Next generation lineage discovery: a case study of tuberous Claytonia L.

PREMISE OF THE STUDY: 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.
METHODS: 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.
KEY RESULTS: Samples mainly aggregated into groups representing each of the previously recognized species in each of the genetic data sets. Compared to the double digest RADseq dataset, 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.
CONCLUSIONS: 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.

研究背景：物种形成是生殖隔离的直观结果，但由于基因流、形态连续性、杂交或多倍化，以及新近分化支系间序列变异度较低，界定物种形成过程中产生的类群往往颇具难度。尽管如此，物种复合群（species complexes）广泛存在，对其进行分类对于理解生物多样性如何影响生态系统功能至关重要。
研究方法：本研究借助现代测序技术识别多年生春美草属（Claytonia L.）支系，并评估遗传支系与形态、生态变异之间的对应关系。从63个种群中选取18个类群的子集，分别开展三项实验：(a) 利用网络分析与溯祖分析进行支系识别；(b) 借助椭圆傅里叶分析与排序分析开展叶形分析；(c) 通过方差分析（ANOVA）与排序分析开展生态分析（涵盖土壤化学、气候因子）。
主要研究结果：各遗传数据集的样本主要聚为与此前已认定的各个物种相对应的类群。与双酶切RADseq（double digest RADseq）数据集相比，基因组浅层测序（genome skimming）数据具备更高的分辨率，为探究核基因组与叶绿体基因组多样性模式提供了更多契机。在所研究的类群间，形态与生态关联均存在显著差异（尽管存在过渡渐变）。基于本文呈现的形态学数据，本文描述了一个新物种——克劳福德春美草（Claytonia crawfordii）。
研究结论：本研究呈现的遗传数据，是首次对新近分化的多年生春美草属植物的系统发育关系开展解析的研究之一，并暗示了茎干状物种与块茎状物种间曾发生过杂交事件。鉴于此前学界在界定新近分化的植物支系的物种边界时曾遭遇诸多困难，本案例研究证明了高通量测序（high throughput sequencing）为系统分类学研究带来的革命性突破。