Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China.
Syst Biol. 2011 Mar;60(2):175-87. doi: 10.1093/sysbio/syq090. Epub 2011 Jan 20.
The monophyletic group Caniformia (dog-like carnivores) in the order Carnivora comprises 9 families. Except for the general consensus for the earliest divergence of Canidae and the grouping of Procyonidae and Mustelidae, conflicting phylogenetic hypotheses exist for the other caniformian families. In the present study, a data set comprising > 22 kb of 22 nuclear intron loci from 16 caniformian species is used to investigate the phylogenetic utility of nuclear introns in resolving the interfamilial relationships of Caniformia. Our phylogenetic analyses support Ailuridae as the sister taxon to a clade containing Procyonidae and Mustelidae, with Mephitinae being the sister taxon to all of them. The unresolved placements of Ursidae and Pinnipeds here emphasize a need to add more data and include more taxa to resolve this problem. The present study not only resolves some of the ambiguous relationships in Caniformia phylogeny but also shows that the noncoding nuclear markers can offer powerful complementary data for estimating the species tree. None of the newly developed introns here have previously been used for phylogeny reconstruction, thus increasing the spectrum of molecular markers available to mammalian systematics. Interestingly, all the newly developed intron data partitions exhibit intraindividual allele heterozygotes (IIAHs). There are 115 cases of IIAHs in total. The incorporation of IIAHs into phylogenetic analysis not only provides insights into the interfamilial relationships of Caniformia but also identifies two potential hybridization events occurred within Ursidae and Otariidae, respectively. Finally, the powers and pitfalls of phylogenetics using nuclear introns as markers are discussed in the context of Caniformia phylogeny.
食肉目（犬形类）中的单系群 Caniformia 包括 9 个科。除了犬科最早的分歧和浣熊科与鼬科的分组得到普遍共识外，其他犬形类科的系统发育假说存在冲突。在本研究中，使用了一个包含来自 16 种犬形类物种的>22 kb 的 22 个核内含子位点的数据集，来研究核内含子在解决犬形类科内关系中的系统发育效用。我们的系统发育分析支持浣熊科是包含浣熊科和鼬科的进化枝的姐妹群，而臭鼬科是它们的姐妹群。熊科和鳍足类的未解决位置强调需要添加更多的数据并包括更多的分类群来解决这个问题。本研究不仅解决了犬形类系统发育中的一些模糊关系，还表明非编码核标记可以为估计种系发生树提供有力的补充数据。这里没有一个新开发的内含子以前被用于系统发育重建，因此增加了可用于哺乳动物系统学的分子标记的范围。有趣的是，所有新开发的内含子数据分区都表现出个体内等位基因杂合子（IIAHs）。总共存在 115 个 IIAHs 情况。将 IIAHs 纳入系统发育分析不仅提供了对犬形类科内关系的深入了解，还分别确定了在熊科和海狮科内发生的两个潜在的杂交事件。最后，在犬形类系统发育的背景下，讨论了使用核内含子作为标记进行系统发育的优缺点。
