BIOEE 1780 1st Edition Lecture 6Outline of Previous Lecture I. Finish activityA) ClarifyB) Create taxonomic treeC) DiscussII. Phylogenetic TerminologyIII. Further notesOutline of Current LectureI. ReviewII. Molecular treesA) Neutral theoryB) Coalescence III. MitochondriaCurrent lectureI. Review*Synapomorphy: shared derived traitII. Molecular trees*Tips are presents day alleles*Can see clades*Branch length reflects numbers of state transitions/mutationsA) Neutral theory (of molecular evolution)*Most new mutations are not favored or disfavored*For example, many DNA nucleotide substitutions are synonymous (variants code for the same amino acid)*Neutral mutations arise at random, genetic drift determine their fate in a population*They arise at an average rate and can be used to date nodes on a molecular phylogeny*Example: HIV analyzed, turned into a best-fit line, node estimated at 1910-ish-This means that 1910 is around when HIV arose.B) Coalescence*The process by which, looking back through time, the paths of any pair of homologous alleles merge in a common ancestorC) Gene trees vs species trees (Gene trees do not necessarily match species trees)Allele splits hereSpecies split hereIII. Mitochondria*Mitochondria only comes from mom (our mitochondria are clones of our mother’s)*We can trace our mitochondria back to a “mitochondrial Eve”*There also exists a “y-chromosome
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