Data from: European colonisation, not Polynesian arrival, impacted population size and genetic diversity in the critically endangered New Zealand Kākāpō

Island endemic species are often vulnerable to decline and extinction following human settlement, and the genetic study of historical museum specimens can be useful in understanding these processes. The kākāpō (Strigops habroptilus) is a critically endangered New Zealand parrot that was formerly widespread and abundant. It is well established that both Polynesian and European colonization of New Zealand impacted the native avifauna, but the timeframe and severity of impacts have differed depending on species. Here, we investigated the relative importance of the 2 waves of human settlement on kākāpō decline, using microsatellites and mitochondrial DNA (mtDNA) to characterize recent kākāpō genetic and demographic history. We analyzed samples from 49 contemporary individuals and 54 museum specimens dating from 1884 to 1985. Genetic diversity decreased significantly between historical and contemporary kākāpō, with a decline in mean number of microsatellite alleles from 6.15 to 3.08 and in number of mtDNA haplotypes from 17 to 3. Modeling of demographic history indicated a recent population bottleneck linked to the period of European colonization (approximately 5 generations ago) but did not support a major decline linked to Polynesian settlement. Effective population size estimates were also larger for historical than contemporary kākāpō. Our findings inform contemporary kākāpō management by indicating the timeframe and possible cause of the bottleneck, which has implications for the management of extant genetic diversity. We demonstrate the broader utility of a historical perspective in understanding causes of decline and managing extinction risk in contemporary endangered species.岛屿特有物种在人类定居后往往极易出现种群衰退乃至灭绝，而对馆藏历史标本开展遗传学研究，有助于解析这类过程的发生机制。鸮鹦鹉（kākāpō，*Strigops habroptilus*）是一种极度濒危的新西兰鹦鹉，曾广泛分布且种群数量庞大。已有研究证实，波利尼西亚人与欧洲人对新西兰的殖民活动均对本土鸟类区系造成了影响，但不同物种所受影响的时间尺度与严重程度存在差异。本研究以微卫星标记（microsatellites）与线粒体DNA（mtDNA）为手段，解析鸮鹦鹉近期的遗传与种群历史，以此探究人类两次殖民浪潮对鸮鹦鹉种群衰退的相对影响程度。我们共分析了49份当代个体样本，以及54份采集于1884年至1985年的馆藏标本。相较于历史种群，当代鸮鹦鹉的遗传多样性显著下降：微卫星标记的平均等位基因数从6.15降至3.08，线粒体DNA单倍型数量也从17种减少至3种。种群历史模型分析显示，近期的种群瓶颈事件与欧洲殖民时期（约5个世代前）高度相关，但未发现与波利尼西亚殖民活动相关的大规模种群衰退证据。历史种群的有效种群大小估算值也高于当代种群。本研究明确了种群瓶颈的发生时间与潜在诱因，可为当代鸮鹦鹉的保护管理提供参考，同时对现存遗传多样性的管护工作具有指导意义。本研究同时证实了历史标本视角在解析濒危物种种群衰退原因、管控当代濒危物种灭绝风险方面的广泛应用价值。