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phylogeny1 - Phylogeny Analysis Christopher Lee Phylogeny...

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Phylogeny Analysis Christopher Lee
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Phylogeny: Reconstructing Evolutionary History Goal: infer past history that produced a set of modern characters (sequences, typically). • Ingredients: – Characters: e.g. sequence differences – Evolutionary model Distance metric Probabilistic model of evolution Output: an evolutionary tree
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Phylogenetic Analysis: Overview phylogenetic inference evolutionary model Chimp Human Gorilla Macaque sequence data Summary Statistics Orangutan Squirrel Evolutionary tree
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What is a Tree? A tree is a connected graph consisting of nodes (sequences) and edges (that each connect a pair of nodes) with no cycles (path of edges that returns to its starting point). There exists a single unique path between any pair of nodes. Not a tree, due to cycle Modern sequences Ancestral sequences
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Interpreting Phylogenetic Trees: Characters Any set of objects (species; genes; proteins) can be analyzed for their evolutionary relationships. Call them the “operational taxonomic units” (OTU). Phylogeny is based on differences between the OTUs: characters . These could be sequence differences; anatomical differences, etc.
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Character Differences Branch Lengths and Order Chimp ..AGC T A A A G GGT C AGG G GAA G GG C A .. Gorilla ..AGC A T A GG GGT C AGG G GAA A GG C T .. Human ..AGC AA A A G GGT C AGG G GAA G GG G A .. Macaque ..AGC T C A T C GGT A AGG A GAA A GG A T .. Orangutan ..AGC CC A T C GGT C AGG A GAA A GG A T .. Squirrel ..AGC GG A CC GGT A AGG A GAA A GG A C .. Ch H Gor O M S Branch length represents the extent of change - expected number of substitutions per nucleotide site. The longer the branch the more change Characters Phylogenetic Tree •Length of a branch is proportional to number of differences •Tree shows order of divergences
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Phylogeny: Standard Assumptions •Sequences diverge by bifurcation events (no trifurcations etc.). (Model forms a tree). •Sequences are essentially independent once they diverge from their common ancestor. •The probability of observing nucleotide k at site j in the future depends only on the current nucleotide at site j . (Markov Chain assumption). •Different sites (characters) within a sequence evolve independently.
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Character Differences Sequence Distances Chimp ..AGC T A A A G GGT C AGG G GAA G GG C A .. Gorilla ..AGC A T A GG GGT C AGG G GAA A GG C T .. Human ..AGC AA A A G GGT C AGG G GAA G GG G A .. Macaque ..AGC T C A T C GGT A AGG A GAA A GG A T .. Orangutan ..AGC CC A T C GGT C AGG A GAA A GG A T .. Squirrel ..AGC GG A CC GGT A AGG A GAA A GG A C .. Characters Chimp Gor Hum Mac Orang Sq Chimp 5 2 8 8 9 Gor 5 7 6 8 Hum 9 8 9 Mac 2 4 Orang 5 Distances
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Sequence Distances Branch Lengths and Order Chimp ..AGC T A A A G GGT C AGG G GAA G GG C A .. Human ..AGC AA A A G GGT C AGG G GAA G GG G A ..
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