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.

中文翻译：

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基因流在东南亚斑点溪蛙复合体中产生了一种神秘物种。

大多数新的隐性物种是使用常规的基于树和距离的物种定界方法（SDM）来描述的，该方法依赖于系统发育的安排和遗传差异的度量。但是，尽管已知许多因素（如种群结构和基因流）会混淆系统发育推断和物种定界，但并不经常评估这些过程的影响。使用FrogCap序列捕获协议获得的大量外显子，内含子和超保守元件，我们将常规SDM与更健壮的基因组分析进行了比较，这些分析评估了种群结构和基因流，以表征东南亚蛙类复合体（Pulchrana picturata）中的物种边界）。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水平的分化（线粒体DNA的差异高达10％）。杂种种群被推定为独立的（单子）进化枝，与邻近种群（7％–10％）和与异种种群异常相似（<3％）非常不同。这种异常模式在东南亚的两栖动物中并不少见，这使人们怀疑在其他两栖动物群体中观察到的高水平的隐性多样性是否反映了不同的隐性物种，或者是高度混合和结构化的种群种群。我们的结果还为发散（有时是非姐妹）同胞血统的难题提供了另一种解释-这种模式已被赞誉为指示真正的神秘物种。