Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK.
Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
Nat Commun. 2023 Jul 18;14(1):4020. doi: 10.1038/s41467-023-39532-z.
Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.
平行进化提供了强有力的证据，表明自然选择通过局部环境变化进行了适应性进化。然而，平行进化的过程的时间顺序和模式仍然存在争议。在这里，我们利用古基因组学的时间分辨率来解决这些长期存在的问题，比较了起源于中全新世（距今 8610-5626 年）的基因组与当代宽吻海豚沿海-远洋生态型的成对样本。我们发现，随着样本年龄的降低，古代样本与沿海种群的亲和力增加。我们评估了在先前推断为受到沿海生境平行选择的地点的最年轻的基因组（距今 5626 年），发现它包含了沿海相关基因型。因此，沿海相关变体的频率升高到接近沿海生境出现时可检测到的频率。混合图分析揭示了远洋和沿海种群之间的网状进化历史，共享了有助于快速适应新出现的沿海生境的遗传变异。
