Phylogenetics

How we make sense out of the whole group?
How do we decide what organisms to group together?

I. Early Classification

Can we find a way of categorizing and classifying mammals that sets them apart as a distinct taxonomic group and shows the evolutionary relationships among the different kinds of mammals?

  1. Aristotle (384-322 BC):
    Believed that reality is manifested in physical objects that are knowable through experience
    Wrote numerous treatises on the natural world

    Mammals were viviparous animals with red blood.
    Recognized five categories of vertebrates, with humans as a separate category:

  2. John Ray (1693)
    An Anglican priest
    Believed in "natural theology," the idea that he could better understand God through studying the natural world
    Recognized mammals as having

    Recognized that fossils represented organisms that were once alive.

  3. Carolus Linnaeus, the "Father of Taxonomy" (wrote Systema naturae, 1758)
    1. Systema naturae, early editions:
      • hairy bodies
      • quadrupedal
      • viviparous
      • females made milk
    1. Systema naturae, 10th edition: "Mammalia," Linnaeus basically adopts Ray's definition

      WORKSHEET: Historical definitions


    2. Linnaeus devised the Linnaean system

      A hierarchical system
      Seven obligate categories of classification
        Kingdom
          Phylum
            Class
              Order
                Family
                  Genus
                    Species

      Can also have optional (=intermediate) categories
        "super-"
          [category]
            "sub-"
              "infra-"

      A taxon can refer to any category of classification


    3. Nomenclature
      System is used world-wide; avoids mix-ups and confusion such as occur when common names are used

      1. Latinized words
      2. Name usually means something (ex. Carnivora="flesh eaters")
      3. Endings often depend on level of classification
        "-idae" indicates it's at the level of Family
        "-inae" indicates it's at the level of Subfamily
      4. Specific names are 2 words: Genus species


  1. ca. 1799: An early attempt at a classification scheme for mammals based on locomotion

    Think-Pair-Share: What other types of observable characteristics could you use to classify mammals? Are any of these categories any better or worse than any other types of observable characteristics?

  1. Early 1800's, Recognized three distinct subgroups of mammals: Monotremes/Marsupials/Placentals
    By the late 1800's, these became known by the present-day terms: Prototheria/Metatheria/Eutheria
    Be aware that there have been other proposed organization schemes for mammals, including some recent ones, that use different terminology (e.g., Bell/McKenna and Luo, Kielan-Jaworowska, and Cifelli)

  2. George Gaylord Simpson (ca. 1928-1929): Three very distinct groups of mammals


II. The science of classification

  1. Earliest approaches were simply to give everything a name.

    taxonomy=the science of naming and classifying organisms

    1. Common criteria for classifying
      1. Ways of life (aquatic, terrestrial, volant)
      2. Environmental adaptations (hooves, flippers, wings)
      3. Morphological traits (hierarchy based on shared structural features)

    2. Lower levels (root): widely shared features

    3. Higher levels (tips: more unique features (eg, species-specific features)


      George Gaylord Simpson ( The principles of classification and a classification of mammals, 1945): A classification scheme for Eutherians
    Unguiculata share many primitive features,
    evolutionarily ancient,
    diverse specializations     		shrews, bats, primates, flying lemurs, anteaters, sloths, etc.
    Glires   rodents, rabbits and hares
    Mutica aquatic whales and dolphins
    Ferungulata   carnivores, aardvark, elephants, hyraxes, sirenians, perissodactyls (odd-toed ungulates) and artiodactyls (even-toed ungulates)



  2. Problems with this type of approach: Similarities among organisms can occur for a variety of reasons.
  1. A major development in classification was the use of evolution as the basis for the structure of the hierarchy.

    1. Species grouped together have more recent common ancestor
    2. Shared characteristics are explained on the basis of shared evolutionary history (homology)

  1. The field is now called systematics or phylogenetics (the two terms are basically used interchangeably).

    systematics= the scientific study of the kinds and diversity of organisms and of any and all relationships among them

    phylogenetics=systematics, with the organizing principle being evolution

    1. Phylogeny

      1. Definition: A series of relationships between species; inferred based on their shared and unique characteristics; also called a tree
      2. Describes a series of evolutionary changes
      3. "Trunk" (root) is the common ancestor for the whole group
      4. "Leaves" (tips) are individual taxa
      5. Branching points (nodes) are common ancestors
      6. Location of node approximates how long ago divergence occurred
      7. Groups that are most closely related to each other are sister taxa
      8. Represents a monophyletic group, rather than a paraphyletic or polyphyletic group



      WORKSHEET: Pruned trees


    2. What kind of characters do we use to construct the tree?

      1. Choice of characters affects shape of tree
      2. Homologous traits are useful, convergent traits are not

    3. Types of characters that can be used

      1. Morphology
        1. skeletal features
        2. soft tissue features (e.g., type of uterus)
      2. Molecules
        1. Proteins (especially relatively conserved enzymes with a small number of variants that are fixed in different species)
        2. DNA electrophoresis
        3. Gene sequences (Nuclear or Mitochondrial)
        4. Whole genomes

    4. What kind of data should we use to construct mammalian phylogenies?

      1. Morphological data

        Advantages

        • Can get estimates of the time of divergence of lineages using fossil data and C14 dating
        • Enables us to understand the morphology and ecology of extinct, ancestral species (or at least speculate about it)

        Disadvantages

        • Morphological characteristics are more likely to be convergent
        • Patterns of inheritance of morphological traits not always clear
        • The fossil record is spotty due to the scarcity of fossils in some environments and for small bodied species
        • There are less data to use
        • Different character states sometime hard to differentiate (subjective and arbitrary) except in the case of presence/absence of a trait


      2. Molecular data

        Advantages

        • There's more of it!
        • Patterns of inheritance are straightforward
        • Molecular traits are less susceptible to convergence because
          • the genetic code is redundant (there are multiple ways to get the same result, so phenotypic traits that appear identical may have different genetic bases
          • much of the genome consists of non-coding DNA that may not be under selection
        • The number of potential point mutation differences between species is likely to be very large, so even if there are independent identical mutations (i.e., convergence in DNA sequence), those will be outweighed by the number of dissimilar mutations
        • The number of mutations can be used to measure time because we can calculate a rate of mutation. This allows us to estimate time of divergence for different lineages, even in the absence of fossil data.

        Disadvantages

        • Different character states are usually easy to measure (but alignment is a complicating issue...)
        • Provides little information about what extinct species were like, in terms of their morphology and ecology


      3. Mix and match?

        Advantages

        • More data points (use all available information)

        Disadvantages

        • If any of your data are correlated, then those data may have a disproportionate influence over the results (this is termed pseudoreplication)

    5. Major recent developments

      1. Growing availability of molecular data
      2. Development of strict mathematical rules for constructing trees and for choosing amongst different trees
      3. Use of powerful computers has made it possible to increase
        • the number of characteristics being used
        • the number of species included in the analysis








Mammal phylogeny from Bininda-Emonds et al. (2007)

III. The challenge of reconstructing eutherian mammalian phylogenies

  1. Problems

    1. More than 5,000 mammalian species
    2. Many orders whose relationships need to be figured out (~28)
    3. Some orders are speciose (e.g., rodents and bats) while others consist of very small numbers of species (e.g., Tubulidentata)
    4. There are ~1028 different possible trees but only one is correct

  2. First attempts to reconstruct mammalian phylogeny led to "bushy" trees because



    WORKSHEET: Modern phylogenetic trees






IV. Tutorials and other relevant links