Deriving the genomic tree of life in the presence of horizontal gene transfer: Conditioned reconstruction

摘要: The horizontal gene transfer (HGT) being inferred within prokaryotic genomes appears to be sufficiently massive that many scientists think it may have effectively obscured much of the history life recorded in DNA. Here, we demonstrate tree can reconstructed even presence extensive HGT, provided processes genome evolution are properly modeled. We show dynamic deletions and insertions genes occur during evolution, including those introduced by modeled using techniques similar used model nucleotide substitutions sequence evolution. In particular, appropriately designed general Markov models reasonable tools for reconstructing These studies indicate that, contain assumptions met, is possible reconstruct life. also consider fusion genomes, a process not encountered derive method identification reconstruction events. Genomic reconstructions well-defined classical four-genome problem, root multicellular animals, method, when conjunction with paralinear/logdet distances, performs remarkably well relatively unaffected recently discovered big artifact.