Bardeleben Carolyne, Moore Rachael L, Wayne Robert K
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-1606, USA.
Mol Phylogenet Evol. 2005 Dec;37(3):815-31. doi: 10.1016/j.ympev.2005.07.019. Epub 2005 Oct 5.
We have reconstructed the phylogenetic relationships of 23 species in the dog family, Canidae, using DNA sequence data from six nuclear loci. Individual gene trees were generated with maximum parsimony (MP) and maximum likelihood (ML) analysis. In general, these individual gene trees were not well resolved, but several identical groupings were supported by more than one locus. Phylogenetic analysis with a data set combining the six nuclear loci using MP, ML, and Bayesian approaches produced a more resolved tree that agreed with previously published mitochondrial trees in finding three well-defined clades, including the red fox-like canids, the South American foxes, and the wolf-like canids. In addition, the nuclear data set provides novel indel support for several previously inferred clades. Differences between trees derived from the nuclear data and those from the mitochondrial data include the grouping of the bush dog and maned wolf into a clade with the South American foxes, the grouping of the side-striped jackal (Canis adustus) and black-backed jackal (Canis mesomelas) and the grouping of the bat-eared fox (Otocyon megalotis) with the raccoon dog (Nycteruetes procyonoides). We also analyzed the combined nuclear+mitochondrial tree. Many nodes that were strongly supported in the nuclear tree or the mitochondrial tree remained strongly supported in the nuclear+mitochondrial tree. Relationships within the clades containing the red fox-like canids and South American canids are well resolved, whereas the relationships among the wolf-like canids remain largely undetermined. The lack of resolution within the wolf-like canids may be due to their recent divergence and insufficient time for the accumulation of phylogenetically informative signal.
我们利用来自六个核基因座的DNA序列数据，重建了犬科23个物种的系统发育关系。通过最大简约法（MP）和最大似然法（ML）分析生成了个体基因树。总体而言，这些个体基因树的分辨率不高，但有几个相同的分组得到了不止一个基因座的支持。使用MP、ML和贝叶斯方法对包含六个核基因座的数据集进行系统发育分析，得到了一棵分辨率更高的树，这棵树与之前发表的线粒体树一致，发现了三个明确的分支，包括赤狐类犬科动物、南美狐和狼类犬科动物。此外，核数据集为几个先前推断的分支提供了新的插入缺失支持。核数据得出的树与线粒体数据得出的树之间的差异包括：鬃狼和薮犬与南美狐归为一个分支；侧纹胡狼（Canis adustus）和黑背胡狼（Canis mesomelas）归为一个分支；蝠耳狐（Otocyon megalotis）与貉（Nycteruetes procyonoides）归为一个分支。我们还分析了核基因+线粒体基因的联合树。在核基因树或线粒体基因树中得到强烈支持的许多节点，在核基因+线粒体基因联合树中仍然得到强烈支持。包含赤狐类犬科动物和南美犬科动物的分支内的关系得到了很好的解析，而狼类犬科动物之间的关系在很大程度上仍未确定。狼类犬科动物内部缺乏分辨率可能是由于它们最近才分化，且没有足够的时间积累系统发育信息信号。
