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Abstract PremiseA family‐specific probe set for sunflowers, Compositae‐1061, enables family‐wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization. MethodsWe developed a Hyb‐Seq probe set, Compositae‐ParaLoss‐1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genusPackera. We performed Hyb‐Seq with Compositae‐ParaLoss‐1272 for 19Packerataxa that were previously studied using Compositae‐1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support. ResultsWe report that Compositae‐ParaLoss‐1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae‐1061. Most notably, Compositae‐ParaLoss‐1272 recovered substantially fewer paralogous sequences than Compositae‐1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae‐1061. DiscussionGiven the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae‐ParaLoss‐1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.
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An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae
PremiseHybrid capture with high‐throughput sequencing (Hyb‐Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family‐specific Hyb‐Seq probe set and the outcomes of different phylogenetic analyses are investigated here. MethodsHyb‐Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non‐paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. ResultsAlignments of the Asteraceae family‐wide Hyb‐Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DiscussionThe approach used to build a Hyb‐Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb‐Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage‐specific.
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- Award ID(s):
- 1745197
- PAR ID:
- 10459812
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Applications in Plant Sciences
- Volume:
- 7
- Issue:
- 10
- ISSN:
- 2168-0450
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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