Applications of phylogenetic incongruence to detecting and reconstructing interspecific recombination and horizontal gene transfer

[摘要] In bacteria and viruses, recombination and horizontal gene transfer (HGT) permit the direct exchange or acquisition of DNA into the genome from species other than the ;;parent;;. Two major challenges face attempts at reconstructing non-treelike evolution: (1) multiple sources of gene tree incongruence exist, making various reconciliation scenarios possible, and (2) reconstructing a given reconciliation scenario is computationally hard. In this thesis, we address the latter problem, describing new methods for reconstructing recombination and HGT events: RECOMP and RIATA-HGT. RECOMP is a recombination detection method, faster than all existing algorithms and as accurate as the best. RIATA-HGT is the first polynomial-time heuristic that reconstructs unrestricted HGT events based on gene tree incongruence. We also describe two studies characterizing the sources of statistical error in phylogenetic incongruence: ortholog inference and phylogeny estimation. These studies identify computational problems whose revision will improve the overall accuracy of phylogenetic incongruence-based, non-treelike evolution reconstruction tools.

[发布机构] Rice University

[效力级别] Computer