Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
Mol Phylogenet Evol. 2020 Feb;143:106667. doi: 10.1016/j.ympev.2019.106667. Epub 2019 Oct 30.
Golden moles (Family Chrysochloridae) are small subterranean mammals, endemic to sub-Saharan Africa, and many of the 21 species are listed as threatened on the IUCN Red List. Most species have highly restricted ranges; however two species, the Hottentot golden mole (Amblysomus hottentotus) and the Cape golden mole (Chrysochloris asiatica) have relatively wide ranges. We recently uncovered cryptic diversity within A. hottentotus, through a phylogeographic analysis of this taxon using two mitochondrial gene regions and a nuclear intron. To further investigate this cryptic diversity, we generated nuclear SNP data from across the genome of A. hottentotus, by means of double-digest restriction-site associated DNA sequencing (ddRADSeq), and mapped reads to the Cape golden mole genome. We conducted a phylogenetic analysis and investigated population differentiation. Our results support the distinctiveness of A. h. meesteri. Furthermore, we provide evidence from nuclear SNPs in support of our previous finding that Central coastal samples represent a unique cryptic lineage that is highly divergent from A. h. pondoliae farther south. Although mtDNA suggests that Umtata may represent a unique lineage sister to A. h. longiceps, mito-nuclear discordance from our RADseq data indicate that these samples may instead be closer to A. h. pondoliae, and therefore may not represent a distinct lineage. We stress the importance of recognizing that understudied populations, such as that of Umtata, may represent populations or ESUs under threat and in need of conservation attention. We present a high-quality filtered SNP dataset, comprising thousands of SNPs, which may serve as a useful resource for future golden mole studies. We have thus added to the growing body of research demonstrating the power and utility of RADseq to investigate population differentiation.
金鼹（Chrysochloridae 科）是一种小型地下哺乳动物，分布于撒哈拉以南非洲，其中 21 个物种被列入 IUCN 红色名录，属于濒危物种。大多数物种的分布范围非常有限；然而，有两个物种，霍屯督金鼹（Amblysomus hottentotus）和海角金鼹（Chrysochloris asiatica）的分布范围相对较广。我们最近通过对这个分类群使用两个线粒体基因区域和一个核内含子进行系统地理学分析，揭示了 A. hottentotus 内部的隐存多样性。为了进一步研究这种隐存多样性，我们通过双酶切限制位点相关 DNA 测序（ddRADSeq）在 A. hottentotus 的整个基因组中生成了核 SNP 数据，并将读取数据映射到海角金鼹基因组。我们进行了系统发育分析和种群分化研究。我们的结果支持 A. h. meesteri 的独特性。此外，我们还提供了来自核 SNP 的证据，支持我们之前的发现，即中部沿海样本代表了一个独特的隐存谱系，与更南部的 A. h. pondoliae 高度分化。尽管 mtDNA 表明乌姆塔塔可能代表与 A. h. longiceps 姐妹的独特谱系，但我们的 RADseq 数据显示，这些样本可能更接近 A. h. pondoliae，因此可能不代表一个独特的谱系。我们强调认识到，像乌姆塔塔这样研究不足的种群，可能代表着受到威胁的种群或 ESUs，需要得到保护关注。我们提供了一个高质量的过滤 SNP 数据集，包含数千个 SNP，这可能成为未来金鼹研究的有用资源。因此，我们增加了越来越多的研究，证明了 RADseq 在研究种群分化方面的强大功能和实用性。
