Bioregion heterogeneity correlates with extensive mitochondrial DNA diversity in the Namaqua rock mouse, Micaelamys namaquensis (Rodentia: Muridae) from southern Africa--evidence for a species complex.

RESEARCH ARTICLE Open Access
Bioregion heterogeneity correlates with extensive
mitochondrial DNA diversity in the Namaqua rock
mouse, Micaelamys namaquensis (Rodentia:
Muridae) from southern Africa - evidence for a
species complex
Isa-Rita M Russo1,2,4*, Christian T Chimimba2,3†, Paulette Bloomer1†
Abstract
Background: Intraspecific variation within the diverse southern African murine rodents has not been extensively
investigated, yet cryptic diversity is evident in several taxa studied to date. The Namaqua rock mouse, Micaelamys
namaquensis Smith, 1834 is a widespread endemic murine rodent from the subregion. Currently, a single species
with four subspecies is recognised, but in the past up to 16 subspecies were described. Thus, this species is a
good candidate for the investigation of patterns and processes of diversification in a diverse but under-studied
mammalian subfamily and geographic region. Here, we report genetic differentiation based on mitochondrial DNA
(mtDNA) cytochrome b (cyt b) sequences among samples collected over an extensive coverage of the species’
range.
Results: Cytochrome b sequences of 360 widely sampled individuals identified 137 unique maternal alleles. Gene
tree and phylogeographic analyses of these alleles suggest the presence of at least eight lineages or haplogroups
(A-H), with varying degrees of intra-lineage diversity. This differentiation is in contrast with the most recent
taxonomic treatment based on cranial morphometrics which only recognised four subspecies. The mtDNA diversity
strongly supports earlier views that this taxon may represent a species complex. We further show statistical support
for the association of several of these lineages with particular vegetation biomes of southern Africa. The time to
the most recent common ancestor (TMRCA) dates to the Pliocene (~5 Mya) whereas coalescent-based divergence
time estimates between lineages vary between 813 Kya [0.22 - 1.36] and 4.06 Mya [1.21 - 4.47]. The major
diversification within lineages occurred during the Pleistocene. The identification of several regions of sympatry of
distinct lineages offers future opportunities for the elucidation of the underlying speciation processes in the
suggested species complex.
Conclusions: Similar to other African murine rodents, M. namaquensis radiated during the Pliocene and
Pleistocene coinciding with major periods of aridification and the expansion of savanna habitats. The suggested
species complex is represented by at least eight lineages of which the majority are confined to only one or a few
neighbouring biomes/bioregions. Contrasting intra-lineage phylogeographic patterns suggest differences in
adaptation and responses to Plio-Pleistocene climatic and vegetation changes. The role of ecological factors in
driving speciation in the group needs further investigation.
* Correspondence: RussoIM@Cardiff.ac.uk
† Contributed equally
1Molecular Ecology & Evolution Programme (MEEP), Department of Genetics,
University of Pretoria, Pretoria, 0002 South Africa
Full list of author information is available at the end of the article
Russo et al. BMC Evolutionary Biology 2010, 10:307
http://www.biomedcentral.com/1471-2148/10/307
© 2010 Russo et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.

Background
Globally the order Rodentia represents the richest mam-
malian diversity [1], yet species and higher level classifi-
cation within the order remains to be resolved due
to controversies surrounding morphological character
evolution in the group [2-5]. The Old World subfamily
Murinae is the most diverse within the species-rich
family Muridae [3]. Africa is one of the centres of ende-
mism of the subfamily and based on combined mito-
chondrial and nuclear gene data, it has been suggested
that the major African radiation occurred in the Miocene
(7 - 9 Mya) [3]. The latter and other recent studies [6,7]
of African murids highlighted the impact of Miocene and
Pliocene climatic changes on vegetation and landscape
composition (see also [8]) and linked the rapid radiation
within several taxa to the expansion of savanna habitats.
Murid diversity within the southern African subregion
remains underestimated as few local taxa have been
assessed for intraspecific variation. Most of the earlier
studies were based on traditional morphometrics and/or
qualitative morphology, e.g. studies on species within the
genera Acomys [9], Saccostomus [10], Mastomys [11],
Aethomys [12-15] and Micaelamys (formerly designated
as Aethomys [2]). Recently molecular studies investigated
Otomys [16], Mastomys [17,18], Micaelamys [19], Rhabd-
omys [20] and Saccostomus [21]. These molecular studies
suggest high levels of cryptic diversity, a feature also
reported for other African murids (cf [6,7]).
In general, small mammals such as rodents have
restricted dispersal abilities [22-24] and many display patchy
distributions. Smaller rodents in particular show adaptation
to specific micro-habitats and would likely be more sensi-
tive to environmental changes [24,25]. Indeed, habitat selec-
tion, dispersion and inter-specific competition are proposed
to be amongst the most important factors influencing the
co-existence of species [23,26]. In addition, karyotypic
changes have been implicated in the speciation of several
rodent species (e.g., Otomys [27] and Rhabdomys [20]).
The focus of the present study is the Namaqua rock
mouse, Micaelamys namaquensis Smith, 1834, originally
described from Witwater, Little Namaqualand in the
Northern Cape Province of South Africa [28]. The genus
Aethomys Thomas, 1915 was formerly subdivided into two
African endemic subgenera namely Micaelamys and Aeth-
omys [2]. Recent molecular studies [19,29,30] reported the
paraphyly of the genus and the two subgenera have since
been elevated to full generic rank [2]. The genus Micaela-
mys Ellerman, 1941 includes M. namaquensis and M.
granti Wroughton, 1908, while Aethomys includes the
remaining nine species. The close relationship between M.
namaquensis and M. granti is evident from dental mor-
phology [31], karyology [32], gross sperm and bacular
morphology [32] and cranial phenetic analysis [33].
Fossil species of Aethomys have been recorded from
Langebaanweg (Western Cape Province, South Africa)
[34]. It is noteworthy that the smaller of the two fossil
species closely resembles the extant M. namaquensis,
which may be indicative of the long-term presence of this
species in the subregion [34]. The oldest known repre-
sentatives of the genus, A. adamanticola and A. moder-
nis, have been recorded in South Africa and date to
between the Early Pleistocene and Late Miocene [35,36].
Micaelamys namaquensis is widely distributed in
southern African (south of the Zambezi/Cunene Rivers),
but has also been recorded to the north of the subregion
in Angola, Zambia, Malawi and northern Mozambique
[2]. These rodents are catholic in their habitat require-
ments but where there are rocky outcrops or hillsides
they will use these in preference to any other type of
habitat [2]. The social structure of the species has not
been elucidated but colonies appear to live in rock cre-
vices, in or under fallen logs or in holes in trees [2].
They are mostly granivores [2] and breed during the
warmer spring and summer months [37]. They are
known for unstable population cycles associated with
high mortality and high reproductive potential [38].
Such cycles would likely leave clear ‘footprints’ in the
distribution of genetic diversity in the species.
The Namaqua rock mouse shows considerable geo-
graphic variation such as in pelage colouration, tail length
and body size throughout its distributional range
[2,37,39,40]. This variation suggested that M. namaquen-
sis may reflect either a complex of species [40] or subspe-
cies [37,39]. Earlier reports [41,42] recognised 16
subspecies within M. namaquensis (Figure 1). However,
these distinctions were primarily based on a limited num-
ber of geographically restricted samples [37,43], with lit-
tle or no assessment of patterns of geographic variation
over the entire distributional range of the species.
A comprehensive intraspecific morphometric study
within M. namaquensis from southern Africa [15] sug-
gested the recognition of four subspecies differing in
both cranial size and shape: M. n. namaquensis Smith,
1834, M. n. lehocla Smith, 1836, M. n. alborarius Peters,
1852 and M. n. monticularis Jameson, 1909. This study
also suggested that the geographical limits of the pro-
posed subspecies broadly coincide with the major phyto-
geographical zones of southern Africa [44,45] (Figure 1):
the subspecies namaquensis was shown to be largely
associated with a combination of the Succulent Karoo,
Fynbos and the southern coastal Savanna/Grassland
region of the Eastern Cape, KwaZulu-Natal and eastern
Mpumalanga Provinces of South Africa, while the sub-
species alborarius and lehocla were shown to be asso-
ciated with the Savanna and Upper/Lower Karoo
biomes, respectively [15]. The subspecies monticularis
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was largely confined to the Grassland biome of southern
Africa [15] (see inset in Figure 1).
Given its wide distribution and past indications of
cryptic diversity, we investigated the cyt b variation of
M. namaquensis as a potential model for murine diver-
sification in southern Africa. Our objectives are: 1) to
evaluate the phylogeographic structure in this wide-
spread species; 2) to compare patterns of genetic varia-
tion with previously described morphological variation;
3) to evaluate the geographical association between the
observed diversity and environmental features of the
region and 4) to consider the divergence times in terms
of the climatic and vegetation changes characterising
southern Africa over the recent evolutionary past.
Results
The 5’ end of the cyt b gene (631 bp) was sequenced for
360 M. namaquensis individuals. All sequences obtained
were of the mtDNA cyt b gene with conserved domains
and nucleotide composition biases typical of this
mtDNA protein coding gene [46-48]. As expected, most
of the substitutions were silent, with only 36 of the 210
amino acid sites being variable. The 176 variable nucleo-
tide positions defined 137 maternal alleles (Additional
file 1), the allele frequencies and geographic distribu-
tions are indicated in Additional file 2. Sequence diver-
gence values based on uncorrected p-distances ranged
from 0.16% to 7.74% between the alleles. Only four
widespread and high frequency alleles were recorded
(NH014, NH100, NH113 and NH115), while most of
the remaining alleles were locality-specific (107 alleles).
The overall nucleotide diversity was 3%, while the allelic
diversity value of 0.91 corresponded to those reported
for other rodents [49].
Unique lineages were defined based on the joint inter-
pretation of a Bayesian gene tree (Figure 2), an ultra-
metric analysis in BEAST (Figure 3) and an allele
network as estimated in TCS (Figure 4) (see Additional
file 3 for a summary of the comparison). We thus pro-
pose the presence of eight lineages (A-H) with varying
Figure 1 Major biomes of southern Africa [see [44,45]]. Background colours for the eight major biomes are indicated in the legend; major
lakes and saltpans are also included. The yellow star indicates the type locality for the species and the blue stars indicate the type localities for
the 16 previously described subspecies. The inset shows the geographic distribution of the phenetic diversity within Micaelamys namaquensis
from southern Africa [15]. The purple, orange, yellow and green zones correspond with the subspecies M. n. alborarius, M. n. lehocla, M. n.
monticularis and M. n. namaquensis, respectively.
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Figure 2 A Bayesian inference (BI) tree based on 631 bp of the mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene of Micaelamys
namaquensis from southern Africa. The BI posterior probability values for internal branches are given at each node with either an asterisk (*)
or a circle (). Asterisks indicate BI posterior probability values ≥ 0.95 and circles indicate BI posterior probability values ≥ 0.90. Aethomys
chrysophilus and A. ineptus were used as outgroups. Lineages A - H mainly correspond to different biomes or bioregions of southern Africa
(Figures 1 and 5; see text for some minor exceptions). Colours correspond to those in Figures 3, 4 and 5.
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degrees of intra-lineage diversity. We do not present
individual lineage phylogeographic patterns in detail but
indicate some of the subdivisions (e.g. in lineages A and
B) and use lineages A2 and D to illustrate heteroge-
neous and homogeneous diversity patterns, respectively.
The Bayesian phylogram (Figure 2) is characterised by
short internal branches suggesting a rapid radiation of
lineages. This is supported by the relatively short time-
frame over which these lineages became established dur-
ing the Early Pleistocene and Late Pliocene (2.3 - 4.06
Mya) (Figure 3). Two major periods of subsequent
radiation within the lineages is evident at approximately
1.4 - 1.7 Mya (diversification within lineages A, B, C
and H) and from 176 Kya to 1 Mya (lineages D - G).
With the exception of lineage H, the monophyly of
the respective lineages are statistically supported by the
Bayesian posterior probability values (Figure 2). Sister
relationships are not consistent across the phylogenetic
analyses and statistical support is largely lacking (see
Figures 2 and 3 and Additional file 3). However, lineages
A and B and lineages C, D and E are potential sister
clades. In addition, these two clades appear to share a
common history. The BEAST analysis further suggest a
sister relationship between G and H; these two distinc-
tive lineages are consistently placed sister to the remain-
der of the lineages. The position of lineage F is
inconsistent between the different analyses.
The TCS analysis connected alleles separated by up to
10 mutational steps (95% confidence limit); only lineage
H and a subset of the lineage B alleles (B3) could not be
joined to the remainder of the network (Figure 4). Line-
age D shows a star-like pattern of 31 closely related
alleles recorded over a large geographic area. Seven of
the alleles were shared between two to six localities;
Figure 3 A phylogenetic tree for 137 representative mitochondrial DNA (mtDNA) cytochrome b (cyt b) alleles of Micaelamys
namaquensis from southern Africa as obtained by BEAST analysis. Divergence dates (epochs) are indicated in the grey-scale key at the
bottom of the figure. Lineages A - H mainly correspond to different biomes or bioregions of southern Africa (Figures 1 and 5; see text for some
minor exceptions). Colours correspond to those in Figures 2, 4 and 5.
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