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Molecular characterization of Acomys louisae from Somaliland: a deep divergence and contrasting genetic patterns in a rift zone

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Abstract

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.

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Acknowledgements

Special thanks are due to her Excellency Mrs Shukri Haji Ismail (Minister of Environment & Rural Development, Republic of Somaliland) for issuing the collection and export permit (Ref. MOERD/M/I/251/2017, MOERD/M/I/721/2019). We would like to thank Abdinasir Hussein (Ministry of Environment & Rural Development, Hargeisa, Somaliland). David Král, David Sommer and Pavel Just (Charles University, Prague, CZ), Martin Häckel (Czech University of Life Sciences, Prague, CZ), Daniel Berti, Petr Kabátek and František Kovařík (Prague, CZ), Tomáš Mazuch (Dříteč, CZ) and Abdisalaan Shabeele (Hargeisa, Somaliland) were excellent companions in the fieldwork during both expeditions. We are obliged to Hynek Kmoníček (Ministry of Foreign Affairs of the Czech Republic, CZ) who introduced us to Somaliland authorities. We thank also Mohamoud Y. Muse (President of University of Hargeisa, Somaliland), M. A. Sulub (Corporate Communication Directorate, University of Hargeisa, Somaliland), Suleiman Ahmed Gulair (President of Amoud University), Ahmed A. Boqore, Mohamed M. Jibail (Vice Presidents of Amoud University), and local authorities of Boorama, Las Geel, Sheikh, Erigavo, Mader Mage, Rugay, Buq, Ruqi, Jidhi, Quljeet, Ali Haid, Dacar Budhuq and Agabar settlements (Republic of Somaliland) for their help and support. We are obliged to Iveta Štolhoferová for critical reading of the manuscript. Computational resources were supplied by the project “e-Infrastruktura CZ” (e-INFRA LM2018140) provided within the program Projects of Large Research, Development and Innovations Infrastructures. This project was supported by the Czech Science Foundation (Project No. 20-21608S). Contribution of P.F. has been supported by Charles University Research Centre program No. 204069.

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Author notes

  1. Daniel Frynta, Klára Palupčíková are Co-first authors, the contribution of these authors is equal.

Authors and Affiliations

  1. Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague 2, Czech Republic

    Daniel Frynta, Klára Palupčíková & Petra Frýdlová

  2. Amoud University, Borama, Somaliland

    Hassan Sh Abdirahman Elmi

  3. Hargeisa University and Candlelight for Environment, Education and Health (CEEH), Hargeisa, Somaliland

    Ahmed Ibrahim Awale

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  1. Daniel Frynta
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Conceived and designed the research DF, collected the data in the field DF, PF, HAE, performed molecular analyses KP, curation of the molecular data KP, analysed the data KP, DF, interpreted the results DF, KP, wrote the paper KP, DF, PF, commented earlier versions of the MS HAE, AIA, suggested suitable localities and provided permissions HAE, AIA, all co-authors approved the final version of MS.

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Correspondence to Petra Frýdlová.

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Frynta, D., Palupčíková, K., Elmi, H.S.A. et al. Molecular characterization of Acomys louisae from Somaliland: a deep divergence and contrasting genetic patterns in a rift zone. Mamm Biol 100, 385–398 (2020). https://doi.org/10.1007/s42991-020-00045-7

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