Brito Patrícia H, Edwards Scott V
Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
Genetica. 2009 Apr;135(3):439-55. doi: 10.1007/s10709-008-9293-3. Epub 2008 Jul 24.
We review recent trends in phylogeography and phylogenetics and argue that these two fields stand to be reunited by the common yardstick provided by sequence and SNP data and by new multilocus methods for phylogenetic analysis. Whereas the modern incarnation of both fields was spawned by PCR approaches applied to mitochondrial DNA in the late 1980s, the two fields diverged during the 1990s largely due to the adoption by phylogeographers of microsatellites, in contrast to the adoption of nuclear sequence data by phylogeneticists. Sequence-based markers possess a number of advantages over microsatellites, even on the recent time scales that are the purview of phylogeography. Using examples primarily from vertebrates, we trace the maturation of nuclear gene phylogeography and phylogenetics and suggest that the abundant instances of gene tree heterogeneity beckon a new generation of phylogenetic methods that focus on estimating species trees as distinct from gene trees. Whole genomes provide a powerful common yardstick on which both phylogeography and phylogenetics can assume their proper place as ends of a continuum.
我们回顾了系统地理学和系统发育学的近期趋势，并认为这两个领域有望通过序列和单核苷酸多态性（SNP）数据提供的共同标准以及新的多位点系统发育分析方法重新结合。虽然这两个领域的现代形式都是在20世纪80年代末将聚合酶链反应（PCR）方法应用于线粒体DNA时产生的，但在20世纪90年代，这两个领域出现了分歧，主要原因是系统地理学家采用了微卫星，而系统发育学家采用了核序列数据。基于序列的标记相对于微卫星具有许多优势，即使在系统地理学所涉及的近期时间尺度上也是如此。我们主要以脊椎动物为例，追溯核基因系统地理学和系统发育学的成熟过程，并表明基因树异质性的大量实例呼唤新一代专注于估计物种树（与基因树不同）的系统发育方法。全基因组提供了一个强大的共同标准，系统地理学和系统发育学都可以在这个标准上作为一个连续统一体的两端占据其应有的位置。
