Koepfli Klaus-Peter, Wayne Robert K
Department of Organismic Biology, Ecology and Evolution, 621 Charles E. Young Drive South, University of California, Los Angeles, California 90095-1606, USA.
Syst Biol. 2003 Oct;52(5):571-93. doi: 10.1080/10635150390235368.
We compared the utility of five nuclear gene segments amplified with type I sequence-tagged site (STS) primers versus the complete mitochondrial cytochrome b (cyt b) gene in resolving phylogenetic relationships within the Mustelidae, a large and ecomorphologically diverse family of mammalian carnivores. Maximum parsimony and likelihood analyses of separate and combined data sets were used to address questions regarding the levels of homoplasy, incongruence, and information content within and among loci. All loci showed limited resolution in the separate analyses because of either a low amount of informative variation (nuclear genes) or high levels of homoplasy (cyt b). Individually or combined, the nuclear gene sequences had less homoplasy, retained more signal, and were more decisive, even though cyt b contained more potentially informative variation than all the nuclear sequences combined. We obtained a well-resolved and supported phylogeny when the nuclear sequences were combined. Maximum likelihood and Bayesian phylogenetic analyses of the total combined data (nuclear and mitochondrial DNA sequences) were able to better accommodate the high levels of homoplasy in the cyt b data than was an equally weighted maximum parsimony analysis. Furthermore, partition Bremer support analyses of the total combined tree showed that the relative support of the nuclear and mitochondrial genes differed according to whether or not the homoplasy in the cyt b gene was downweighted. Although the cyt b gene contributed phylogenetic signal for most major groupings, the nuclear gene sequences were more effective in reconstructing the deeper nodes of the combined tree in the equally weighted parsimony analysis, as judged by the variable-length bootstrap method. The total combined data supported the monophyly of the Lutrinae (otters), whereas the Melinae (badgers) and Mustelinae (weasels, martens) were both paraphyletic. The American badger, Taxidea taxus (Taxidiinae), was the most basal taxon. Because hundreds of type I STS primer sets spanning the complete genomes of the human and mouse have been published and thus represent many independently segregating loci, the potential utility of these markers for molecular systematics of mammals and other groups is enormous.
我们比较了用I型序列标签位点（STS）引物扩增的五个核基因片段与完整的线粒体细胞色素b（cyt b）基因在解决鼬科系统发育关系中的效用。鼬科是一个大型且生态形态多样的肉食性哺乳动物家族。对单独和组合数据集进行最大简约法和似然分析，以解决关于位点内和位点间同塑性、不一致性和信息含量水平的问题。由于信息变异量低（核基因）或同塑性水平高（cyt b），所有位点在单独分析中分辨率都有限。尽管cyt b包含的潜在信息变异比所有核序列之和还多，但核基因序列单独或组合起来同塑性更低，保留的信号更多，也更具决定性。当核序列组合在一起时，我们得到了一个分辨率良好且得到支持的系统发育树。对总组合数据（核和线粒体DNA序列）进行的最大似然法和贝叶斯系统发育分析比等权重最大简约法分析能更好地处理cyt b数据中的高同塑性水平。此外，对总组合树的分区布勒默支持分析表明，根据是否对cyt b基因的同塑性进行加权，核基因和线粒体基因的相对支持度有所不同。尽管cyt b基因对大多数主要类群贡献了系统发育信号，但根据可变长度自展法判断，在等权重简约分析中，核基因序列在重建组合树的更深节点方面更有效。总组合数据支持水獭亚科（水獭）的单系性，而獾亚科（獾）和鼬亚科（鼬、貂）都是并系的。美洲獾（Taxidea taxus，獾亚科）是最基部的分类单元。由于已经发表了数百个跨越人类和小鼠完整基因组的I型STS引物组，因此这些标记物在哺乳动物和其他类群的分子系统学中的潜在效用巨大。
