title: A scalable and flexible approach for investigating the genomic landscapes of phylogenetic incongruence.
abstract: Analyses of DNA sequence datasets have repeatedly revealed inconsistencies in phylogenetic trees derived with different data. This is termed phylogenetic incongruence, and may arise from a methodological failure of the inference process or from biological processes, such as horizontal gene transfer, incomplete lineage sorting, and introgression. To better understand patterns of incongruence, we developed a method (PartFinder) that uses likelihood ratios applied to sliding windows for visualizing tree-support changes across genome-sequence alignments, allowing the comparative examination of complex phylogenetic scenarios among many species. As a pilot, we used PartFinder to investigate incongruence in the Homo-Pan-Gorilla group as well as Platyrrhini using high-quality bacterial artificial chromosome (BAC)-derived sequences as well as assembled whole-genome shotgun sequences. Our simulations verified the sensitivity of PartFinder, and our results were comparable to other studies of the Homo-Pan-Gorilla group. Analyses of the whole-genome alignments reveal significant associations between support for the accepted species relationship and specific characteristics of the genomic regions, such as GC-content, alignment score, exon content, and conservation. Finally, we analyzed sequence data generated for five platyrrhine species, and found incongruence that suggests a polytomy within Cebidae, in particular. Together, these studies demonstrate the utility of PartFinder for investigating the patterns of phylogenetic incongruence.
authors.affiliation: Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, United States. aprasad@nhgri.nih.gov
authors.forename: Arjun B
authors.initials: AB
authors.lastname: Prasad
authors.forename: James C
authors.initials: JC
authors.lastname: Mullikin
authors.forename: Eric D
authors.initials: ED
authors.lastname: Green
mesh_terms: D000818:Animals; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D002965:Classification / Q000379:methods*; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D016678:Genome / Q000235:genetics*; D006801:Humans; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D010802:Phylogeny; D011323:Primates / Q000235:genetics; D012107:Research Design; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA; D012984:Software