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

脊椎动物物种间系统发育关系的研究目前主要依赖于线粒体基因序列的分析，而对核基因的分析则相对较少。爱荷华州州立大学的Gavin Naylor博士正在探索几个候选的核基因，这些基因被认为是单拷贝的或来自基因的小家族（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，将选择10个左右的候选基因，构建扩增引物以提取和扩增片段，然后对鱼类、鸟类和哺乳动物的几个模式分类群的基因进行测序。在比较来自不同生物体的基因序列之间的突变差异时，将使用已知的模式分类群的系统发育树在测试中评估诸如核苷酸碱基组成均匀性、自由变化的位点的比例、突变位点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可能产生信息丰富的结果，但很少有明确的候选基因的特性测试，以确定事先有用的基因来源。将要进行的工作将确定具有使它们在遗传学上有用的特性的基因，并将提供对其效用的经验性测试。 随着测序技术的改进和更多基因组的完整测序，生物信息学将转向比较基因组学，以挖掘隐藏在全基因组比较中的信息。 这一奋进将大大加强与正在比较的基因组之间的系统发育关系的准确理解，反过来，强大的，可靠的系统发育将取决于从几个核以及线粒体基因的数据。

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.