Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany.
Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
Sci Rep. 2017 Mar 3;7:43562. doi: 10.1038/srep43562.
Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver's masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data).
解决有问题的系统发育关系通常需要高质量的基因组数据。然而，对于许多生物来说，这些数据仍然不可用。在啮齿动物中，海狸的系统发育位置一直引起特别关注。海狸的咬肌（闭颌肌）的排列曾经表明它与某些松鼠科啮齿动物（如松鼠）有很强的亲和力，将它们置于松鼠形亚目。然而，现代分子数据表明，海狸与代表与老鼠有关的进化枝的物种关系更为密切，但实际上没有来自同源性免费标记（例如反转录转座子插入）的关于海狸的确切位置的重要数据。我们从已存入的基因组 Illumina 配对末端读取中获得了一个大体的基因组组装，并使用新的生物信息学坐标提取器 fastCOEX 提取了数千个潜在的系统发育信息反转录转座子标记，使我们能够评估海狸系统发育位置的不同假设。比较结果为海狸（海狸科）和袋鼠鼠科相关物种（地鼠科）（p < 0.0015，6 个标记，没有冲突数据）之间的明显关系提供了重要支持，在一个得到高度支持的与老鼠有关的进化枝（包括 Myodonta、Anomaluromorpha 和 Castorimorpha）（p < 0.0015，6 个标记，没有冲突数据）内。
