Effective and census size, connectivity and the temporal dimension of genetic diversity in aquatic organisms

了解种群中有多少个体是保护和进化生物学的基本第一步。人口普查人口规模（Nc）的概念相对容易理解，因为它通常是指人口中的个人总数。然而，这种概念上的简单性掩盖了这样一个事实，即在大多数情况下，精确而无偏差地估计丰度是极其困难的。在管理被开发的海洋种群方面，以及在保护濒临灭绝的小种群方面，这尤其是个问题。在海洋渔业中，对丰度的估计传统上依赖于每单位努力的渔获量（CPUE），这是一个受偏见和不确定性影响的指标，往往是不可靠的和有争议的。我的目标之一是用基因组学来估计人口普查的规模。人口规模很重要，但它本身只能部分回答管理和保护的问题。在进化生物学中，最重要的往往不是总丰度，而是种群的有效规模（Ne）。这是一个理想群体的大小，表现出与所研究群体相同的遗传特性。因此，有效和普查规模这两个参数及其关系（Ne/Nc）都很重要，因为它们的相对大小可用于评估中性过程与自适应过程在塑造所研究系统的遗传组成方面的相对作用。***在这个建议中，我着重于对Nc和Ne的估计。我计划使用基因组学和近亲属标记重新捕获（CKMR）框架来估计Nc。该方法使用的原理是，个体的基因型可以被认为是对其每个父母的基因型的“再捕获”，然后在标记-再捕获框架中分析父母-后代对（POP）的数量和模式。假设对后代和父母的抽样是相互独立的，那么在两个群体的大量收集中鉴定出的持久性有机污染物的遗传数量可用于估计丰度。我计划用四个独立的系统来做这个实验，这些系统在数量和交配行为上都不同，因此，在繁殖成功的预期模式上也不同。这包括交配几乎是随机的系统[条纹鲈鱼]，中等[如溪鳟，大西洋鲑鱼]和高度[如灰海豹]歪斜繁殖成功的系统。我的目标是评估生活史特征（特定年龄的存活率和繁殖率）估计中的不确定性对丰度估计的精度和偏差在一系列丰度估计和生殖倾斜上的影响。对于所有四种系统，基因组数据还将用于估计有效种群规模，并在可行的情况下使用一种需要了解标记之间重组率的方法来估计它们的时间轨迹。该研究将有助于验证CKMR框架，以估计管理种群和数据有限种群的丰度

Knowing how many individuals there are in a population is a fundamental first step in conservation and evolutionary biology. The concept of census population size (Nc) is relatively easy to understand as it generally refers to the total number of individuals in a population. This conceptual simplicity, however, belies the fact that estimating abundance with precision and without bias is in most cases extremely difficult. It is particularly a problem in the management of exploited marine populations, as well as in the conservation of small populations under risk of extinction. In marine fisheries, the estimation of abundance has traditionally relied on catch per unit effort (CPUE), a metric that is subject to bias and uncertainty and can often be unreliable and contentious. One of my goals is to estimate census population size, Nc, using genomics. ***Population size is important but by itself provides only a partial answer to questions in management and conservation. In evolutionary biology, what often matters most is not total abundance, but the effective size of the population (Ne). This is the size of an ideal population that exhibits the same genetic properties as the population under study. Both parameters, effective and census size and their relationship (Ne/Nc) are thus important as their relative magnitudes can be used to assess the relative roles of neutral vs. adaptive processes in moulding the genetic composition of the system under study. ***In this proposal I focus on the estimation of both, Nc and Ne. I plan to estimate Nc using genomics and the Close Kin Mark Recapture (CKMR) framework. This method uses the principle that an individual's genotype can be considered a “recapture” of the genotypes of each of its parents, and then analyses the number and pattern of parent-offspring pairs (POP) in a mark-recapture framework. Assuming the sampling of offspring and parents is independent of each other, the number POPs genetically identified in a large collection of both groups can be used to estimate abundance. I plan to do this with four independent systems differing in abundance and mating behavior and thus, in expected patterns of reproductive success. This includes systems where mating is nearly random [striped bass] to systems with moderately [e.g., brook trout, Atlantic salmon] and highly [e.g., grey seals] skewed reproductive success. My goal is to assess the consequences of uncertainties in the estimation of life history traits (age specific survival and fecundity rates) on precision and bias of the abundance estimates over a range of abundance estimates and reproductive skew. For all four systems, the genomic data will also be used to estimate effective population sizes and where feasible their temporal trajectory using a method that requires knowledge of recombination rates among markers. The research will assist in validating the CKMR framework to estimate abundance in managed and data limited populations.**