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<p>Investigating genetic differentiation within a distinct geographic region contributes to a better understanding of the speciation process. <i>Niviventer sacer</i> was recently elevated from subspecies to species and is restricted to Shandong Province, China. However, the reported phylogenetic relationships of <i>N. sacer</i> based on mitochondrial and nuclear gene data by different researchers exhibit a phenomenon of mitonuclear discordance. We utilized nuclear SNPs and mitochondrial genome data to explore the evolutionary history of <i>N. sacer</i> and evaluated whether there is introgression among <i>Niviventer</i> species. Additionally, we analyze the correlation between genotypes and geographical/environmental variables, revealing the isolating factors behind genetic differentiation. Results indicate that <i>N. sacer</i> is most closely related to <i>N. confucianus</i>. <i>N. confucianus</i> has undergone introgressive hybridization with other <i>Niviventer</i> species and among its populations, which led to a reduction in mitochondrial genetic diversity. However, <i>N. sacer</i> has limited gene flow with other <i>Niviventer</i> species. The divergence between <i>N. sacer</i> and <i>N. confucianus</i> began ~ 1.2&#xa0;Ma, and nearby geological and climatic shifts isolated <i>N. sacer</i> in lowland plain habitats, potentially leading to speciation. Our results provide a detailed description of phylogeographic isolation in rodent a species restricted to lowland plains, which has important significance in zoogeographical studies.</p>

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RAD-seq data confirms that mitochondrial genes do not accurately reflect the phylogenetic position of Niviventer sacer (Rodentia: Muridae)

  • 期刊论文

  • 发表日期：

    2025年12月1日

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  • Yaoyao Li,
  • Xinghan Lin,
  • Haotian Li,
  • Yiqiao Li,
  • Chao Ma,
  • Yuchun Li

摘要

Investigating genetic differentiation within a distinct geographic region contributes to a better understanding of the speciation process. Niviventer sacer was recently elevated from subspecies to species and is restricted to Shandong Province, China. However, the reported phylogenetic relationships of N. sacer based on mitochondrial and nuclear gene data by different researchers exhibit a phenomenon of mitonuclear discordance. We utilized nuclear SNPs and mitochondrial genome data to explore the evolutionary history of N. sacer and evaluated whether there is introgression among Niviventer species. Additionally, we analyze the correlation between genotypes and geographical/environmental variables, revealing the isolating factors behind genetic differentiation. Results indicate that N. sacer is most closely related to N. confucianus. N. confucianus has undergone introgressive hybridization with other Niviventer species and among its populations, which led to a reduction in mitochondrial genetic diversity. However, N. sacer has limited gene flow with other Niviventer species. The divergence between N. sacer and N. confucianus began ~ 1.2 Ma, and nearby geological and climatic shifts isolated N. sacer in lowland plain habitats, potentially leading to speciation. Our results provide a detailed description of phylogeographic isolation in rodent a species restricted to lowland plains, which has important significance in zoogeographical studies.