Ghosts of a Structured Past: Impacts of Ancestral Patterns of Isolation-by-Distance on Divergence-Time Estimation.
Ghosts of a Structured Past: Impacts of Ancestral Patterns of Isolation-by-Distance on Divergence-Time Estimation.
复制标题
DOI：
10.1093/jhered/esaa042
复制
发表时间：
2020-12-07
期刊：
影响因子：
--
通讯作者：
Blackmon H
中科院分区：
文献类型：
--
作者：
Hancock ZB;Blackmon H
距离隔离是自然界中普遍存在的一种模式，它描述了亚种群之间的遗传相关性随着地理距离的增加而减少。在种群祖先到现代姐妹种的种群中，由于祖先种群末端亚种群的等位基因频率差异，这种模式可能会假设种群分化时间估计过高。在此研究中，我们分析了当祖先种群模型为线性垫脚石时，到最近共同祖先的时间与种群分化时间之间的关系。利用聚结模拟，我们比较了聚结时间与种群散度时间在种群大小上的不同比率。接下来，我们模拟全基因组获得单核苷酸多态性（SNPs），并使用贝叶斯聚结程序SNAPP估计分化时间。我们发现，当邻近种群间的迁移速率降低时，从末端种群中取样时，聚结时间明显大于种群分化时间。当散度与种群规模比< 10且迁移率较低时，SNAPP的散度时间高估会变得严重。最后，我们利用巴西特有鳞片（troidurus）的经验数据集证明了祖先距离隔离对发散时间估计的影响。我们的结论是，估计分化时间的研究应该在明确的空间背景下认识到潜在的祖先种群结构，否则就有可能严重高估种群分裂的时间。
Isolation-by-distance is a widespread pattern in nature that describes the reduction of genetic correlation between subpopulations with increased geographic distance. In the population ancestral to modern sister species, this pattern may hypothetically inflate population divergence time estimation due to allele frequency differences in subpopulations at the ends of the ancestral population. In this study, we analyze the relationship between the time to the most recent common ancestor and the population divergence time when the ancestral population model is a linear stepping-stone. Using coalescent simulations, we compare the coalescent time to the population divergence time for various ratios of the divergence time over the population size. Next, we simulate whole genomes to obtain single nucleotide polymorphisms (SNPs), and use the Bayesian coalescent program SNAPP to estimate divergence times. We find that as the rate of migration between neighboring demes decreases, the coalescent time becomes significantly greater than the population divergence time when sampled from end demes. Divergence-time overestimation in SNAPP becomes severe when the divergence-to-population size ratio < 10 and migration is low. Finally, we demonstrate the impact of ancestral isolation-by-distance on divergence-time estimation using an empirical dataset of squamates (Tropidurus) endemic to Brazil. We conclude that studies estimating divergence times should be cognizant of the potential ancestral population structure in an explicitly spatial context or risk dramatically overestimating the timing of population splits.
登录
查看更多内容
影响因子：
4.3
作者：
Kelleher J;Etheridge AM;McVean G
通讯作者：
McVean G
DOI：
10.1098/rspb.2000.0970
发表时间：
2000-01-07
影响因子：
4.7
作者：
Gaggiotti, OE;Excoffier, L
通讯作者：
Excoffier, L
DOI：
10.1073/pnas.1704949114
发表时间：
2017-07-25
影响因子：
11.1
作者：
Ceballos, Gerardo;Ehrlich, Paul R.;Dirzo, Rodolfo
通讯作者：
Dirzo, Rodolfo
影响因子：
0.5
作者：
DOBZHANSKY, T
通讯作者：
DOBZHANSKY, T
影响因子：
10.7
作者：
ArisBrosou, S;Excoffier, L
通讯作者：
Excoffier, L