Data from: The demographic history of Atlantic Salmon (Salmo salar) across its distribution range reconstructed from Approximate Bayesian Computations

Understanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. Here, we investigated the demographic history of Atlantic Salmon across the entire species range using 2035 anadromous individuals from North America and Eurasia. By combining results from admixture graphs, geo-genetic maps and an Approximate Bayesian Computation (ABC) framework, we validated previous hypotheses pertaining to secondary contact between European and Northern American populations, but also identified secondary contacts in European populations from different glacial refugia. We further identified the major sources of admixture from the southern range of North America into more northern populations along with a strong signal of secondary gene flow between genetic regional groups. We hypothesize that these patterns reflects the spatial redistribution of ancestral variation across the entire North American range. Results also support a role for linked selection and differential introgression that likely played an under-appreciated role in shaping the genomic landscape of species in the Northern hemisphere. We conclude that studies between partially isolated populations should systematically include heterogeneity in selective and introgressive effects among loci to perform more rigorous demographic inferences of the divergence process.

阐明种群分化构建过程中种群动态过程与选择过程的双重作用，是进化生物学领域最具挑战性的研究课题之一。本研究针对分布于全球物种分布范围内的大西洋鲑（Atlantic Salmon），利用采自北美与欧亚大陆的2035尾溯河洄游个体，解析其种群历史动态。本研究结合混合图谱（admixture graphs）、地理遗传图谱（geo-genetic maps）以及近似贝叶斯计算（Approximate Bayesian Computation, ABC）框架的分析结果，不仅验证了此前关于欧洲与北美北部种群间次级接触的假说，还发现欧洲种群内部存在来自不同冰期避难所（glacial refugia）的次级接触事件。本研究进一步明确了北美南部种群向北部种群的主要基因混合来源，并检测到遗传区域类群间存在显著的次级基因流信号。我们推测上述模式反映了祖先遗传变异在北美全域范围内的空间重分布过程。研究结果同时证实了连锁选择（linked selection）与差异化渐渗（differential introgression）的作用——这两类过程可能在塑造北半球物种基因组景观（genomic landscape）的过程中发挥了此前未被充分重视的作用。本研究总结指出，针对部分隔离种群的研究应系统纳入位点间选择效应与渐渗效应的异质性，从而对分化过程开展更为严谨的种群动态推断。