The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine
This content will become publicly available on December 28, 2023
- Award ID(s):
- 1655683
- NSF-PAR ID:
- 10451914
- Editor(s):
- Ruane, Sara
- Date Published:
- Journal Name:
- Systematic Biology
- Volume:
- 72
- Issue:
- 1
- ISSN:
- 1063-5157
- Page Range / eLocation ID:
- 161 to 178
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Kubatko, Laura (Ed.)Abstract Many recent phylogenetic methods have focused on accurately inferring species trees when there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of these methods, and for phylogenetic methods in general, the data for each locus are assumed to consist of orthologous, single-copy sequences. Loci that are present in more than a single copy in any of the studied genomes are excluded from the data. These steps greatly reduce the number of loci available for analysis. The question we seek to answer in this study is: what happens if one runs such species tree inference methods on data where paralogy is present, in addition to or without ILS being present? Through simulation studies and analyses of two large biological data sets, we show that running such methods on data with paralogs can still provide accurate results. We use multiple different methods, some of which are based directly on the multispecies coalescent model, and some of which have been proven to be statistically consistent under it. We also treat the paralogous loci in multiple ways: from explicitly denoting them as paralogs, to randomly selecting one copy per species. In all cases, the inferred species trees are as accurate as equivalent analyses using single-copy orthologs. Our results have significant implications for the use of ILS-aware phylogenomic analyses, demonstrating that they do not have to be restricted to single-copy loci. This will greatly increase the amount of data that can be used for phylogenetic inference.[Gene duplication and loss; incomplete lineage sorting; multispecies coalescent; orthology; paralogy.]more » « less
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