Classification and Phylogeny

1. Biological classification
   1. Romans developed categories for animals living on land, in water or in air
   2. Carolus Linnaeus (1707-1778) wrote Systema Naturae (1758) and created the Linnaean system, a hierarchical naming system which is still in use today
      1. Binomial nomenclature - all species are identified with a Genus and species name
      2. Each species is grouped with other species in higher categories:
         1. Kingdom (King) Animalia Plantae
         2. Phylum (Philip) Chordata Tracheophyta
         3. Class (Came) Mammalia Angiospermae
         4. Order (of) Primates Rosales
         5. Family (fairly) Hominidae Rosaceae
         6. Genus species (good size) Homo sapiens Rosa elegans
      3. Although still in use, does not always indicate evolutionary relationships. Widespread agreement that classification system should reflect evolution. This has spurned an active research effort to develop a phylogenetic classification system.
2. Concept of phylogeny
   1. What is a phylogenetic tree?
      1. Indicates evolutionary relationships
      2. Often attempt to be strictly dichotomous
      3. Can indicate branching patterns and/or branch lengths, e.g. evolutionary time
      4. A rooted tree indicates the order in which events occurred. Roots can be established
         1. outgroup - taxa that are unrelated, but share enough features to indicate what ancestor looked like
         2. fossil
      5. Phylogeny is specified by the branching pattern, not the order of the tips
   2. What characters are used to build trees?
      1. Independent - two characters should be able to evolve separately
      2. Homologous - traits are evolutionarily related, e.g. forelimb, not wings, should be derived homologies. Ancestral homologies do not provide information.
      3. Minimize homoplasy, where homoplasy means traits look the same, but are not homologous. Caused by
         1. convergence
         2. parallelism (convergence in recently diverged species)
         3. reversals - can occur easily in DNA
      4. available in large numbers
   3. Phylogenetic systematics
      1. Cladistics (Willi Hennig - 1950)
         1. Identify monophyletic groups on the basis of shared derived traits, e.g. mammals have fur and milk which were inherited from a common ancestor, termed synapomorphies. Determine if traits are derived using
            1. outgroups - did they possess the trait?
            2. fossils
         2. Synapomorphies identify evolutionary branch points
         3. Synapomorphies are nested
         4. If there are no homoplasies (reversals), then tree-building is easy
         5. If homoplasies are present, then use parsimony- fewest number of character changes
            1. Minimizes homoplasy
            2. Characters must be discrete
            3. Example using sequence data
      2. Phenetics
         1. Minimize distance defined in character space
         2. cannot detect homoplasies
         3. different distance metrics can produce different trees
         4. example using distances on x-y plot
         5. tends to work reasonably well with lots of characters and constant rates of change
3. Using phylogenies
   1. Scaling branch lengths for time
      1. Align nodes with fossil dates
         1. Homind evolution - predict Homo-Pan split at 15 MYA
      2. Molecular clock
         1. Zuckerkandl and Linus Pauling (1962) - amino acid seqs of hemoglobin and cyt C
         2. 1977 - Vince Sarich and Allan Wilson - predicted Homo-Pan split at 5 MYA using albumin aa sequence
         3. a clock is justified if
            1. change is neutral
            2. mutation is equally likely throughout the sequence
            3. substitutions then occur due to drift
         4. many genes show evidence of clock-like behavior
         5. But, each gene often has a different clock, as do some lineages
         6. clocks need to be calibrated against the fossil record
   2. Reconciling phylogeny and taxonomy (evolutionary taxonomy)
      1. Current taxonomy is based on phenetics
         1. does not always produce monophyletic groups, for example
         2. reptiles: lizards, snakes, turtles & crocodiles: share
            1. internal fertilization
            2. scaly skin
            3. 4 chambered heart
            4. membrane bound (amniotic) egg
         3. birds - differ by having feathers, not scaly skin
         4. cladistic approach shows that birds evolved from dinosaurs, reptiles are not monophyletic
      2. Current taxonomy is being overhauled
         1. GENBANK is using phylogenetic scheme
         2. Now 8 kingdoms, whereas there were 5 last year!