Determining the genetic diversity and differentiation among populations is a critical element of conservation biology, but for many aquatic, data-deficient species with small population sizes, this is not possible. Closely related species may therefore provide a model. For the first time, using over 4000 single-nucleotide polymorphism loci, we characterise the population genetic diversity and structure of one of the world’s rarest marine fish, the spotted handfish (Brachionichthys hirsutus), a species which is also a member of the most threatened marine bony fish family (Brachionichthyidae). Fin clips were taken from 170 live spotted handfish across seven disjunct sites within the only known estuary (in Tasmania, Australia) where multiple populations of the species are found. Spatially discrete populations clustered into three genetic groupings and a significant variance in allele frequencies among populations (overall F_ST = 0.043), even at the small scale of the estuary, was observed. Furthermore, low contemporary migration rate estimates suggest low genetic homogeneity between locations. Because of the low genetic connectivity, population clusters of spotted handfish within the estuary should be considered as separate conservation management units. This insight should be considered for management and conservation strategies of other data-deficient and threatened species in the family.

确定种群之间的遗传多样性和分化是保护生物学的一个关键要素，但对于许多种群规模较小的水生、数据不足的物种来说，这是不可能的。因此，密切相关的物种可以提供一个模型。我们首次使用超过 4000 个单核苷酸多态性位点，表征了世界上最稀有的海洋鱼类之一斑点手鱼（Brachionichthys hirsutus）的种群遗传多样性和结构。)，该物种也是最受威胁的海洋硬骨鱼科 (Brachionichthyidae) 的成员。鳍夹取自 170 条活斑手鱼，分布在唯一已知的河口（在澳大利亚塔斯马尼亚州）的七个不同地点，在该河口发现了该物种的多个种群。空间离散的种群聚集成三个遗传分组，种群之间的等位基因频率存在显着差异（总体F _ST = 0.043)，即使在河口的小范围内，也被观察到。此外，较低的当代迁移率估计表明地点之间的遗传同质性较低。由于遗传连通性低，河口内的斑点手鱼种群应被视为单独的保护管理单位。这种见解应该被考虑用于家庭中其他缺乏数据和受威胁物种的管理和保护策略。