Insights from a general, full‐likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging*
Insights from a general, full‐likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging*
复制标题
从基因组数据推断共享进化事件的通用全似然贝叶斯方法的见解：推断共享人口统计事件具有挑战性*
DOI：
10.1111/evo.14052
复制
发表时间：
2020
期刊：
影响因子：
3.3
通讯作者：
Cobb, Kerry A.
中科院分区：
文献类型：
--
作者：
Oaks, Jamie R.;L'Bahy, Nadia;Cobb, Kerry A.
影响物种分布、丰富度和多样性的因素可以同时影响群落内或群落间的多个进化谱系。这些变化包括环境变化或种间生态相互作用，导致多个物种的范围缩小、扩大或碎片化。这样的过程预测了跨物种的时间集群进化事件，例如同步的种群分化和/或种群大小的变化。已经开发了许多方法来推断共同的种群差异或种群规模的变化，但不是两者都有，而后者仅限于近似方法。我们介绍了一种全似然贝叶斯方法，该方法使用基因组数据来估计种群分化和种群大小变化的任意组合的时间聚集性。使用模拟数据，我们发现，估计人口变化的时间和共享往往不准确，并且对先前的假设敏感，这与对共享分歧时间的准确、精确和稳健的估计形成对比。我们还表明，先前对阿拉斯加五个三棘刺鱼(Gasterbone Us Aculeatus)种群之间共扩张的估计可能是由先前的假设和忽略不变特征驱动的。最后，我们讨论了改进人口同步变化估计的潜在途径。
Factors that influence the distribution, abundance, and diversification of species can simultaneously affect multiple evolutionary lineages within or across communities. These include changes to the environment or inter-specific ecological interactions that cause ranges of multiple species to contract, expand, or fragment. Such processes predict temporally clustered evolutionary events across species, such as synchronous population divergences and/or changes in population size. There have been a number of methods developed to infer shared divergences or changes in population size, but not both, and the latter has been limited to approximate methods. We introduce a full-likelihood Bayesian method that uses genomic data to estimate temporal clustering of an arbitrary mix of population divergences and population-size changes across taxa. Using simulated data, we find that estimating the timing and sharing of demographic changes tends to be inaccurate and sensitive to prior assumptions, which is in contrast to accurate, precise, and robust estimates of shared divergence times. We also show that previous estimates of co-expansion among five Alaskan populations of three-spine sticklebacks (Gasterosteus aculeatus) were likely driven by prior assumptions and ignoring invariant characters. We conclude by discussing potential avenues to improve the estimation of synchronous demographic changes across populations.