Chan Kin O, Hutter Carl R, Wood Perry L, Grismer L L, Das Indraneil, Brown Rafe M
Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, Singapore.
Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.
Mol Ecol. 2020 Oct;29(20):3970-3987. doi: 10.1111/mec.15603. Epub 2020 Sep 14.
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
大多数新的隐存物种是使用传统的基于树和距离的物种界定方法（SDMs）来描述的，这些方法依赖于系统发育排列和遗传分化度量。然而，尽管已知诸如种群结构和基因流等众多因素会混淆系统发育推断和物种界定，但这些过程的影响却不常被评估。我们使用通过FrogCap序列捕获协议获得的大量外显子、内含子和超保守元件，将传统的SDMs与更稳健的基因组分析进行了比较，后者评估种群结构和基因流以刻画东南亚蛙类复合体（饰纹姬蛙）的物种边界。我们的结果表明，基因流和基因渗入可以产生类似于不同物种的系统发育模式和分化水平（线粒体DNA中高达10%的分化）。杂交种群被推断为独立的（单系）分支，与相邻种群高度分化（7%-10%），且与异域种群异常相似（<3%）。这种异常模式在东南亚两栖动物中并不罕见，这使得人们质疑在其他两栖动物类群中观察到的高水平隐存多样性是反映了不同的隐存物种，还是相反，是高度混合和结构化的集合种群谱系。我们的结果还为分歧的（有时是非姐妹的）同域谱系这一难题提供了另一种解释——这种模式一直被视为真正隐存物种形成的标志。基于这些发现，我们建议，对连续分布的“隐存”类群进行物种界定时，不应仅依赖传统的SDMs，而必须考察种群结构和基因流，以避免分类膨胀。
