National Research Council - Institute of Marine Biological Resources and Biotechnologies, Messina, Italy.
Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, PSL Université Paris, Paris, France.
J Evol Biol. 2021 Jun;34(6):856-865. doi: 10.1111/jeb.13871.
Research on the genomics of adaptation is rapidly changing. In the last few decades, progress in this area has been driven by methodological advances, not only in the way increasingly large amounts of molecular data are generated (e.g. with high-throughput sequencing), but also in the way these data are analysed. This includes a growing appreciation and quantitative treatment of covariation among units within the same data type (e.g. genes) or across data types (e.g. genes and phenotypes). The development and adoption of more and more integrative tools have resulted in richer and more interesting empirical work. This special issue - comprising methodological, empirical, and review papers - aims to capture a 'snapshot' of this rapidly evolving field. We discuss in particular three important themes in the study of adaptation: the genetic architecture of adaptive variation, protein-coding and regulatory changes, and parallel evolution. We highlight how more traditional key themes in the study of genetic architecture (e.g. the number of loci underlying adaptive traits and the distribution of their effects) are now being complemented by other factors (e.g. how patterns of linkage and number of loci interact to affect the ability to adapt). Similarly, apart from addressing the relative importance of protein-coding and regulatory changes, we now have the tools to look in-depth at specific types of regulatory variation to gain a clearer picture of regulatory networks. Finally, parallel evolution has always been central to the study of adaptation, but now we are often able to address the question of whether - and to what extent - parallelism at the organismal or phenotypic level is matched by parallelism at the genetic level. Perhaps most importantly, we can now determine what mechanisms are driving parallelism (or lack thereof) across levels of biological organization. All these recent methodological developments open up new directions for future studies of adaptive changes across traits, levels of biological organization, demographic contexts and time scales.
适应的基因组学研究正在迅速发展。在过去的几十年中，该领域的进展不仅得益于方法学的进步，即如何越来越多地生成大量分子数据（例如高通量测序），还得益于如何分析这些数据。这包括对同一数据类型（例如基因）或跨数据类型（例如基因和表型）中单位之间的共变进行越来越多的认识和定量处理。越来越多的综合工具的开发和采用导致了更丰富和更有趣的经验工作。本期特刊——包括方法、实证和综述论文——旨在捕捉这一快速发展领域的“快照”。我们特别讨论了适应研究中的三个重要主题：适应性变异的遗传结构、蛋白质编码和调控变化以及并行进化。我们强调了在遗传结构研究中更为传统的关键主题（例如，适应性状的潜在基因座数量及其效应的分布）如何现在正在得到其他因素的补充（例如，连锁模式和基因座数量如何相互作用以影响适应能力）。同样，除了探讨适应性状的遗传结构的相对重要性外，我们现在还拥有深入研究特定类型的调控变化的工具，以更清楚地了解调控网络。最后，并行进化一直是适应研究的核心，但现在我们通常能够解决生物体或表型水平的并行性是否以及在何种程度上与遗传水平的并行性相匹配的问题。也许最重要的是，我们现在可以确定是什么机制在推动不同层次的生物组织之间的并行性（或缺乏并行性）。所有这些最近的方法学进展为跨性状、生物组织层次、人口背景和时间尺度的适应性变化的未来研究开辟了新的方向。
