Blouin M S, Yowell C A, Courtney C H, Dame J B
Department of Zoology, Oregon State University, Corvallis 97331-2914, USA.
Mol Biol Evol. 1998 Dec;15(12):1719-27. doi: 10.1093/oxfordjournals.molbev.a025898.
Only relatively recently have researchers turned to molecular methods for nematode phylogeny reconstruction. Thus, we lack the extensive literature on evolutionary patterns and phylogenetic usefulness of different DNA regions for nematodes that exists for other taxa. Here, we examine the usefulness of mtDNA for nematode phylogeny reconstruction and provide data that can be used for a priori character weighting or for parameter specification in models of sequence evolution. We estimated the substitution pattern for the mitochondrial ND4 gene from intraspecific comparisons in four species of parasitic nematodes from the family Trichostrongylidae (38-50 sequences per species). The resulting pattern suggests a strong mutational bias toward A and T, and a lower transition/transversion ratio than is typically observed in other taxa. We also present information on the relative rates of substitution at first, second, and third codon positions and on relative rates of saturation of different types of substitutions in comparisons ranging from intraspecific to interordinal. Silent sites saturate extremely quickly, presumably owing to the substitution bias and, perhaps, to an accelerated mutation rate. Results emphasize the importance of using only the most closely related sequences in order to infer patterns of substitution accurately for nematodes or for other taxa having strongly composition-biased DNA. ND4 also shows high amino acid polymorphism at both the intra- and interspecific levels, and in higher level comparisons, there is evidence of saturation at variable amino acid sites. In general, we recommend using mtDNA coding genes only for phylogenetics of relatively closely related nematode species and, even then, using only nonsynonymous substitutions and the more conserved mitochondrial genes (e.g., cytochrome oxidases). On the other hand, the high substitution rate in genes such as ND4 should make them excellent for population genetics studies, identifying cryptic species, and resolving relationships among closely related congeners when other markers show insufficient variation.
直到最近，研究人员才开始转向分子方法来重建线虫的系统发育。因此，我们缺乏像其他类群那样广泛的关于线虫不同DNA区域进化模式和系统发育有用性的文献。在这里，我们研究了线粒体DNA（mtDNA）在重建线虫系统发育中的有用性，并提供可用于先验特征加权或序列进化模型中参数设定的数据。我们通过对毛圆科4种寄生线虫（每个物种38 - 50个序列）的种内比较，估计了线粒体ND4基因的替换模式。结果模式表明对A和T有强烈的突变偏向，且转换/颠换比低于其他类群通常观察到的情况。我们还给出了第一、第二和第三密码子位置的相对替换率信息，以及从种内到目间比较中不同类型替换的相对饱和率信息。沉默位点极其迅速地饱和，可能是由于替换偏向以及或许还有加速的突变率。结果强调了仅使用亲缘关系最密切的序列来准确推断线虫或其他具有强烈组成偏向性DNA的类群的替换模式的重要性。ND4在种内和种间水平都显示出高氨基酸多态性，在更高水平的比较中，可变氨基酸位点有饱和的证据。总体而言，我们建议仅将mtDNA编码基因用于亲缘关系相对密切的线虫物种的系统发育研究，即便如此，也仅使用非同义替换和更保守的线粒体基因（如细胞色素氧化酶）。另一方面，像ND4这样的基因中的高替换率应使其非常适合群体遗传学研究、识别隐存种以及在其他标记显示变异不足时解析亲缘关系密切的同属物种之间的关系。
