Genomic insights into the critically endangered King Island scrubtit

Small, fragmented or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of < 100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analysed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct.小型、碎片化或隔离的种群因近交与遗传漂变引发的适合度代价，面临种群衰退风险。金岛刷尾刺嘴雀（Acanthornis magna greeniana）是指名亚种塔斯马尼亚刷尾刺嘴雀（A. m. magna）的极危亚种，估计种群数量不足100只，仅残存于三片沼泽林斑块中。塔斯马尼亚刷尾刺嘴雀在塔斯马尼亚大陆的湿林中广泛分布。本研究采用PacBio HiFi技术对刷尾刺嘴雀基因组进行测序，并利用包含5239个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点的双酶切限制性位点相关DNA（double-digest restriction site-associated DNA, ddRAD）数据集，对金岛与塔斯马尼亚刷尾刺嘴雀开展群体基因组学研究。该基因组总长1.48 Gb，包含1518个重叠群（contig），N50值为7.715 Mb。金岛刷尾刺嘴雀构成整体四个遗传聚类之一，但在单独与塔斯马尼亚刷尾刺嘴雀分组分析时，可分为三个不同的亚种群。金岛刷尾刺嘴雀亚种群间的两两FST值高于多数塔斯马尼亚刷尾刺嘴雀亚种群。金岛刷尾刺嘴雀的遗传多样性低于除一个塔斯马尼亚刷尾刺嘴雀亚种群外的所有群体，近交系数则高于该亚种群之外的所有群体。我们在15只金岛刷尾刺嘴雀中观察到8只存在头顶秃斑，而55只塔斯马尼亚刷尾刺嘴雀均未出现该表型。共有6个位点与秃斑表型显著相关，其中一个位点位于DOCK11基因内，该基因与早期羽毛发育密切相关。当前金岛刷尾刺嘴雀亚种群间几乎不存在基因交流，需开展进一步野外监测以量化其种群规模小、遗传多样性低以及近交程度高所带来的适合度后果，进而可在该类群灭绝前实施循证保护行动。