Fenner School of Environment and Society, Australian National University, Canberra 2601, Australia.
School of Molecular and Life Sciences, Curtin University, Perth 6845, Australia.
J Hered. 2024 Aug 20;115(5):552-564. doi: 10.1093/jhered/esae029.
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 analyzed 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.
小种群、碎片化或孤立的种群由于与近亲繁殖和遗传漂变相关的适合度成本而面临种群减少的风险。金岛灌丛鹪鹩（Acanthornis magna greeniana）是塔斯马尼亚灌丛鹪鹩（A. m. magna）的一个极度濒危亚种，估计有<100 只个体存在于三个沼泽森林斑块中。塔斯马尼亚灌丛鹪鹩广泛分布于塔斯马尼亚大陆的潮湿森林中。我们使用 PacBio HiFi 对灌丛鹪鹩基因组进行了测序，并使用 5,239 个 SNP 位点的双酶切限制位点相关 DNA（ddRAD）数据集对金岛和塔斯马尼亚灌丛鹪鹩进行了群体基因组研究。基因组长 1.48 Gb，由 1,518 个 contigs 组成，N50 为 7.715 Mb。金岛灌丛鹪鹩形成了四个总体遗传群之一，但在与塔斯马尼亚灌丛鹪鹩分开分析时，分为三个不同的亚群。金岛灌丛鹪鹩亚群之间的成对 FST 值大于大多数塔斯马尼亚灌丛鹪鹩亚群之间的 FST 值。金岛灌丛鹪鹩的遗传多样性较低，近交系数较高，除一个塔斯马尼亚灌丛鹪鹩亚群外，均高于其他所有亚群。我们在 15 只金岛灌丛鹪鹩中有 8 只观察到冠秃，但在 55 只塔斯马尼亚灌丛鹪鹩中没有观察到。6 个位点与秃发显著相关，包括一个位于 DOCK11 基因内的位点，该基因与早期羽毛发育有关。金岛灌丛鹪鹩亚群之间不太可能存在当代基因流，需要进一步的实地监测来量化其小种群规模、低遗传多样性和高近交率的适应度后果。然后可以实施基于证据的保护行动，以免该分类单元灭绝。
