Chapter 4: Taxonomy and Phylogeny of Animals

[[Linnaeus and Taxonomy[[

Taxonomy: The study of the principles of systematic ordering and naming of organisms

  • Part of a broader science of systematics
    • Study of variation among animal populations to reveal their evolutionary relationships
  • Provides evolutionary biology
    • Adjusting system to accommodate evolution has produced many problems
  • Carl von Linne
    • (Latin pen name: Carolus Linnaeus) (1707-1778)
    • Produced extensive system of taxonomy for both plants and animals
    • Binomial Nomenclature
      • 2 names: genus name + species epithet/name
      • Species grouped in hierarchical categories
      • Taxa (singular: taxon)

   How Animals are Classified

  # [[Species[[

  • Difficult to define
    • Important criteria for recognition of species
  1. Common Descent

   

  1. Members of a species must trace their ancestry to a common ancestral population
    1. Species must be the smallest distinct groupings of organisms sharing patterns of descent and ancestry

   

  1. To ID such groupings:

       1. Morphological characters 2. Chromosomal characters 3. Molecular characters

  1. Members of a species must form a reproductive community that excludes members of other species

==Concepts of Species:==

  • Most influential: Biological Species Concept
    • Inspired by Darwinian evolutionary theory
    • “A species is a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature.” - Ernst Mayr, 1983
  • Species = interbreeding population of individuals having common descent
    • Not based on organismal morphology
    • But can still help to diagnose biological species
    • Variation should be relatively smooth and continuous within species and discontinuous between them
  • Criticisms
    • Refers to contemporary populations
    • How can we trace the temporal duration of a species’ lineage through its past history?
    • Example: Humans
      • When are human fossils no longer Homo sapiens, but different species?
    • Species do not exist in groups of organisms that reproduce only asexually
    • How much reproductive divergence is necessary to consider two populations separate species?

Evolutionary Species Concept

  • Proposed by George Gaylord Simpson in the 1940s
  • Adds evolutionary time dimension to the biological species concept
  • “A single lineage of ancestor-descendant populations that maintains its identity from other such lineages and that has its own evolutionary tendencies and historical fate”
  • Applies both to sexually and asexually reproducing organisms
  • Abrupt changes in diagnostic features mark a boundary between different species in evolutionary time
  • Updated in 1989 by Alan Templeton
    • Population geneticist
    • Included the expectation that populations of a species evolve as a genetically cohesive unit by natural selection and genetic drift
    • Cohesion Species Concept
    • Any individual in a species is a possible common ancestor of the entire species at some future time

Phylogenetic Species Concept

  • Irreducible (basal) grouping of organisms diagnosably distinct from other such groupings and within which there is a parental pattern of ancestry and descent
  • Emphasizes common descent
  • Both asexual and sexual groups covered
  • Any spatially separated population that has undergone character evolution that distinguishes it is recognized as a species
  • Would describe a larger # of species than would any other concept

Current disagreements about species definitions are exciting.

  • Will lead to enormous advances in biology and fundamental reconsiderations of the meaning of species

==DNA Barcoding of Species==

Does not resolve the definition of species

  • Useful for Identifying an unknown organism

DNA Barcoding

  • Technique for diagnosing organisms to species using sequence information from a standard gene present in all animals
    • COI (cytochrome c oxidase subunit 1)
    • Mitochondrial gene
    • Standard “barcode” region for animals
    • Process
    • DNA extracted
    • Gene targeted
      • Many copies made
      • Sequenced
    • Sequence checked against a public reference library of identified species (database)
      • Can ID unknown species

[[Taxonomic Characters and Reconstruction of Phylogeny[[

Once species are named, how do we decide where each one fits on our tree (phylogeny)?

  • Based on characters that vary among species
    • Any feature that a taxonomist uses to study variation within or among species
    • Can be morphological, chromosomal, and/or molecular
    • Homologous characters are useful for constructing phylogenies
    • Similar features that are the result of common ancestry

 Homologous Characters

  • Similarity does not always reflect common ancestry
    • Homoplasy
    • Result of independent or convergent evolution
    • Analogous Characters

 Analogous Characters

[[Using Character Variation to Reconstruct Phylogeny[[

==First Step:==

  • For each character, which character state was present in the most recent common ancestor of the entire taxon?
    • Ancestral Character State
    • Contrasting states =  Derived Character States
    • Derived characters shared by all members of a clade = synapomorphies
    • Clade = fundamental unit of the phylogenetic grouping of species
      • Ancestral lineage + all descendants from lineage
    • Basic Method
    • Compare characters in group of interest (= ingroup) to those of an outgroup
      • Reference group
      • Known to be related to the study organisms
      • Less closely related to any member of the ingroup than the outgroups are to each other
      • Ancestral for ingroup

==Next Steps:==

  • Use synapomorphies as evidence of homology to infer that a particular group of species forms a clade
  • Pattern formed by all synapomorphies within ingroup reveals a nested hierarchy of clades within clades
    • Goal: Identify all clades nested within ingroup
    • Could reveal the structure of common descent among species
    • Diagram = cladogram
    • Not the same as a phylogenetic tree
    • Needs more info
    • Duration of evolutionary lineage, ancestor info, etc.

 Cladogram

[[Theories of Taxonomy[[

2 currently popular theories of taxonomy

  • Both based on evolutionary and phylogenetic principles
    • Difference: how those evolutionary principles are used
  1. ==Evolutionary Taxonomy==
    • Predates phylogenetic systematics
    • Retains many aspects of Linnean taxonomy
      • Species grouped in a nested hierarchy of increasingly more inclusive higher taxa
      • All taxa must:
      • Have a single evolutionary origin
      • Include the most recent common ancestor of all members of the taxon
  2. ==Phylogenetic Systematics (cladistics)==
    • Developed in the mid-20th century by Willi Hennig
    • Emphasizes criterion of common descent
      • All taxa must be monophyletic
      • Includes common ancestor and ALL descendants
      • Members are linked by nested sets of characters that trace the evolutionary history of the group
      • These principles underpin cladistics
        • Method of investigating evolutionary relationships based on analyses of the distribution of characters

Our Approach:

  • Emphasize monophyletic taxa
  • Consistent with the criteria of both theories

[[Major Divisions of Life[[

All life is categorized into 3 monophyletic domains:

  1. Bacteria
    • Prokaryotes
  2. Archaea
    • Prokaryotes
    • Differ from bacteria in membrane structure and ribosomal RNA sequences
  3. Eukarya
    • All eukaryotes

 Monophyletic Domains