Smouse Peter E, Whitehead Michael R, Peakall Rod
Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, 08901-8551, USA.
Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia.
Mol Ecol Resour. 2015 Nov;15(6):1375-84. doi: 10.1111/1755-0998.12422. Epub 2015 May 20.
Reconstructing evolutionary history for emerging species complexes is notoriously difficult, with newly isolated taxa often morphologically cryptic and the signature of reproductive isolation often restricted to a few genes. Evidence from multiple loci and genomes is highly desirable, but multiple inputs require 'common currency' translation. Here we deploy a Shannon information framework, converting into diversity analogue, which provides a common currency analysis for maternally inherited haploid and bi-parentally inherited diploid nuclear markers, and then extend that analysis to construction of minimum-spanning networks for both genomes. The new approach is illustrated with a quartet of cryptic congeners from the sexually deceptive Australian orchid genus Chiloglottis, still in the early stages of speciation. Divergence is more rapid for haploid plastids than for nuclear markers, consistent with the effective population size differential (N(ep) < (N(en)), but divergence patterns are broadly correlated for the two genomes. There are nevertheless intriguing discrepancies between the emerging plastid and nuclear signals of early phylogenetic radiation of these taxa, and neither pattern is entirely consistent with the available information on the sexual cues used by the orchids to lure the pollinators enforcing reproductive isolation. We describe possible extensions of this methodology to multiple ploidy levels and other types of markers, which should increase the range of application to any taxonomic assemblage in the very early stages of reproductive isolation and speciation.
重建新出现的物种复合体的进化历史非常困难，新分离出的分类群在形态上往往难以区分，而生殖隔离的特征通常仅限于少数几个基因。来自多个基因座和基因组的证据非常有必要，但多个输入需要“通用货币”转换。在这里，我们采用香农信息框架，将其转换为多样性类似物，为母系遗传的单倍体和双亲遗传的二倍体核标记提供通用货币分析，然后将该分析扩展到构建两个基因组的最小生成网络。通过来自具有性欺骗性的澳大利亚兰花属 Chiloglottis 的一组难以区分的同属物种（仍处于物种形成的早期阶段）对这种新方法进行了说明。单倍体质体的分歧比核标记更快，这与有效种群大小差异（N(ep) < (N(en))）一致，但两个基因组的分歧模式大致相关。然而，这些分类群早期系统发育辐射中出现的质体和核信号之间存在有趣的差异，而且这两种模式都不完全与兰花用于吸引传粉者以加强生殖隔离的性信号的现有信息一致。我们描述了这种方法可能扩展到多个倍性水平和其他类型的标记，这应该会增加其在生殖隔离和物种形成非常早期阶段对任何分类组合的应用范围。
