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

\