited from distant ancestors. E.G. From the point of view of Primates, having five fingers is a plesiomorphy. (Symplesiomorphies are "shared ancestral states.")
        • Apomorphies: A derived (evolved) character state. E.G. From the point of view of Primates, having an opposable thumb is an apomorphy.
          • Synapomorphies: are "shared derived states." E.G. the presence of an opposable thumb is a synapomorphy of humans, chimpanzees, monkeys, lemurs, and other lineages of primate.
          • Autapomorphies: Unique derived character state. E.G. The enlarged braincase of humans is an autapomorphy, not shared with other animals.

          The History of Phylogenetic Systematics (Cladistics)

          Ideally, we would like to have some non-arbitrary, natural organizing principle for a taxonomic system that natural scientists can use. Indeed, Darwin, in the Origin noted that the Linnean system of taxonomy, based on general similarity, ought to be superceded by one based on closeness of common ancestry. Alas, on a practical level, such an undertaking was impossible until the invention of digital computers.

            Numerical taxonomy (Phenetics) : Introduced by Robert Sokal and Peter Sneath in late 1950s. Attempted to base classification on similarity alone, viewing the tree of evolution as fundamentally unknowable. Often called Phenetics. Pheneticists tend to use continuous numerical measurements in multivariate statistical analyses to identify groups.

          By the mid 1970s, cladistics had eclipsed phenetics. By the 90s it was the dominant school of taxonomic thought. In North America, the 1980s were the heady era of taxonomic revolution in which cladistic revolutionaries in institutions such as the University of California at Berkeley and the American Museum of Natural History shaped the future of systematics. A revealing document from this era is:

          DeQueiroz 1988 key concepts:


          CHARACTERS VERSUS THEIR TOKENS

          Some of the problems described above may arise from the fact that symbols like ‘0’ and ‘−’ (as a ‘minus’ sign) have connotative associations with concepts such as absence or loss, which originate from usages in other (i.e. non-phylogenetic) contexts. A common thread among these problems is the implication that ‘0’ is treated as inherently different from any nonzero state, perhaps even standing in for primitiveness. This is perhaps a result of the frequent use of ‘0’ for the states of the root taxon as a matter of convention. The possibility arises that the convention sometimes gets mistaken (consciously or unconsciously) for a procedural necessity. The purpose of reviewing some details of phylogenetic counting algorithms earlier was to underscore the fact that the tokens only indicate an identity. This helps to evaluate not only how the above scoring procedures are problematic, but also how we choose among alternative ways of dealing with these problems, as described in the subsequent section.

          It is important not to confuse ‘0’ with a statement of primitiveness when drafting character lists and scoring matrices, especially for unordered characters. In theory, it makes no difference whether absence is represented by ‘−’, ‘+’, ‘0’, or ‘1’. Assuming you have not ordered or weighted characters, you could swap all instances of ‘0’ for ‘1’ and vice versa and you will still obtain the same result as before. The only thing that matters is that taxa that share the same conditions are coded the same way. Because of the default assumptions of transformational symmetry, there is no difference between 0 scores and non-0 scores where the assessment of a transformation cost takes place. States 1, 2, 3, etc., are not derived states until a phylogenetic analysis has been conducted and returns that result, and the Fitch algorithm will not add any additional steps if each appears independently in the tree or together. Similarly, state 0 is not the ‘plesiomorphic state’ simply because it is labelled 0. ‘Derived’ and ‘plesiomorphic’ are properties that are exposed as the phylogenetic algorithm assigns optimal values of the characters to internal nodes. They can be represented by any token the investigator chooses. It is the investigator's responsibility to ensure that the tokens accurately reflect the character information in a truly symmetric manner because the parsimony algorithm (unless given specific commands otherwise) will treat character transformations symmetrically. The consequence of failing to account for this symmetry will be a loss of grouping information.


          Living Fossils

          The principal misunderstanding to deal with, here, is that no living thing is &ldquomore evolved&rdquo than any other. Whether bacterium or human being, both share a common ancestor at least 3.4 billion years ago, and both have been evolving ever since.

          Truly, there is a fascination about certain organisms &ndash a brachiopod called Lingula, horseshoe crabs, coelacanths, the New Zealand tuatara, . &ndash which seem little changed from their fossilised ancestors, but this is really just a conceit. To quote from Richard Fortey&rsquos book, Survivors &ldquo. I have been rather cautious about using the tag &lsquoliving fossil&rsquo too readily. Just as it is untrue that evolution erases the past, it is also the case that no organism remains completely unchanged through long periods of geological time. The horseshoe crab may carry an ancient carapace on its back [he&rsquos speaking figuratively here, people], but it has still moved with the ages. Even the tuatara has evolved at the genomic level for all that its obscurely smiling visage seems to speak directly of the Triassic&rdquo (Fortey 2011, p. 280-281).


          BIOL 3300

          Same nucleotide at given position due to descent from common ancestor Or convergent evolution? E.g. independent mutations in divergent lineages just happened to both produce a C or T at a particular site?

          Only 4 character states (nucleotides)

          • Good chance that independent mutations will occur
          • And multiple substitutions at same site : Therefore, distinguish homology from homoplasy by "preponderance of evidence"
          • -Models, computer programs meant to improve objectivity of molecular phylogenetic analysis
          • -e.g. Kimura's two-parameter model -Corrects for multiple substitutions at the same time
          • -And differences in frequency of transitions to transversions
          • Closely-related species
          • - Nucleotide difference = 16/924 = 1.73%
          • - K2P = 1.76% K2P
          • More distantly-related species
          • - Nucleotide difference = 144/924 = 15.58%
          • - K2P = 17.67%K2P
          • Multiple substitutions at same site increase with time since divergence due to convergent evolution and reversals
          • Difference between sequences saturates at approx. 75%
          • Estimates taxonomic affinities from overall
          • similarity
          • Compares as many characters as possible
          • With no weighting or phylogenetic assumptions (e.g., regarding homology or polarity of character states)
          • Assumes that contribution of homology to overall similarity should be swamped by degree of homology if enough characters compared
          • But critics argue that overall similarity not reliable index of relatedness
          • More closely related if shared ancestor more recently
          • e.g. using Kimura's 2-parameter model
          • Length of branch indicates genetic distance
          • Distance method
          • Represents phenetic approach
          • Clusters taxa so that themost similar forms are grouped together
          • Rooting with outgroup can allow inferences about direction of change
          • Many possible trees but preferred one minimizes the total distance among taxa
          • Not the most accurate method, but reasonably good, and has advantage of being fast, even with large data sets
          • Argues that degree of relatedness ≠degree of similarity
          • Classifies organisms according to order that branches arose along a dichotomous phylogenetic tree
          • Parsimony analysis of synapomorphies determines which phylogeny would require fewest changes to illustrate evolutionary relationships
          • Therefore, only shared, derived characters (synapomorphies) are informative
          • Parsimony informative characters are shared by two or more taxa
          • Characters unique to one lineage are parsimony uniformative
          • Need outgroup to identify synapomorphies
          • i.e. to know what is ancestral (plesiomorphic) and what is derived (apomorphic)
          • Only branch order important
          • Length of branch not important
          • Trees dichtomous
          • e.g. Maximum parsimony analysis in MEGA
          • Computerprograms compare all possible trees
          • Computationally more challenging than Neighbour joining tree
          • Even with 8 species, more than 10,000 possible trees
          • How much confidence should we place in any particular branch point?
          • Evalutae statistically using bootstrapping
          • Builds replicate trees by creating new data sets from existing one by repeated sampling ("pseudoreplication")
          • Generates artificial data sets by random sampling, with replacement, from the ctual data set
          • e.g. if 300 bp in sequence, randomly selects one site and uses it
          • as first entry in new data set
          • Randomly selects second site etc., up to 300 sites
          • New sequence random subset of original
          • Used to estimate phylogeny
          • Repeated 1000 times
          • i.e. 1000 different trees built with differnt subset of data
          • Generates consensus tree indicating in what percentage of the trees each particular branch occurred
          • If results are being biased by a few nucleotide sites, branch values will be low
          • Can the rate at which DNA mutations accumulate be used to date when major events occurred ?
          • e.g. when two taxa diverged (i.e. last shared an ancestor) based on degree of genetic differentiation between them
          • Yes : if we can calibrate this 'molecular clock'
          • Measure geneti distance between two taxa whose divergence is known from:
          • Fossil record
          • Geological record e.g. divergence between marine organisms on wither side of Isthmus of Panama
          • Brown et al. - estimated 2% sequence divergence per million years in mammals using fossil record across mt genome
          • Bermingham and Lessios - estimated divergence in sister species of sea urchins found on either side of Isthmus of Panama (1.8%-2.2% per million years)
          • Similar in butterflies (Brower)
          • And Birds (Shields and Wilson Weir and Schluter)

          Suggestions that mutation rate faster in organisms with: Short generation times warm-blooded vs. cold-blooded organisms

          • And different rates at which substitutions become fixed lead to differences within mt genome (across genes)
          • - Some genes and gene regions more conserved than others
          • And estimates not necessarily applicable across all time scales (for both closely and distantly related taxa)
          • - e.g. due to saturation
          • - If rate is underestimated, divergence times will be overestimated
          • Closest living relative of cetaceans difficult to determine since they are so specialized for aquatic life
          • Relationship between cetaceans and ungulates, suggested by structure of internal organs and skeletal characters
          • Based on dentitions, perhaps sister group to artiodactyls?
          • Which would make ungulates paraphyletic
          • i.e. whales are in the ungulate clade
          • Whale (cetaceans) not just within ungulate clade
          • But also within artiodactyl clade
          • Suggests cetaceans are sister taxon to hippos (Gatesy et al.)
          • i.e. that whales are artiodactyls
          • Suggests that traits of hippos and whales
          • That were thought to be convergent adaptations for aquatic life (hippo = river horse)
          • Might actually be synapomorphies
          • Additional fossil data:
          • Several synapomorphies identify Artiodactyla as descendants of common ancestor
          • Notably smooth, pulley-shaped astragalus
          • But fossil whales (with hindlimbs) found
          • With pulley-shaped astragalus (Thewissen and Madar, Thewissen et al.)
          • But second, conclusive fossil find
          • Two species where size and shape of ear bones clearly identified them as whales
          • And pulleylike astragalus marked them as artiodactyls

          Presence or absence of homologous SINEs and LINEs (short or long interspersed elements)

          • Convergence unlikely:
          • Unlikely that inserted into two independent host lineages at exactly same location
          • Reversal detectable:
          • When lost, usually lose part of host genome too
          • Therefore, extremely reliable characters(="complex")
          • Support whale and hippo as sister taxa (Nikaido et al.)
          • Now order Cetartiodactyla generally recognized
          • 47.5 million-year-old fossils discovered in Pakistan
          • Male and female of new species (Maiacetus inuus)
          • With four flippers like limbs modified for foot-powered swimming could support their weight but probably couldn't travel far on land
          • Female with fetus positioned for head-first delivery, like land mammals but unlike modern whales = indicating birth on land
          • Size difference of male and female only moderate - suggesting that males didn't control territories or command harems
          • of females
          • 200 year old mystery of world's biggest yuckiest flower solved using molecular phylogeny
          • The Rafflesiaceae have giant blooms, which look and smell like decomposing meat to attract carrion flies that pollinate them
          • Are also parasitic (gaining nutrients from tissue of the tropical grape vine rather than photosynthesis)
          • Using DNA analysis, found to belong to the Euphorbiaceae family
          • Which includes the rubber tree, castor oil plant, and the cassava schrub
          • They fall in the middle of this group with minute flowers
          • Big, odour flowers likely evolved because these plants occur in dimly-lit tropical rainforest understoreys
          • Davis et al.
          • Can tumor cells move from patient to patient?
          • Canine transmissible venereal tumor (CTVT)
          • Question:
          • a) Are the tumor cells transmitted from dog to dog?
          • b) or is each tumor an obnormal growth of each dog's own cells (caused perhaps by a virus that is transmitted)?
          • If a), genetic analysis will show tumor cells to be monophyletic
          • If b), the dogs and their tumors will each be monophyletic
          • Stong support for (a)
          • To answer, Kittler et al reasoned thatbody lice (which lives in clothing) arose from head lice around the time humans started wearing clothing
          • Therefore, estimated when body lice arose by estimating genetic distance between body lice and head lice in humans from aroundt the world.
          • - To convert genetic divergence into chronological divergence, needed to "calibrate" molecular clock
          • - Reasoned that head lice that parasitized humans and lice that parasitized chimps diverged when their host species diverged (approx. 5.5 million years ago, according to fossil record) to calculate "conversion factor"
          • Therefore, estimated that body lice (and therefore clothing) originated approx. 72,000 yrs ago
          • Associated with spread of early humans outof Africa?
          • smallest evolutionarily independent unit
          • Essence of speciation is lack of gene flow
          • Separate gene pools
          • But practical criteria for identifying when populations are evolving independently?
          • Assumes reproductively isloated populations will accumulate morphological differences
          • But not all differences are species-level differences
          • - Sexual dimorphism
          • - Life cycle differences
          • - Environmental effects
          • - Intraspecific polymorphisms (e.g. eye colout) and polyphenisms (e.g. queen, worker, solder ants)
          • And some species may be cryptic
          • DNA barcoding uncovering many cryptic species
          • Species are smallest identifiable units that are diagnostic and monphyletic
          • Many possible monophyletic groups
          • Different criterion than BSC to establish whether lack of gene flow
          • PSC detects species tat have been evolutionarily independent long enough for diagnostic traits to emerge
          • Can be based on numerous characters (not just morphological - but not just genetic characters )
          • Any type of organisms
          • Testable
          • Criterion is reproductive isloation
          • Separate species if they do not hybridize regularly in nature or if they fail to prodcue viable fertile offspring whenthey do
          • Widely accepted since Ernst Mayr "championed it" in 1942 e.g. legal definition used in U.S.Endangered Species Act 1973
          • Lack of gene flow "litmus test" for evolutionary independence
          • More common than previously thought
          • - Hard to detect prior to use of genetic methods, especially with backcrossing
          • Many well-known hybrids are generally sterile
          • - But not always (e.g."beefalo")
          • Particularly common in plants (more later)
          • Hybridization in wild often result of anthropogenic change
          • - introduction of non-natives
          • - removal of isolating barriers
          • - range shifts
          • e.g. Hybrid grizzly-polar bears a worrisome sign of the North's changing climate
          • And difficult totest and apply:
          • - In populations that don't co-occur
          • - In fossil forms
          • - Irrelevant in asexual organisms
          • Have to make inferences (based on morphological, genetic, or behavioural differeces) about whether they might be reproductively isolated
          • -> Have to understand causes of reproductive isloation

          1. Copepods

            Morphologically, single species
        • Molecular phylogeny showed at least 8 species
        • Different phylogenies species unable to produce fertile offspring (even where they overlap in distribution)
        • At least 8 cryptic species by both BSC, PSC
          • 2. Elephants
          • Traditionally African and Asian elephants
          • Two African types (forest and grasslan) but don't interact to test BSC
          • PSC showed them to be distinct species
            Diatoms responsible for harmful algal blooms (genus Pseudo-nitzchia)
          • Two morphological species using light microscopy
          • But TEM (transmission electron microscopy) and phylogenetic analysis using DNA sequence data revealed 8 spp.
          • Mating trials agreed
          • Production of neurotoxin during algal blooms variable
          • Perhaps due to different species compositions at different times
          • 4. Cryptic skate species
          • Generally considered single species (common skate)
          • Molecular phylogenetic analysis revealed two distinct species (blue skate and flapper skate)
          • - Which weren't even sister species
          • Further investigation showed species:
          • - Could be morphological distinguished (by tooth shape)
          • - Had different geographicaldistributions
          • Important for conservation purposes
          • Classically, speciation in 3 steps:
          • 1. Isolation
          • 2. Divergence
          • 3. Reproductive isolation (RI)
          • a) Allopatric speciation (geographic speciation)
          • Evolutionary independence begins with cessation of gene flow due to physical separation of populations
          • Populations then develop intrinsic genetic differences especially if conditions different on each side of barrier)
          • RI if secondary contact

          Divergence begins after the founding event, resulting from genetic drift and natural selection

          • e.g. Hawaiian Drosophila
          • >1000 spp. (Many island endemics)
          • Each island likely founded by small number of individuals or even single gravid female
          • - Genetic drift and natural selection on genes responsible for courtship displays and habitat use
          • Supported by phylogenetic evidence : suggests that islands were colonized in sequence ("island hopping")
          • Considered general mechanism for initiating speciation
          • Especially in motile animals (or with resting stages)
          • e.g. invasive species in ballast water of ships
          • and plants
          • e.g. small number of seeds to new habitats by wind or water currents or by the feet, feathers, and digestive tracts of birds and other mammals
          • Can be slow process (e.g. rise of moutain range, glaciers) or rapid (e.g. lava flow)
          • - Includes human-caused habitat fragmentation
          • - Whether barrier to gene flow depends on species
          • e.g. Snapping shrimp
          • On either side of isthmus of Panama (Land bridge closed approx. 3 mya)
          • Morphological sister species on either side of isthmus
          • Confirmed phylogenetically (DNA)
          • And mating study showed pairs no longer capable of interbreeding
          • Speciation complete

          Parapatric speciation

          When a population enters new habitat within range of parent species

          No physical separation between populations (i.e. no extrinsic barrier)

          Instead, speciation results from evolution of other mechanisms that reduce gene flow between populations

          e.g. banded and unbanded water snakes: mainland banded many on islands unbanded

          • Allopatric speciation if water currents completely prevented migration
          • But parapatric because frequent migration from mainland and hybridization
          • - With selection against banded on islands
          • Outcome dependent on balance between gene flow and selection
          • Speciation most likely in small populations when gene flow is low, selection for divergence is strong (intrinsic barriers)
          • Occurs entirely within range of parent species
          • Therefore, must be intrinsic barriers to gene flow
          • i) Polyploidy and other chromosome changes as barrier to gene flow
          • - Whole genome duplication
          • - Largest scale of mutation possible
          • Error in meiosis produces diploid (unreduced) gametes
          • Gametes with different chromosome numbers normally incompatible (3N low fertility)
          • Immediate reproductive isolation between parental and daughter populations
          • Polyploidy common in plants since capable of self-fertilization
          • 70% angiosperms, 95% ferns with polypoidy in history
          • Polyploidization in animals relatively rare, although self-fertilization and parthenogenesis in many groups
          • e.g. whiptail lizards : polyploidy produced by hybridization between species (allopolyploidy)
          • e.g. Each species may arise independently multiple times
          • Not whole genome duplication
          • But any differences in chromosome number still usually prevent formation of fertile offspring
          • e.g. butterfly genus Agrodiaetus
          • - Species with chromosome number ranging from 10 to 134
          • - Sympatric species with same number of chromosomes rare, suggesting that differences are important in maintaining isolation

          Other intrinsic barriers to gene flow in sympatry include temporal reproductive isolation (e.g. differences in flowering time), host or pollinator specilization, or anatomical or behavioural isolation

          • e.g. Japanese winter moth
          • - In N. Japan (where deep snow and extreme cold preclude reproduction in midwinter), one species reproduces late fall/early winter and other reproduces late winter/early spring
          • Species are genetically divergent despite geographic overlap
          • But in S. Japan (where reproduction possible throughout winter), no temporal isolation and single interbreeding population
          • e.g. two species of monkeyflowers : one pollinated by bees, other by hummingbirds
          • - No opportunity for hybridization even where they co-occur
          • e.g. Japanese land snail (genus Euhadra)
          • - Single gene controls whether shell shows left-handed or right-handed coiling
          • - Mutation producing other handedness results in immediate reproductive isolation "due to anatomical reproductive incompatibility
          • - Phylogeny suggests right-handedness has arisen multiple times
          • Natural selection becoming recognized as most important factor promoting divergence
          • Different selection pressures on each population in different habitats, using different resources
          • e.g. Apple and hawthorn maggot flies
          • - Incipient speciation in sympatry
          • - Species first observed on apples in mid-1800s
          • - Host trees occur together and flies search widely for host
          • - Not morphologically distinct
          • But strong host preference
          • Therefore, assortative mating since they mate on host

          Divergence just result of genetic drift due to reproductive isolation?

          • Or two "races" exposed to different selection pressures?
          • Evdence suggests selection driven by difference in when fruit from each host ripens
          • - Apples ripen 3-4 weeks before hawthorns
          • - Therefore, still warm when apple fly larvar pupate vs. cool (prewinter) temperature for hawthorn larvae
          • Deer mice from Sand Hills in Nebraska
          • Light colour coded by a single gene (agouti)
          • Estimated that gene appeared approx. 4,000 years ago (few thousand years after colonization by dark mice)
          • New gene has since become very common
          • Used owl predation experiments to estimate strength of selection pressure : paler mice have 0.5% survival advantage
          • Linnen et al.
          • 1. Sticklebacks
          • - Independent armour loss in isolated lakes
          • - Reduced ion availability and lower predation intensity

          Likewise, parallel divergence of benthic and limnetic pairs (Rundle et al.)

          • 2. Walking stick insects
          • Unstriped morph more common on host plant with broad leaves
          • Striped morph more common on host with thin, needle-like leaves
          • Predation by birds and lizards
          • Divergence in body size, shape, host preference, behaviour
          • Driven by intense divergent selection for crypsis (Nosil et al.)
          • Not genetic drift
          • Special type of natural selection acting on phenotypes involved in mate choice
          • Assortative mating due to direct mate choice (not by-product of ecological selection)
          • Can contribute to reproductive isolation that may lead to speciation
          • e.g. Hawaiian cricket genus Laupala
          • - Females choose males of their species based on song pulse rate
          • - Differences important in maintaining RI among 38 species
          • - Genetic basis not known but male song and female preference tightly linked
          • e.g. Cichlids
          • >500 species in Lake Malawi alone
          • Can direct mate choice (based on differences in male colour) prevent interbredding or is RI result of habitat segregation?
          • Yes : complete assortative mating, even in lab
          • Highly significant genetic differences indicate RI
          • In some situations, mating preferences and environmental factors interact
          • In Lake Victoria, where water clarity poor, males of both species have similar colour patterns and are less genetically divergent
          • Two general mechanisms reduce interbreeding and hybridization:
          • 1) Prezygotic isolation Mostly premating isolation - temporal isolation (e.g. Japanese winter moth), host or pollinator specialization, anatomical reproductive incompatibility (Japanese land snails), mate choice (e.g. assortative mating in cichlids, crickets)
          • Also gametic isolation (e.g. Drosophila)
          • Expect RI between good species (according to BSC)
          • But hybridization between recently-diverged species not uncommon (e.g. following secondary contact)
          • - e.g. over 700 introduced plant species in British Isles hybridize with native species
          • - And at least half of these produce fertile hybrids
            2. When equally fit, divergence between parental populations erased
          • 3. Higher fitness (e.g. in intermediate or new habitat)
          • - Creating a distinct population of their own
          • - Either stable hybrid zone (higher fitness at boundary of parental ranges) or new species (in novel habitats)

          Evolution of mechanisms that prevent interbreeding between newly interacting incipient species (prezygotic)

          • If hybrids are less fit: (postzygotic)
          • Parental populations under different selection pressures
          • Changes in mating systems
          • Or if fixation of alleles that don't work well together when heterozygous
          • Selection against hybrids should reinforce selection for assortative mating (prezygotic RI)
          • And finalize the speciation process
          • Minimizes "gamete" wastage
          • e.g. Drosophila santomea and D. yacuba
          • Should be selection for evolution of prezygotic isolation in sympatry since hybrid males are sterile
          • In allopatric populations, females produce about equal numbers of offspring sired by males of each species
          • But in sympatric populations, females produce mostly eggs sired by males of own species, even if mated first with male of other species = gametic isolation
          • Pheromones in 2 species chemically different when sympatric But not when allopatric
          • BUT : in allopatric populations brought together in lab
          • Pheromones diverged to resemble those found in sympatric species
          • In 9 generations
          • Two divergent lineages isolated in N and S rainforest refugia during Pliocene and Pleistocene
          • Reconnected ca. 6500 years ago in contact zone
          • Selection against hybridization through mate choice greater in contact zones than in allopatric area = reproductive character displacement Post-mating reproductive isolation:
          • - S females x N males inviable
          • - N females x S males viable but with slower development
          • Greater "penalty" if S female choose wrong male
          • Led to pre-mating reproductive isolation (reinforcement):
          • - S females better than N females at choosing own males
          • e.g. One stickleback population
          • Breakdown of benthic-limnetic species pair into hybrid swarm (Gow et al. 2006)
          • Likely due to environmental change in lake
          • Exotic crayfish introduced in early 1990s (Taylor et al)
          • e.g. cichlids in Lake Victoria
          • Increased turbidity causing breakdown of pre-mating reproductive barriers (Seehausen et al)
          • Hendry et al - possible human impacts on adaptive radiation : beak size bimodality in Darwin's finches
          • Divergence with respect to beak size and shape within medium ground finch Geospiza fortis
          • Biomodal distribution evident in 1940s-1960s
          • Few with intermediate beak size
          • No intrinsic genetic incompatibility
          • Presumably disruptive selection due to selection against hybrids
          • Insufficient supply of seeds with intermediate size/hardness
          • Site with increased human presence after 1960
          • Finch feeders with rice that can be cracked by birds having wide range of beak sizes
          • No longer selection against intermediate beaks
          • e.g. big sagebush in Utah
          • 2 subspecies, basin, and mountain, hybridize at intermediate elevations
          • Hybrid zone relatively narrow by stable over time
          • Reciprocal transplant experiments showed that each subspecies did best at its own elevation
          • Hybrids superior in transitional habitat
          • Continue to hybridize at interface
          • e.g. two wildflower species in Colorado
          • Hybrids grew as well or better in transitional habitats
          • Sunflower Helianthus anomalous thought to have been created by hybridization between two other species (H.annuus and H. petiolaris)
          • Reproductive isolation from parental species
          • DNA evidence supports previous hypothesis that Aubodon's warbler (D. auduboni) is a hybrid between two other species (D. coronata and D. nigrifrons)
          • Homoploid hybrid speciation otherwise thought to be rare in tetrapods
          • Researchers recreated Heliconius heurippa in the lab by crossing Heliconius cydno and Heliconius melpomene
          • And natural hybrids show wing patterns very similar to H. heurippa
          • Wing pattern of H. heurippa leads to reproductive isolation from parent species
          • Growing circumstantial evidence for hybrid speciation in Ragoletis fruit flies, swordtail fish and African cichlids
          • And some suspect American red wolf could be product of hybridization between coyotes and gray wolves
          • Hot topic in evolutionary biology research now
          • Including identification of actual genes and mutations
          • e.g. "blonde" deer mice on Sand Hills in Nebraska (Linnen et al. 2009)
          • e.g. "reinforcement" gee in flycatchers (Sether et al)
          • Pied and collared flycatchers
          • Speciation occurred during last ice age reunited when glaciers receded
          • Closely related, look similar, share same territory, but rarely breed together and hybrids are sterile
          • Females prefer conspecific males but about 2% hybridize
          • Studied hybrids to determine if preference genetic or learned through exposure : mechanism of pre-mating RI?
          • Hybrid females prefer males of same species as genetic father hybrid males showed no preference
          • Genes found on sex chromosome (Z) of females (from father)
          • Saether et al. 2007
          • Previously thought that radical reorganization required = "genetic revolution"
          • RI due to genome-wide divergence in allopatry
          • Sequential fixation of large number of genetic changes, each with very small effect (Fisher's geometric model)
          • But recent research shows speciation can also result from : Few large-effect changes
          • - Crickets, cichlids : few genes related to mate choice
          • - Phlox: few genes related to flower colour
          • And speciation can result from both:
          • New mutations:
          • e.g. deer mice from Sand Hills in Nebraska (Linnen et al)
          • e.g. Pelvic reduction in stickbacks (Chan et al.)
          • and Standing variation:
          • e.g. reduced plates in FW sticklebacks (Colosimo et al.)
          • e.g.1 : Beach mice on Florida Gulf Coast
          • Single nucleotide difference in melanocortin-1 receptor gene accounts for up to 36% of the lighter coat colour
          • Same mutation not present in light-coloured Altantic coast mice, suggesting convergent phenotypic evolution
          • Agouti gene involved in blonde deer mice from Sand Hills in Nebraska
          • Hoekstra et al.
          • e.g.2 : Dark pigmentation in rock pocket mice invading lava flows in Arizona vs. New Mexico
          • "Clearly, in nature, independent populations can have different genetic solutions to similar ecological" problems
          • e.g.3 Complete loss of pigment in Mexican cavefish
          • Two populations with different deletions in the ocular albinism 2 gene
          • Other populations show full complementation different gene likely involved
          • Crossing blind cavefish (Astyanax mexicanus) from distant caves can restore some sight
          • Supports idea that blindness evolved convergently in distantly related cavefish populations
          • Mutations in different genes responsible for loss of sight in separate lineages

          e.g.1: Exact same amino acid polymorphism in Mc1r in blonde beach mice and woolly mammoths

          • e.g.2 : Pitx1 gene involved in pelvic reduction in threespine and ninespine sticklebacks
          • Suspected involvement in manatees
          • First metazoans in fossil record approx. 565 Ma
          • e.g. multicellular butsmall and morphologically simple jellyfshes and sponges
          • Then Cambrian "explosion" (545-505 Ma)
          • In time, Cambrian represents <1% of Earth's history
          • But with appearance of most living animal phyla
          • e.g. arthropods, annelids, molluscs, chordates

          Start of Phanerozoic (= visible life) eon

          • 1. Amber and freezing Least altered remains but rare
          • e.g. insects preserved in hardened plant resins
          • e.g. woolly mammoth in permafrost
          • Other environments without weathering, scavenging animals, decomposition
          • e.g. human remains in peat bogs
          • 2. Permineralization and replacement
          • Where dissolved minerals (e.g. calcite, silica, gypsum) replace original mineral content or precipitate in and around it
          • Can preserve 3D details of internal structure
          • 3. Molds and casts Remains decay after being buried in sediment
          • Casts = new material fills space and hardens into rock
          • Molds = unfilled spaces
          • Preserves 3D information about surface shape
          • 4. Compression and impression fossils
          • Organic matter is buried in sediment before it decomposes
          • Under weight of sediment, leaves 2D impression in material below
          • 5. Trace fossils
          • Trackways or burrows (e.g. Tyndall stone)
          • Coprolites (e.g. sloth dung in desert caves)
          • 1. Durability of specimen or protection
          • 2. Burial
          • 3. Lack of oxygen
          • Therefore:
          • Fossils mostly hard structures left where sediments are deposited
          • e.g. river deltas, beaches, floodplains,marshe, sea floors
          • Also anaerobic swamps
          • 1. Habitat bias
          • Sedimentary deposits accumulate mostly in coastal marine areas
          • - Composed of material eroded from landmasses
          • Therefore, mostly marine organisms
          • - To lesser extent, other coastal or floodplain organisms
          • 2. Taxonomic bias
          • Bias towards organisms with mineralized structures (shell or bone)
          • >60% of animal phyla without hard structures are under-repressented
          • Critical plant parts (e.g. flowers) rarely fossilize
          • 3. Temporal bias
          • Old rocks rarer than new rocks as mountains erode and tectonic plates subduct
          • Fidelity of the fossil record better for more recent fossils
          • 4. Collection bias
          • e.g. certain groups of fossils are preferentially collected
          • Hierarchy divided into eons, eras, periods, epochs, and stages
          • early 1800s, intervals arranged by relative ages onlyAbsolute times assigned with development of dating techniques
          • Three eras : Paleozoic, Mesozoic, Cenozoic
          • Within Cenozoic, either:
          • Three periods : Paleogene, Neogene, and Holocene (5th ed.)
          • Life evolved on a world that was itself changing (Freeman and Herron)
          • Rearrangement of continents and oceans due to plate tectonics
          • Resulted in major climatic changes:
          • e.g. climate patterns extreme when continents came together because smaller relative amount of coastline (with its moderating effect on climate)
          • Collision of plates can cause also increased mountain building -> rock weathering -> decreased CO2 -> decreased temperatures and glaciation
          • During times of high CO2, poles free from glaciation
          • Dated 565-544 Ma
          • Discovered in 1940s
          • Named for Ediacara hills, Australia
          • But similar fossil at 20 sites around world
          • Mostly compression and impression fossils or traces
          • Organisms without shells or other hard parts
          • Small sponges, jelyfishes, comb jellies
          • Morphologically simple
          • Asymmetrical or with radial symmetry
          • But were more complex bilaterally symmetric animals present this early?
          • Argument that linear burrows and tracks were made by organism with head and tail
          • Fossilized embryos also suggest bilateral symmetry
          • - e.g. resembling larval sponges
          • - e.g. resembling cleaving arthropod embryos
          • Strong fossil evidence for bilaterally symmetric animals in late Precambrian
          • e.g. mollusc-like Kimberella Together suggests bilaterians small but present
          • Dated 505 Ma
          • Discovered 1909 near Field, BC
          • Described in Stephen Jay Gould's "Wonderful life"
          • Mostly compression and impression fossils
          • Variety of large, complex bilaterally symmetric forms
          • Little overlap with Ediacaran fossils
          • Well-developed segmentation, heads, appendages
          • Complex arthropods (e.g. trilobites)
          • Segmented worms, wormlike priapulids, molluscs
          • Several chordates with segmented trunk muscles, notochord that resemble hagfishes and lampreys
          • Also unusual organisms not obviously related to any extant phyla
          • Sometimes grouped together as "Problematica"
          • Some of which might represent new phyla
          • If so, Cambrian explosion resulted in even greater morphological diversity than realized
          • Many major groups later extinct
          • However, further studies suggest "Problematica" probably member s or close relatives of living phyla
          • e.g. Opabina e.g. Wiwaxia
          • Something unusual happened during the Cambrian
          • That led to earliest members of virtually all major animal lineages appearing relatively suddenly
          • At same time, in many parts of the world
          • Diversification in terms of Morphological innovations
          • Locomotion
          • Feeding

          Major divergences shown between Ediacaran fauna and Burgess Shale Fauna

          • 1. Radially or asymmetric (diploblastic) e.g. Jellyfishes, comb jellies
          • vs.
          • Bilaterally-symmetric (triploblastic) = Bilatera e.g. arthropods, nematodes, molluscs, chordates
          • 2. Protostome vs. deuterostome
          • Protostome:
          • Gastrulation forms mouth first
          • e.g. arthropods, nematodes, molluscs, annelids, flatworms
          • vs.
          • Deuterostome : first opening becomes anus
          • e.g. echinoderms, chordates
          • How long did these traits exist before appearing in fossil record?
          • Use molecular clock to date events not dated in fossil record
          • Wray et al. used 7 different genes, all independently calibrated
          • Estimated that chordates and echinoderms diverged 1000 Ma
          • Protostomes and deuterostomes diverged 1200 Ma
          • i.e. divergences occurred hundreds of millions of years before first appearance in fossil record
          • If so, fossils of bilaterians, protostomes, and deuterostomes should eventually be found in Proterozoic rocks
          • Cooper and Fortey, Smith
          • Suggested that the lineages leading to the living Bilatera diverged over prolonged period in Proterozoic
          • But most were small organisms that left no fossil trace
          • If so, what lit the fuse?
          • What aused dramatic change in body size in multiple lineages, during same brief time?
          • May have been connected with ecological changes (e.g. in atmosphere or oceanic geochemistry)
          • Especially rising oxygen concentrations in seawater due to increase in photosynthetic algae during Proterozoic
          • Knoll and Carroll suggested mass extinction of much Ediacaran fauna just before Cambrian
          • At same time as rise in atmospheric oxygen
          • Allowed tiny bilaterians to evolve in response to changed conditions
          • Geological evidence for rise in oxygen (e.g. Knoll and Carroll)
          • But additional predictions still untested:
          • No fossil evidence of small-bodied protostomes and deuterostomes in Proterozoic
          • No evidence of mass extinction of Ediacaran fauna

          Large evolutionary change

          Fossil record shows composition of biota has changed "radically" over time

          • Single or small group of ancestral species rapidly diversifies into large number of descendant species
          • Usually occupy wide variety of niches
          • Lack of competitors permits diversification to fill unoccupied niches
          • a) Following colonization of new, depauperate environment
          • e.g. Galapagos finches Fish in postglacial lakes
          • b) Extinction of other taxa
          • e.g. diversification of mammals after dinosaurs became extinct at end of Cretaceous period
          • e.g. Diversification of Bilatera after extinction of many Ediacaran fauna
          • e.g. diversification of arthopods due to jointed limbs
          • e.g. adaptive radiation among land plants
          • 1. Radiation of terrestrial plants from aquatic ancestors (400 Ma)
          • - Key morphological features (e.g. waxy cuticles, stomata)
          • 2. Radiation of angiosperms (110 Ma)
          • - Flower key innovation since it made pollination so efficient
          • Absence of evolutionary changein one or more characters for some period of evolutionary time
          • New morphospecies appear suddenly in fossil record
          • Then persist for millions of years without apparent change
          • Darwin emphasized gradual nature of evolution by natural selection to contrast instantaneous creation of new forms presented in Theory of Special Creation
          • Attributed lack of transitional forms to incompletedness of fossil record
          • Gradualism accepted patternfor next century
          • Gradualism opposed by Eldredge and Gould
          • Claimed stasis is real pattern in fossil record
          • Morphology is static within species
          • And morphological variation occurs at time of speciation (cladogenesis)
          • Tested in bryozoans
          • Abundant in fossil record for past 100 my
          • Phylogeny well known
          • Confident that morphospecies designations reflect phylogent
          • Cheetham, Jackson and Cheetham Caribbean bryozoans from 20 my -present
          • 19 extinct and living species in two genera
          • Estimated phylogeny for each genus
          • None of the populations showed traits intermediate between species
          • Characteristics of species were stable through time
          • i.e. Shows unequivocal patterns of stasis
          • - Punctuated by rapid morphological change
          • Erwin and Anstey reviewed 58 studies for evidence of punctuated equilibrium
          • Wide variety of taxa and period
          • Varied in ability to meet criteria for testing stasis
          • But number of studies may compensate for this

          e.g. Why would morphology of bryozoans remain unchanged for 5-10 million years?

          Address using so-called "living fossil"

            Species or clades that show little or no measurable change over millions of years
          • Although don't necessarily retain all of the "primitive" features of ancestral lineage
          • 1. Ginkgo biloba Single extant species with no close living relatives
          • Leaves similar to 40 Ma impression fossils
          • Thought for centuries to be extinct in wild but is now known to grow wild in at least two small areas in eastern China
          • 2. Horsetail
          • Approx. 15% extant species in genus Equisetum with no close living relatives
          • Much larger and more diverse group 350-300 Ma before seed plants became dominant
          • 3. Coelacanth
          • Prehistoric fish believed extinct for 65 million years
          • Until live specimen was found off east coast of South Africa in 1938
          • Once successful group with many genera and species
          • Abundant fossil record from 400-65 Ma
          • 4. Horseshoe Crab Extant species in genus Limulus virtually identical to fossil species from 150 Ma
          • Is it due to a lack of genetic variation?
          • No, according to Avise et al:
          • Compared mtDNA variation in horseshoe crabs to that of king hermit crab clade
          • Same (or more) genetic variation within horseshoe
          • Instead, likely due to relatively stable environment
          • Stabilizing selection around an optimal phenotype
          • 5 major extinction episodes during Phanerozoic
          • ca. 20-55% families went extinct
          • ca. 60-95% species went extinct in 1 million year span
          • Global in extent
          • Involved wide range of organisms
          • Rapid relative to expected life span of taxa
          • Although "The Big Five" responsible for only 4% of all extinctions during Phanerozoic
          • Other 96% extinctions occurred at normal or background rates:
          • - Taxa with restricted ranges and limited dispersal more likely to go extinct
          • 5 mass extinction events recognized in early 1800s
          • 1. Terminal-Ordovician (ca. 440 Ma)
          • 2. Late-Devonian (ca. 365 Ma)
          • 3. Permian-Triassic (252 Ma)
          • 4. End-Triassic Extinction(215 Ma)
          • 5. Cretaceous-Paleogene (65 Ma)
          • 440 Ma
          • Extinction of >100 families of marine inverts
          • e.g. brachiopods, bryozoans, reef-building fauna
          • Probably caused by glaciation of southern supercontinent Gondwana
          • Glacial deposits from this period found in Sahara Desert
          • Glaciation also caused lowering of sea level and reduced availability of continental shelf habitat
          • 365 Ma
          • Mostly affected warmwater marine species (e.g. rugose corals, brachiopods, trilobites)
          • Perhaps caused by another episode of global cooling
          • With accompanying lowering of sea level
          • Glacial deposits of this age in northern Brazil
          • Meteorite impacts also suggested
          • But evidence inconclusive
          • 252 Ma
          • End of Paleozoic
          • Biggest of big five
          • Mother of mass extinctions (Erwin 1993)
          • Extinction of 90-95% of marine species
          • Primarily affcted marine inverts
          • e.g. foraminifera, trilobites, bryozoans, brachiopods, echinoderms
          • And also vertebrates such as pelycosaurs
          • - Mammal-like reptiles e.g. Dimetrodon Fossils found many places worldwide
          • Especially Texas and Oklahoma
          • Where much of oil derived from Permian fossils
          • Still debated bytnumerous theories
          • 1. Glaciation on Gondwana
          • 2. Reduction of shallow continental shelf habitat due to formation of supercontinent Pangea
          • - Which occurred in early and middle Permian
          • 3. Large volanic eruptions in Siberia
          • - evidence of silica-rich lava flows dated to this time
          • 215 Ma
          • Particularly severe in the oceans
          • e.g. brachiopods, gastropods, molluscs severely affected
          • Some terrestrial groups affected
          • e.g. some reptile and amphibian groups
          • Precise cause not known
          • But huge volcanic eruptions occurred ca. 208-213 Ma as supercontinent Pangea began to break apart
          • Triassic extinctions allowed dinosaurs to become dominant
          • 65 Ma
          • End of the Mesozoic
          • Marine plankton and invert affected
          • And (non-avian) dinosaurs, pterosaurs, large-bodied marine reptiles (ichthyosaurs, plesiosaurs) wiped out
          • Evidence that huge asteroid hit the earth
          • - High concentration of iridium at K-Pg boundary
          • - Iridium rare in Earth's crust but abundant in extra-terrestrial objects
          • Amount of iridium suggests asteroid 10-15 km wide
          • Also presence of two other minerals at K-Pg bounday:
          • - Shocked quartz particles
          • - Microtektites (tiny glass particles melted by heat of an impact)
          • Known from other well-documented meteorite crash sites
          • Shocked quatz and microtektitea at K-Pg boundary in Caribbean
          • Site of impact found in early 1990s from magnetic and gravitational anomalies in Yucatan peninsula
          • Crater 180 km in diameter
          • Dater 65 Ma

          10 km asteroid striking ocean would have produced series of events affecting climate, atmosphere, and oceanic chemistry worldwide


          What is an apomorphy? What is a plesiomorphy? Can someone confirm these definitions? - Biology

          widowpenalties 1 10000 aggedbottom ewpage

          Week 2: Vegetative Morphology & Keys

          Flowering plants are the culmination of an amazing cascade of evolutionary innovations. This laboratory aims to place them in the context of the diverse array of vascular plants and trace the evolution of some basic aspects of their morphology.

          The first section of this laboratory aims to illustrate the less specialised organisation of the plant body found in the non-flowering plants and from which angiosperm morphology has been derived, while the latter part of the lab introduces the use of identification keys. The rest of the course concentrates on the flowering plants, and will consider form and function of the various organs of this group in more detail.

          The purpose of many of the questions in this lab is to encourage you to look carefully at your material to see what is really there. Today's focus is on leaves, buds, and stems. In different species they make look very different. There are also some specialized terms for discussing different types of leaves it's not necessary to memorize these terms but it is good to know they exist and where to find definitions when you need them.

          In today's lab we will do a very brief tour of leaves across all the major groups of vascular plants from whisk ferns, ferns, gymnosperms, and finishing with the angiosperms.

          ![Terms for different leaf shapes. Figure from N.C.W. Beadle, O.D. Evans & R.C. Carolin (1982) Flora of The Sydney Region. Reed, Sydney.](Fig. 2 Leaf shape .tif)

          ![Leaf arrangements simple and compound leaves. Figure from N.C.W. Beadle, O.D. Evans & R.C. Carolin (1982) Flora of The Sydney Region. Reed, Sydney.](Fig. 3 Leaf margins, simple & compound.tif)

          ##A basal group of ferns: the whisk ferns

          The earliest known vascular plants consisted of a system of cylindrical axes. The cortical tissues of the above ground parts had stomata and a cuticle and were photosynthetic, while the epidermis of the underground parts had no cuticle but produced hair-like outgrowths to aid absorption of water and minerals. Such plants are only known from the fossil record, but there are two living genera that approach this simple level of organisation. These are Psilotum and Tmesipteris, which are both "whisk ferns" and native to Australia.

          It consists of a stem system bearing small microphylls. The stem grows by a single apical "initial" rather than a meristem (a group of initials).

          • Examine the branching of the stem. This type of branching, where there is no main axis bearing laterals, is termed dichotomous. It is the oldest form of branching in plants, and is still common in the algae. Can you distinguish a main axis bearing lateral branches, or are all branches of equal size and growth?
          • Determine what, if any, relationship exists between microphyll and branch position. Does this plant have axillary buds? If there are no actual buds, from which point and in what manner do branches form?

          Members of this group have roots, stems and leaves, but the latter are megaphylls, and are not homologous with the microphylls of the previous group. In the ferns there is no main root system, the roots being lateral organs borne on the stems (adventitious roots).

          Examine Lygodium scandens.

          The stem grows horizontally below the surface of the ground (it is a rhizome) only the leaves are visible. Each leaf grows for one year, climbing on other plants towards the light, but eventually dies back to be replaced by a new one the next year.

          • Note the growing apex of a leaf is coiled up to protect the initial cell that is responsible for the growth. All fern leaves uncoil at the apex like this why is this adaptive?
          • Use the drawings in Figs.1.1. and 1.2 to identify the primary and secondary leaflets (pinnae and pinnules), and the primary and secondary rachises.
          • How would you describe the primary branching in the leaf? Is there any evidence of dichotomous branching in these leaves?
          • Note that the veins in the leaflets (pinnules) are in the form of an open system where the branches end blindly rather than joining to form a net.
          • What, if any, part of Psilotum nudum would be homologous with the leaf of Lygodium scandens? Is any organ of the latter homologous with the microphylls of the former?

          Note the small fibrous adventitious roots that arise at any point along the stem, and the large divided (compound) megaphylls. These leaves uncoil during growth.

          • Determine the relationship (if any) between leaf positions and branching of the stem. Does this species have axillary buds? How are branches initiated in the stem system?
          • Use the diagrams in Fig. 1 to determine what type of branching is present in the leaf. How many orders of branching are there in a leaf? Identify the primary, secondary and tertiary rachises.
          • Compare a one-year-old leaf with a two-year-old leaf. Is there any evidence of indeterminate growth in these leaves?
          • Examine the apex of the rhizome (underground stem). Does this plant have an apical bud? Is there any protection of the growing apex?

          These are seed plants without fruit or flowers. They are thought to have dominated the world's vegetation during the cooler and drier period that followed the Carboniferous.

          Examine Podocarpus elatus

          Podocarpus elatus (Plum Pine) is a conifer native to the closed forests of eastern Australia.

          The leaves of conifers are also interpreted as megaphylls, i.e. as having evolved from a lateral branch that has become determinate in growth and flattened to enhance interception of light.

          • Note the simple leaves that characterise the order. Are the leaves strictly determinate in growth? How are they arranged? What term(s) best describe the phyllotaxis (leaf arrangement)?
          • Hold a leaf up against the light and examine the pattern of the veins with a hand lens. Can you detect any lateral veins branching from the midrib? These leaves have a continuous sheet of tracheid-like cells between the adaxial and abaxial mesophyll tissue that distributes water laterally through the lamina from the single midvein.
          • Examine the pattern of branching of the stem. Look for axillary buds in leaf axils. Does this plant have axillary branching as in angiosperms or apical branching as in ferns?

          Examine the growing apex closely. Rather than a naked apical meristem, this group has the meristem protected within a bud. Note that the bud consists of a meristem enclosed with embryonic leaves, but that these are themselves enclosed within a group of bud scales, ie., reduced and hardened leaves that protect the bud. When the apex starts growing next spring, the bud scales fall off (leaving scars where they were attached) and the new vegetative leaves expand as the stem grows out of the bud. The positions of previous winter buds can be seen at intervals down the stem. They appear as rings of scars where the bud scales were attached.

          • Given that each winter bud marks the end of a year's growth, how old is the basal internode of the specimen you are examining?

          Angiosperms -- Flowering Plants

          Fill in the appropriate information in Table 1.1 and 1.2 as you examine the angiosperms in the lab today.

          There are many orders of flowering plants. All are characterised by the possession of a carpel, pollination at a distance from the micropyle of the ovule, and double fertilisation via a pollen tube. Like the previous two divisions their leaves are megaphylls, although there is some evidence that the megaphyll evolved separately in each group. Unlike conifers, the leaves of angiosperms may be simple or compound.

          Note that it has simple leaves with a short petiole, and that the laminas of these are mostly arranged in the one plane, spreading out either side of the stem. Note carefully how leaves are attached at successive nodes.

          • Using a hand lens and holding the leaf against the light, examine the venation pattern in the leaf lamina.
          • Are there any free vein endings in the leaf? Which term best describes this pattern? How does this pattern differ from that in the leaflet of a fern?
          • Examine the relationship between stems, leaves and branches. How do branches arise on the stem? Does this plant have axillary branching? Does each leaf axil contain a bud? How can you distinguish a branch of Abelia bearing two rows of simple leaves from a single pinnate leaf?

          Examine the the pea seedlings (Pisum sativum) on your bench.

          Each leaf is compound, consisting of a petiole terminating in a rachis bearing several pairs of rounded leaflets.

          • Identify the pair of large rounded stipules associated with each node, and resembling a basal pair of leaflets that are attached directly to the stem. Note how they enclose the apical bud of the main axis. What possible adaptive value could these stipules have?

          Examine Acacia elata (Cedar Wattle).

          How much constitutes a leaf? Look for axillary buds that may arise in the axils of leaves, but never in the axils of leaflets. Also look for the largest repeated unit of organisation. The leaf is the largest determinate unit of organisation, as distinct from the indeterminate stem system.

          • Identify the petiole, rachis, primary leaflets (pinnae) and secondary leaflets (pinnules). Are the primary and secondary leaflets strictly paired?
          • Look for the doughnut- or volcano-shaped glands (nectaries) that are a characteristic feature of the petiole and/or the rachis of Acacia species. What could be the adaptive value of such nectaries?
          • Compare the form of these leaves with those of Gleichenia. In which respects do they differ? Which of these two forms of leaf most closely resembles a stem system? (ie., which is the more primitive megaphyll?) Which features of the Acacia do you consider to be advanced, and which do you consider primitive?

          Examine specimens A, B, and C

          In some angiosperms the process of adaptation has blurred the functional distinction between leaves and stems. Some such examples are considered below.

          In each of specimens A, B and C, use your knowledge of the relationship between stems, leaves and axillary branches to work out what constitutes a leaf, and then enter in Table 1.1 the appropriate terminology from Fig 1.2 to describe the form and arrangement of the leaves.

          In the following cases, some part of the plant has been modified to serve as an aid to climbing.

          Examine the tendrils on the young pea plants supplied. Each tendril arises from near the end of a compound leaf, in the position in which you find a leaflet (CHECK THIS) on a leaf that has no tendril.

          Hence, we can conclude that the development has been modified so that the tissues that normally develop into the leaflet grow into a tendril instead (ie., the tendril is a modified leaflet/pinna).

          Now examine the tendrils on the branch of Cissus sp. Each arises on the stem opposite a leaf. This suggests that the plant originally had leaves in opposite pairs, and that one has been modified to form the tendril.

          To check this explanation, find a node at which no tendril has been formed.

          This shows that our initial interpretation is wrong. The tendril cannot be a modified leaf.

          If it is neither a modified leaf nor a modified axillary branch, it must in fact be a modification of the tip of the main axis.

          In this species, each time a tendril is formed it uses up the apical meristem in the apical bud, so continued growth of the plant can only come from an axillary bud emerging from the axil between the last leaf and the tendril. As it grows, the axillary branch pushes the tendril to the side, and forms a continuation of the vertical axis of the plant. So the plant axis is formed by a new "side branch" at each node bearing a tendril. This pattern of growth is described as sympodial growth. Sympodial growth is also seen in some plants where the apical bud is used up to form a flower.

          Examine specimens D, E and F

          Determine in each case whether the climbing structure (tendril or claw) represents an apical bud, and axillary bud, a leaf or part of a leaf. Enter your answers in Table 1.2.

          TABLE 1 Leaf morphology in angiosperms. For form of leaf write down the shape, apex, base, and veneation using the terms from Figure 1.1 and 1.2.

          Species hspace <20 mm>Form of Leafhspace <20 mm>Arrangement of leaves hspace <15 mm>Stipules

          TABLE 2 Modifications to aid climbing. For form of leaf write down the shape, apex, base, and veneation using the terms from Figure 1.1 and 1.2.

          Species hspace <13 mm>Form of leaf hspace <10 mm>Modification to aid climbing hspace<10 mm>Organ modified

          Check your answers with demonstrators / lecturers / classmates

          Introduction to the use of an identification key

          Plant identification almost always is based on a key. The aims of this exercise are to learn how to use an identification key, and also to become familiar with a range of common vegetative features of plants. Use the preceding section and the glossary to understand all the terms in the key.

          A key is a device that progressively eliminates possibilities until the identification is complete. At each step in the process it asks you to choose which of a pair of contrasting conditions or characters occurs in your specimen, and then directs you to the next appropriate choice depending on the condition chosen. It is important to realise that you do not have to use all the possible alternatives for any one specimen. The contrasting alternatives can be arranged in either of the following ways:

          In Bracketed Keys the contrasting alternatives are placed together, usually under a single number. Each alternative directs you to the numbered alternative that should be examined next. Hence, the first alternative under number 1 might direct you to 2 (the second pair of contrasting conditions), while the second alternative under 1 may direct you to 13, omitting all the intervening pairs (2 to 12).

          In Indented Keys the contrasting alternatives are marked with the same symbols (numbers or letters) and indented or inset the same distance from the left hand margin, but are not necessarily placed directly under each other indeed, they can sometimes be on different pages of the book, so one has to search for the alternative. Commonly the first and second alternatives are distinguished as A and *A, B and *B, etc. Having decided which alternative best fits the specimen, proceed to the pair of alternatives that immediately follows the correct alternative (downwards!). Hence, if your specimen fits the second of two alternatives, say *B, ignore all the choices listed below B and go to the first choice listed under *B.

          In both types, it is essential to -

          1. always proceed downwards
          2. read all alternatives carefullybefore deciding which best fits the specimen, and check any unfamiliar terms in the glossary. Never decide that the first alternative is correct before you read the second of the contrasting pair!

          Now turn to the key at the back of the lab manual. This is a key that uses only vegetative characters. The advantage of such a key is that it does not require you to have flowers or fruit, which are only on the tree in certain seasons. Use this key to identify at least two of the specimens.

          Week 3: Floral Morphology and Inflorescences

          Reference: Raven, P.H., Evert, R.F. & Eichhorn, S.E. 2013. The Biology of Plants 8$^$ edition pp 478-492.

          In this practical, we will examine the floral characters of typical angiosperms. In addition, we will introduce you to sufficient terminology that you can use identification keys based on reproductive characters.

          The radiation of floral structure within Angiosperms has lead to a wide variety in both floral structures and inflorescences. In part this is due to chance evolutionary events and in part it is do to selection pressures that arise from a particular pollination mechanism.
          Sometimes the pollinators are animals that are evolving themselves, meaning the evolution of floral structure can only be understood in the context of co-evolution--both the plant and the animal are evolving at the same time and in response to each other.

          The floral diversity in angiosperms is staggering, but with some practice it's also useful---it can be of great assistance in plant identification. With a few terms and some practice.

          As you will see, flowers are complex, highly specialised, and exhibit tremendous morphological diversity across taxa. Botanists have a number of ways of describing floral structure.

          The basic floral structure comprises four whorls, each comprising 3-5 segments, but this varies greatly among species. A 'whorl' is a group of appendages arising from the same point on an axis. The identity of each floral whorl is determined by its position and function. The inner-most and upper-most whorl is the gynoecium, followed by the androecium, corolla and calyx (the outer-most and lowest whorl of the flower.

          Make sure you know these terms (consult the glossary at the back of the manual):

          determinate and indeterminate growth

          radial and bilateral symmetry

          perianth, petal, corolla, sepal, calyx

          A floral formula can express the number, fusion and insertion of floral parts.

          The symbols used are as follows:

          K : calyx (sepals)

          C : corolla (petals)

          P refers to the perianth, when calyx (K) and corolla (C) are not different.

          A : androecium i.e. the number and arrangement of stamens and staminodes.

          G : gynoecium i.e. the number and arrangement of carpels.

          G What is an apomorphy? What is a plesiomorphy? Can someone confirm these definitions? - Biology,[nobr][H1toH2]

          CHARACTERS VERSUS THEIR TOKENS

          Some of the problems described above may arise from the fact that symbols like ‘0’ and ‘−’ (as a ‘minus’ sign) have connotative associations with concepts such as absence or loss, which originate from usages in other (i.e. non-phylogenetic) contexts. A common thread among these problems is the implication that ‘0’ is treated as inherently different from any nonzero state, perhaps even standing in for primitiveness. This is perhaps a result of the frequent use of ‘0’ for the states of the root taxon as a matter of convention. The possibility arises that the convention sometimes gets mistaken (consciously or unconsciously) for a procedural necessity. The purpose of reviewing some details of phylogenetic counting algorithms earlier was to underscore the fact that the tokens only indicate an identity. This helps to evaluate not only how the above scoring procedures are problematic, but also how we choose among alternative ways of dealing with these problems, as described in the subsequent section.

          It is important not to confuse ‘0’ with a statement of primitiveness when drafting character lists and scoring matrices, especially for unordered characters. In theory, it makes no difference whether absence is represented by ‘−’, ‘+’, ‘0’, or ‘1’. Assuming you have not ordered or weighted characters, you could swap all instances of ‘0’ for ‘1’ and vice versa and you will still obtain the same result as before. The only thing that matters is that taxa that share the same conditions are coded the same way. Because of the default assumptions of transformational symmetry, there is no difference between 0 scores and non-0 scores where the assessment of a transformation cost takes place. States 1, 2, 3, etc., are not derived states until a phylogenetic analysis has been conducted and returns that result, and the Fitch algorithm will not add any additional steps if each appears independently in the tree or together. Similarly, state 0 is not the ‘plesiomorphic state’ simply because it is labelled 0. ‘Derived’ and ‘plesiomorphic’ are properties that are exposed as the phylogenetic algorithm assigns optimal values of the characters to internal nodes. They can be represented by any token the investigator chooses. It is the investigator's responsibility to ensure that the tokens accurately reflect the character information in a truly symmetric manner because the parsimony algorithm (unless given specific commands otherwise) will treat character transformations symmetrically. The consequence of failing to account for this symmetry will be a loss of grouping information.


          Evolution : Glossary

          Acquired trait A phenotypic characteristic, acquired during growth and development, that is not genetically based and therefore cannot be passed on to the next generation (for example, the large muscles of a weightlifter). (PBS evolution Glossary)

          Adaptation the evolutionary process whereby a population becomes better suited to its habitat. Can also refer to a feature which is especially important for an organism's survival. For example, the adaptation of horses' teeth to the grinding of grass, or their ability to run fast and escape predators. Such adaptations are produced in a variable population by the better suited forms reproducing more successfully, that is, by natural selection. (Wikipedia)

          Adaptationism or panselectionism a set of methods in the evolutionary sciences for distinguishing the products of adaptation from traits that arise through other processes. It is employed in fields such as ethology and evolutionary psychology that are concerned with identifying adaptations. Critics (most notably Richard Lewontin and Stephen Jay Gould) contend that the adaptationists (John Maynard Smith, W.D. Hamilton and Richard Dawkins being frequent examples) have over-emphasized the power of natural selection to shape individual traits to an evolutionary optimum, and ignored the role of developmental constraints, and other factors to explain extant morphological and behavioural traits. (Wikipedia)

          Adaptive radiation the rapid expansion and diversification of a group of organisms as they fill unoccupied ecological niches, evolving into new species or sub-species the classic example being Darwin's finches. This occurs as a result of different populations becoming reproductively isolated from each other, usually by adapting to different environments. Radiations specifically to increase in taxonomic diversity or morphological disparity, due to adaptive change or the opening of ecospace, may affect one clade or many, and be rapid or gradual The term can also be applied to larger groups of organisms, as in "the adaptive radiation of mammals" (see diagram below), although in this context it is perhaps better referred to as evolutionary radiation. Evolutionary radiation in this context refers to a larger scale radiation whereas rapid radiation driven by a single lineage's adaptation to their environment is adaptive radiation proper. Adaptive and evolutionary radiations in this latter context follow mass-extinctions, as when during the early Cenozoic mammals and large flightless birds filled ecological roles previously occupied in the Mesozoic by dinosaurs.

          Spindle diagram showing the adaptive radiation of placental mammals in the Cenozoic (Geological timeline at top of diagram). Placentals radiated rapidly after the extinction of the dinosaurs, and the modern diversity of form was established within the first 10 million years of the Tertiary (during the Paleocene). (Based on Gingerich 1984.)

          Advanced some evolutionary scientists and systematists reject terms like "primitive" or "advanced" when discussing fossil or recent organisms. It is felt that these terms imply ascent or teleology, and that terms like primitive and advanced terms suggest some degree of "improvement" or superiority in the case of organisms considered advanced in relation to those considered primitive. Such associations are of especial concern in cladistics, where an emphasis is on only verifiable empirical methodology. Hence value-neutral words like "derived" are used as an alternative. However, it could be argued that evolution can indeed refer to an increase in complexity and emergence of new characteristics. This being so, there is no reason why these terms cannot be used. (MAK)

          Allele Different versions of the same gene. For example, humans can have A, B or O blood type alleles. (W. R. Elsberry talk.origins via W.J. Hudson)

          Allometry The relation between the size of an organism and the size of any of its parts, first outlined by Otto Snell in 1892 and Julian Huxley in 1932. Allometric growth is the phenomenon where parts of the same organism grow at different rates. For example in various insect species (e.g., the Hercules Beetle), where a small change in overall body size can lead to an enormous and disproportionate increase in the dimensions of appendages such as legs, antennae, or horns. Allometric relations can be studied during the growth of a single organism, between different organisms within a species, or between organisms in different species. Contrast with isometric growth.

          Amino acid The molecular building blocks of proteins. The properties of a protein are determined by its particular amino acid sequence. There are 20 amino acids in the proteins of life on Earth.

          Anagenesis the evolutionary transformation of one species over time into another, or in other words , the emergence of a new character or attribute (which in in this case a new species) from an older one. One of the two main parameters of evolutionary change, the other being branching (either cladogenesis or budding). O'Keefe & Sander 1999 provide a case study of among mid Triassic pachypleurosaurs, and its interpretation using phenetic, cladistic, and stratigraphic methodologies. The diagram at the right by Paul Olsen, Lecture 5 Evolution, showing the relation between anagenesis and cladogenesis. See also fig. 1 at Talk Origins: Macroevolution showing anagenesis and cladogenesis as complementary parameters (see also ancestor, descendant). (MAK)

          Analogy/analogous structure Structures having similar function or superficial appearance, but have a different evolutionary origin. For example the wings of insects and the wings of birds. Contrast with homologous structures.

          The Ancestor's Tale popular science book written by Richard Dawkins. The book charts the evolutionary history of life, which is illustrated as a pilgrimage backward in time heading towards the origin of life. This creates of series of 40 "rendezvous" by following man, as the selected currently existing creature, through the most recent common ancestors (called 'concestor'). The basic structure of the book is modeled after Chaucer's Canterbury Tales. (EvoWiki)

          1880 photo of the Berlin Archaeopteryx specimen

          From Vogt, C. 1880. "Archaeopteryx macrura, an Intermediate Form between Birds and Reptiles". Ibis 4:434-456.

          Archaeopteryx arguably the most famous of all transitional forms, Archaeopteryx is the earliest and most primitive known bird, most of whose fossil remains were recovered in the 19th century, from the Jurassic Solnhofen limestone in Bavaria. Perfectly intermediate between reptile (or more correctly, theropod dinosaur) and modern bird, its discovery was powerful evidence for Darwinian evolution. (MAK). Wikipedia page (detailed coverage)

          Arms race in evolutionary biology just as is the case between two rival nations, positive feedback between two or more evolutionary lineages coevolving in such a way that each, in turn, develops more and more extreme/efficient defenses and weapons in response to the others' attributes. For example, a predator may evolve larger teeth or claws, resulting in the prey species developing faster speed, larger size or protective armour, requiring the predator lineage itself to develop further to be able to capture its prey. In addition to predator and prey, can also occur with the co-evolution of a parasite and its host. Alternatively, the arms race may be between members of the same species, as in sexual selection or Red Queen effects. See also escalation hypothesis. (MAK, Wikipedia)

          Artificial selection Selectively breeding animals and cultivate crops to select the most desirable traits in a plant or animal population. Most domesticated and agricultural species have been produced by artificial selection. It was Darwin's observations in this area that inspired the idea of natural selection (without human intervention)

          Ascent The premise that evolution directional, moving from primitive and less perfect to more complex and perfect forms, the whole constituting a sort of hierarchical gradation, usually with man at the top. The progression from (what is anthropocentrically considered) a lower to a higher form of life. Zallinger's iconic and often misinterpreted (it was never intended to portray a strictly linear model of evolution) March of Progress gives the classic representation of the layman's conception of evolution, showing man's progression from an ape-like ancestor through various intervening stages of ape-men, to modern human. . According to popular science writers like Stephen Jay Gould, thes idea of evolution as a straight-line from the slime to man and beyond is a concept that really has very little to do with true Darwinism, despite superficial appearances to the contrary. On the other hand, modern fields such as systems theory and the study of biodiversity through time shows that evolution is indeed directional in that it does progress to more complex forms (while simpler organisms such as bacteria continue alongside, it is a misinterpretation to assume that Darwinian thought and evolutionary theory in general support a naive anthropocentric hierarchy of being.

          The Evolution as Progress meme is however immensely influential in human thinking. It appears in Marxism, in Theosophy, in Humanism, in Transhumanism, and elsewhere besides. It is criticized and rebuked by anti-evolutionist religious creationists, who think they are opposing Darwinism, when they are actually opposing something that has nothing to do with Darwinism. Some popular thinkers, such as Teilhard de Chardin, have argued for an anthropocentric cosmology, culminating in a future omega point. (MAK)

          Asexual reproduction (also called Vegetative Reproduction) A form of duplication using only mitosis. Example, a new plant grows out of the root or a shoot from an existing plant. This process produces only genetically identical offspring since all divisions are by mitosis. 1. offspring called clones meaning that each is an exact copy of the original organism 2. this method of reproduction is rapid and effective allowing the spread of an organism 3. Since the offspring are identical, the only mechanism for introducing genetic diversity is mutation. (W.J. Hudson)

          Base The information coding part of DNA, the letters of the genetic code. The DNA molecule is a chain of nucleotides each consisting of a backbone made of a sugar and a phosphate group, with a nitrogenous base attached. There are four bases ("letters" so to speak) in the DNA "language": adenine (A), guanine (G), cytosine (C), or thymine (T). In RNA, uracil (U) is used instead of thymine. A and G belong to the chemical class called purines C, T, and U are pyrimidines. In a strand of DNA, bases are paired and are lined up across from one another: A pairs with T and G pairs with C. The sequence of bases along the DNA molecule determines what the DNA codes for (such as making a protein, or turning on or off a gene). In protein-coding regions, three base pairs code for a single amino acid. For example, the base pair sequence ATG codes for the amino acid methionine. (adapted from UCMP Understanding Evolution Glossary, and PBS evolution Glossary)

          Batesian mimicry A form of mimicry in which one non-poisonous species (the Batesian mimic) has evolved to imitate the warning signals of a harmful or poisonous species, to deter a predator. It is named after the English naturalist Henry Walter Bates, after his work in the rainforests of Brazil. Contrasted with Müllerian mimicry, a form of mutually beneficial convergence between two or more harmful species. (adapted from Wikipedia)

          Biological species concept An integral part of the modern evolutionary synthesis, defines a species as "a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature." BSC applies well to sexually reproducing animals, but not as well to plant life because there is greater gene flow between plant species. It is also difficult if not impossible to apply to the fossil record. Fossils are divided into species based on taxonomic classification (similarity of physical characteristics—see morphological species concept. See also cladistic species concept, ecological species concept, phenetic species concept, and recognition species concept. (W.J. Hudson. Kutschera & Niklas 2004 p.263).

          Bottleneck, bottleneck effect A form of genetic drift that occurs when a population's size is greatly reduced. Gene frequencies in the population are likely to change just by random chance and many genes may be lost from the population, reducing the population's genetic variation. When the population later expands in numbers, the resulting gene frequencies may be distinctly different from those before the bottleneck. (See also Founder effect.) (UCMP Understanding Evolution Glossary, M. W. Strickberger)

          Branching for the sake of convenience I use this term as the counterpole to anagenesis. See also Multiplication of species.

          Budding in a phylogenetic context, the origin of a new taxon (population group, species, or group of species), that does not affect the existence and attributes of the parental taxon (stem population group, or stem group of species). (Horandl & Stuessy 2010, p.1643). Mayr & Bock (2002) coined this term for divergence of a small group of populations, while the rest of the populations remain unchanged. Most obvious are cases of peripatric speciation after geographical isolation of a small group of populations. This is expected to happen mostly after colonizing events by a few individuals, then followed by rapid speciation and adaptation to new environments. Recent evidence from biogeographical studies on both animals and plants suggests that peripatric speciation may be more common than previously thought, since dispersal, even transoceanic dispersal, explains many disjunct distributional patterns. Buddings of this kind are often connected to a high amount of phenotypic change in the derivative species, which undergoes drift and adaptive change in the new ecological situation. In contrast, the source populations are neither in any novel environment, nor under any novel selective pressure." Contrast anagenesis, cladogenesis. (Horandl & Stuessy 2010, p.1644)

          Cambrian explosion The sudden appearance of all current animal phyla during the Early and Middle Cambrian.

          Cladogenesis (also called Splitting): The division of an ancestral parental lineage into two or more daughter lineages or species, rather than the transformation of the ancestral species in toto (anagenesis). In contrast to budding, splitting leads to extinction of the parental lineage. (W. R. Elsberry talk.origins via W.J. Hudson Horandl & Stuessy 2010, p.1643). As shown by the diagram (right) from Moore, Lalicker, & Fischer 1952 cladogenesis was recognised, along with anagenesis, as one of the two types of gradual evolution. This evolutionary paradigm was replaced in the 1970s and 80s by cladistics. The highly formalised trees that cladistics rely on do not allow for anagenesis, as a result cladogenesis (and then only a division into two daughter species) becomes the standard form of speciation . However, according to Horandl & Stuessy 2010, p.1644 (who argue for recognition of paraphyly): "only a portion of known speciation processes can be categorized as a split of a species in two or more isolated population groups. Allopatric speciation, whereby, e.g., a geographic barrier isolates population groups, does result in a complete disappearance of the original species. Allopatric speciation has been long advocated as the main speciation mechanism, especially in the zoological literature (Coyne & Orr, 2004). This mode of speciation occurs over longer time dimensions, and it divides the ancestral species into more or less equal portions. Allopatric speciation, therefore, fits well the cladistic model of symmetrical divergence, but this is no longer regarded as the predominant mode of speciation, especially in plants (e.g., Rieseberg & Brouillet, 1994). Other evolutionary processes, especially budding and merging, enhance asymmetrical divergence and therefore occurrence of paraphyly." . See also multiplication of species, adaptive radiation. (MAK)

          Codon a three base unit of DNA that specifies an amino acid or the end of a protein.

          Co-evolution Evolution in two or more species, such as predator and its prey or a parasite and its host, in which evolutionary changes in one species influence the evolution of the other species. See also evolutionary arms race. (PBS evolution Glossary)

          Co-extinction the loss of one species due to the extinction of another for example, the extinction of parasitic insects following the loss of their hosts. Co-extinction can also occur when a flowering plant loses its pollinator, or through the disruption of a food chain. (Wikipedia)

          Common ancestor The ancestral species that gave rise to two or more descendant lineages, and thus represents the ancestor they have in common.

          Common descent the premise that every group of organisms descended from a common ancestor, and that all groups of organisms, including animals, plants, and microorganisms, ultimately go back to a single origin of life on earth. (W.J. Hudson)

          Convergence of forms between placentals (left) and marsupials (right).

          Convergent evolution, Convergence process in which two or more distinct lineages independently evolve similar characteristics of one another. In other words, there is an evolutionary convergence between two unrelated or only distantly related types. This often occurs because both lineages face similar environmental challenges and selective pressures. A form of homoplasy. Compare Parallel Evolution: e.g. the shark, tuna, ichthyosaur, and dolphin all evolved a similar streamlined shape as large aquatic fast-swimming predators. (adapted from UCMP Understanding Evolution Glossary) Two types of convergence that could be distinguished are analogy (convergent modifications of a non-homologous structure or behaviour, e.g. the wings of insects (presumably derived from tergal paranota) and the wings of birds (derived from the vertebrate fore legs)) and homoiology (convergent modifications of a homologous structure or behaviour—e.g. The wings of pterosaurs, birds, and bats represent such a homoiology, since they are homologous as tetrapod fore leg, but were convergently modificated to flight devices (wings)). (Glossary of Phylogenetic Systematics by Günter Bechly)

          Creation The bringing forth of matter from nothing, or the development of life from non-living systems. cf. abiogenesis. (W. R. Elsberry in talk.origins via W.J. Hudson)

          Crossover The exchange of nucleotides between pairs of homologous chromosomes during mitosis or especially meiosis. (W. R. Elsberry in talk.origins)

          Darwin, Charles 19th-century naturalist considered the father of the science of evolution. His landmark work, On the Origin of Species, published in 1859, presented a wealth of facts supporting the idea of evolution and proposed a viable theory for how evolution occurs, via the mechanism he called "natural selection" (as a natural process analogous to artificial selection) Also published important works on coral reefs and on the geology of the Andes, and a popular travelogue of his five-year voyage aboard HMS Beagle, and a comprehensive scientific study of barnacles. (adapted from PBS evolution Glossary)

          Darwin's theory of evolution through natural selection can be summarised by means of three principles:

          1. Principle of variation. Among individuals within any population, there is variation in morphology, physiology, and behavior.
          2. Principle of heredity. Offspring resemble their parents more than they resemble unrelated individuals.
          3. Principle of selection. Some forms are more successful at surviving and reproducing than other forms in a given environment.

          (Griffiths AJF, Miller JH, Suzuki DT, et al. "Introduction", in An Introduction to Genetic Analysis. 7th edition. New York: W. H. Freeman 2000)

          Darwinian Of or pertaining to natural selection, or Darwin's theory of evolution in general. Sometimes taken to mean natural selection with gradualist assumptions, although it is now considered doubtful that Darwin was a uniformitarian to this degree. (modified from W. R. Elsberry in talk.origins)

          Darwinian classification see Evolutionary systematics.

          Darwinian evolution See Darwinism.

          Darwinism In 1859 Charles Darwin supplied a mechanism, namely natural selection, that could explain how evolution occurs. Darwin's theory of natural selection helped to convince most people that life has evolved and this point has not been seriously challenged in the past one hundred and forty years. It is important to note that Darwin's book "The Origin of Species by Means of Natural Selection" did two things. It summarized all of the evidence in favor of the idea that all organisms have descended with modification from a common ancestor, and thus built a strong case for evolution. In addition Darwin advocated natural selection as a mechanism of evolution. Biologists no longer question whether evolution has occurred or is occurring. That part of Darwin's book is now considered to be so overwhelmingly demonstrated that is is often referred to as the fact of evolution. However, the mechanism of evolution is still debated. cf. Modern Synthesis. (W.J. Hudson). Historically, Darwinism represented the stage in the development of evolutionary thought that began with the 1859 publication of On the Origin of Species. "Specifically, it refers to the Darwin/Wallace principle of natural selection as the major driving force in evolution. Since Darwin (1859, 1872) accepted Lamarck's principle of the inheritance of acquired characteristics as a source of biological variability, it is equally fair to call this the "Lamarck/Darwin/Wallace" period of evolutionary thought. (Kutschera & Niklas 2004, p.259–260)

          Descendent in this context, a population, lineage, or species, that arises through evolution from an ancestor (an earlier species or taxon). Where a number of descendants share the same ancestor (cladogenesis), the ancestor is called a common ancestor. (MAK)

          Diploid Having two alleles for every gene at every locus, one from the mother and one from the father. Most animals, including humans, are diploid. (W.J. Hudson)

          Directionality (in evolution) as here defined, the premise that evolution begins with simple or primitive structures or forms of life and moves to greater complexity or perfection hence some forms of life are more complex, advanced, or evolved relative to others see Systems Theory's definition of evolution. Results in a tree or hierarchy in which—depending on your perspective—multicellular life, vertebrate animals, or human beings, or self-consciousness, culture, or omega point are at its apex. Whilst the emergence of complexity is a self-evident fact, philosophers and scientists are divided over whether evolution itself is directional. See also complexification, emergence, great story. (MAK)

          DNA Deoxyribonucleic acid, the molecule that contains genetic information.

          Escalation hypothesis a hypotheses put forward by Geerat J. Vermeij. It states that organisms are in constant conflict with one another and therefore devote a lot of resources to thwarting the adaptations evolution brings to all competing organisms as time advances. This is in contrast to adaptations evolution may bring that are unrelated to competition with other organisms such as adapting to ecological niches based upon other factors such as geology and climate. Vermeij's extensive work with the characteristics of marine gastropod fossils informed his development of thoughts on escalation. One prediction of the Escalation Hypothesis is that individual species having fewer adaptations that enable them to compete with other life forms are more likely to survive a mass extinction event such as one of The Big Five. This is because there is more flexibility to fit into new ecological niches that arduous adaptations such as heavy shells or energy consuming venom production would hinder. (Wikipedia)

          Evolution (Biology) A change in the gene pool of a population over time. The process of evolution can be summarized in three sentences: Genes mutate. Individuals are selected. Populations evolve. (W.J. Hudson) A subset of Evolution (Systems Theory). See also Darwinism, Modern Synthesis . Note that in the biological context, evolution does not apply to individuals (in contrast with the premises of Conscious evolution). (MAK)

          Evolutionary game theory (EGT) is the application of game theory to interaction dependent strategy evolution in populations. EGT is useful in a biological context by defining a framework of strategies in which adaptive features can be modeled. It originated in 1973 with John Maynard Smith and George R. Price's formalization of evolutionarily stable strategies as an application of the mathematical theory of games to biological contexts, arising from the realization that frequency dependent fitness introduces a strategic aspect to evolution. EGT differs from classical game theory by focusing on the dynamics of strategy change more than the properties of strategy equilibria. Despite its name, evolutionary game theory has become of increasing interest to economists, sociologists, anthropologists, and philosophers.

          In Smith's and Price's paper, "The Logic of Animal Conflict", a computer model was used to show why animals had not adapted a "total war" strategy. Adaptations for males focused on maximizing their ability to compete with each other in order to maximize their dominance over a territory and better compete for mates. Using game theory, they were able to test a variety of evolutionary strategies to see which one emerged with the highest average payoff, explaining why animals have only evolved limited war strategy, in which risk of serious injury is low. (Wikipedia)

          Evolutionary psychology branch of psychology or evolutionary science that examines psychological traits—such as memory, perception, or language—from a modern evolutionary perspective. It seeks to identify which human psychological traits are evolved adaptations , that is, the functional products of natural selection or sexual selection. Evolutionary psychology has its historical roots in Charles Darwin's theory of natural selection.[4] Darwin's theory inspired William James's functionalist approach to psychology. Along with W.D. Hamilton's (1964) seminal papers on inclusive fitness, E. O. Wilson's Sociobiology (1975) helped to establish evolutionary thinking in psychology and the other social sciences. (Wikipedia)

          Evolutionary radiation see Adaptive radiation.

          Evolutionary synthesis see Modern Synthesis.

          Evolutionary Theory (or Evolutionary Mechanism Theory) Any one of several theories in biology dealing explicitly with some aspect of evolution or cumulative evolution. Examples include Sewall Wright's "shifting-balance theory", Eldredge and Gould's "punctuated equilibrium theory", the theory of common descent, Darwin's "descent with modification", Henry Fairfield Osborn's "orthogenesis", and "Gene Flow". While "evolutionary theory" is equivalent, the point that mechanisms are proposed and tested in evolutionary mechanism theories is worthy of stress and repetition. Some mechanisms increase genetic variation ( cf. mutation, recombination, gene flow ) and some decrease genetic variation ( cf. natural selection, genetic drift). (W. R. Elsberry talk.origins via W.J. Hudson)

          Fitness the ability of an individual organism to both survive and reproduce a central element of evolutionary theory. Fitness is equal to the average contribution to the gene pool of the next generation that is made by an average individual of the specified genotype or phenotype. If differences between alleles at a given gene affect fitness, then the frequencies of the alleles will change over generations the alleles with higher fitness become more common (in other words, natural selection). (Wikipedia)

          Fitness landscape Sewall Wright proposed that populations occupy adaptive peaks on a fitness landscape. In order to evolve to another, higher peak, a population would first have to pass through a valley of maladaptive intermediate stages. A given population might be "trapped" on a peak that is not optimally adapted. (Wikipedia)

          Founder effect Changes in gene frequencies that usually accompany starting a new population from a small number of individuals. The newly founded population is likely to have quite different gene frequencies than the source population because of sampling error (i.e., genetic drift). The newly founded population is also likely to have a less genetic variation than the source population. For a more detailed explanation, see our resource on adaptation in Evolution 101. (UCMP Understanding Evolution Glossary)

          Gene The fundamental physical and functional unit of heredity which carries information from generation to the next. (W. R. Elsberry talk.origins via W.J. Hudson)

          Gene family A set of related genes occupying various loci in the DNA, almost certainly formed by duplication of an ancestral gene and having a recognizably similar sequence. Members of a gene family may be functionally very similar or differ widely. The globin gene family is an example. (PBS evolution Glossary)

          Gene flow An evolutionary mechanism theory. Gene Flow states that new organisms may enter a population by migration from another population. If they mate within the population, they can bring new alleles to the local gene pool. In some closely related species, fertile hybrids can result from interspecific matings. These hybrids can vector genes from species to species. (W.J. Hudson)

          Gene frequency The frequency in the population of a particular gene relative to other genes at its locus. Expressed as a proportion (between 0 and 1) or percentage (between 0 and 100 percent). (PBS evolution Glossary)

          Gene selection, "selfish gene" theory, or gene-centered view of evolution theory that genes are the unit of selection. The theory states that although individuals are the object of selection, because of crossing over and recombination which shuffles genes around, it is the genes which are selected for over time. The alternatives to gene selection are group selection and individual selection.

          Gene selection theory is central to the understanding of contemporary evolutionary theory, and has developed from population genetics and the modern synthesis, and was established as the leading theory of natural selection during the Williams revolution. The revolution was based on the findings of population genetics, and other principal architects of the revolution include W.D. Hamilton, John Maynard Smith, Robert Trivers and Richard Dawkins, who popularised the revolution in The Selfish Gene.

          There is still some scientific debate about gene selection, which leading biologists such as Ernst Mayr rejecting the theory. Mayr (2000) states that the gene can not be the object of selection because it is the whole organism that lives, reproduces and dies, not individual genes. This, however, is not a problem for gene selectionism, which has always maintained that part of the environment in which genes are selected includes the other genes in the population, but because of recombination no combination of genes exist more than once, so although individuals may be the object of selection, genes are the units, and evolution consists of a change in independent allele frequencies in populations. (EvoWiki)

          Genetic diversity resulting from sources of genetic variation, it is the variety of alleles and genotypes within a population or species.

          Genetic drift Random changes in the frequency of genes in the population that are not due to selective pressure. This may occur because the different genotypes do not have a noticeable effect on the relative fitness of individuals (such as different mitochondrial haplotypes), or selection may not be strong enough to affect transmission of the genotype (for instance, on a recently-colonised island without predators). Genetic drift is a factor in neutral evolution. The significance of genetic drift in evolution is uncertain. In a large population, most of the factors affected by genetic drift will be minor, and drift is probably not significant over the population as a whole. However, in a small, isolated population drift may have a significant effect on the makeup of the population. CKT061201

          Genetic engineering Removing genes from the DNA of one species and splicing them into the DNA of another species using the techniques of molecular biology. (PBS evolution Glossary)

          Genetic recombination see Recombination.

          Genetics The branch of science which deals with elucidating the attributes and mechanisms of heredity in living systems. On Earth, this involves research into RNA and DNA. (W. R. Elsberry in talk.origins)

          Genome complete haploid complement of DNA (including all genes) from the chromosomes of the nucleus of an organism. (Developmental Biology 376 Glossary)

          Genotype The heritable information contained in an individual. (W. R. Elsberry in talk.origins) The set of two genes possessed by an individual at a given locus. More generally, the genetic profile of an individual. (PBS evolution Glossary)

          according to Moore, Lalicker, & Fischer

          Gradualism or phyletic gradualism evolutionary mechanism theory, based on the premise that evolutionary change takes place through the gradual change of populations and not by the sudden (saltational) production of new individuals that represent a new type. New species evolve through the steady and gradual transformation of the entire population. The standard evolutionary paradigm prior to the early 1970s, as shown by the diagram (right) from Moore, Lalicker, & Fischer 1952. This view is usually attributed to Darwin because of his being influenced by uniformitarian geology by Eldredge and Gould, who instead argued for Punctuated Equilibria. But Richard Dawkins explained that such constant-rate gradualism is not present in the professional literature, thereby the term only serves as a straw-man for punctuated equilibrium advocates. In his book The Blind Watchmaker, Dawkins argues against the idea that Charles Darwin himself was a constant-rate gradualist, as suggested by Niles Eldredge and Stephen Jay Gould. See also comments by John Wilkins and Larry Moran. (MAK W.J. Hudson, Wikipedia)

          Group selection theory that alleles can become fixed or spread because of the benefits they bestow on groups, regardless of the fitness of individuals within that group. Group selectionist ideas have been around since Darwin mentioned it in the Descent of Man as a possible mechanism of evolution of human altruism but were further elaborated by V.C. Wynne-Edwards in the 1960s.

          More correctly, group selection is defined as the differential survival and reproduction of groups (Wade 1977). A response to group selection occurs when the differences among groups has a heritable basis. For group selection this means not only single locus allelic differences, but also epistatic genetic differences, differences in genetically based interactions among individuals, and even potentially cultural differences. Thus, it is simplistic to speak of group selection simply in terms of the spread of an altruistic allele.

          Critiques, particularly by George C. Williams (1966), John Maynard Smith (1964) and C.M. Perrins (1964) cast serious doubt on group selection as a major mechanism in evolutionary history. These responses were part of the lead up to the Williams revolution in which gene selection theory became the prominent paradigm. (EvoWiki)

          Haploid having only half the normal complement of chromosomes. (W. J. Hudson)

          Heterozygous Having two different alleles at a given locus. (W. J. Hudson)

          Heredity the passing of traits to offspring (from its parent or ancestors). This is the process by which an offspring cell or organism acquires or becomes predisposed to the characteristics of its parent cell or organism. Through heredity, variations exhibited by individuals can accumulate and cause some species to evolve. Evolution in organisms occurs through changes in heritable traits—particular characteristics of an organism. In humans, for example, eye colour is an inherited characteristic and an individual might inherit the "brown-eye trait" from one of their parents. Inherited traits are controlled by genes and the complete set of genes within an organism's genome is called its genotype. The complete set of observable traits that make up the structure and behaviour of an organism is called its phenotype. These traits come from the interaction of its genotype with the environment. As a result, many aspects of an organism's phenotype are not inherited. For example, suntanned skin comes from the interaction between a person's genotype and sunlight thus, suntans are not passed on to people's children. The study of heredity in biology is called genetics. See also Modern Synthesis, Mendelian inheritance. (Wikipedia)

          Homoiology Convergent modifications of a homologous structure (or behaviour). The wings of pterosaurs, birds, and bats represent such a homoiology, since they are homologous as tetrapod fore leg, but were convergently modificated to flight devices (wings). (Glossary of Phylogenetic Systematics by Günter Bechly

          Homologous chromosomes chromosome pairs of the same length, centromere position, and staining pattern, with genes for the same characteristics at corresponding loci. One homologous chromosome is inherited from the organism's mother the other from the organism's father. (Wikipedia)

          Homology/homologous structure coined by Richard Owen to refer to essential similarity, rather than analogy. With the rise of evolutionary theory, came to mean similarity due to sharing a common evolutionary origin (Rieppel, 1993, pp.2–3). In this definition, which is still the one used, homology refers to a character shared by a set of species and present in and inherited, with or without modification, from their common ancestor. For example, the bones in a bat's wing, a dog's front leg, and a human arm, are the same, although modified to serve different functions (see following diagram). Contrast with homoplasious and analogous.

          The principle of homology illustrated by the evolutionary radiation of the forelimb of mammals. All conform to the basic pentadactyl pattern but are modified for different usages. The third metacarpal is shaded throughout the shoulder is crossed-hatched.

          Homoplasy in relation to apomorphy, autapomorphy, synapomorphy, plesiomorphy and symplesiomorphy

          Homoplasy having an independent evolutionary origin. Features that are similar but not the result of inheritance from a common ancestor. The two main causes of homoplasious characters are convergent evolution (appearance of the same character in at least two distinct lineages) and character reversion (the return to an ancestral character). Use of homoplasies when building a cladogram is sometimes unavoidable but is to be avoided when possible. (modified from Wikipedia and UCMP Understanding Evolution Glossary)

          Homozygous Having two identical alleles at a given locus. (W.J. Hudson)

          Hopeful monster termed coined by the German-born geneticist Richard Goldschmidt, who thought that small gradual changes could not bridge the divide between microevolution and macroevolution. In The Material Basis of Evolution (1940), Goldschmidt wrote "the change from species to species is not a change involving more and more additional atomistic changes, but a complete change of the primary pattern or reaction system into a new one, which afterwards may again produce intraspecific variation by micromutation." His thesis however was universally rejected and has been widely ridiculed within the biological community, which favored the neo-Darwinian explanations of R.A. Fisher, J. B. S. Haldane and Sewall Wright. (Wikipedia)

          Horizontal gene transfer (HGT) or Lateral gene transfer (LGT) any process in which an organism incorporates or transfers genetic material to or from another organism, without being the offspring of that organism. Often, the transference is between members of different species. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g., its parent or a species from which it has evolved. Most thinking in genetics has focused upon vertical transfer, but there is a growing awareness that horizontal gene transfer is a highly significant phenomenon and amongst single-celled organisms perhaps the dominant form of genetic transfer. Bacteria, for example, frequently pass copies of particular genes to one another and pick up foreign genetic material from their environment, resulting in horizontal transfer. Mechanisms include Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA), a process relatively common in bacteria, less so in eukaryotes, and used in laboratories to insert novel genes into bacteria for experiments or for industrial or medical applications (genetic engineering) Transduction, the process in which bacterial DNA is moved from one bacterium to another by a virus Bacterial conjugation, a process in which a bacterial cell transfers genetic material to another cell by cell-to-cell contact and Gene transfer agents, virus-like elements encoded by the host that are found in the alphaproteobacteria order Rhodobacterales. (Wikipedia, UCMP Understanding Evolution Glossary) "has had an important role in eukaryotic genome evolution, but its importance is often overshadowed by the greater prevalence and our more advanced understanding of gene transfer in prokaryotes. Recurrent endosymbioses and the generally poor sampling of most nuclear genes from diverse lineages have also complicated the search for transferred genes. Nevertheless, the number of well-supported cases of transfer from both prokaryotes and eukaryotes, many with significant functional implications, is now expanding rapidly." (Keeling & Palmer 2008, abstract)

          Hybrid an offspring resulting from cross-breeding between two different species. Animal hybrids are often infertile. The mule for example is a cross of female horse and a male donkey. The hinny, a cross between a female donkey and a male horse (mule and hinny are reciprocal hybrids). However there are also fertile hybrids, e.g. between coyotes, wolves, dingoes, jackals and domestic dogs. Plant species hybridize more readily than animal species, and the resulting hybrids are more often fertile hybrids and may reproduce, though there still exist sterile hybrids and selective hybrid elimination where the offspring are less able to survive and are thus eliminated before they can reproduce. A number of plant species are the result of hybridization and polyploidy with many plant species easily cross pollinating and producing viable seeds, the distinction between each species is often maintained by geographical isolation or differences in the flowering period. (Wikipedia)

          Inclusive fitness theory in evolutionary biology and evolutionary psychology it holds that an organism can improve its overall genetic success by cooperative, social behavior. The theory defines the inclusive fitness of an organism as the sum of its classical fitness (how many of its own offspring it produces and supports) and the number of equivalents of its own offspring it can add to the population by supporting others. (PBS evolution Glossary)

          Inheritance of acquired characteristics theory proposed by Jean Baptiste Lamarck, according to whom evolution occurs through the inheritance of traits or abilities an organism acquires in life. For example, the ancestral giraffe stretched its neck to reach the leaves of trees, and as a result passed on a slightly longer neck and legs to its offspring. Also referred to as the "use–disuse theory." Despited being rejected by Weismannian Neo-Darwinism, Lamarckism remained popular well into the early twentieth century, especially in France, but was supplanted by the synthesis of Darwinian and Mendellian theory.

          Intron "intervening sequence," a stretch of nucleic acid sequence spliced out from the primary RNA transcript before the RNA is transported to the cytoplasm as a mature mRNA can refer either to the RNA sequence or the DNA sequence that from which the RNA is transcribed. See also exon. (Developmental Biology 376 Glossary)

          Lineage in this context, an evolutionary lineage, a sequence of ancestors and descendants (which may be cells, genes, populations, species) that evolve through time.

          Locus The location of a gene on a chromosome. At any locus there can be many different alleles in a population, more alleles than any single organism can possess. For example, no single human can simultaneously carry the A, B and an O blood-type allele. (W.J. Hudson)

          Macroevolution Evolution at or above the species level. The boundary between macro- and micro- is fuzzy, as some researchers prefer to include speciation in micro- and others reason that the only macro-process that gives distinctive events is speciation. Speciation events are thus, to many scientists, examples of macroevolution. Another definition is evolution too imperceptible to be observed within the lifetime of one researcher . (W. R. Elsberry in talk.origins via W. J. Hudson) link: Macroevolution Its Definition, Philosophy and History by John Wilkins

          By Wikipedia users Seb951 and Stannered.

          Mass extinction Event involving higher extinction rates than the usual degree of background extinction. See Big Five for diagram of extinction rates, and synopsis of five major extinctions.

          Meiosis A process which converts a diploid cell to a haploid gamete, and cause a change in the genetic information to increase diversity in the offspring. (W.J. Hudson). In the first stage of sexual reproduction, which is meiosis, the number of chromosomes is reduced from a diploid number (2n) to a haploid number (n). During fertilization, haploid gametes come together to form a diploid zygote and the original number of chromosomes (2n) is restored. (Wikipedia graphic by Stannered)

          Meme controversial concept proposed by Richard Dawkins. A meme is a "a unit of cultural inheritance, hypothesized as analogous to the particulate gene and as naturally selected by virtue of its 'phenotypic' consequences on its own survival and replication in the cultural environment." A meme can be an idea, skill, story, or custom, which is passed from one person to another by imitation or teaching. Some theorists argue that memes are the cultural equivalent of genes, and reproduce, mutate, are selected, and evolve in a similar way. The study of memes is called memetics. (Mavericks of the Mind PBS evolution Glossary)

          Mendelian inheritance The mode of genetic inheritance of all diploid species, and therefore of nearly all multicellular organisms. Inheritance is controlled by genes, which are passed on to the offspring in the same form as they were inherited from the previous generation. At each locus an individual has two genes—one inherited from its father and the other from its mother. The two genes are represented in equal proportions in its gametes. (PBS evolution Glossary) For quite some time, the rediscovery of Mendel's work was considered to be the conclusive nail in the Darwinian coffin, killing off the idea of natural selection as Darwin proposed it. Since by the publication of the sixth edition of Darwin's "Origin of Species," Darwin had almost inextricably bound natural selection with his hypothesis on the mechanism of heredity, "pangenesis," this view was quite understandable. However, by the early 1940's, the neo-Darwinian synthesis had met and addressed the criticisms of the Mendelists. (Peter J. Bowler. 1984. Evolution: the history of an idea. University of California Press. Review by W. R. Elsberry link)

          Table showing how genes exchange according to segregation or independent assortment during meiosis and how this translates into the Mendel's Laws.

          Microevolution Evolution within the species level, or a change in allele frequency in a population over time. Note that this connotation is equivalent to evolution. All "Scientific Creationists" so far admit that microevolution is observed. Some Theistic Anti-Evolutionists may not. (W. R. Elsberry in talk.origins via W. J. Hudson)

          Mimicry imitative behavior, one species resembling one another, and gaining advantages as a result. For example harmless flies that have the same colouration as bees and wasps. Because predators know that wasps sting they tend to avoid anything that looks like them. See Batesian mimicry and Müllerian mimicry. (Wikipedia glossary)

          Mitochondria (sing. mitochondrion): A a small round organelle found in most cells in nearly all eukaryotes. They are surrounded by two membranes, the inner of which is folded into invaginations called cristae, where aerobic respiration takes place. Mitochondria produce enzymes that convert food to energy. They contain DNA that codes for some mitochondrial proteins. Because mitochondria are generally carried in egg cells but not in sperm, mitochondrial DNA is inherited from mothers but not fathers. Hence it is possible to trace ancestry through the mother's line (see also mitochondrial Eve). (PBS evolution Glossary, Wikipedia)

          Mitosis Cell division. All cell division in multicellular organisms occurs by mitosis except for the special division called meiosis that generates the gametes. (PBS evolution Glossary)

          Modern Synthesis Also referred to as "evolutionary synthesis", "synthetic theory", and especially modern evolutionary synthesis. The 1920s saw the emergence of an expanded version of Darwinism, which was founded by Ronald Fisher, J. B. S. Haldane and Sewall Wright. They reconciled the idea of evolution by natural selection with the discontinuous, particulate nature of genes. This was the essence the modern synthesis of Darwin's theory and Mendelian genetics. The new synthesis continued to develop in the 1940s, notably with Julian Huxley's, Evolution: The Modern Synthesis (1942) and Bernhard Rensch's, Evolution Above the Species Level (1947). Natural selection was seen as the dominant force shaping evolutionary change. Rensch expressed the view that nothing in biological nature suggests that any evolutionary processes other than natural selection work on the natural genetics of variation within populations. The Great Debate: Darwinism Today. The synthetic paradigm revolution was much broader than the neo-Darwinian concept of Weismann and Wallace, incorporating facts from such fields as genetics, systematics, and paleontology. (Kutschera & Niklas 2004, p.256)

          The Modern Synthesis is a theory about how evolution works at the level of genes, phenotypes, and populations whereas Darwinism was concerned mainly with organisms, speciation and individuals. Modern Synthesis differs from Darwinism in three important aspects: 1. It recognizes several mechanisms of evolution in addition to natural selection. One of these, random genetic drift, may be as important as natural selection. 2. It recognizes that characteristics are inherited as discrete entities called genes. Variation within a population is due to the presence of multiple alleles of a gene. 3. It postulates that speciation is (usually) due to the gradual accumulation of small genetic changes. This is equivalent to saying that macroevolution is simply a lot of microevolution. (W. R. Elsberry in talk.origins via W. J. Hudson)

          Mosaic evolution Because evolution does not occur uniformly, but rather different characteristics evolve at different rates, transitional organisms tend to have a mosaic of characteristics of both ancestral/primitive and more specialised descendants. So for example early tetrapods had both fish-like and amphibian features, and Archaeopteryx possessed both dinosaur and bird-like features. (MAK)

          Multiplication of species The theory that species multiply, either by splitting into daughter species or by "budding", that is, by the establishment of geographically isolated founder populations that evolve into new species. (W. R. Elsberry in talk.origins via W. J. Hudson)

          Mutation An error in duplication of genetic material which results in a different sequence of and/or a different number of base pairs in the copy than were in the original. Mutation creates new alleles. (W. R. Elsberry in talk.origins via W. J. Hudson)

          Morphology The study of the form and structure of organisms, such as animals and plants and their fossil remains. For example, comparing the shape of the femur in different grazing mammals is a morphological study. (UCMP Understanding Evolution Glossary). Gross morphology refers to the collective structures or an organism as a whole as a general description of the form and structure of an organism, taking into account all of its structures without specifying an individual structure. Anatomy is the study of the form and structure of internal features of an organism. Comparative Morphology is analysis of the patterns of the locus of structures within the body plan of an organism, and forms the basis of taxonomical categorization. Functional Morphology: the study of the relationship between the structure and function of morphological features. Experimental Morphology is study of the effects of external factors upon the morphology of organisms under experimental conditions, such as the effect of genetic mutation. (Wikipedia Morphology pertains to the phenotype rather than the genome ("molecular morphology" has been used for some time for describing the structure of compound molecules, such as polymers and RNA, is a distinct field).

          Natural selection The differential reproduction and, thereby, transmission of alleles between generations, of individuals in a population, due to heritable variation in a trait or traits which they possess. This is one mechanism by which evolution can occur. (W. R. Elsberry in talk.origins via W. J. Hudson). Conceived independently and then jointly published by Darwin and Wallace, and substantially elaborated upon in the early part of the twentieth century with the rediscovery of Mendelian genetics and then advances in population genetics. (Kutschera & Niklas 2004, p.256)

          Neo-Darwinism historically, term coined by Romanes (1895) to refer to the incorporation of Weismann's ideas on heredity into Darwin's theory of natural selection, showing how biological variation is generated and rejecting the Lamarckian inheritance of the earlier Darwinism. (Kutschera & Niklas 2004, p.260). The term is also used as a synonym for Modern Synthesis, or even any modern approach to evolutionary theory

          Neutral theory of molecular evolution The neutral theory of molecular evolution was first formally suggested by Motoo Kimura in 1968, and maintains that the majority of mutations occurring within a population are selectively neutral (i.e. have neither a positive or negative effect), and that genetic drift rather than natural selection is a major factor in differences between populations. While debate still occurs about the relative importance of these two processes, the neutral theory has become the null hypothesis for tests of whether natural selection has occurred in a given lineage. One major implication of this theory is that mutations should accumulate at a fairly constant rate, and therefore the divergence times between lineages should be calculable from the degree of divergence—the so-called molecular clock. The usefulness and correct application of molecular clocks remains a highly contentious subject in studies of evolution. References: Kimura, M. 1968. Evolutionary rate at the molecular level. Nature 217: 624–626. pdf Wikipedia: Neutral theory of molecular evolution. CKT070830

          Neo-Lamarckism Popular alternative to Darwinism during the late 19th and early 20th centuries, based on Lamarck's idea of acquired characteristics. Neo-Lamarckism was supported by natural theology, popular in America at the turn of the century. Spencer supported neo-Lamarckism. "Against selection itself Spencer [1893] used an argument that had considerable force when measured against the pregenetical selection theory (Ridley, 1982a). He pointed out that when a new structure evolved, all the rest of the body would have to accommodate the new development. Thus a series of variations would be required to adjust the overall structure in a manner correlated to the new organ. What would be the chance of all these variations appearing together at the right time, if the species had to depend on random variation? Selection might explain the changes in a single organ, but not an integrated transmutation of the whole body." Lamarckism, as Spencer pointed out, could provide an explanation for the integrated development or elimination of organs. This was seen to be a weakness of natural selection. "The law of "acceleration of growth" was first published in Cope's "On the origin of genera" of 1867 (reprinted in Cope, 1887) and in Hyatt (1868). According to this law, evolution progresses by a series of sudden additions to the growth of the individual. At certain points in time, every individual in a species begins to exhibit a new phase of growth that advances all to the form of a new species. To make room for this addition, the old adult form is compressed back to an earlier phase of growth, hence the "acceleration" of growth to accommodate an extra stage before maturity. Cope denied that evolution on a small scale is a branching process, claiming instead that each genus represents a group of species that have reached the same point in the historical development of their group. Their close relationship is not a sign of common descent but of identical position in the scheme of development." "Cope postulated a growth-force named "bathmism" concentrated in those parts of the body most in use, it developed them at the expense of other areas. By the last decade of the century, this Lamarckism had been developed to considerable depth (Cope, 1887, 1896 Hyatt, 1880, 1884, 1889)." Referring to the case of the midwife toad: "Was the india ink added by someone wishing to preserve the original marks, or was it deliberate sabotage, perhaps a Nazi plot to discredit evidence hostile to their racial theories? Koestler certainly has suggested that Kammerer's experiments may have been genuinely successful, although others think he was simply dishonest. (Aronson, 1975)." (Peter J. Bowler. 1984. Evolution: the history of an idea. University of California Press. Review by W. R. Elsberrylink)

          Nondirectionality (in evolution) as here defined, the premise that evolution does not have a direction, that nature does not tend towards greater complexity, that it is misleading to speak of "lower", "simpler", or "primitive", and that all attempts to impose a narrative are hold-overs of Victorian ideas such as ascent. Non-directionality is favoured by some evolutionists such as Steven Jay Gould. See also cosmicism, reductionism. Contrast with anthropocentrism, ascent, directionality, Evolution (Systems Theory) and teleology. (MAK)

          Non-missing link Although creationists often claim that no transitional forms are known in the fossil record, in fact the reverse is the case. (see Link). As it would be oxymoronic to refer to these intermediate species by their popular moniker as "missing link" (e.g. link link) I have coined the informal term "non-missing link". See also anagenesis, ancestor, common ancestor, basal taxon, stem group. Note that even though, in view of the vagaries of the fossil record, the non-missing link may not necessarily be the actual, literal, common ancestor of all later species in that lineage (although in some cases where stratigraphic preservation is very good it might), but it would certainly be a closely related form. (MAK)

          Ontogeny The process of the development and growth of an individual from zygote to adult. (W. R. Elsberry in talk.origins). See also developmental biology, evo-devo, morphogenesis.

          Ontogeny recapitulates phylogeny See Recapitulation.

          Orthogenesis a conjecture related to Lamarckism. "The crucial difference is that the trends of orthogenesis are not adaptive. Far from being a positive response to the environment, they represent a nonutilitarian force that can in some cases drive the species to extinction. In this there is a similarity to Hyatt's concept of racial senility." "A famous case was that of the recently extinct "Irish elk", thought to have died out because its antlers became too large as a result of an internal trend (Gould, 1974b). It seemed as though the trend that produced the antlers, perhaps originally for some useful purpose, had acquired a momentum of its own that had carried it far beyond the point of utility. This "overdevelopment" theory of extinction became widely popular among non-Darwinian paleontologists in the early twentieth century." "Strong support for orthogenesis came from the Russian biologist Leo S. Berg (translation 1926), but perhaps its best known exponent was the American paleontologist Henry Fairfield Osborn." Aristogenesis—Osborn's own term for orthogenesis. Mendelism was originally viewed as an alternative to selection. (Peter J. Bowler. 1984. Evolution: the history of an idea. University of California Press. Review by W. R. Elsberry link)

          Organism individual member of a species, that is, a single biological entity, either unicellular (single-celled) or multicellular (many-celled). A living system such as animal, plant, fungus, or eukaryote or prokaryote micro-organism, capable of response to stimuli, reproduction, growth, and maintenance of homeostasis as a stable whole. Colloquially and informally, the term might also be used in evolutionary narratives to refer to a species or population, rather than just an individual. (from Wikipedia, MAK, Fossil Mall)

          Parallel evolution the development of a similar trait or traits in related, but distinct, species descending from the same ancestor, but from different clades or lineages. For example:

          • Old and New world porcupines shared a common ancestor, both evolved strikingly similar quill structures this is also an example of convergent evolution as similar structures evolved in hedgehogs, echidnas and tenrecs.
          • Contemporaneous evolution of browsing horses and paleotheres both of which shared the same environmental space.
          • Upright posture independently developed among several lines of TriassicArchosaurs.
          • Internal fertilization has evolved independently in sharks, some amphibians and amniotes.
          • The Patagium is a fleshy membrane that is found in gliding mammals such as: flying lemurs, flying squirrels, sugar gliders and the extinct Volaticotherium. These mammals acquired the patagium independently.
          • South American Pyrotherians have evolved a body plan (graviportal limbs, trunk, tusks) similar to early proboscideans. indicates that the lophophore, a complex feeding structure, evolved independently among bryozoa and brachiopod, two phyla previously grouped together but now considered only distantly related.

          One of the most spectacular examples of parallel evolution is provided by the two main branches of the mammals, the placentals and marsupials, which have followed independent evolutionary pathways following the break-up of land-masses such as Gondwana roughly 100 million years ago. In South America, marsupials and placentals shared the ecosystem (prior to the Great American Interchange) in Australia, marsupials prevailed and in the Old World the placentals won out. However, in all these localities mammals were small and filled only limited places in the ecosystem until the mass extinction of dinosaurs sixty-five million years later. At this time, mammals on all three landmasses began to take on a much wider variety of forms and roles. While some forms were unique to each environment, surprisingly similar animals have often emerged in two or three of the separated continents. Examples of these include the litopterns and horses, whose legs are difficult to distinguish the European sabre-toothed cat (Machairodontinae) and the South American marsupial sabre-tooth (Thylacosmilus) the Tasmanian wolf and the European wolf likewise marsupial and placental moles, flying squirrels, and (arguably) mice. (modified from Wikipedia)

          Phenotype The set of measurable or detectable physical or behavioral features of an individual. The phenotype represents the expression of the genotype of the individual as modified by environmental conditions during the individual's ontogeny. (W. R. Elsberry in talk.origins)

          Phylogeny term coined by Haeckel (Haeckel 1866): the study of the family history of life, the evolutionary relationships among groups of organisms, often illustrated with a branching evolution tree. More

          Piltdown Man famous 1912 hoax of early fossil man, consisting of a human skull, ape jaw, and filed down teeth. Had a significant detrimental impact on early research on human evolution: discoveries of Australopithecine fossils found in the 1920s in South Africa were ignored and instead the popular (but erroneous) theory argued that the human brain expanded in size before the jaw adapted to new types of food. rather than the reverse. Definitively exposed as a forgery by scientists back in 1953. (MAK, Wikipedia)

          Polyploidy containing more than two paired (homologous) sets of chromosomes. (Wikipedia)

          Population A group of potentially inter-breeding individuals of the same species found in the same place at the same time (Booth et al. 2003). A group of organisms, typically a single species, and typically isolated from other members of its species in some manner. (W.J. Hudson)

          Plasmid A genetic element that exists (or can exist) independently of the main DNA in the cell. In bacteria, plasmids can exist as small loops of DNA and be passed between cells independently. (PBS evolution Glossary)

          Primitive ancestral, similar or identical to the original forms, basal or stem member of a lineage, tends to be a generalist, lacks the specialised features of its descendants. Cladistics rejects terms like "primitive", instead using the more technical and (to outsiders and non-paleo geeks) obscure plesiomorphy. Nevertheless "primitive" does not have to equate anthropomorphically with advancement, technology, etc, compare "primeval" or "primordial". See also my comments re "advanced". (MAK)

          Gradual and Punctuated evolution

          Punctuated equilibria (More popularly known as punctuated evolution): an evolutionary theory that argues that new species evolve suddenly and in geographically isolated areas. Most speciation involves cladogenesis rather than anagenesis, and occurs via peripatric speciation. Hence speciation is rarely found in the fossil record, because established, populous and widespread species (the sort that are most likely simply through greater numbers to leave fossil remains) usually change slowly, if at all, during their time of residence. New species tend to develop in a geographically limited region and stratigraphically limited extent, which is small in relation to the overall time and distribution of the species. Sampling of the fossil record will reveal a pattern of most species in stasis, with abrupt appearance of newly derived species being a consequence of ecological succession and dispersion. Adaptive change in lineages occurs mostly during periods of speciation, and trends in adaptation occur mostly through the mechanism of species selection. See punctuated equilibria FAQ on the talk.origins archive site. (W. R. Elsberry in talk.origins via W. J. Hudson, modified).
          Right: Gradual and Punctuated evolution. Gradual evolution (or phyletic gradualism) occurs where change is small and constant punctuated evolution where change is very rapid, while most of the time there is virtually no change. (Diagram by Paul Olsen, Lecture 5 Evolution—url main reference: Eldredge & Gould 1972)

          Protein the building blocks of cells large molecules made up of a sequence of amino acids. Many of the important large molecules in living organisms—for example, enzymes—are proteins. (Fossil Mall glossary, MAK)

          Quasispecies Darwinian evolution of self-replicating entities within the framework of physical chemistry. Put simply, a quasispecies is a large group or cloud of related genotypes that exist in an environment of high mutation rate, where a large fraction of offspring are expected to contain one or more mutations relative to the parent. This is in contrast to a species, which from an evolutionary perspective is a more-or-less stable single genotype, most of the offspring of which will be genetically accurate copies.

          The quasispecies model is useful in providing a qualitative understanding of the evolutionary processes of self-replicating macromolecules such as RNA or DNA or simple asexual organisms such as bacteria or viruses (viral quasispecies), and is helpful in explaining something of the early stages of the origin of life. Quantitative predictions based on this model are difficult because the parameters that serve as its input are hard to obtain from actual biological systems. The quasispecies model was put forward by Manfred Eigen and Peter Schuster based on initial work done by Eigen. (Wikipedia)

          r-selection, r-selected species A species that produces a large number of off-spring, each of which receives little care (quantity rather than quality). R-selected species are better suited for variable or unpredictable environments. (Wikipedia glossary)

          Racial senility intriguing but long refuted theory that certain long-lived lineages became old and "senile", by analogy with individual development, as their evolutionary novelty is used up. Developed by Alpheus Hyatt to explain the exotic shapes of some Cretaceous ammonite shells, horns and plates on dinosaurs, and so on. (MAK)

          Random Unpredictable in some way. Mutations are "random" in the sense that the sort of mutation that occurs cannot generally be predicted based upon the needs of the organism. However, this does not imply that all mutations are equally likely to occur or that mutations happen without any physical cause. Indeed, some regions of the genome are more likely to sustain mutations than others, and various physical causes (e.g., radiation) are known to cause particular types of mutations. (UCMP Understanding Evolution Glossary)

          Recapitulation The theory of recapitulation, also called the biogenetic law or Embryological parallelism, and often expressed as the phrase "ontogeny recapitulates phylogeny". The hypothesis that in developing from embryo to adult, animals go through stages resembling or representing successive stages in the evolution of their remote ancestors. Therefore, each phase of the ontogeny of an individual directly represents the adult phase of some ancestor species in the phylogeny of the species to which the individual belongs. With different formulations, such ideas have been applied to several fields, including biology, anthropology and education theory. In biology, there are several examples of embryonic stages showing features of ancestral organisms, but a "strong" formulation of the concept has been discredited. The concept originated in the 1790s among the German Natural philosophers and, as proposed by Étienne Serres in 1824–26, became known as the "Meckel–Serres Law". In 1866, the German zoologist Ernst Haeckel proposed that the embryonic development of an individual organism (its ontogeny) followed the same path as the evolutionary history of its species (its phylogeny). This principle is recognized to be inaccurate in several respects, and its use is now generally deprecated. The turn of phrase is attributed to Ernst Haeckel, while the "biogenetic law" upon which it was based can be traced back to von Baer. (W. R. Elsberry in talk.origins, Wikipedia)

          Recognition species concept A definition of a species as a set of organisms that recognize one another as potential mates they have a shared mate recognition system. Compare with biological species concept, cladistic species concept, ecological species concept, and phenetic species concept. (Fossil Mall glossary) See other species definitions.

          Recombination Recombination creates new combinations of alleles. Recombination primarily occurs through sexual reproduction, where diploid cells form haploid gametes. The organism inherits one gamete each from the mother and the father, and the gametes are 'recombined' to form a new diploid chromosome. Recombination can occur not only between genes, but within genes as well. Recombination within a gene can form a new allele. (cf. mutation ) Recombination is a mechanism of evolution because it adds new alleles and combinations of alleles to the gene pool. (W.J. Hudson)

          Red Queen's Hypothesis or Red Queen Effect is an evolutionary hypothesis. The term is taken from the Red Queen's race in Lewis Carroll's Through the Looking-Glass. The Red Queen said, "It takes all the running you can do, to keep in the same place." The Red Queen Principle can be stated thus: In reference to an evolutionary system, continuing adaptation is needed in order for a species to maintain its relative fitness amongst the systems being co-evolved with. The hypothesis is intended to explain two different phenomena: the advantage of sexual reproduction at the level of individuals, and the constant evolutionary arms race between competing species. In the first (microevolutionary) version, by making every individual an experiment when mixing mother's and father's genes, sexual reproduction may allow a species to evolve quickly just to hold onto the ecological niche that it already occupies in the ecosystem. In the second (macroevolutionary) version, the probability of extinction for groups of organisms is hypothesized to be constant within the group and random among groups. It's counterpart is the Court Jester Hypothesis, which proposes that macroevolution is driven mostly by abiotic events and forces. (Wikipedia)

          Reproductive isolation Isolation of one species or population from another species or population by differences in reproductive traits or habits. The two species or populations may or may not share the same environmental range. An example of two species being reproductively isolated are similar species of animals that breed at different times of the year. (W.J. Hudson)

          Ring species A situation in which two reproductively isolated populations living in the same region are connected by a geographic ring of populations that can interbreed. (PBS evolution Glossary)

          Ribonucleic acid (RNA): A molecule similar to DNA, but with only a single strand, by which the genetic code of DNA is converted into proteins in cells. It has three forms: Messenger RNA, ribosomal RNA, and transfer RNA. Some viruses carry RNA as their genetic material instead of DNA. There has been speculation that an "RNA world" preceded current life on Earth.

          Selective pressure any environmental factors such as scarcity of food or extreme temperatures that favour the survival of only those organisms with characteristics that provide resistance or adaptability. (based on PBS evolution Glossary)

          Sexual selection a trait that makes an individual more likely to find a mate than others. A microevolutionary process. (Wikipedia: Glossary of ecology). This process may produce traits that seem to decrease an organism's chance of survival, while increasing its chances of mating. (UCMP Understanding Evolution Glossary)

          Shifting Balance Theory Sewall Wright's 'Shifting Balance' theory argues that populations are often divided into smaller subpopulations. Drift could cause allele frequency differences between subpopulations if gene flow was small enough. If a subpopulation was small enough, the population could even drift through fitness valleys in the adaptive landscape. Then, the subpopulation could climb a larger fitness hill. Gene flow out of this subpopulation could contribute to the population as a whole adapting. (W.J. Hudson)

          Social Darwinism a 19th century political philosophy which attempted to explain differences in social status (particularly class and racial differences) on the basis of evolutionary fitness. Based on the misinterpretation of Darwinian theory, Social Darwinism is generally considered unscientific by modern philosophers of science. (Wikipedia glossary)

          Species Highly controversial term given a variety of definitions by biologists. Currently, the Biological Species Concept (BSC) is widely popular: Groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups (Mayr, 1963, Animal Species and Evolution). More (W. R. Elsberry in talk.origins via W. J. Hudson) See also cladistic species concept, ecological species concept, phenetic species concept, and recognition species concept. See other species definitions. (Fossil Mall glossary)

          Speciation The the basic process of evolution by which new species appear. Although the theory of evolution is a century and a half old the precise mechanism by which new species make their appearance in the biosphere is still a field of active research, with all the disagreements and debates that go with it. A number of types of speciation have been proposed:

          Allopatric speciation is supposed to be caused by the physical separation of specimens of what was one and the same species. The classical example is Darwin's work on the finches of the Galapagos Islands. The presumed scenario is that an ancestral species of finch reached the various islands and evolved in about as many different species as there are islands. The critical factor causing the speciation is usually assumed to be the severing of the gene flow between the population on an island and the mother population on the mainland. Mayr also stressed the small size of the new population and contended that e.g. the emergence of the Isthmus of Panama did not lead to much speciation of biota of the shallow seas at either side because both represented a far too large gene pool to allow allopatric speciation to occur. Jcwf100131

          Peripatric speciation is taken to occur in the same geographic area—without severance of the gene flow—due to ecological differences, e.g. the existence of two different ecological niches into which an existing species can specialize. Jcwf100131. Alternatively, a population of an ancestral species in a geographically peripheral part of the ancestral range is modified over time until even when the ancestral and daughter populations come into contact, there is reproductive isolation. See also cladogenesis, anagenesis, punctuated equilibria. (W. J. Hudson)

          Tierra Artificial life simulation of Tom Ray's which demonstrates the utility of natural selection in computer implementations for finding novel approaches to difficult problems. This is prima facie evidence that A. E. Wilder-Smith was premature in declaring "simulations of natural selection 'jam' the best computers". (W. R. Elsberry in talk.origins)

          Transitional form, or transitional fossil A fossil or group of organisms that are intermediate and a link between a more primitive or ancestral group and a more advanced or specialised one, possessing characteristics or traits of both (see Mosaic evolution). Generally any evolutionary lineage constitutes a series of transitional forms for example in the evolution of birds from dinosaurs, or whales from terrestrial ancestors, there are a number of intermediate forms or non-missing links.An important aspect of evolutionary systematics, see also anagenesis. Note that strict application of cladistics rejects the possibility of identifying transitional forms (it doesn't deny the reality of evolution of course, just that it is possible to know for sure which fossils represent transitional forms) (Systematics and Biogeography: Paraphyly Watch 3: Transitional Fossils, Microbes & Patrocladistics). An alternative approach (given in Wikipedia) would be to make a distinction between "transitional" and "intermediate". Transitional forms do not have a significant number of unique derived traits, so it is morphologically close to the actual common ancestor it shares with its more derived relative (see also basal taxon and stem group). Intermediate can be used for those forms with a larger number of uniquely derived traits. According to this definition, Archaeopteryx is transitional whereas the platypus (an specialised egg laying mammal, descended from very primitive mammals) is intermediate. But rather than multiply terminology, it would be better to retain intermediate in the informal but more grammatically correct sense of meaning the same as "transitional". Some intermediate/transitional forms linking major groups of vertebrates include the fish/amphibian sequence from Eusthenopteron (fish) to Panderichthys to Tiktaalik to Acanthostega to fully developed amphibians (Devonian period), transitional reptile/mammal forms such as the cynodont Thrinaxodon and other mammal-like reptiles that show a blend of mammalian and reptilian characteristics (Triassic), Velociraptor and relatives, and even more so Microraptor, a four-winged gliding dromaeosaurid, and even more advanced forms such as Anchiornis and Scansoriopteryx, representing an intermediate stage between the flightless theropods and primitive birds such as Archaeopteryx (Jurassic) Pezosiren, an intermediate form of a primitive seacow with both terrestrial (land mammal) and aquatic adaptations (Eocene) Pakicetus, Ambulocetus, Rodhocetus and similar forms constitute links between amphibious and terrestrial artiodacyl (even-toed) ungulates and aquatic whales (Eocene) and Sahelanthropus, indicating it is close to the common ancestor of chimpanzees and modern humans) the most basal ape-like African hominid. mosaic of primitive (chimpanzee-like) and derived hominid features (Miocene) See Transitional vertebrate fossils FAQ, at the TalkOrigins Archive, and Wikipedia: List of transitional fossils for a much more detailed lists. (MAK Kutschera & Niklas 2004, p.259).

          Unicellular organism a living system consisting of only a single cell. May be simple, as with bacteria, or complex, as with protists. In the case of protists, different parts of the cell takes on the functions that organs and other systems fulfill in multicellular (many-celled) organisms. (MAK)

          Uniformitarianism Assumption that processes acting in the past are the same as those acting in the present. proposed the late 18th century theory of James Hutton that the natural forces now changing the shape of the earth's surface have been operating in the past much in the same way. The most important implication is that the earth is very old (deep time) and that the present is the key to understanding the past. Developed by Charles Lyell in the 19th century, who in turn influenced Darwin. Contrast with catastrophism, punctuated equilibrium.

          Universal tree of life See tree of life.

          Variation differences between individual organisms, or populations. An individual organism's phenotype results from both its genotype and the influence from the environment it has lived in. A substantial part of the variation in phenotypes in a population is caused by the differences between their genotypes. The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will fluctuate, becoming more or less prevalent relative to other forms of that gene. Evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when a new allele reaches the point of fixation, when it either disappears from the population or replaces the ancestral allele entirely. Variation comes from mutations in genetic material, migration between populations (gene flow), and the reshuffling of genes through sexual reproduction. Variation also comes from exchanges of genes between different species for example, through horizontal gene transfer in bacteria, and hybridisation in plants. Despite the constant introduction of variation through these processes, most of the genome of a species is identical in all individuals of that species. However, even relatively small changes in genotype can lead to dramatic changes in phenotype: for example, chimpanzees and humans differ in only about 5% of their genomes. (Wikipedia)

          Vestigial, vestigial structure A non-functional anatomical component retained merely as a matter of contingent history. (W. R. Elsberry in talk.origins) Usually, vestigial structures are formed when a lineage experiences a different set of selective pressures than its ancestors, and selection to maintain the elaboration and function of the feature ends or is greatly reduced. UCMP Understanding Evolution Glossary, Many organisms have vestigial organs, which are the remnants of fully functional structures in their ancestors. As a result of changes in lifestyle the organs became redundant, and are either not functional or reduced in functionality. With the loss of function goes the loss of positive selection, and the subsequent accumulation of deleterious mutations. Since any structure represents some kind of cost to the general economy of the body, an advantage may accrue from their elimination once they are not functional. Examples: wisdom teeth in humans the loss of pigment and functional eyes in cave fauna the loss of structure in endoparasites. (Wikipedia)

          Vicariance a process in which a species' range is divided even though the species has remained in place. This might happen through tectonic action, geologic activity (like the rise of a mountain range or shift in the course of a river), or other processes. Vicariance is usually contrasted with dispersal as a biogeographic mechanism. (UCMP Understanding Evolution Glossary)

          Virus infectious agent that can replicate only inside the living cells of organisms, and infect all types of organisms, from animals and plants to bacteria. Most viruses are too small to be seen directly with a light microscope. Since the initial discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, about 5,000 viruses have been described in detail, although there are millions of different types. Viruses are found in almost every ecosystem on Earth and are the most abundant type of biological entity. An enormous variety of genomic structures can be seen among viral species as a group they contain more structural genomic diversity than plants, animals, archaea, or bacteria. A virus has either DNA or RNA genes and is called a DNA virus or a RNA virus respectively. The vast majority of viruses have RNA genomes. Plant viruses tend to have single-stranded RNA genomes and bacteriophages tend to have double-stranded DNA genomes. Viruses are not typically considered to be organisms because they are incapable of "independent" or autonomous reproduction or metabolism. Their origins are unclear: some may have evolved from plasmids, others from bacteria. Viruses are an important means of horizontal gene transfer, which increases genetic diversity. The study of viruses is known as virology, a sub-speciality of microbiology. (Wikipedia)

          Web of life conventionally refers to the food chain or trophic network, describes the feeding relationships between different species in an ecosystem. However, in reference to horizontal gene transfer can also refer to genetic transfer and evolution by non-hereditary means especially common among bacteria.

          Williams revolution paradigm shift of the 1960s which saw the gene become the focus of evolutionary thinking, which saw evolutionary biology united with genetics. The revolution is named after George C. Williams, whose 1966 book Adaptation and Natural Selection popularised the theory. Previously most evolutionary thinkers considered selection to favour individuals, groups (group selection) and species, such as individuals acting "for the good of the species". The Williams revolution, however, established gene selection as the principal process of selection, and showed that because genes were the units of selection, selection would favour genes which maximised their own survival, not that of the group or species. (EvoWiki)

          Zygote The cell formed by the fertilization of male and female gametes. (PBS evolution Glossary)


          Watch the video: Synapomorphy. Wikipedia audio article (May 2022).