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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.

Russo IR, Chimimba CT, Bloomer P - BMC Evol. Biol. (2010)

Bottom Line: 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.The role of ecological factors in driving speciation in the group needs further investigation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Ecology & Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, 0002 South Africa. RussoIM@Cardiff.ac.uk

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.

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Geographic distribution of Micaelamys namaquensis mitochondrial DNA (mtDNA) cytochrome b (cyt b) lineages in the biomes of southern Africa (see legend for colours). The circles indicate the number of individuals sampled at each locality (see legend for scale); the size of the pie charts represents allele frequencies. Stars indicate the type localities of the species/subspecies. The inset shows a topographical map of southern Africa. Colours correspond to those in Figures 2, 3 and 4.
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Figure 5: Geographic distribution of Micaelamys namaquensis mitochondrial DNA (mtDNA) cytochrome b (cyt b) lineages in the biomes of southern Africa (see legend for colours). The circles indicate the number of individuals sampled at each locality (see legend for scale); the size of the pie charts represents allele frequencies. Stars indicate the type localities of the species/subspecies. The inset shows a topographical map of southern Africa. Colours correspond to those in Figures 2, 3 and 4.

Mentions: Most lineages form separate geographical units displaying an allopatric/parapatric pattern of distribution (Figure 5). Major physical features of the southern African landscape (rivers and mountains) do not appear to separate the lineages (see inset Figure 5 for the general topography). One exception is the enigmatic lineage F that appears to be restricted to high elevations of the Great Escarpment. However, most lineages and in some instances also the sub-clades within them, appear to be associated with different vegetation types of southern Africa: lineage A (A1 - A5) with different bioregions of the Grassland and Savanna biomes; B2 with Albany Thicket; B3 with the western Fynbos; C with the Bushmanland/Upper Karoo bioregion (Nama-Karoo/Savanna); D with the Nama-Karoo; E with the Kalahari Duneveld (Nama-Karoo); F with the Sub-Escarpment Grassland bioregion (Grassland); G with the Eastern Kalahari Bushveld (Savanna); and H with Savanna. Names in parenthesis (for example Nama-Karoo/Savanna) refer to biomes as indicated in Figure 1. For bioregion names not referred to in Figure 1 and for more detailed maps see [45].


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.

Russo IR, Chimimba CT, Bloomer P - BMC Evol. Biol. (2010)

Geographic distribution of Micaelamys namaquensis mitochondrial DNA (mtDNA) cytochrome b (cyt b) lineages in the biomes of southern Africa (see legend for colours). The circles indicate the number of individuals sampled at each locality (see legend for scale); the size of the pie charts represents allele frequencies. Stars indicate the type localities of the species/subspecies. The inset shows a topographical map of southern Africa. Colours correspond to those in Figures 2, 3 and 4.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2967545&req=5

Figure 5: Geographic distribution of Micaelamys namaquensis mitochondrial DNA (mtDNA) cytochrome b (cyt b) lineages in the biomes of southern Africa (see legend for colours). The circles indicate the number of individuals sampled at each locality (see legend for scale); the size of the pie charts represents allele frequencies. Stars indicate the type localities of the species/subspecies. The inset shows a topographical map of southern Africa. Colours correspond to those in Figures 2, 3 and 4.
Mentions: Most lineages form separate geographical units displaying an allopatric/parapatric pattern of distribution (Figure 5). Major physical features of the southern African landscape (rivers and mountains) do not appear to separate the lineages (see inset Figure 5 for the general topography). One exception is the enigmatic lineage F that appears to be restricted to high elevations of the Great Escarpment. However, most lineages and in some instances also the sub-clades within them, appear to be associated with different vegetation types of southern Africa: lineage A (A1 - A5) with different bioregions of the Grassland and Savanna biomes; B2 with Albany Thicket; B3 with the western Fynbos; C with the Bushmanland/Upper Karoo bioregion (Nama-Karoo/Savanna); D with the Nama-Karoo; E with the Kalahari Duneveld (Nama-Karoo); F with the Sub-Escarpment Grassland bioregion (Grassland); G with the Eastern Kalahari Bushveld (Savanna); and H with Savanna. Names in parenthesis (for example Nama-Karoo/Savanna) refer to biomes as indicated in Figure 1. For bioregion names not referred to in Figure 1 and for more detailed maps see [45].

Bottom Line: 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.The role of ecological factors in driving speciation in the group needs further investigation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Ecology & Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, 0002 South Africa. RussoIM@Cardiff.ac.uk

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.

Show MeSH
Related in: MedlinePlus