"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2009 University of California, Berkeley B.D. Mishler Feb. 24, 2009. Molecular Evolution Aims: (1) phylogeny reconstruction (2) study of evolution at the molecular level per se Mutation, recombination, and gene conversion Transposable elements Repetitive elements (microsatellites) Natural selection vs neutrality detecting selection Different genomes organellar vs. nuclear gene movement Comparing genomes synteny, rearrangements, indels the "annotation" problem Exon shuffling Introns (different types) Multigene families paralogy vs orthology the fate of duplicated genes: ghost genes, subfunctionalization Polyploidy - genome size RNA and secondary structure Transition-transversion bias purines A G pyrimidines C T U Protein evolution ("proteomics") Codon usage bias G+C content Simplified cladogram of the 'many-to-many' relationships of classical nuclear receptors. Triangles indicate expansion within one lineage; bars represent single members. Numbers in parentheses indicate the number of paralogues in each group.From: Biochemistry & Molecular Biology of Plants. edited by Bob B. Buchanan, Wilhelm Gruissem, Russell L. Jones. 2000. “inparalogs” vs. “outparalogs” Erik Sonnhammer. Trends in Genetics Vol.18 No.12, 2002 Synteny Orthology vs.
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