CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France.
MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France.
J Anim Ecol. 2022 Jun;91(6):1180-1195. doi: 10.1111/1365-2656.13623. Epub 2021 Nov 18.
Climate influences population genetic variation in marine species. Capturing these impacts remains challenging for marine fishes which disperse over large geographical scales spanning steep environmental gradients. It requires the extensive spatial sampling of individuals or populations, representative of seascape heterogeneity, combined with a set of highly informative molecular markers capable of revealing climatic-associated genetic variations. We explored how space, dispersal and environment shape the genomic patterns of two sympatric fish species in the Mediterranean Sea, which ranks among the oceanic basins most affected by climate change and human pressure. We hypothesized that the population structure and climate-associated genomic signatures of selection would be stronger in the less mobile species, as restricted gene flow tends to facilitate the fixation of locally adapted alleles. To test our hypothesis, we genotyped two species with contrasting dispersal abilities: the white seabream Diplodus sargus and the striped red mullet Mullus surmuletus. We collected 823 individuals and used genotyping by sequencing (GBS) to detect 8,206 single nucleotide polymorphisms (SNPs) for the seabream and 2,794 for the mullet. For each species, we identified highly differentiated genomic regions (i.e. outliers) and disentangled the relative contribution of space, dispersal and environmental variables (climate, marine primary productivity) on the outliers' genetic structure to test the prevalence of gene flow and local adaptation. We observed contrasting patterns of gene flow and adaptive genetic variation between the two species. The seabream showed a distinct Alboran sea population and panmixia across the Mediterranean Sea. The mullet revealed additional differentiation within the Mediterranean Sea that was significantly correlated to summer and winter temperatures, as well as marine primary productivity. Functional annotation of the climate-associated outlier SNPs then identified candidate genes involved in heat tolerance that could be examined to further predict species' responses to climate change. Our results illustrate the key steps of a comparative seascape genomics study aiming to unravel the evolutionary processes at play in marine species, to better anticipate their response to climate change. Defining population adaptation capacities and environmental niches can then serve to incorporate evolutionary processes into species conservation planning.
气候影响海洋物种的群体遗传变异。对于那些在广阔的地理范围内扩散，跨越陡峭环境梯度的海洋鱼类来说，捕捉这些影响仍然具有挑战性。这需要对个体或种群进行广泛的空间采样，这些个体或种群代表着海洋景观的异质性，同时还需要结合一组高度信息丰富的分子标记，这些标记能够揭示与气候相关的遗传变异。我们探讨了空间、扩散和环境如何塑造地中海两种共生鱼类的基因组模式，地中海是受气候变化和人类压力影响最大的海洋盆地之一。我们假设，在移动性较低的物种中，种群结构和与气候相关的选择基因组特征会更强，因为受限的基因流往往有利于局部适应等位基因的固定。为了检验我们的假设，我们对两种具有不同扩散能力的鱼类进行了基因分型：白鲷 Diplodus sargus 和条纹红鲻 Mullus surmuletus。我们采集了 823 个个体，并使用测序基因分型（GBS）检测到白鲷的 8206 个单核苷酸多态性（SNP）和红鲻的 2794 个 SNP。对于每个物种，我们确定了高度分化的基因组区域（即异常值），并厘清了空间、扩散和环境变量（气候、海洋初级生产力）对异常值遗传结构的相对贡献，以检验基因流和局部适应的普遍性。我们观察到两种鱼类之间存在着截然不同的基因流和适应性遗传变异模式。白鲷显示出明显的阿尔沃兰海种群和在地中海的泛化混合群体。红鲻在地中海内部显示出更多的分化，这种分化与夏季和冬季温度以及海洋初级生产力显著相关。然后对与气候相关的异常 SNP 进行功能注释，确定了参与耐热的候选基因，这些基因可以进一步研究，以更好地预测物种对气候变化的反应。我们的研究结果说明了比较海洋景观基因组学研究的关键步骤，旨在揭示海洋物种中起作用的进化过程，更好地预测它们对气候变化的反应。确定种群的适应能力和环境小生境可以将进化过程纳入物种保护规划中。
