Abstract：
Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective \"evolve and resequence\" natural experiments using sedaDNA.
摘要：
在自然生态系统中，很少可能直接观察适应生态变化的时间顺序和速度。沉积的古代DNA（sedaDNA）已被证明是长期死亡的生物1,2,3的基因组规模数据的可处理来源，从而有可能提供对过去种群进化史的理解。从sedaDNA重建了生态系统生物多样性的时间序列，通常使用从少于1克沉积物中产生的DNA元编码或鸟枪序列数据。6,7这里，wemaximizedsequencecoveragebyextracingDNAfrom~50xmoresessionpersamplethanthemajorityofpreviousstudies1,2,3toachievegeneticallyresolution.从海洋到淡水生态系统的晚更新世沉积物的时间序列中，我们比较了在这种转变的关键时间点从三刺棘背的环境基因组重建的适应性基因型。我们发现了一个交错的时间动态，其中淡水等位基因在已知的基因座上对三头棘鱼的海洋淡水发散有很大影响（例如，EDA）8在隔离盆地形成的微咸阶段已经建立。然而,在大多数海洋淡水发散相关基因座中仍然检测到海洋等位基因，即使在湖泊与海洋入侵完全隔离之后。我们的回顾性方法是在最后一个冰期结束时研究三头棘鱼环境基因组的适应性，这补充了当代实验方法9,10,11，并强调了使用sedaDNA进行回顾性“进化和测序”自然实验的未开发潜力。
