Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics
Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics
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DOI：
10.1093/oxfordjournals.molbev.a025898
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发表时间：
1998-12-01
影响因子：
10.7
通讯作者：
Dame, JB
中科院分区：
文献类型：
--
作者：
Blouin, MS;Yowell, CA;Dame, JB
直到最近，研究人员才转向分子方法来重建线虫的生殖系统。因此，我们缺乏广泛的文献的进化模式和系统发育的有用性不同的DNA区域线虫，存在其他类群。在这里，我们研究的有用性线粒体DNA的线虫发育重建和提供的数据，可用于先验字符加权或参数规格的序列进化模型。我们估计的线粒体ND 4基因的替代模式，从种内比较在四种寄生线虫从家庭毛圆线虫科（38-50序列每种）。由此产生的模式表明一个强大的突变偏向A和T，和一个较低的转换/颠换比通常观察到的其他类群。我们还介绍了在第一，第二和第三密码子位置的相对取代率和不同类型的取代的相对饱和率的比较，从种内interordinal。沉默位点的饱和速度非常快，这可能是由于替换偏好，也可能是由于突变率加快。结果强调的重要性，只使用最密切相关的序列，以准确地推断模式的替代线虫或其他类群具有强烈的成分偏见的DNA。ND 4还显示在种内和种间水平上的高氨基酸多态性，并且在更高水平的比较中，存在可变氨基酸位点饱和的证据。一般来说，我们建议只使用mtDNA编码基因用于相对密切相关的线虫物种的遗传学，即使这样，也只使用非同义替换和更保守的线粒体基因（例如，细胞色素氧化酶）。另一方面，ND 4等基因的高替代率使其非常适合群体遗传学研究，识别隐藏物种，并在其他标记显示变异不足时解决密切相关的同源物之间的关系。
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.