Botany Department, Field Museum of Natural History, Chicago, IL 60605, USA; The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532, USA.
Botany Department, Field Museum of Natural History, Chicago, IL 60605, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.
Mol Phylogenet Evol. 2014 Oct;79:359-67. doi: 10.1016/j.ympev.2014.06.026. Epub 2014 Jul 8.
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.
确定非常近缘物种之间的系统发育关系一直是进化生物学家面临的挑战，因为基因座间系统发育分歧和获得可变标记物的困难。在这里，我们使用了一种基于测序的基因分型（GBS）方法来采样减少的代表性基因组数据集，并推断了 Cyperaceae 属中七个密切相关的 Carex 物种的系统发育关系。过去尝试重建这些物种的系统发育关系产生了相互矛盾且支持度不高的结果。我们基于超过 3000 个 GBS 基因座和超过 1300 个 SNPs（每个个体的最小序列深度为 10），使用最大似然法和贝叶斯推断法推断出一个稳健的系统发育树。我们还使用 D 统计量检验测试了历史上的基因渗入。我们将这些分析与分区 RAD 分析进行了比较，后者旨在识别可能被数据中主导信号掩盖的次优树，这些信号反映了次要的系统发育信号。系统发育分析产生了具有高支持度的完全解决的树。我们发现了两个主要分支，一个分支聚集了 Carex scoparia 种群和 C. waponahkikensis，另一个分支聚集了 C. longii、C. vexans、C. suberecta 和 C. albolutescens。我们检测到 C. scoparia 和 C. suberecta 或 C. albolutescens 之间存在边缘显著的基因渗入信号，并拒绝了 C. waponahkikensis 的杂种起源假说。我们的结果表明，NGS 数据集在解决传统系统发育标记物失败的一些最困难的系统发育挑战方面具有强大的能力。
