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Abstract Detail


Mason-Gamer, Roberta [1], White, Dawson [2].

Phylogenomic analysis of the wheat tribe Triticeae (Poaceae) based on chloroplast and nuclear data acquired using a Hyb-Seq approach.

The wheat tribe, Triticeae, is a phylogenetically complicated group of grasses. Molecular analyses over the past 25 years have achieved ambiguous results, due to a combination of low resolution from some data sets and phylogenetic conflict among others. While the most striking cases of conflict have involved differences between nuclear and chloroplast gene trees, incongruence has also been recorded in comparisons among individual nuclear loci. The present work builds upon previous results by applying a Hyb-Seq approach, which combines targeted sequence capture of low-copy sequences with skimming of non-targeted, high-copy sequences. We present data from nearly-complete chloroplast genomes, and from over a thousand nuclear coding loci. The 1121 nuclear loci included in the analyses represent a selected subset drawn from over 2000 captured loci; we included only those for which: (1) all 76 sampled individuals—75 ingroup and one outgroup—are represented, and (2) reasonable alignments could be achieved with only low to moderate efforts expended on editing and/or masking. Together, the aligned nuclear data set includes 1,872,973 characters, of which 182,981 are variable. We performed phylogenetic analyses of the chloroplast data (maximum-likelihood search and bootstrap) and the nuclear data (gene tree and quartet-based analyses, and maximum likelihood searches and bootstrap analyses of individual and concatenated loci). Based on these results, we highlight (1) increased phylogenetic resolution of both chloroplast and nuclear trees, including stronger support of deep nodes and clarification of early-diverging lineages; (2) a clearer picture of the extent of chloroplast-nuclear conflict; and (3) underlying phylogenetic patterns within the nuclear data.

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1 - University of Illinois at Chicago, Department of Biological Sciences, MC 066, 845 W. Taylor St., Chicago, IL, 60607, USA
2 - University Of Illinois At Chicago, University Of Illinois At Chicago, 845 West Taylor St. #3256, Department Of Biological Sciences, Chicago, IL, 60607, United States

target enrichment.

Presentation Type: Oral Paper
Session: 36, Phylogenomics III
Location: 107/Mayo Civic Center
Date: Wednesday, July 25th, 2018
Time: 11:00 AM
Number: 36011
Abstract ID:862
Candidate for Awards:None

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