Classification and Phylogeny

1. Binomial nomenclature - all species are identified with a Genus and species name

2. Each species is grouped with other species in higher categories:

a. Kingdom (King) Animalia Plantae
b. Phylum (Philip) Chordata Tracheophyta
c. Class (Came) Mammalia Angiospermae
d. Order (of) Primates Rosales
e. Family (fairly) Hominidae Rosaceae
g. 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.

II. Concept of phylogeny

A. 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.

5. Phylogeny is specified by the branching pattern, not the order of the tips

B. 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

a. convergence
b. parallelism (convergence in recently diverged species)
c. reversals - can occur easily in DNA

4. available in large numbers

C. Phylogenetic systematics

1. Cladistics (Willi Hennig - 1950)

a. Identify monophyletic groups on the basis of shared derived traits (synapomorphies), e.g. mammals have fur and milk which were inherited from a common ancestor. Synapomorphies identify evolutionary branch points.

b. Assume a bifurcating pattern of evolution and traits change over time
c. Determine character polarity, i.e. ancestral (plesiomorphies) or derived (apomorphies) state. Determine if traits are derived by asking if the following possess the trait

i. outgroups - related taxa
ii. fossils

e. Construct tree to maximize the number of shared derived states and minimize cases of character convergence (homoplasies). This is maximum parsimony - fewest number of character changes. Not always easy to do!

i. Minimizes homoplasy
ii. Characters must be discrete

2. Phenetics

a. Minimize distance defined in character space
b. cannot detect homoplasies
c. different distance metrics can produce different trees
d. tends to work reasonably well with lots of characters and constant rates of change

III Using phylogenies

A. Scaling branch lengths for time

1. Align nodes with fossil dates

a. Homind evolution - anthropologists predicted Homo-Pan split at 15 MYA

2. Molecular clock

a. First proposed by Zuckerkandl and Linus Pauling (1962) - amino acid seqs of hemoglobin and cyt C

b. 1977 - Vince Sarich and Allan Wilson - predicted Homo-Pan split at 5 MYA using albumin amino acid sequence

c. a clock is justified if

i. change is neutral
ii. mutation is equally likely throughout the sequence
iii. substitutions then occur due to drift

d. many genes show evidence of clock-like behavior
e. But, each gene often has a different clock, as do some lineages
f. clocks need to be calibrated against the fossil record

B. Reconciling phylogeny and taxonomy (evolutionary taxonomy)

1. Current taxonomy is based on phenetics

a. does not always produce monophyletic groups, for example

b. reptiles: lizards, snakes, turtles & crocodiles: share

i. internal fertilization
ii. scaly skin
iii. membrane bound (amniotic) egg

c. birds - differ by having feathers, not scaly skin

d. but the cladistic approach shows that birds evolved from dinosaurs, reptiles are not monophyletic

2. Current taxonomy is being overhauled

a. GENBANK is using phylogenetic scheme
b. Now 8 kingdoms, whereas there were 5 last year!