ChapterFourteenPhylogeography[3rdpart]例析.ppt

* Definition 1: Demographic inference that takes into account the stochasticity of genetic processes. Definition 2: Studies focused on the processes generating patterns of genetic variation within and among closely related species. Statistical phylogeography 种群突变参数θ = 4Neμ。θ可通过基于溯祖模型的软件（例如，Lamarc: Kuhner, 2006）对已知的DNA序列进行计算获得。当恒定的有效种群大小不是一个合理的假设时，θ值可作为种群增长参数的一个估计值。 The universe of potential historical scenarios that might be considered in statistical phylogeography is huge. As represented here on the surface of the sphere, there is a continuous array of possible demographic processes and associated parameter values. Depending on the trajectory of a population’s history over time (i.e., the path traversed through the sphere), a simple model such as contiguous range expansion (shown on the left) might provide an accurate simplified representation, whereas in other cases, a more complex model that incorporates different evolutionary processes at varying time points (shown on the right) would be needed for statistical phylogeographic analyses. The coalescent process was used to evaluate the probability that n gene lineages would fail to coalesce within population lineages representing purported allopatric ancestral refugial-source populations, hence, producing a discordance between the gene and population tree. purported 传说的, 据说的 Schematic representations of a gene tree contained within a population tree; an arrow identifies the discordance between the gene and population trees. This discord can easily be quantified by counting the number of deep coalescents (Maddison 1997), or the failure of gene lineages to coalesce within their respective population lineages (assuming that there is no gene flow among the populations). The amount of discordance between a gene tree and the population model was measured by s, the minimum number of sorting events required to produce the genealogy within a given model of divergence (Slatkin and Maddison 1989). The s-value is a measure of