Data from: Species delimitation with gene flow: a methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs

Accurately delimiting species boundaries is a non-trivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genome-wide SNPs to identify putative species boundaries by implementing non-coalescent and coalescent-based SDMs (mPTP, iBPP, BFD*). We then tested the validity of putative boundaries by estimating spatiotemporal gene flow (fastsimcoal2, ABBA-BABA) to assess the extent of genetic isolation among putative species. Our results show that the A. larutensis complex runs the gamut of the speciation continuum from highly divergent, genetically isolated lineages (mean Fst = 0.9) to differentiating populations involving recent gene flow (mean Fst = 0.05; Nm > 5). As expected, SDMs were effective at delimiting divergent lineages in the absence of gene flow but overestimated species in the presence of marked population structure and gene flow. However, using a population genomics approach and the concept of species as separately evolving metapopulation lineages as the only necessary property of a species, we were able to objectively elucidate cryptic species boundaries in the presence of past and present gene flow. This study does not discount the utility of SDMs but highlights the danger of violating model assumptions and the importance of carefully considering methods that appropriately fit the diversification history of a particular system.

精准界定物种边界绝非易事，其对后续分析推断可产生显著影响。本研究对比了常用物种界定方法（Species Delimitation Methods, SDMs）以及基于全基因组单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）的群体基因组学方法的效能，用以评估当前被认定为单一物种的马来西亚湍蛙复合体（Amolops larutensis）的谱系分化情况。首先，我们借助形态学、线粒体DNA及全基因组SNPs数据，通过实施非溯祖及基于溯祖的物种界定方法（mPTP、iBPP、BFD*）推定物种边界；随后，通过估算时空基因流（fastsimcoal2、ABBA-BABA）检验推定边界的有效性，以此评估推定物种间的遗传隔离程度。本研究结果显示，A. larutensis复合体覆盖了物种形成连续体的全部区间，从高度分化、遗传隔离的谱系（平均Fst=0.9），到存在近期基因流的分化群体（平均Fst=0.05；Nm>5）。正如预期，物种界定方法在无基因流的情况下可有效界定分化谱系，但在存在显著群体结构与基因流时会高估物种数量。然而，结合群体基因组学方法与“将物种定义为独立演化的集合种群谱系是物种唯一必要属性”的核心概念，我们得以在存在过往与当前基因流的背景下，客观阐明隐存物种边界。本研究并未否定物种界定方法的应用价值，而是凸显了违反模型假设的潜在风险，以及仔细选择适配特定类群演化历史的研究方法的重要性。