Graduate School of Environmental Science, Hokkaido University, N10W5, Sapporo City, 060-0810, Hokkaido Prefecture, Japan.
Graduate School of Environmental Science, Hokkaido University, N10W5, Sapporo City, 060-0810, Hokkaido Prefecture, Japan.
Theor Popul Biol. 2022 Dec;148:76-85. doi: 10.1016/j.tpb.2022.11.001. Epub 2022 Nov 17.
Predicting temporal dynamics of genetic diversity is important for assessing long-term population persistence. In stage-structured populations, especially in perennial plant species, genetic diversity is often compared among life history stages, such as seedlings, juveniles, and flowerings, using neutral genetic markers. The comparison among stages is sometimes referred to as demographic genetic structure, which has been regarded as a proxy of potential genetic changes because individuals in mature stages will die and be replaced by those in more immature stages over the course of time. However, due to the lack of theoretical examination, the basic property of the stage-wise genetic diversity remained unclear. We developed a matrix model which was made up of difference equations of the probability of non-identical-by-descent of each life history stage at a neutral locus to describe the dynamics and the inter-stage differences of genetic diversity in stage-structured plant populations. Based on the model, we formulated demographic genetic structure as well as the annual change rate of the probability of non-identical-by-descent (denoted as η). We checked if theoretical expectations on demographic genetic structure and η obtained from our model agreed with computational results of stochastic simulation using randomly generated 3,000 life histories. We then examined the relationships of demographic genetic structure with effective population size N, which is the determinants of diversity loss per generation time. Theoretical expectations on η and demographic genetic structure fitted well to the results of stochastic simulation, supporting the validity of our model. Demographic genetic structure varied independently of N and η, while having a strong correlation with stable stage distribution: genetic diversity was lower in stages with fewer individuals. Our results indicate that demographic genetic structure strongly reflects stable stage distribution, rather than temporal genetic dynamics, and that inferring future genetic diversity solely from demographic genetic structure would be misleading. Instead of demographic genetic structure, we propose η as an useful tool to predict genetic diversity at the same time scale as population dynamics (i.e., per year), facilitating evaluation on population viability from a genetic point of view.
预测遗传多样性的时间动态对于评估长期种群存续至关重要。在具有阶段结构的种群中，特别是在多年生植物物种中，通常使用中性遗传标记比较生命史各阶段（如幼苗、幼体和开花个体）之间的遗传多样性。各阶段之间的比较有时被称为人口遗传结构，它被认为是潜在遗传变化的代表，因为随着时间的推移，成熟个体将死亡并被更不成熟的个体所取代。然而，由于缺乏理论检验，阶段遗传多样性的基本性质仍不清楚。我们开发了一个矩阵模型，该模型由中性基因座中每个生命史阶段非一致遗传的概率差分方程组成，以描述阶段结构植物种群中遗传多样性的动态和各阶段之间的差异。基于该模型，我们将人口遗传结构以及非一致遗传概率的年变化率（表示为η）公式化。我们检查了从我们的模型中获得的人口遗传结构和η的理论预期是否与使用随机生成的 3000 个生命史进行的随机模拟的计算结果相符。然后，我们检验了人口遗传结构与有效种群大小 N 的关系，N 是每代时间多样性损失的决定因素。η和人口遗传结构的理论预期与随机模拟的结果非常吻合，支持了我们模型的有效性。人口遗传结构独立于 N 和 η 而变化，而与稳定的阶段分布密切相关：个体数量较少的阶段遗传多样性较低。我们的结果表明，人口遗传结构强烈反映稳定的阶段分布，而不是时间遗传动态，仅从人口遗传结构推断未来遗传多样性可能会产生误导。我们建议使用 η 而不是人口遗传结构作为预测与种群动态（即每年）相同时间尺度的遗传多样性的有用工具，从而从遗传角度评估种群生存能力。
