A scalable and flexible approach for investigating the genomic landscapes of phylogenetic incongruence
| Autor: | Nisc Comparative Sequencing Program, James C. Mullikin, Eric D. Green, Arjun B. Prasad |
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| Rok vydání: | 2013 |
| Předmět: |
Primates
Polytomy Chromosomes Artificial Bacterial Molecular Sequence Data Inference Introgression Biology DNA sequencing Coalescent theory Genetics Animals Humans Computer Simulation Molecular Biology Phylogeny Ecology Evolution Behavior and Systematics Likelihood Functions Bacterial artificial chromosome Genome Base Sequence Phylogenetic tree Sequence Analysis DNA Classification Research Design Evolutionary biology Data Interpretation Statistical Horizontal gene transfer Sequence Alignment Software |
| Zdroj: | Molecular Phylogenetics and Evolution. 66:1067-1074 |
| ISSN: | 1055-7903 |
| DOI: | 10.1016/j.ympev.2012.11.023 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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