Genes for Phylogenies: Identifying Genes with Intrinsically Good Properties for Phylogenetic Estimation

目前，脊椎动物物种间系统发育关系的研究主要依赖于线粒体基因序列的分析，而较少依赖于核基因的分析。爱荷华州立大学的Gavin Naylor博士正在研究几个候选的核基因，这些基因被认为是单拷贝的，或者来自基因的小家族（重复），以便为脊椎动物的系统发育分析找到可靠的特征来源。从基因序列数据库中超过7000个基因的初步调查中，选择10个左右的候选基因，构建扩增引物来提取和扩增片段，然后对几个模式分类群的基因进行测序，包括鱼类、鸟类和哺乳动物。在比较不同生物基因序列之间的突变差异时，将使用已知的模型分类群的系统发育树进行测试，以评估诸如核苷酸碱基组成均匀性、自由变化位点的比例、位点间速率变化和密码子使用等特性。在系统发育分析中，并非所有的基因都同样有可能产生信息丰富的结果，但很少有对候选基因特性的明确测试，以事先确定有用的基因来源。将要开展的工作将确定具有使其易于在系统发育上有用的特性的基因，并将对其效用进行实证检验。随着测序技术的进步和越来越多的基因组被完整测序，生物信息学将转向比较基因组学，以挖掘全基因组比较中隐藏的信息。这一努力将大大加强对基因组之间系统发育关系的准确理解，而反过来，稳健、可靠的系统发育将依赖于从几个核基因和线粒体基因中提取的数据。

The study of phylogenetic relationships among species of vertebrate animals relies heavily at present on analyses of mitochondrial gene sequences, and less so on analyses of nuclear genes. Dr. Gavin Naylor of Iowa State University is exploring several candidate nuclear genes, presumed to be single-copy or from small families (duplications) of genes, in order to find sources of reliable characters for phylogenetic analysis of vertebrates. From initial surveys of over 7000 genes in gene-sequence databases, ten or so candidates will be selected, amplification primers constructed to extract and amplify the segments, and the genes then sequenced for several model taxa of fishes, birds, and mammals. In comparing mutational differences between gene sequences from different organisms, such properties as nucleotide base compositional evenness, the proportion of sites free to vary, the among-site rate variation, and codon usage will be evaluated in tests using a known phylogenetic tree for the model taxa. Not all genes are equally likely to yield informative results in phylogenetic analyses, but there has been little explicit testing of properties of candidate genes, to determine beforehand useful gene sources. The work to be carried out will identify genes with properties that predispose them to be phylogenetically useful and will provide empirical tests of their utility. As sequencing technology improves and as more genomes are sequenced in their entirety, bioinformatics will turn to comparative genomics to mine information that is buried in the comparison of whle-genomes. This endeavor will be greatly enhanced with an accurate understanding of the phylogenetic relationships among the genomes being compared, and in turn robust, reliable phylogenies will depend upon data drawn from several nuclear as well as mitochondrial genes.