Adaptation and drift in the deep sea - investigating the evolution of diversity in a 'uniform' environment

保护生物多样性是必要的，以使自然人口有可能对不断变化的环境作出反应，并防止因丧失多样性而丧失适宜性。了解基本流程对于促进有效的可转让管理战略是必要的。这在海洋环境中尤其重要，因为在海洋环境中，基因流动几乎没有明显的边界。通过漂移和定向选择，生物多样性在种群内丧失，并通过相同的过程在种群之间保留。岛屿种群的大小有助于确定主导过程，因为在小种群中，漂移比选择更强。众所周知，许多自然多样性是通过这些过程在同种种群之间划分的，但这种多样性的碎片化结构往往是神秘的，特别是在像深海这样知之甚少的环境中。我们通常根据地理距离和明显的自然边界来先验地定义人口。然而，除了空间因素外，环境特征还可以通过影响基因流动的速度和方向来影响连接模式，这种影响将随着环境的变化而变化。环境特征也推动了局部选择，即使在基因持续流动的情况下，选择也可以保持种群之间的差异。如果不了解当地人口如何适应当地环境，我们仍然无法将这种类型的生物多样性纳入保护战略，并解决其对物种长期生存的潜在重要性。要了解生物多样性的功能和价值，就需要更好地了解导致生物多样性进化和丧失的选择和漂移的相互作用过程。虽然许多相关理论已经确立，但需要经验数据来检验理论并确定环境因素如何与自然系统中的进化过程相互作用。在这项研究中，我们将使用第二代测序技术来研究环境因素如何与深海种群结构和物种形成的进化相关，包括中性和功能基因座。重点将特别放在栖息地深度和按距离隔离的问题上，但其他环境因素将在收集地点根据最近经社理事会联合研究期间从相同地点收集的数据进行量化(在此期间为拟议的研究收集样本)。研究的物种将是珊瑚属的鱼，这是一种看似有名无实的深海鱼类属，其中一些是重要的商业渔业物种(包括本研究的主要重点物种--C.rupestris)。初步研究表明，系统发育谱系划分与栖息地深度相关。其他工作表明，在这些物种中的一些物种中，与压力适应相关的基因进行了选择。在比较种群基因组学研究中，将对两个珊瑚科局部物种进行调查。这两个种，C.rupestris和C.brevibarbis是共生的，但前者发现的深度比后者浅。我们将测试关于栖息地按深度或其他特征(例如，当前系统或地理距离)划分如何通过漂移(通过与扩散相关的不同环境压力)和选择来决定种内和种间多样性(包括使用扩展的系统发育评估在该属的多个栖息地专家物种之间)的进化的假设。据预测，深海栖息地的连通性更强，这可能导致更大的有效种群规模，并促进适应性进化。综上所述，这些数据将为我们提供新的见解，了解漂移和选择在多样性进化过程中的交互作用，并提供关于深海多样性结构的可转移推断。

The conservation of biodiversity is necessary to provide natural populations with the potential to respond to a changing environment, and to prevent the loss of fitness associated with lost diversity. An understanding the underlying processes is necessary to promote effective transferable management strategies. This is especially important in the marine environment where there are few obvious boundaries to gene flow. Biodiversity is lost within populations by drift & directional selection, and retained among populations by the same processes. The size of insular populations helps to determine the dominant process, since drift is stronger than selection in small populations. It is known that much natural diversity is divided among conspecific populations by these processes, but the fragmented structure of this diversity is often cryptic, especially in poorly understood environments like the deep sea. We typically define populations a priori by geographic distance and according to apparent physical boundaries. However, in addition to spatial factors, environmental characteristics can affect patterns of connectivity by affecting the rate and direction of gene flow, and this influence will vary as environments change over time. Environmental characteristics also drive local selection, and selection can maintain differences among populations even with continuing gene flow. Without knowledge about how local populations may have adapted to local environments, we remain unable to incorporate that type of biodiversity into conservation strategy, and to address its potential importance to the long-term survival of species. Understanding the function and value of biodiversity requires a better understanding of the interacting processes of selection and drift leading to its evolution and loss. While much of the relevant theory is well established, empirical data are required to test theory and determine how environmental factors interact with evolutionary processes in natural systems. In this study we will employ second generation sequencing technologies to investigate how environmental factors are associated with the evolution of population structure and speciation in the deep sea, at both neutral and functional loci. The particular focus will be on habitat depth and isolation by distance, however other environmental factors will be quantified at collection sites based on data collected from the same sites during the recent ECOMAR consortium study (during which samples for the proposed study were collected). The study species will be fish in the genus Coryphaenoides, a specious genus of deep demersal fishes, some of which are commercially important fisheries species (including the primary focal species in this study, C. rupestris). Initial studies have shown phylogenetic lineage division correleted to habitat depth. Other work has indicated selection at genes associated with adaptation to pressure in some of these species. Two focal Coryphaenoides species will be investigated in a comparative population genomics study. These species, C. rupestris and C. brevibarbis are sympatric, but the former is found at shallower depths than the latter. We will test hypotheses about how habitat division by depth or other characteristics (e.g. current systems or geographic distance) may determine the evolution of intra- and inter-specific diversity (including among multiple habitat-specialist species in the genus using an extended phylogenetic assessment) both by drift (through differential environmental pressures associated with dispersal) and by selection. Greater connectivity is predicted in the abyssal habitat, which may lead to larger effective population sizes and facilitate adaptive evolution. Taken together these data will provide novel insight into the interactive role of drift and selection during the evolution of diversity, and transferable inference about how diversity is structured in the deep sea.