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.

精准界定物种边界并非易事，其结果会对后续推断产生显著影响。本研究比较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，以评估当前被认定为单一物种的马来西亚湍蛙复合群（Amolops larutensis）的谱系分化情况。首先，我们通过实施非溯祖及基于溯祖的SDMs（mPTP、iBPP、BFD*），结合形态学数据、线粒体DNA数据及全基因组SNPs数据，初步推定物种边界。随后，我们通过估算时空基因流（fastsimcoal2、ABBA-BABA）来验证推定边界的有效性，以评估推定物种间的遗传隔离程度。我们的研究结果显示，A. larutensis复合群覆盖了物种形成连续体的完整谱系：从高度分化、遗传隔离的谱系（平均Fst值为0.9），到存在近期基因流的分化种群（平均Fst值为0.05；Nm > 5）。正如预期，在无基因流的情况下，SDMs可有效界定分化谱系；但在存在显著群体结构与基因流的场景中，SDMs会高估物种数量。然而，我们采用群体基因组学方法，并以"物种是独立演化的集合种群谱系"作为物种唯一的必要属性，能够在存在过往及当前基因流的场景中，客观阐明隐存物种边界。本研究并未否定SDMs的应用价值，而是强调了违反模型假设的风险，以及审慎选择适配特定类群分化历史的研究方法的重要性。