Rodents are the most speciose mammalian order and comprise almost half of all mammalian species diversity .
Within Rodentia, the most diverse assemblage is the superfamily
Muroidea, with a global membership of 1300 living species and a natural
distribution that includes all continents except Antarctica and all but
the most remote islands. This remarkable group also includes the
commensal rats and mice, long despised as human pests and agents of
disease , but now highly valued as model organisms for research related to human health [3,4].
Not surprisingly, morphology-based classifications of muroid rodents
were beset by problems of parallel evolution, with many common
adaptations evolving independently on different landmasses. Molecular
phylogenetic analyses are much less constrained by this problem and
recent studies using slowly evolving nuclear genes have done much to
clarify the membership and structure of Muroidea [5-7]. Recent classifications of this group recognize five or six family level lineages [7,8]. The speciose family Muridae Illiger, 1811 (150 genera and 730 species) is divided by Musser and Carleton 
into five subfamilies, of which the Murinae Illiger, 1811 is the most
diversified (126 genera, 561 species). Within the family Muridae, there
is strong molecular support for three subfamilies (Deomyinae,
Gerbillinae, Murinae) [subfamily Leimacomyinae of Musser and Carleton 
has not yet been surveyed], and for a link between Deomyinae and
Gerbillinae, with these as a sister clade to Murinae (this latter
subfamily encompassing otomyines) [5-7].
The subfamily Murinae has a natural distribution that spans the Old
World, including all of Africa and Eurasia, and extending to Australia,
New Guinea and many islands of the western Pacific (we do not consider
here the human-mediated distribution of a few commensal rodents of the
genera Mus and Rattus in the Americas and throughout oceanic islands). More than 500 species are currently recognised , with centers of diversity and endemism in each of Tropical Africa, Southeast Asia, and the Australo-Papuan region [9,10].
Despite the obvious significance of this group for biogeographic
studies, previous molecular studies have either had specific regional
foci (e.g. Africa [11-13]; Philippines: ; Australia: [15,16] ; Eurasia: [17,18]) or employed immunological methods of uncertain reliability .
These studies have encouraged regionally-based classifications at
tribal or subfamilial level, especially within the Australasian and
Philippine regions where various higher level groupings are sometimes
recognized (e.g. Anisomyini, Conilurini, Hydromyini, Phloeomyinae,
Pseudomyinae, Rhynchomyinae). In Africa, Ducroz et al.  designated a tribe Arvicanthini for one well-supported monophyletic group. The most recent, global classification of Murinae 
abandons the tribal level of classification in favour of a less formal
arrangement of genera into divisions, following and improving a system
already employed by Misonne . Specifically, Musser and Carleton  (2005: pages 902 – 905) organize the 126 genera of the subfamily Murinae into 29 divisions, and consider the living taxa Myotomys, Otomys, and Parotomys as members of the subfamily Otomyinae.
Africa supports more than 25% of all living murine species including representatives of 32 endemic genera .
All African murines are endemic at species level and only two genera
are shared between Africa and Eurasia. One of these is the genus Mus, which is widespread across Eurasia and is represented in Africa by an endemic subgenus, Nannomys, the African pigmy mice [19-21]. The second is the primarily African genus Myomyscus which has one species (M. yemeni) native to the Arabian Peninsula. A single origin for all African Murinae, except possibly Dasymys, was proposed by Watts and Baverstock  based on their analyses of albumin microcomplement fixation. In contrast, Chevret's 
studies using the DNA/DNA hybridization method found a minimum of three
ancient African lineages within Murinae, each associated with Eurasian
taxa. Later studies using direct sequencing methods supported the
notion of polyphyly for African Murinae, e.g. [12-14,16,24]. Jansa et al.  identified three distinct groups: the 'Arvicanthines' (sensu Ducroz et al. ), a 'Praomys group' (sensu Lecompte et al. ) and the genus Malacomys. The 'otomyines', a dentally distinctive African lineage with three genera (Myotomys, Otomys,Parotomys), are variously associated in molecular studies with either the Praomys group  or the arvicanthines [6,11,12,16,24]. Ducroz et al.  suggested recognition of this group at tribal rank, as Otomyini. However, Musser and Carleton  follow more traditional practice by recognizing a distinct subfamily Otomyinae within Muridae.
Numerous questions thus remain unresolved concerning the pattern and
timing of African Murinae diversification. In particular, the
relationships of the various African lineages with Asian genera are
enigmatic, and the timing of most cladogenic events remains poorly
resolved or understood. The latter issue is critical to understanding
the history of faunal interchange via the Arabian plate following the
collision of Africa with Asia around 16 and 20 Million years ago (Mya) [26,27].
Notably, the murine palaeontological record attests to the presence of
some shared genera in Africa and Asia during the late Miocene and the
but whether this is due to multiple faunal exchanges between Asia and
Africa, to the presence of ancient shared lineages followed by
vicariance, or else to convergent evolution, remains a matter of
To more adequately assess the pattern and timing of faunal exchanges
between Africa and Asia, it is necessary to first establish a more
complete phylogenetic framework including all of the key African and
Eurasian lineages, and then to derive reliable estimates of divergence
times. The main objectives of our study are: (1) to provide a robust
and comprehensive phylogeny of the extant African murines and to infer
their relationships with the Asian Murinae using mitochondrial and
nuclear gene sequences, (2) to provide a new systematic framework that
accurately reflects the phylogeny of Murinae; (3) to estimate times of
origin and diversification for the African murines lineages; and (4) to
place this phylogeny in an historical and geographical context to gain
insight into the origin and maintenance of African murine diversity.