Journal
MOLECULAR PHYLOGENETICS AND EVOLUTION
Volume 79, Issue -, Pages 359-367Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2014.06.026
Keywords
Carex section Ovales; D-statistic test; Genotyping-by-sequencing; Hybridization; Introgression
Funding
- US National Science Foundation (NSF) [1255901, 1146488]
- Marie Curie IOF fellowship [301119]
- Direct For Biological Sciences
- Division Of Environmental Biology [1146488] Funding Source: National Science Foundation
- Division Of Environmental Biology
- Direct For Biological Sciences [1255901] Funding Source: National Science Foundation
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Determining phylogenetic relationships among very closely related species has remained a challenge for evolutionary biologists due to interlocus phylogenetic discordance and the difficulty of obtaining variable markers. Here, we used a Genotyping-by-Sequencing (GBS) approach to sample a reduced representation genomic data set and infer the phylogeny of seven closely related species in the genus Carex (Cyperaceae). Past attempts to reconstruct phylogenetic relationships among these species produced conflicting and poorly-supported results. We inferred a robust phylogeny based on >3000 GBS loci and >1300 SNPs (with a minimum sequence depth within individuals of 10) using maximum likelihood and Bayesian inference. We also tested for historical introgression using the D-statistic test. We compared these analyses with partitioned RAD analysis, which is designed to identify suboptimal trees reflecting secondary phylogenetic signal that may be obscured by the dominant signal in the data. Phylogenetic analyses yielded fully resolved trees with high support. We found two main clades, one grouping Carex scoparia populations and C. waponahkikensis, and a second clade grouping C. longii, C. vexans, C. suberecta and C. albolutescens. We detected marginally significant signals of introgression between C. scoparia and C. suberecta or C. albolutescens, and we rejected a hybrid origin hypothesis for C. waponahkikensis. Our results demonstrate the power of NGS data sets for resolving some of the most difficult phylogenetic challenges where traditional phylogenetic markers have failed. (C) 2014 Elsevier Inc. All rights reserved.
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