Phylogeographic patterns in the Horn of Africa have recently attracted researchers searching for hidden diversity and explaining the evolutionary history of this region. In this paper, we focus on spiny mouse Acomys louisae. We examined 88 samples from 13 localities across Somaliland and sequenced CYTB, control region and IRBP genes. Phylogenetic analysis confirmed clear distinctness of A. louisae from the other clades of Acomys, but it also revealed deep splits within A. louisae clade. Samples from Central and Eastern Somaliland, including those from the type locality, form a clearly distinct Somaliland clade while remaining ones from the very NW of Somaliland and 5 previously published sequences from Djibouti and E Ethiopia form a Djibouti group. At two localities in the contact zone, we detected sympatric occurrence of both. The clades exhibit sharply contrasting patterns of variability, the Somaliland clade is characterized by a sufficient mitochondrial haplotype diversity, but low sequence divergence. The population parameters and haplotype networks suggest that the populations belonging to the Somaliland clade probably underwent a recent expansion of its range and population size. It may be explained by a repopulation after the interglacial period providing poor environmental conditions for spiny mice in E and C Somaliland. In contrast, the Djibouti group shows extremely high nucleotide diversity besides that of haplotype one. This suggests a long-term persistence of large and/or structured populations. It may be attributed to a specific history of the Ethiopian Rift and Afar. The results emphasize the importance of the Horn of Africa as a region preserving high endemism.

中文翻译：

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来自索马里兰的 Acomys louisae 的分子特征：裂谷带中的深度分化和对比遗传模式

非洲之角的系统地理学模式最近吸引了研究人员寻找隐藏的多样性并解释该地区的进化历史。在本文中，我们关注多刺小鼠 Acomys louisae。我们检查了来自索马里兰 13 个地点的 88 个样本，并对 CYTB、控制区和 IRBP 基因进行了测序。系统发育分析证实了 A. louisae 与 Acomys 的其他进化枝的明显区别，但它也揭示了 A. louisae 进化枝内的深裂。来自中部和东部索马里兰的样本，包括来自典型地区的样本，形成了一个明显不同的索马里兰进化枝，而剩下的来自索马里兰西北部的样本和来自吉布提和埃塞俄比亚东部的 5 个先前公布的序列形成了一个吉布提组。在接触区的两个地方，我们检测到两者的同域发生。进化枝表现出鲜明对比的变异模式，索马里兰进化枝的特征是足够的线粒体单倍型多样性，但序列差异低。种群参数和单倍型网络表明，属于索马里兰进化枝的种群最近可能经历了其范围和种群规模的扩大。这可能是由于间冰期后的重新种群为索马里兰东部和中部的多刺小鼠提供了恶劣的环境条件。相比之下，除了单倍型 1 之外，吉布提组还显示出极高的核苷酸多样性。这表明大型和/或结构化种群的长期存在。这可能归因于埃塞俄比亚裂谷和阿法尔的特定历史。