423f11-phylogeny

423f11-phylogeny - Phylogeny CMSC 858s Tree of Life / LUA...

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Phylogeny CMSC 858s
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Tree of Life / LUA
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Salzberg, Kingsford, et al., 2007 H5N1 Infuenza Strains
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Salzberg, Kingsford, et al., 2007 bootstrap support H5N1 Infuenza Strains
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How many times has a feature arisen? been lost? How is a disease evolving to avoid immune system? What is the sequence of ancestral proteins? What are the most similar species? What is the rate of speciation? Is there a correlation between gain/loss of traits and environment? with geographical events? Which features are ancestral to a clade, which are derived? What structures are homologous, which are analogous? Questions Addressable by Phylogeny
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Taxon sampling: how many individuals are used to represent a species? how is the “outgroup” chosen? Can individuals be collected or cultured? Marker selection: Sequence features should: be Representative of evolutionary history (unrecombined) [mitochondrial & chloroplast dna] have a single copy be able to be ampliFed with PCR able to be sequenced change enough to distinguish species, similar enough to perform MSA Study Design Considerations
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Convergent Evolution Bird & bat wings arose independently (analogous) Bone structure has common ancestor (homologous) “Has wings” is thus a “bad” trait for phylogenetic inference
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“Divergent” Evolution “Obvious” phenotypic traits are not necessarily good markers
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423f11-phylogeny - Phylogeny CMSC 858s Tree of Life / LUA...

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