IST Austria (Institute of Science and Technology Austria), Klosterneuburg, Austria.
Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland.
Mol Ecol Resour. 2022 Nov;22(8):2941-2955. doi: 10.1111/1755-0998.13676. Epub 2022 Jul 15.
Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that F , a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when N is large, therefore longer run times are needed to estimate N than F . Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size.
空间显式群体遗传模型已经发展了很长时间，但很少被用于检验关于遗传多样性空间分布或群体间遗传分化的假设。在这里，我们使用空间显式的合并模拟，在时空变化的居群大小的各种场景下，探索岛屿模型和二维踏脚石模型的性质。我们避免模拟遗传数据，而是利用在研究的模型下，遗传多样性和分化的综合统计数据可以从合并时间近似得出这一事实。我们使用 gridCoal 进行模拟，gridCoal 是本文开发的软件 msprime (Kelleher 等人，2016，理论种群生物学，95，13) 的灵活空间包装器。在 gridCoal 中，居群大小可以在空间和时间上任意变化，以及个体居群之间的迁移率。我们确定了不同的因素，这些因素可能导致与理论预期的偏差，例如与有效居群大小相比的模拟时间，以及网格上的时空自相关。我们的结果强调，F，衡量群体结构强度的一个指标，主要取决于近期的人口统计学，这使得它对居群大小的时间变化具有稳健性。相比之下，遗传多样性的数量取决于当 N 很大时的遥远过去，因此，与 F 相比，需要更长的运行时间来估计 N。最后，我们使用 gridCoal 对一个现实世界的例子进行了说明，即银冷杉（Abies alba Mill.）自末次冰期以来的范围扩张，使用了不同程度的时空变化的居群大小。
