Center for the Environment and Department of Biological Sciences, Plymouth State University, 17 High Street, Plymouth, NH, 03264-1594, USA.
Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Am J Bot. 2018 Mar;105(3):536-548. doi: 10.1002/ajb2.1061. Epub 2018 Apr 19.
Species formation is an intuitive endpoint of reproductive isolation, but circumscribing taxa that arise during speciation can be difficult because of gene flow, morphological continuity, hybridization or polyploidization, and low sequence variation among newly diverged lineages. Nonetheless, species complexes are ubiquitous, and their classification is essential for understanding how diversity influences ecosystem function.
We used modern sequencing technology to identify lineages of perennial Claytonia L. and assessed correspondence between genetic lineages and morphological/ecological variation. Subsets of 18 taxa from 63 populations were used for (a) lineage discovery using network and coalescent analyses, (b) leaf shape analyses using elliptical Fourier analysis and ordination, and (c) ecological analyses (soil chemistry, climate) using ANOVA and ordination.
Samples mainly aggregated into groups representing each of the previously recognized species in each of the genetic data sets. Compared to the double-digest restriction-site-associated DNA sequencing data set, genome skimming data provided more resolution and further opportunity to probe into patterns of nuclear and chloroplast genome diversity. Morphological and ecological associations are significantly different (albeit intergrading) among the taxa investigated. A new species, Claytonia crawfordii, is described based on morphological data presented here.
Genetic data presented in this study provide some of the first insights into phylogenetic relationships among recently diverged perennial Claytonia and are suggestive of past hybridization among caudicose and tuberous species. Given prior difficulties in understanding species boundaries among newly diverged plant lineages, this case study demonstrates the revolutionary breakthrough for systematics research that high throughput sequencing represents.
物种形成是生殖隔离的直观终点，但由于基因流、形态连续性、杂交或多倍体化以及新分化谱系之间的低序列变异，界定在物种形成过程中出现的分类群可能具有挑战性。尽管如此，物种复合体还是普遍存在的，它们的分类对于理解多样性如何影响生态系统功能至关重要。
我们使用现代测序技术来鉴定多年生 Claytonia L. 的谱系，并评估遗传谱系与形态/生态变异之间的对应关系。从 63 个种群中选择了 18 个分类群的子集，用于（a）使用网络和合并分析发现谱系，（b）使用椭圆傅里叶分析和排序进行叶形分析，以及（c）使用 ANOVA 和排序进行生态分析（土壤化学、气候）。
样本主要聚集在代表每个遗传数据集之前识别的物种的组中。与双酶切限制位点相关的 DNA 测序数据集相比，基因组掠过数据集提供了更多的分辨率，并进一步有机会探测核和叶绿体基因组多样性的模式。所研究的分类群之间的形态和生态关联明显不同（尽管存在混合）。根据本文提出的形态数据，描述了一个新物种 Claytonia crawfordii。
本研究中提供的遗传数据为最近分化的多年生 Claytonia 之间的系统发育关系提供了一些初步见解，并暗示了在具地下茎和块茎物种之间存在过去的杂交。鉴于先前在理解新分化植物谱系的物种边界方面存在困难，本案例研究展示了高通量测序为系统学研究带来的革命性突破。
