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·Ò룺 The concept of population genomics was introduced to describe the process of sampling numerous loci within a genome to identify locus-specific effects from genome-wide effects. Likewise, ¡°genomic phylogeography¡± describes the simultaneous sampling numerous loci across the genome to infer population history and estimate demographic parameters. Genomic phylogeography is distinguished from multilocus phylogeography by scale and degree. Multilocus studies usually focus on a few tens of markers; although a considerable improvement over single-locus analyses, such studies still only sparsely sample the full heterogeneity of the drift process, and inferences may be driven by a few outlier loci. In genomic phylogeography, by contrast, enough loci are screened to accurately estimate sampling distributions across loci, and locus-specific effects will be represented on the extreme values while genome-wide effects will fall into the centers of the distribution. Such locus-specific effects may be due to selection, mutation, or recombination, whereas genome-wide effects are due to demographic processes such as gene flow, inbreeding, population growth, or bottle necks, and that informs population history. Two main steps are involved in this process: (1) estimating genome-wide effects and (2) detecting outlier loci. Luikart et al.(2003) and Storz(2005) review ways for identifying outlier loci that uses simulated or empirical null distribution of summary statistics such as Fst or homozygosity. These genomic approaches have been successfully applied to model species such as humans, drosophila, and maize. The empircal distribution requires that enough loci be sampled to build robust null distributions and avoid erroneous identifications of perfectly good neutral loci. Examples or methods that use theoretical distributions are Ewens-Watterson test for neutrality, and the Fst outlier test developed by Beaumont and Nichols. |
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