Bayesian models for long-range population genetics

在物种进化问题上可以采取两种截然不同的观点。历史的观点包括在化石证据和分子序列比较的基础上重建所有现存物种（生命之树）的进化史。这就是系统发育学的任务。最近，它推动了重要的统计工作，以提供可靠的树木重建。另一方面，人口统计学和机械学的观点更关注于理解突变、选择和随机漂移之间复杂的相互作用如何决定现存物种的进化模式，直至分子水平。它还试图了解一个物种所经历的生态因素（如其种群规模）如何影响这种相互作用。群体遗传学为这种理解提供了理论框架。经典群体遗传学主要通过观察种内遗传多样性（多态性）的分布来实现其目的。然而，人们逐渐认识到，从系统发育学家进行的大规模比较分析中也可以得到非常有价值的信息。这一信息不如从多态性中得到的信息详细。然而，它追溯到更久远的时间，提出了一种令人兴奋的可能性，即通过阅读它，人们可以重建沿着生命之树的物种所经历的基本生态因素的进化。

Two quite different perspectives can be taken on the problem of species evolution. The historical perspective consists in reconstructing the evolutionary history of all living species (the tree of life), based on fossil evidence and molecular sequence comparisons. This is the task of phylogenetics. Recently, it has motivated important statistical efforts so as to provide reliable tree reconstructions. The demographic and mechanistic perspective, on the other hand, is more concerned with understanding how the intricate interplay between mutation, selection and random drift determines the mode of evolution of extant species, down to the molecular level. It also tries to understand how the ecological factors experienced by a species (such as its population size) influence this interplay. Population genetics provides the theoretical framework for such an understanding. Classical population genetics achieves its aims mainly by observing the distribution of intra-specific genetic diversity (polymorphisms). However, it is progressively understood that very valuable information can also be derived from the large-scale comparative analyses performed by phylogeneticists. This information is less detailed than that derived from polymorphisms. However, it reaches much further back in time, raising the exciting possibility that by reading it out, one could reconstruct the evolution of essential ecological factors experienced by species along the tree of life.