系统发育基因组学.pptx

Phylogenomics Reporter : Shu Hao-yue Laboratory of Pollution and Restoration Ecology Content Background Current methods for phylogenomics Bottleneck Background History The idea of phylogeny follows directly from the theory of evolution presented by Charles Darwin in The Origin of Species At first, the reconstruction of evolutionary History relies on using fossil record to provide a window to the evolutionary history of life on our planet Phylogenetic reconstruction based on the analysis of morphological or ultrastructural characters The introduction of the use of molecular data in phylogenetics led to a revolution in the late 1980s Background theory of evolution Molecular clock Neutral theory of molecular evolution At the molecular level most evolutionary changes and most of the variation within and between species is not caused by natural selection but by random drift of mutant alleles that are neutral Background assumption 1. All sites evolve identically and independently and that all substitutions are equally likely 2. Two sequences share a common ancestor and originated by speciation Tips : gene mutation Background Basic steps 1. Homologous characters 2. Phylogeny reconstructed using tree-building methods Distance methods Maximum parsimony Likelihood methods paralogs orthologs Background Limitations Deep evolutionary histories can be hard to reconstruct from molecular sequence data The further back one goes in time, the harder the alignment of sequences becomes and the greater the impact of homoplasy(multiple point mutations at the same position) Topological conflicts between phylogenies based on individual genes Problems: different genes may follow different evolutionary paths Background Phylogenomics the use of data at the genomic scale to reconstruct the phylogeny of organism Current methods for phylogenomics Phylogenomic reconstruction methods Sequence-based methods Supertree Supermatrix whole-genome features based method