The deep oceans of the Southern Hemisphere are home to several elusive and poorly studied marine megafauna. In the absence of robust observational data for these species, genetic data can aid inferences on population connectivity, demography and ecology. A previous investigation of genetic diversity and population structure in Gray's beaked whale (Mesoplodon grayi) from Western Australia and New Zealand found high levels of mtDNA diversity, no geographic structure and stable demographic history. To further investigate phylogeographic and demographic patterns across their range, we generated complete mitochondrial and partial nuclear genomes of 16 of the individuals previously analysed and included additional samples from South Africa (n = 2) and South Australia (n = 4), greatly expanding the spatial range of genomic data for the species. Gray's beaked whales are highly elusive and rarely observed, and our data represents a unique and geographically broad dataset. We find relatively high levels of diversity in the mitochondrial genome, despite an absence of population structure at the mitochondrial and nuclear level. Demographic analyses suggest these whales existed at stable levels over at least the past 1.1 million years, with an approximately twofold increase in female effective population size approximately 250 thousand years ago, coinciding with a period of increased Southern Ocean productivity, sea surface temperature and a potential expansion of suitable habitat. Our results suggest that Gray's beaked whales are likely to be resilient to near-future ecosystem changes, facilitating their conservation. Our study demonstrates the utility of low-effort shotgun sequencing in providing ecological information on highly elusive species.

南半球的深海是数个难以捉摸且研究不足的海洋大型动物的家园。在缺乏有关这些物种的可靠观测数据的情况下，遗传数据可有助于推断种群连通性，人口统计学和生态学。先前对来自西澳大利亚州和新西兰的格雷喙喙鲸（Mesoplodon grayi）的遗传多样性和种群结构的调查发现，mtDNA多样性水平高，没有地理结构，人口统计历史稳定。为了进一步研究其范围内的系统地理学和人口统计学模式，我们生成了之前分析的16位个体的完整线粒体和部分核基因组，并包括了来自南非（n = 2）和南澳大利亚（n= 4），大大扩展了物种基因组数据的空间范围。格雷的喙鲸非常难以捉摸，很少被观察到，我们的数据代表了一个独特的且地理分布广泛的数据集。尽管在线粒体和核水平上没有种群结构，但我们在线粒体基因组中发现了相对较高的多样性。人口统计学分析表明，这些鲸鱼至少在过去110万年中一直稳定存在，大约25万年前，女性有效种群数量增加了约两倍，这与南大洋生产力，海面温度和潜在海平面上升的时期相吻合。扩大合适的栖息地。我们的结果表明，格雷的喙鲸可能对近期生态系统的变化具有韧性，促进他们的保护。我们的研究证明了省力shot弹枪测序在提供高度易捕物种的生态信息方面的实用性。