State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
Genome Biol Evol. 2017 Aug 1;9(8):1998-2012. doi: 10.1093/gbe/evx147.
The interordinal relationships of Laurasiatherian mammals are currently one of the most controversial questions in mammalian phylogenetics. Previous studies mainly relied on coding sequences (CDS) and seldom used noncoding sequences. Here, by data mining public genome data, we compiled an intron data set of 3,638 genes (all introns from a protein-coding gene are considered as a gene) (19,055,073 bp) and a CDS data set of 10,259 genes (20,994,285 bp), covering all major lineages of Laurasiatheria (except Pholidota). We found that the intron data contained stronger and more congruent phylogenetic signals than the CDS data. In agreement with this observation, concatenation and species-tree analyses of the intron data set yielded well-resolved and identical phylogenies, whereas the CDS data set produced weakly supported and incongruent results. Further analyses showed that the phylogeny inferred from the intron data is highly robust to data subsampling and change in outgroup, but the CDS data produced unstable results under the same conditions. Interestingly, gene tree statistical results showed that the most frequently observed gene tree topologies for the CDS and intron data are identical, suggesting that the major phylogenetic signal within the CDS data is actually congruent with that within the intron data. Our final result of Laurasiatheria phylogeny is (Eulipotyphla,((Chiroptera, Perissodactyla),(Carnivora, Cetartiodactyla))), favoring a close relationship between Chiroptera and Perissodactyla. Our study 1) provides a well-supported phylogenetic framework for Laurasiatheria, representing a step towards ending the long-standing "hard" polytomy and 2) argues that intron within genome data is a promising data resource for resolving rapid radiation events across the tree of life.
有蹄类哺乳动物的洲际关系是哺乳动物系统发育中最具争议的问题之一。以前的研究主要依赖于编码序列（CDS），很少使用非编码序列。在这里，我们通过挖掘公共基因组数据，编译了一个包含 3638 个基因的内含子数据集（从一个蛋白质编码基因的所有内含子都被视为一个基因）（19055073bp）和一个包含 10259 个基因的 CDS 数据集（20994285bp），涵盖了有胎盘类哺乳动物的所有主要分支（除了穿山甲目）。我们发现，内含子数据比 CDS 数据包含更强、更一致的系统发育信号。与这一观察结果一致，内含子数据集的串联和种系发生分析产生了分辨率良好且一致的系统发育，而 CDS 数据集则产生了支持较弱且不一致的结果。进一步的分析表明，从内含子数据推断出的系统发育对数据抽样和外群变化具有高度稳健性，但在相同条件下，CDS 数据产生了不稳定的结果。有趣的是，基因树统计结果表明，CDS 和内含子数据最常观察到的基因树拓扑结构是相同的，这表明 CDS 数据中的主要系统发育信号实际上与内含子数据中的一致。我们有蹄类哺乳动物系统发育的最终结果是（Eulipotyphla,((Chiroptera, Perissodactyla),(Carnivora, Cetartiodactyla)))，支持蝙蝠目和奇蹄目之间的密切关系。我们的研究 1）为有胎盘类哺乳动物提供了一个支持良好的系统发育框架，代表着朝着结束长期存在的“硬”多系性迈出的一步，2）认为基因组内的内含子是解决生命之树中快速辐射事件的有前途的数据资源。
