Kergoat Gaël J, Silvain Jean-François, Delobel Alex, Tuda Midori, Anton Klaus-Werner
INRA, Centre de Biologie et de Gestion des Populations (CBGP-UMR1062), Campus International de Baillarguet, 34988 Montferrier-sur-Lez, France.
Mol Phylogenet Evol. 2007 Apr;43(1):251-69. doi: 10.1016/j.ympev.2006.11.026. Epub 2006 Dec 9.
In this study, we have investigated the limits of taxonomic conservatism in host-plant use in the seed-beetle genus Bruchus. To reconstruct the insect phylogeny, parsimony and multiple partitioned Bayesian inference analyses were conducted on a combined data set of four genes. Permutation tests and both global and local maximum-likelihood optimizations of host preferences at distinct taxonomic levels revealed that host-fidelity is still discernible beyond the host-plant tribe level, suggesting the existence of more important than previously thought evolutionary constraints, which are further discussed in details. Our tree topologies are also mostly consistent with extant taxonomic groups. Through the analysis of this empirical data set we also provide meaningful insights on two methodological issues. First, Bayesian inference analyses suggest that partitioning by using codon positions greatly increase the accuracy of phylogenetical reconstructions. Regarding reconstruction of ancestral character states through maximum likelihood, the present study also highlights the usefulness of local optimizations. The issue of over-parameterization is also addressed, as the optimizations with the most parameter-rich models have returned the most counterintuitive results.
在本研究中,我们调查了豆象属布鲁楚斯在寄主植物利用方面的分类保守性限度。为了重建昆虫系统发育,对四个基因的组合数据集进行了简约法和多重分区贝叶斯推断分析。置换检验以及在不同分类水平上对寄主偏好的全局和局部最大似然优化表明,寄主专一性在寄主植物族水平之上仍然是可辨别的,这表明存在比先前认为的更重要的进化限制,将对此进行详细讨论。我们的树形拓扑结构也大多与现存分类群一致。通过对这个经验数据集的分析,我们还对两个方法学问题提供了有意义的见解。首先,贝叶斯推断分析表明,按密码子位置进行分区大大提高了系统发育重建的准确性。关于通过最大似然法重建祖先特征状态,本研究还强调了局部优化的有用性。还讨论了过参数化问题,因为使用参数最丰富的模型进行优化得到了最违反直觉的结果。