title: Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: a case study in Carex (Cyperaceae).
abstract: 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.
authors.affiliation: Botany Department, Field Museum of Natural History, Chicago, IL 60605, USA; The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532, USA.
authors.forename: Marcial
authors.initials: M
authors.lastname: Escudero
authors.affiliation: Botany Department, Field Museum of Natural History, Chicago, IL 60605, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.
authors.forename: Deren A R
authors.initials: DA
authors.lastname: Eaton
authors.affiliation: The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532, USA.
authors.forename: Marlene
authors.initials: M
authors.lastname: Hahn
authors.affiliation: The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532, USA; Botany Department, Field Museum of Natural History, Chicago, IL 60605, USA. Electronic address: ahipp@mortonarb.org.
authors.forename: Andrew L
authors.initials: AL
authors.lastname: Hipp
mesh_terms: D001499:Bayes Theorem; D005075:Biological Evolution; D031255:Carex Plant / Q000145:classification* / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D051456:Gene Flow; D005838:Genotype; D006824:Hybridization, Genetic; D016013:Likelihood Functions; D009656:North America; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: Carex section Ovales; D-statistic test; Genotyping-by-sequencing; Hybridization; Introgression