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

水生生物遗传多样性的有效和普查规模、连通性和时间维度

• 批准号: RGPIN-2019-04679
• 负责人: Ruzzante, Daniel
• 金额: $ 3.42万
• 依托单位: Dalhousie University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2021
• 资助国家: 加拿大
• 起止时间: 2021-01-01 至 2022-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=737781
• 关键词: Effective; census; size; connectivity; temporal

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.

了解一个种群中有多少个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，因为它通常指的是人口中的总人数。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，准确而无偏见地估计丰度是极其困难的。在管理被开发的海洋种群以及保护濒临灭绝的小种群方面，这是一个特别大的问题。在海洋渔业中，对丰度的估计传统上依赖于单位努力渔获量(CPUE)，这一指标容易受到偏见和不确定性的影响，往往不可靠和有争议。我的目标之一是利用基因组学估计北卡罗来纳州的人口普查规模。人口规模很重要，但它本身只提供了管理和保护问题的部分答案。在进化生物学中，最重要的往往不是总的丰度，而是种群的有效规模(Ne)。这是一个理想种群的大小，它表现出与正在研究的种群相同的遗传特性。因此，有效和人口普查规模及其关系(Ne/Nc)这两个参数都很重要，因为它们的相对大小可以用来评估中性过程和适应性过程在塑造所研究系统的遗传组成方面的相对作用。在这项建议中，我着重于Nc和Ne的估计。我计划使用基因组学和近亲标记重新捕获(CKMR)框架来估计NC。该方法利用个体的基因可以被认为是对其每个亲本的基因类型的“再捕获”的原理，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。假设后代和双亲的样本是相互独立的，在两个群体的大量集合中从基因上识别的持久性有机污染物数量可以用来估计丰度。我计划用四个独立的系统来做这件事，这些系统在丰度和交配行为上不同，因此在预期的繁殖成功模式上也不同。这包括交配几乎是随机的(条纹石斑鱼)的系统，到繁殖成功程度中等[如河豚、大西洋鲑鱼]和高度[如灰海豹]的系统。我的目标是评估生活史特征估计(特定年龄的存活率和繁殖率)中的不确定性对丰度估计的精确度和偏差的影响，以及对一系列丰度估计和生殖偏差的影响。对于所有四个系统，基因组数据还将被用来估计有效的种群规模，并在可行的情况下，使用一种需要了解标记间重组率的方法来估计其时间轨迹。这项研究将有助于验证CKMR框架，以估计受管理和数据有限的人口的丰度。