The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large‐mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long‐read sequencing and long‐range scaffolding methods with long‐ and short‐read RNA sequencing to generate a near error‐free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome‐length autosome scaffolds and the X‐chromosome scaffold, with a scaffold N50 of 115 Mb. Genome‐wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long‐term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long‐term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

中文翻译：

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最濒危海洋哺乳动物小头鼠海豚的参考基因组和人口统计历史

小头鼠海豚是最濒危的海洋哺乳动物，野外仅存不到 19 只。小头鼠海豚于 1958 年首次被描述，20 多年来，由于越来越多地使用大网孔刺网而导致意外死亡，因此小头鼠海豚数量迅速减少。为了了解小头鼠海豚的进化和人口统计历史，我们将长读长测序和长程支架方法与长读长和短读 RNA 测序相结合，从来自于女性个体。基因组组装由 99.92% 的组装序列组成，这些序列包含在 21 个几乎无间隙的染色体长度常染色体支架和 X 染色体支架中，支架 N50 为 115 Mb。全基因组杂合度是迄今为止分析的任何哺乳动物物种中最低的（0.01%），但是杂合性在染色体上均匀分布，与遗传平衡下的长期小种群规模一致，而不是由于最近的种群瓶颈或近亲繁殖导致的低多样性。小头鼠海豚的历史人口统计表明，其人口长期稳定在 5,000 (Ne ) 超过 200,000 年。总之，这些分析表明，小头鼠海豚基因组有足够的机会清除高度有害的等位基因，并可能保持种群健康所需的多样性。