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

目前对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，而对核基因的分析较少。爱荷华州立大学的加文·奈勒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或来自小家族(重复)的基因，目的是为脊椎动物的系统发育分析寻找可靠的特征来源。从基因序列数据库的7000多个基因的初步调查中，将选择10个左右的候选基因，构建扩增引物来提取和扩增这些片段，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。在比较不同生物基因序列之间的突变差异时，将使用模式分类群的已知系统发育树在测试中评估核苷酸碱基组成的均衡性、可自由变化的位置比例、位置间速率差异和密码子使用等属性。并不是所有的基因都有可能在系统发育分析中产生信息丰富的结果，但几乎没有对候选基因的性质进行明确的测试，以提前确定有用的基因来源。即将开展的工作将识别具有使其在系统发育上有用的特性的基因，并将提供对其实用性的经验测试。随着测序技术的进步和更多的基因组被完整测序，生物信息学将转向比较基因组学，以挖掘隐藏在鲸鱼基因组比较中的信息。随着对正在比较的基因组之间的系统发育关系的准确理解，这一努力将得到极大的加强，反过来，稳健、可靠的系统发育将取决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.