Evolution & Cladistics

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jeromesh
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203900
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Evolution & Cladistics
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2013-03-10 18:37:18
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evolution cladistics
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For memorizing terms relating to evolution & cladistics
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  1. apomorphy (adj. apomorphic)
    A derived character state, inferred to have been transformed from a different, ‘primitive’ character state in an ancestor.
  2. autapomorphy (plur. autapomorphies)
    A derived character state (Apomorphy) unique to, or independently derived in one taxon.
  3. character matrix
    A grid showing, for a given set of taxa (usually listed down its side), the coded character states of their characters (usually listed along the top). It is the formal database from which cladograms are constructed.

  4. character state
    One of two or more alternative states recognised for a given character for the purposes of cladistics. Analysis of polarity may allow character states to be categorised as primitive (plesiomorphic) or derived (apomorphic) relative to one another, the latter inferred to have arisen by transformation or mutation from the former.
  5. clade
    A single whole branch of a phylogeny, comprising a common ancestral species and all its descendants, in practice recognised as a (monophyletic) grouping of all taxa that share a given synapomorphy or set of synapomorphies.

  6. cladistics
    The analysis of phylogenetic relationships based on recognising a hierarchy of nested clades, each defined by shared possession of derived character states (synapomorphies).
  7. cladogram
    A rooted tree-like diagram that arranges taxa (placed at the terminations of its branches) in a nested series of clades within clades.

  8. consensus tree
    A tree that combines the preferred groupings from competing cladograms for a given set of taxa, while condensing contentious groupings into multiple branching points.
  9. convergent evolution (convergence)
    The independent (homoplasious) evolution of superficially similar features in separate evolutionary lineages normally through adaptation to a common function, though usually formed in different ways.
  10. homology (adj. homologous)
    Correspondence of characters (morphological or molecular) in different taxa inferred to be due to inheritance from a common ancestor because of similarities in fundamental organisation, and corroborated by congruence with most other putative homologies according to the most parsimonious cladogram(s).
  11. homoplasy (adj. homoplasious)
    Analogy of characters in different taxa inferred to be due to convergent evolution or independently repeated base substitution (in DNA), not common ancestry, and corroborated by repetition on unconnected branches in the most parsimonious cladogram(s).
  12. ingroup
    A group of related taxa whose character state polarity, hence cladistic relationships, are to be resolved by reference to a more distantly related, outgroup taxon.

  13. ontogeny
    The development of an individual organism from a zygote.
  14. node
    A branchpoint on a cladogram.

  15. outgroup comparison
    A means of inferring the polarity of character states based on comparison of a group of related taxa (the ingroup) with a more distantly related taxon, or taxa (the outgroup). Character states in the ingroup that are shared with the outgroup are most parsimoniously considered primitive within the ingroup. Hence other states present among the ingroup are regarded as derived.
  16. ontogenetic criterion
    An indicator of character state polarity that relies on the generalisation that special traits restricted to certain taxa, i.e. derived states, tend to appear later in development than more general, primitive states.
  17. monophyletic
    Applied to a taxonomic grouping that comprises all descendants of a common ancestral species, together with the common ancestor (i.e. an entire clade). In practice, it is recognised as a grouping of all taxa united at a given node in the most parsimonious cladogram(s), and which share some diagnostic synapomorphy or set of synapomorphies.

  18. paraphyletic
    Applied to a taxon that is effectively a monophyletic grouping from which one or more sub-groups have been removed, usually because they are considered to have achieved a new evolutionary ‘grade’ compared with other members of the group. They feature commonly in traditional classifications (e.g. ‘fish’ and ‘reptiles’), but are avoided in cladistic schemes of classification.

  19. parsimony, principle of
    A fundamental working principle in cladistics, whereby the (or a) cladogram with the smallest number of inferred character transformations (i.e. shortest tree length) is taken as the preferred hypothesis for reconstructing phylogenetic relationships, because it involves the least conjecture.
  20. phylogeny (plur. phylogenies)
    Conceptual representation of the history of evolutionary relationships between given organisms, usually depicted as some form of tree-like diagram showing the sequence (and sometimes absolute dates) of branching events between divergent descendants.
  21. polarity
    In cladistics, the inferred sense of evolutionary change in a character. Alternative character states may be identified as primitive or derived by reference either to the ontogenetic criterion or to outgroup comparison.
  22. polytomy (plur. polytomies)
    A node in a cladogram bearing multiple branches, in contrast to the dichotomous branching normally shown.
  23. symplesiomorphy
    A shared primitive character state.
  24. plesiomorphy (adj. plesiomorphic)
    A character state designated the primitive condition within a group of taxa.
  25. sister group (or taxon)
    Each of the pair of species or clades yielded by a branching node on a cladogram.

  26. synapomorphy
    A shared derived character state, i.e. a character state that has been modified from an ancestral (‘primitive’) condition and is shared by two or more taxa as a consequence of having been inherited from a common ancestor in which it is inferred to have arisen. Synapomorphies determine the branching nodes on cladograms and are thus the key to cladistics.
  27. trichotomy
    A threefold branching node on a cladogram.
  28. neutral theory of evolution
    a theory that proposes that most DNA sequence evolution is as a result of genetic drift rather than natural selection.
  29. base substitution
    A type of mutation involving replacement or substitution of a single nucleotide base with another in DNA or RNA molecule (substitution of A, C, G or T with one of the other).
  30. transition (base substitution)
    A mutation that involves the substitution of a purine (A or G) for a purine, or a pyrimidine (C or T) for a pyrimidine.

    • A <----> G
    •       or
    • C <----> T

    Transitions are more common than transversions.
  31. transversion (base substitution)
    A mutation that involves the substitution of a purine (A or G) for a pyrimidine (C or T), or vice versa.

    • A ----> C or T
    • G ----> C or T
    • C ----> A or G
    • T ----> A or G

    Transversions are less common that transitions.
  32. purine
    Base A or G (adenine or guanine).
  33. pyramidine
    Base C or T (cytosine or thymine).
  34. invariant sites
    Sites that do not vary in genetic information and do not help in determining phylogeny.
  35. phylogenetically neutral sites
    Sites where there is an autapomorphy.
  36. phylogenetically informative sites
    Sites where 2 taxa show a synapomorphy.
  37. binary state characteristics
    A character state that can have two qualities eg: presence or absence.
  38. multistate characteristics
    A character state that can have a number of difference states eg: the number of spots.
  39. adenine
    Base A.
  40. base A
    Adenine.
  41. guanine
    Base G.
  42. base G
    Guanine.
  43. cytosine
    Base C.
  44. base C
    Cytosine.
  45. thymine
    Base T.
  46. base T
    Thymine.
  47. base
    One of the purines (A - adenine or G - guanine) or one of the pyramidines (C - cytosine or T - thymine).
  48. phylogram
    A tree-like diagram that summarizes in graphic form the evolutionary history of a group of organisms, in which taxa are placed at the terminations of its branches and the branch lengths are generally proportional to the amount of character change.

  49. consensus tree
    A tree that combines the preferred groupings from competing cladograms for a given set of taxa, while condensing contentious groupings into multiple branching points (polytomies).

  50. strict consensus tree
    Only those clades present in all of the trees in the tree source will be present in the consensus tree.
  51. semi-strict consensus tree
    Only those clades that are present in at least one of the trees, and not contradicted by any of the trees, are present in the consensus tree.
  52. majority rule consensus tree
    Only those clades present in the majority of the trees will be present in the consensus tree.
  53. polytomy (plur. polytomies)
    A node in a cladogram bearing multiple branches, in contrast to the dichotomous branching normally shown.
  54. tree length
    The total number of character transformations revealed by the most parsimonious arrangement of character states on a given cladogram.
  55. consistency index
    The proportion of character transformations that are not repeated. A value of 1 indicates no homoplasy. Lesser values show the extent of homoplasious repetition.

    The consistency index is raised by uninformative derived character states and by informative derived character states.
  56. retention index
    An estimate of the extent of synapomorphies.
  57. Bootstrap test
    A statistical test by which random duplication and omission of characters is used to determine the faithfulness of the cladogram. A robust cladogram is relatively immune to the effect of random change. Cannot be used to benchmark across different trees as parameters are likely to vary.
  58. Bremer Support test
    A measure of how unparsimonious different trees are.
  59. limitation of evolutionary timescales
    If the evolutionary timescale is too short, synapomorphies might not appear making distinguishment more complex.

    If the evolutionary timescales are too long, synapomorphies might evolve out making relationships less easy to determine.
  60. hybridisation
    The production of offspring following mating between a male and a female that are from different populations or species. Can give rise to new species, particularly in plants, but also occasionally in animals. A large proportion of the genome is involved.
  61. reticulate evolution
    The mixing of genes and other heritable components from different species through hybridisation or symbiotic integration.

  62. horizontal gene transfer
    Incorporation of individual genes from one species into the genome of another, usually through the agency of viruses (or humans in the case of genetic modification) in eukaryotes, or by various modes of exchange among prokaryotes. Same as lateral gene transfer.
  63. lateral gene transfer
    Incorporation of individual genes from one species into the genome of another, usually through the agency of viruses (or humans in the case of genetic modification) in eukaryotes, or by various modes of exchange among prokaryotes. Same as horizontal gene transfer.

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