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Diversity, Evolution, and Distribution of Selected African Rodents, with Focus on East African Savannahs

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Diversity, Evolution, and Distribution of Selected African Rodents, with Focus on East African Savannahs School of Doctoral Studies in Biological Sciences University of South Bohemia in České Budějovice Faculty of Science Diversity, evolution, and distribution of selected African rodents, with focus on East African savannahs Ph.D. Thesis Mgr. Vladimír Mazoch Supervisor: doc. Mgr. Radim Šumbera, Ph.D. Institute of Zoology, University of South Bohemia, České Budějovice, the Czech Republic Co-supervisor: doc. Mgr. et Mgr. Josef Bryja Ph.D. Institute of Vertebrate Biology, the Czech Academy of Sciences, Brno, the Czech Republic České Budějovice 2018 This thesis should be cited as: Mazoch, V., 2018: Diversity, evolution, and distribution of selected African rodents, with focus on East African savannahs. Ph.D. Thesis Series, No. 13. University of South Bohemia, Faculty of Science, School of Doctoral Studies in Biological Sciences, České Budějovice, Czech Republic, 117 pp. Annotation The thesis describes genetic diversity and phylogeography in several species of African rodents. It examines cryptic diversity, origin of these taxa together with colonization routes, refugia, barriers to gene flow and other historical factors influencing their current geographical distribution. Molecular genetic analyses detected considerably higher diversity of small mammals than previously expected. Several candidates for new species have been suggested and many new localities for known species have been discovered. Observed phylogeographic structure revealed geographical barriers to gene flow and current contact zones between neighboring taxonomical units (Zambezi-Kafue river system, Rukwa Rift, Eastern Arc Mountains, Limpopo river valley, etc.). Molecular dating, evidence for expansion and contraction of population size, and species distribution modeling suggest connection of main lineage splits with rapid fluctuations in forest/savanna biomes during the Late Pleistocene. Declaration [in Czech] Prohlašuji, že svoji disertační práci jsem vypracoval samostatně pouze s použitím pramenů a literatury uvedených v seznamu citované literatury. Prohlašuji, že v souladu s § 47b zákona č. 111/1998 Sb. v platném znění souhlasím se zveřejněním své disertační práce, a to v úpravě vzniklé vypuštěním vyznačených částí archivovaných Přírodovědeckou fakultou elektronickou cestou ve veřejně přístupné části database STAG provozované Jihočeskou univerzitou v Českých Budějovicích na jejích internetových stránkách, a to se zachováním mého autorského práva k odevzdanému textu této kvalifikační práce. Souhlasím dále s tím, aby toutéž elektronickou cestou byly v souladu s uvedeným ustanovením zákona č. 111/1998 Sb. zveřejněny posudky školitele a oponentů práce i záznam o průběhu a výsledku obhajoby kvalifikační práce. Rovněž souhlasím s porovnáním textu mé kvalifikační práce s databází kvalifikačních prací Theses.cz provozovanou Národním registrem vysokoškolských kvalifikačních prací a systémem na odhalování plagiátů, provozovanou Národním registrem vysokoškolských kvalifikačních prací a systémem na odhalování plagiátů. České Budějovice, ....................... …….…….….…………………………… Mgr. Vladimír Mazoch……. This thesis originated from a partnership of Faculty of Science, University of South Bohemia; and Institute of Vertebrate Biology, Czech Academy of Sciences. Financial support This thesis was financially supported by the projects of the Czech Science Foundation, nos. P506/10/0983 and 15-20229S. Acknowledgements The completion of this thesis could not have been possible without the support, assistance, and patience of many people who have accompanied me in recent years as I have worked on this thesis. To all of them, whose names are to be listed here, I wish to express my sincere thanks. I would like to express my gratitude to my supervisor Radim Šumbera for professional guidance, encouragement, and advice he has provided throughout my time as his student, to Pepa Bryja and Ondra Mikula for their constructive suggestions and insightful comments during the writing of the manuscript. I wish to thank to my friend and colleague Hana Konvičková for introduction to lab work and phylogenetic analyses. I am thankful to Molly McDonough and Sophie Gryseels for providing me an opportunity to work with them on their respective manuscripts. I would like to thank my fellow doctoral students Mates Lövy, Honza Šklíba, Ema Hrouzková, Honza Zima, Ondra Kott, Džája Smiešková, Táňa Aghová, and once again Sophie for their feedback, cooperation, and of course friendship, especially during field expeditions. Field work would not be possible without our local colleagues, namely Yonas Meheretu, Kiros Welegerima, Abdul Katakweba, and Ramos Tseu. All of them and many others were not only great field workers but provided many valuable advices during writing of the manuscripts. A very special gratitude goes out to teachers and staff at the University of South Bohemia and Research Facility of Institute of Vertebrate Biology in Studenec for providing fascinating lectures and access to the laboratory and research facilities. I am also grateful to my significant other, my family, and friends for their support and encouragement throughout my prolonged studies. List of papers and author’s contributions The thesis is based on the following papers: I. Mazoch V., Mikula O., Bryja J., Konvičková H., Russo I. R., Verheyen E. & Šumbera R. (2018). Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion. Mammalia, 82(4), 373-387. (IF 2017 = 0.714). Vladimír Mazoch (VM) provided, together with Josef Bryja and Radim Šumbera, substantial contribution to conception and design of the manuscript, drafted first version of the manuscript to the coauthors, revised critically important content, performed laboratory work, collaborate on statistical analysis, and contributed to field work. II. McDonough M. M., Šumbera R., Mazoch V., Ferguson A. W., Phillips C. D., & Bryja J. (2015). Multilocus phylogeography of a widespread savanna-woodland-adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa's Zambezi region. Molecular Ecology, 24(20), 5248-5266. (IF 2017 = 6.131). VM was involved in data collection, ecological niche modelling analysis and interpretation, and provided a revision of the manuscript. III. Bryja J., Mikula O., Šumbera R., Meheretu Y., Aghová T., Lavrenchenko L. A., Mazoch V., Oguge N., Mbau J. S., Welegerima K., Amundala N., Colyn M., Leirs H. & Verheyen E. (2014). Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa. BMC Evolutionary Biology, 14(1), 256. (IF 2017 = 3.027). VM contributed to data analyses, fieldwork, and contributed to writing of the manuscript. IV. Bryja J., Mazoch V., Patzenhauerová H., Mateke C., Zima J. Jr, Šklíba J. & Šumbera R. (2012). Revised occurrence of rodents from the tribe Praomyini (Muridae) in Zambia based on mitochondrial DNA analyses: implications for biogeography and conservation. Folia Zoologica, 61(3/4), 268-283. (IF 2017 = 0.467). VM performed laboratory work, contributed to preparation, analysis of the dataset, manuscript editing, and manuscript review. Content General Introduction ..................................................................... 1 1. Introduction ............................................................................... 2 1.1. General background ................................................................. 2 1.2. East(ern) Africa ........................................................................ 3 1.3. The East African Rift System ................................................ 6 1.4. Climatic fluctuations ................................................................ 8 1.5. Rivers, lakes, and drainage evolution .................................. 10 1.6. Vegetation history of East Africa ........................................ 12 1.7. Small mammals as models for phylogeographic studies .... 15 1.8. The practical importance of understanding diversity and phylogeography of East African rodents ..................... 18 2. Aims and scope of the thesis .................................................... 21 3. References ................................................................................ 22 Chapter I. Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion. ......................... 33 Chapter II. Multilocus phylogeography of a widespread savanna-woodland-adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa's Zambezi region. ....................................................................... 49 Chapter III. Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa. ................................................................ 69 Chapter IV. Revised occurrence of rodents from the tribe Praomyini (Muridae) in Zambia based on mitochondrial DNA analyses: implications for biogeography and conservation. ........................................................................... 91 Conclusion and future perspective ............................................. 109 Appendix ................................................................................... 115 GENERAL INTRODUCTION 1. Introduction 1.1. General background An ongoing boom in studies combining molecular genetics and geographical data provides a capable tool for the understanding
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