Ecological genetics of isolated loach populations indicate compromised adaptive potential

Many endangered species live in fragmented and isolated populations with low genetic variability, signs of inbreeding, and small effective population sizes - all features elevating their extinction risk. The flat-headed loach (<i>Oreonectes platycephalus</i>), a small noemacheilid fish, is found widely across southern China, but only in headwaters of hillstreams; as a result, they are spatially isolated from conspecific populations. We surveyed single nucleotide polymorphisms in 16 Hong Kong populations of <i>O. platycephalus</i> to determine whether loach populations from different streams were genetically isolated from each other, showed low levels of genetic diversity and signs of inbreeding, and had small effective population sizes. Estimates of average observed heterozygosity (<i>H</i>_<em>O</em> = 0.0473), average weighted nucleotide diversity (<i>π</i>_<em>w</em> = 0.0546) and effective population sizes (<i>N</i>_<em>e</em> = 10.2 - 129.8) were very low, and several populations showed clear signs of inbreeding as judged from relatedness estimates. The degree of genetic differentiation among populations was very high (average <i>F</i>_<em>ST</em> = 0.668), even over short geographic distances (&lt; 1.5 km), with strong patterns of isolation by distance. These results suggest that Hong Kong populations of <i>O. platycephalus</i> have experienced strong genetic drift and loss of genetic variability because sea-level rise after the last glaciation reduced connectedness among paleodrainages, isolating populations in headwaters. All this, together with the fact that the levels of genetic diversity and current effective population sizes within <i>O. platycephalus</i> populations are lower than most other freshwater fishes, suggests that they face high extinction risk and limited capacity for future adaptation.The DArT-seq report contains all SNPs among 282 <i>O. platycephalus</i> individuals called by <i>Diversity Arrays Technology Pty Ltd, Australia</i>. Analyses in this study were based on the report using the R package <i>dartR v2.7.2</i>. In addition, <i>.vcf</i> files of each population were attached for analysss conducted by <i>vcftools</i>.

诸多濒危物种均呈现种群破碎化与隔离化特征，伴随遗传多样性低下、近交迹象以及较小的有效种群规模——上述因素均会提升其灭绝风险。扁头鳅（*Oreonectes platycephalus*）为小型条鳅科鱼类，广泛分布于中国南方，但仅栖息于山溪上游水域；因此其种群与同种其他种群存在空间隔离。本研究对香港地区16个扁头鳅种群开展单核苷酸多态性（single nucleotide polymorphisms, SNP）分析，旨在明确不同溪流中的扁头鳅种群是否存在遗传隔离、是否呈现遗传多样性低下与近交迹象，以及是否具备较小的有效种群规模。研究结果显示，平均观测杂合度（*H*_*O* = 0.0473）、平均加权核苷酸多样性（*π*_*w* = 0.0546）以及有效种群规模（*N*_*e* = 10.2~129.8）均处于极低水平；且通过亲缘关系评估可知，多个种群存在明确的近交迹象。种群间的遗传分化程度极高（平均*F*_ST = 0.668），即使在地理距离极近（<1.5 km）的种群间亦是如此，且呈现显著的距离隔离模式。上述结果表明，末次冰期后的海平面上升降低了古水系间的连通性，导致山溪上游的扁头鳅种群相互隔离，香港地区的扁头鳅种群因此经历了强烈的遗传漂变与遗传多样性丧失。加之扁头鳅种群的遗传多样性水平与当前有效种群规模均低于多数其他淡水鱼类，这一切均提示该物种面临极高的灭绝风险，且未来的适应能力十分有限。本研究使用的DArT-seq报告包含由澳大利亚Diversity Arrays Technology Pty Ltd公司对282尾扁头鳅个体检测得到的全部单核苷酸多态性位点。本研究的数据分析基于该报告，并使用R包*dartR v2.7.2*完成；此外，本研究还附带了每个种群的.vcf格式文件，以供使用vcftools开展相关分析。