Jansa Sharon A, Forsman Jessica F, Voss Robert S
Bell Museum of Natural History and Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, 55108, USA.
Mol Phylogenet Evol. 2006 Feb;38(2):363-80. doi: 10.1016/j.ympev.2005.06.007. Epub 2005 Jul 27.
Selection at the protein-level can influence nucleotide substitution patterns for protein-coding genes, which in turn can affect their performance as phylogenetic characters. In this study, we compare two protein-coding nuclear genes that appear to have evolved under markedly different selective constraints and evaluate how selection has shaped their phylogenetic signal. We sequenced 1,100+ bp of exon 6 of the gene encoding dentin matrix protein 1 (DMP1) from most of the currently recognized genera of New World opossums (family: Didelphidae) and compared these data to an existing matrix of sequences from the interphotoreceptor retinoid-binding protein gene (IRBP) and morphological characters. In comparison to IRBP, DMP1 has far fewer sites under strong purifying selection and exhibits a number of sites under positive directional selection. Furthermore, selection on the DMP1 protein appears to conserve short, acidic, serine-rich domains rather than primary amino acid sequence; as a result, DMP1 has significantly different nucleotide substitution patterns from IRBP. Using Bayesian methods, we determined that DMP1 evolves almost 30% faster than IRBP, has 2.5 times more variable sites, has less among-site rate heterogeneity, is skewed toward A and away from CT (IRBP has relatively even base frequencies), and has a significantly lower rate of change between adenine and any other nucleotide. Despite these different nucleotide substitution patterns, estimates of didelphid relationships based on separate phylogenetic analyses of these genes are remarkably congruent whether patterns of nucleotide substitution are explicitly modeled or not. Nonetheless, DMP1 contains more phylogenetically informative characters per unit sequence and resolves more nodes with higher support than does IRBP. Thus, for these two genes, relaxed functional constraints and positive selection appear to improve the efficiency of phylogenetic estimation without compromising its accuracy.
蛋白质水平上的选择会影响蛋白质编码基因的核苷酸替换模式，进而影响这些基因作为系统发育特征的表现。在本研究中，我们比较了两个似乎在明显不同的选择约束下进化的蛋白质编码核基因，并评估选择如何塑造了它们的系统发育信号。我们对来自新大陆负鼠（负鼠科）目前大多数已确认属的牙本质基质蛋白1（DMP1）编码基因的第6外显子的1100多个碱基对进行了测序，并将这些数据与来自光感受器间类视黄醇结合蛋白基因（IRBP）的现有序列矩阵和形态特征进行了比较。与IRBP相比，DMP1在强纯化选择下的位点要少得多，并且表现出一些处于正向选择下的位点。此外，对DMP1蛋白的选择似乎保留了短的、酸性的、富含丝氨酸的结构域，而不是一级氨基酸序列；因此，DMP1的核苷酸替换模式与IRBP有显著差异。使用贝叶斯方法，我们确定DMP1的进化速度比IRBP快近30%，可变位点多2.5倍，位点间速率异质性较小，偏向于A而远离CT（IRBP的碱基频率相对均匀），并且腺嘌呤与任何其他核苷酸之间的变化速率显著较低。尽管有这些不同的核苷酸替换模式，但无论是否明确建模核苷酸替换模式，基于对这些基因的单独系统发育分析得出的负鼠科关系估计都非常一致。尽管如此，DMP1每单位序列包含更多的系统发育信息特征，并且比IRBP能以更高的支持度解析更多的节点。因此，对于这两个基因，宽松的功能约束和正向选择似乎提高了系统发育估计的效率，而不会损害其准确性。
