Phylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies & cladograms? How do we read them? How do we estimate them?

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1 Phylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies & cladograms? How do we read them? How do we estimate them?

2 Carolus Linneaus:Systema Naturae (1735) Swedish botanist & natural theologist Hierarchical classification based on ideal of unchanging types. Binomial nomenclature - replaced polynomials Categories: K, P,C, O, F, G, S Assumes a static, unchanging Universe

3 Charles Darwin and Fig. 1 Origin of Species (1859) Species diverge; they do so gradually Articulated idea of shared ancestry, branching of lineages (cladogenesis) and change along branches (anagenesis) Only figure in OS: a dendrogram

4 Problems with Linnean system It does NOT represent ancestor-descendent relationships. Hierarchical categories do not imply degree of evolutionary divergence. Are Rabbits as different from Rodents as they are from Elephants? When should we split groups into separate categories? - splitting vs. lumping How different is different enough to warrant separate groupings? Ex: Dogs & wolves

5 Dendrogram ~ Cladogram Cladistics & Phylogenetics: Method of classifying organisms into groups consisting of an ancestor and ALL their decendents. Cladogram or Phylogenetic tree: Hypothesis (in diagram form) representing evolutionary relationships among populations, species, or larger groups*

6 Why construct cladograms? 1. Provide an understanding of evolutionary history of life 2. Provide a framework for interpreting and valuating diversity 3. Classification & organization system Most efficient way to classify organisms is based on phylogenetic relatedness, because it captures information about shared ancestry.

7 All species coalesce to a common Recall our lab: Just as all genes coalesce to a single ancestral gene, all individuals coalesce to a single ancestor. Like tracing a family tree ancestor:

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15 Tips Branches Nodes Root Most Recent Common Ancestor (MRCA) 1 0

16 Phylogeny of Vertebrates Name another tip Name another node

17 Who is the MRCA of Mammals and Crocodiles? Monophyletic groupings

18 Monophyletic groupings Nodes name monophyletic groups: An ancestor and ALL of its descendents

19 Reading phylogenies 5 of these are identical Which one is not the same?*

20 Tree of Life

21 What data should we use to construct trees? What data do you use? Often do it without understanding why

22 What data should we use to determine evolutionary relationships? Characters: distinguishable variations of an organism 1. Morphologic 2. Developmental 3. Genetic Quantifiable Independent of each other ACGTTGAA ACCTTGTA Homologous: Shared by taxa because their common ancestor evolved the trait

23 Characters Are the bones of the upper limb homologous structures? Are wings of bats, birds and pterosaurs homologous structures?

24 Pitfalls When Similarity Close Relationship! 2 taxa may share a derived character state OR may share an ancestral character state OR may share a character state due to convergence to same phenotype (MRCA did not have the character) These are analogous traits (homoplasies) Bird and bat wings Dermopterans, Flying squirrels, Sugar gliders Only if first case is true will you ALWAYS infer correct phylogenetic relationship.

25 Willi Hennig and Cladistics Grouping scheme based ONLY on phylogenetic relationships Not on degree of similarity or adaptive divergence Used presence of shared derived characters (synapomorphies) to infer evolutionary relationships Based trees upon total weight of ALL synapomorphies

26 Synapomorphies identify monophyletic groups Unite groups with shared, (only among each other) derived (from some ancestral group) characters

27 Problems with characters Which characters are phylogenetically informative? How do we quantify # of possible states & frequency of change among them? How do we establish polarity? How do we deal with continuous traits: Quantify or discard them?

28 States are discrete Ideal character # of states are knowable (across taxa) Transition frequencies (rates of change) are estimable DNA ONLY 4 states; A C G T No polarity Can measure transition frequencies

29 Method of inferring trees Choose the most parsimonious one Parsimony: Methodological reductionism; Explanation which requires the fewest undocumented assumptions is probably correct. Occam s Razor: The easiest explanation is probably the correct one. William of Occam: 14th century Franciscan monk In cladistics/phylogeny: The tree which requires us to postulate the least evolutionary change & fewest homoplasies is probably correct

30 Parsimony Find all possible tree topologies; calculate total number of changes required to produce each topology. Topology with fewest changes = the most parsimonious tree* A B C D C A B D Taxa: A, B, C, D Characters:

31 Placement of Cetaceans Morphology of astragalus unites Artiodactyls Most parsimonious placement = one gain of pulley-shaped astragalus

32 Placement of Cetaceans Mounting genetic evidence suggests Hippos have shared genes with Cetaceans more recently than they have with other Artiodactyls (e.g. deer)

33 Placement of Cetaceans Appearance of SINE s (mutations) throughout the genome suggests that Cetaceans & Hippos are close relatives Rare; Selectively neutral; Once established, lost only via drift

34 Paraphyletic groupings