Today’s lecture Understanding phylogenetic trees What is phylogeny? Phylogeny = the pattern of evolutionary relationships among species, their descent from common ancestors “… the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever-branching and beautiful ramifications.” Charles Darwin, On the Origin of Species (1859) Augustin Augier, 1801 Heinrich Bronn, 1858 Haeckel, 1866 Haeckel, 1874 What is phylogeny? Phylogeny is often presented as a diagram (a phylogenetic tree). 1. Haeckel, 1866 2. Wikipedia 3 3. APweb 4. Gomez, 2010 5. Cameron, 2000 4 1 5 2 Interpreting phylogenetic trees Ingroup Outgroup Group 2 Group 1 H G F E D C B A Tip = extant species Terminal branch Node Internal branch (internode) = ancestral species Root = common ancestor time Ingroup = the lineage under consideration. Outgroup = a lineage that is not part of the ingroup. Sister group = the lineage that is most closely related to the lineage under consideration. Interpreting phylogenetic trees Topology = the branching pattern of a phylogenetic tree Sister relationships are reciprocal; sister groups are each other’s closest relatives (share a more recent common ancestor with each other than with any other group). Interpreting phylogenetic trees H G F E D C B A Monophyletic group (or clade) = a single lineage; a group composed of a common ancestor and all of its descendants. mono = one, phylum = tribe Interpreting phylogenetic trees H G F E D C B A Paraphyletic group = a group containing a common ancestor and some, but not all, of its descendants. para = near, not quite, phylum = tribe Interpreting phylogenetic trees H G F E D C B A Polyphyletic group = multiple lineages; a group that does not contain the common ancestor of its members. poly = many, phylum = tribe Phylogenetic classification Phylogenetic classification = a hierarchical ordering of taxa, according to phylogenetic relationships. The use of phylogeny to produce the classification. Often referred to as cladistics. Our goal is to recognize and name only monophyletic groups, to achieve nested sets that are hierarchically organized. Chordates Amniotes Mammals Phylogenetic classification HomeothermiaHomeothermia (animals: thatan example are “warm of blooded”):a polyphyletic mammals group and birds evolution.berkeley.edu Phylogenetic classification Reptiles: flightlessReptiles, animals dinosaurs: with keratin examples scales Birdsof paraphyletic: flying animals groups with keratin feathers biology.unm.edu Phylogenetic classification Why no polyphyletic groups? – Natural classification should reflect evolutionary relationship Why no paraphyletic groups? – Taxa at same rank should not contain one another – All members of a group should have their closest relative also belong to that group Recognizing monophyletic groups allows greater predictive power xkcd.com( Taxonomic revision Gadek et al., 2000 Alaska yellow cedar Before: Chamaecyparis nootkatensis Xanthocyparis vietnamensis Taxonomic revision Farjon et al., 2002 Alaska yellow cedar Before: Chamaecyparis nootkatensis Now: Xanthocyparis nootkatensis Taxonomic revision tomato Before: Lycopersicon esculentum Now: Solanum lycopersicum Spooner et al., 1993 Reconstructing phylogeny Phylogenetic inference = the process by which the branching pattern of evolutionary relationship (phylogeny) is estimated. A phylogenetic tree is a hypothesis; it is subject to re- evaluation upon the discovery of new evidence. How do we infer phylogeny? Reconstructing phylogeny From comparable similarities (characters); shared traits between species. The characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, all true classification being genealogical.Charles Darwin, On the Origin of Species (1859) Character/trait = a variable characteristic of an Charles Darwin photo by Leonard organism, or group of organisms. Darwin, 1874. From Woodall, 1884: Transactions of the Shropshire Archaeological Society Eg. Body covering; flower color Character states = the different forms a character can take. white yellow scales feathers Reconstructing phylogeny: characters Dial, 1992 Homology = homologous characters are those inherited from a common ancestor. The states of homologous characters are comparable with one another, and may provide insight into evolutionary relationship. Analogy = analogous characters have multiple, independent evolutionary origins. Analogous characters do not provide useful indicators of evolutionary relationship. Reconstructing phylogeny: characters Synapomorphy = shared, derived character. (from Greek: syn—together (shared) + apo—away + morph—form) A derived state shared by two or more lineages, which was present in their common ancestor, and is not found in other organisms. Synapomorphies diagnose monophyletic groups. E.g., angiosperms (flowering plants) Reconstructing phylogeny: characters Ovules enclosed in carpels: synapomorphy defining angiosperms Ovules enclosed in carpels Soltis et al., 2011 Reconstructing phylogeny: characters Symplesiomorphy = shared, ancestral character. (from Greek: syn—together (shared) + plesio—near + morph—form) An ancestral state shared by two or more lineages, which was present in their common ancestor, but is not found in all of its descendants. Symplesiomorphies diagnose paraphyletic groups. E.g., “dicots” vs. monocots Reconstructing phylogeny: characters Two seed leaves: symplesiomorphy defining “dicots” One seed leaf Reconstructing phylogeny: characters Homoplasy = convergent character, analogy. (from Greek: homo—same + plassein—to mold) A state shared by two or more lineages which is not due to common ancestry. Convergent evolution, or parallelism. Convergent characters diagnose polyphyletic groups. E.g., “Amentiferae” Reconstructing phylogeny: characters Wind pollination: multiple origins convergent characters associated with wind pollination, defining “Amentiferae” Reconstructing phylogeny: characters Polarity = direction of evolutionary change. Outgroup comparison Character states in the outgroup = ancestral condition in the ingroup. petals unfused = ancestral The preferred outgroup for determining polarity is the closest lineage to the ingroup: the sister group. Reconstructing phylogeny: in practice Parsimony = the principle that the best explanation is the simplest one. Trait a Trait b Trait c Taxon 1 Absent (0) Present (1) Absent (0) Taxon 2 Present (1) Absent (0) Present (1) Taxon 3 Present (1) Present (1) Present (1) Outgroup Absent (0) Absent (0) Absent (0) out 1 2 3 out 1 3 2 out 1 2 3 c b c b a c a c b c a a a b b 4 steps 5 steps 6 steps Reconstructing phylogeny: in practice In practice: many taxa, many characters; computationally intensive Felsenstein,(1978( Reconstructing phylogeny: in practice Real example with DNA sequence data (nucleotide characters). .