Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation
Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation
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多个独立基因组数据集的一致性揭示了表型变异有限的复合物中的物种
DOI：
10.1093/sysbio/syad024
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发表时间：
2023
影响因子：
6.5
通讯作者：
Verboom, G Anthony
中科院分区：
文献类型：
--
作者：
Wootton, Lara M;Forest, Félix;Verboom, G Anthony
基因组时代的物种划界主要集中在将多种分析方法应用于单一的大规模并行测序(MPS)数据集，而不是利用不同类别的MPS数据提供的独特但互补的见解。在这项研究中，我们展示了使用两个独立的MPS数据集，一个序列捕获数据集和一个通过测序进行基因分型产生的单核苷酸多态(SNP)数据集，如何能够分辨属于草属Ehrharta的三个复合体中的物种，其强大的种群结构和微妙的形态变化限制了传统物种界定方法的有效性。序列捕获数据被用来构建埃赫哈拉塔的全面系统发育树，并解决焦点分支内的种群关系，而SNP数据被用来检测种群之间的基因库共享模式，使用一种新的方法可视化多个K值。鉴于这两个基因组数据集是独立的，它们所解析的簇中的强一致性为所有三个所研究的复合体中的物种边界提供了强有力的批准。我们的方法还能够解析一些单种群物种和可能的杂交物种，这两者都很难使用单个MPS数据集来检测和表征。总体而言，数据揭示了你体内存在的11个物种和5个物种。SetaceaandE.和你在一起的是狂热的困惑。在最终确定物种限制之前，需要进一步采样的分枝复合体。尽管表型分化通常很微妙，但真正的隐语仅限于少数物种对和三胞胎。我们的结论是，在没有强烈的形态分化的情况下，使用多个独立的基因组数据集是必要的，以提供作为综合分类学方法基础的跨数据集证实。[物种定界；基因测序；种群结构；综合分类学；隐蔽种；禾本科)。]
Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study, we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single-nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genusEhrharta,whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree ofEhrhartaand to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualizes multiple values ofK. Given that the two genomic data sets are independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both of which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in theE. setaceaandE. rehmanniicomplexes, with theE. ramosacomplex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach. [Species delimitation; genotyping-by-sequencing; population structure; integrative taxonomy; cryptic species; Ehrharta (Poaceae).]