title: Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa.
abstract: BACKGROUND
  Rodents of the genus Mus represent one of the most valuable biological models for biomedical and evolutionary research. Out of the four currently recognized subgenera, Nannomys (African pygmy mice, including the smallest rodents in the world) comprises the only original African lineage. Species of this subgenus became important models for the study of sex determination in mammals and they are also hosts of potentially dangerous pathogens. Nannomys ancestors colonized Africa from Asia at the end of Miocene and Eastern Africa should be considered as the place of their first radiation. In sharp contrast with this fact and despite the biological importance of Nannomys, the specimens from Eastern Africa were obviously under-represented in previous studies and the phylogenetic and distributional patterns were thus incomplete.
  
  
  RESULTS
  We performed comprehensive genetic analysis of 657 individuals of Nannomys collected at approximately 300 localities across the whole sub-Saharan Africa. Phylogenetic reconstructions based on mitochondrial (CYTB) and nuclear (IRBP) genes identified five species groups and three monotypic ancestral lineages. We provide evidence for important cryptic diversity and we defined and mapped the distribution of 27 molecular operational taxonomic units (MOTUs) that may correspond to presumable species. Biogeographical reconstructions based on data spanning all of Africa modified the previous evolutionary scenarios. First divergences occurred in Eastern African mountains soon after the colonization of the continent and the remnants of these old divergences still occur there, represented by long basal branches of M. (previously Muriculus) imberbis and two undescribed species from Ethiopia and Malawi. The radiation in drier lowland habitats associated with the decrease of body size is much younger, occurred mainly in a single lineage (called the minutoides group, and especially within the species M. minutoides), and was probably linked to aridification and climatic fluctuations in middle Pliocene/Pleistocene.
  
  
  CONCLUSIONS
  We discovered very high cryptic diversity in African pygmy mice making the genus Mus one of the richest genera of African mammals. Our taxon sampling allowed reliable phylogenetic and biogeographic reconstructions that (together with detailed distributional data of individual MOTUs) provide a solid basis for further evolutionary, ecological and epidemiological studies of this important group of rodents.
authors.affiliation: Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic. bryja@brno.cas.cz.|Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic. bryja@brno.cas.cz.|Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Research Facility Studenec, Studenec 122, 675 02, Koněšín, Czech Republic. bryja@brno.cas.cz.
authors.forename: Josef
authors.initials: J
authors.lastname: Bryja
authors.affiliation: Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic. onmikula@gmail.com.|Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Brno, Czech Republic. onmikula@gmail.com.
authors.forename: Ondřej
authors.initials: O
authors.lastname: Mikula
authors.affiliation: Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic. sumbera@prf.jcu.cz.
authors.forename: Radim
authors.initials: R
authors.lastname: Šumbera
authors.affiliation: Department of Biology, College of Natural and Computational Sciences, Mekelle University, Tigray, Ethiopia. meheretu@yahoo.com.
authors.forename: Yonas
authors.initials: Y
authors.lastname: Meheretu
authors.affiliation: Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic. tatiana.aghova@gmail.com.|Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic. tatiana.aghova@gmail.com.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Aghová
authors.affiliation: A.N.Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia. llavrenchenko@gmail.com.
authors.forename: Leonid A
authors.initials: LA
authors.lastname: Lavrenchenko
authors.affiliation: Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic. vladimir.mazoch@prf.jcu.cz.
authors.forename: Vladimír
authors.initials: V
authors.lastname: Mazoch
authors.affiliation: Earth Watch Institute, Nairobi, Kenya. otienoh.oguge@gmail.com.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Oguge
authors.affiliation: College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya. jsyombua04@yahoo.com.
authors.forename: Judith S
authors.initials: JS
authors.lastname: Mbau
authors.affiliation: Department of Biology, College of Natural and Computational Sciences, Mekelle University, Tigray, Ethiopia. lezelalem16@yahoo.com.
authors.forename: Kiros
authors.initials: K
authors.lastname: Welegerima
authors.affiliation: University of Kisangani, Eastern Province, Kisangani, DR, Congo. nicaisedrazo@yahoo.fr.
authors.forename: Nicaise
authors.initials: N
authors.lastname: Amundala
authors.affiliation: CNRS UMR 6552/53, Université de Rennes 1, Station Biologique, Paimpont, France. marc.colyn@univ-rennes1.fr.
authors.forename: Marc
authors.initials: M
authors.lastname: Colyn
authors.affiliation: Evolutionary Ecology Group, Biology Department, University of Antwerp, Antwerpen, Belgium. herwig.leirs@ua.ac.be.
authors.forename: Herwig
authors.initials: H
authors.lastname: Leirs
authors.affiliation: Evolutionary Ecology Group, Biology Department, University of Antwerp, Antwerpen, Belgium. erik.verheyen@naturalsciences.be.|Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, Brussels, Belgium. erik.verheyen@naturalsciences.be.
authors.forename: Erik
authors.initials: E
authors.lastname: Verheyen
mesh_terms: D017954:Africa South of the Sahara; D000818:Animals; D005075:Biological Evolution; D051379:Mice / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D058974:Phylogeography