Data from: Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands

Harnessing the power of genomic scans, we test the debated ‘species pump’ hypothesis that implicates repeated cycles of island connectivity and isolation as drivers of divergence. This question has gone understudied given the limited resolution of past molecular markers for studying such dynamic phenomena. With an average of 32000 SNPs from the genome of 136 individuals from ten populations of a Caribbean flightless ground cricket species (Amphiacusta sanctaecrucis) and a complementary set of statistical approaches, we infer a stepping-stone colonization model and high levels of genetic differentiation across the Virgin Islands, which have been periodically inter-connected until 8 ka. Estimates of divergence times from models based on the site frequency spectrum coincide with a period of repeated connection and fragmentation of the islands at 75–130 ka. These results are consistent with a role of island connectivity cycles in promoting genomic divergence and indicate that the genetic distinctiveness of island populations has persisted despite subsequent and extended interisland connections identified from bathymetric data. We discuss these findings in the broader context of Caribbean biogeography, and more specifically why high levels of genomic divergence across the Virgin Islands associated with repeated connectivity cycles do not actually translate into species diversification.本研究利用基因组扫描技术，检验了存在争议的物种泵假说（species pump hypothesis）——该假说认为岛屿连通与隔离的重复循环是群体分化的驱动因子。由于过往用于研究这类动态现象的分子标记分辨率有限，该议题长期未得到充分探究。本研究对加勒比群岛无翅地蟋物种*Amphiacusta sanctaecrucis*的10个种群共136个个体进行基因组分析，获取了平均32000个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点，并辅以一套互补的统计分析方法，最终推断维尔京群岛存在踏脚石定殖模型，且群体间存在高水平遗传分化——这些岛屿直至距今8千年前仍处于周期性连通状态。基于位点频率谱（Site Frequency Spectrum, SFS）构建的模型所估算的分化时间，与距今7.5万至13万年间岛屿反复连通与碎片化的时期高度吻合。上述结果与岛屿连通循环促进基因组分化的假说一致，同时表明尽管通过水深数据识别出后续存在更持久的岛间连通事件，维尔京群岛各群体的遗传独特性仍得以保留。我们将本研究结果置于加勒比生物地理学的更广泛背景下展开讨论，并具体探讨了：为何与反复连通循环相关的维尔京群岛高水平基因组分化，实际上并未促成物种多样化。