Hancock Zachary B, Bradburd Gideon S
Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103.
bioRxiv. 2025 May 24:2025.05.19.654925. doi: 10.1101/2025.05.19.654925.
In most natural populations, individuals in close proximity are more related on average than those at greater distances; this pattern gives rise to geographic population genetic structure. Despite extensive theoretical work on spatial population genetics, few empirical methods exist to estimate the components of theoretical models of genetic relatedness in continuous space. One classic model of relatedness in continuous space is the Wright-Malécot model, which predicts that the probability of identity-by-descent decays as a function of geographic distances. The shape of this decay curve is dictated by the dynamics of local dispersal and mating, as well as population density. This model can be reformulated to describe the probability of identity-by-state, in which case it decays to an asymptote, the value of which is determined by the historical demography of the population. Collectively, these features can be modeled in a likelihood-based framework to estimate neighborhood size and long-term diversity from pairwise genetic and geographic distance. In this article, we introduce the R package sandwrm (Spatial Analysis of Neighborhood size and Diversity using WRight-Malécot), which takes a Bayesian approach to estimate key parameters of populations that are both dispersal-limited and distributed continuously across a landscape.
在大多数自然种群中，平均而言，近距离的个体比远距离的个体亲缘关系更密切；这种模式导致了地理种群遗传结构的产生。尽管在空间种群遗传学方面有大量的理论研究，但在连续空间中，用于估计遗传相关性理论模型组成部分的实证方法却很少。连续空间中亲缘关系的一个经典模型是赖特 - 马勒科特模型，该模型预测，同源基因的概率会随着地理距离的增加而衰减。这种衰减曲线的形状由局部扩散和交配动态以及种群密度决定。这个模型可以重新表述以描述基因型相同的概率，在这种情况下，它会衰减到一个渐近线，其值由种群的历史人口统计学决定。总体而言，这些特征可以在基于似然性的框架中进行建模，以从成对的遗传距离和地理距离估计邻域大小和长期多样性。在本文中，我们介绍了R包sandwrm（使用赖特 - 马勒科特进行邻域大小和多样性的空间分析），它采用贝叶斯方法来估计在景观中既受扩散限制又连续分布的种群的关键参数。
