Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion

Mazoch, Vladimír; Mikula, Ondřej; Bryja, Josef; Konvičková, Hana; Russo, Isa‐Rita M.; Verheyen, Erik; Šumbera, Radim

doi:10.1515/mammalia-2017-0001

Cited by 20 publications

(15 citation statements)

References 85 publications

(86 reference statements)

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“…2b; see more details in [44]). Similar structure was recently observed in numerous other taxa of sympatric murid and bathyergid rodents living in open habitats of Zambezian region [67–70]. Similarly, the mountains in north-eastern Tanzania (Kilimanjaro, Pare, Usambara) currently delimit distribution for some Acomys lineages ( Wil2 vs. Wil3 or cahirinus vs. spinosissimus groups), and, again, this pattern was found in other savanna rodents (e.g.…”

Section: Discussionsupporting

confidence: 81%

Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny

et al. 2019

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Background Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and evolutionary biology). Despite their importance, large distribution and abundance in local communities, the phylogeny and the species limits in the genus are poorly resolved, and this is especially true for sub-Saharan taxa. The main aims of this study are (1) to reconstruct phylogenetic relationships of Acomys based on the largest available multilocus dataset (700 genotyped individuals from 282 localities), (2) to identify the main biogeographical divides in the distribution of Acomys diversity in dry open habitats in Afro-Arabia, (3) to reconstruct the historical biogeography of the genus, and finally (4) to estimate the species richness of the genus by application of the phylogenetic species concept. Results The multilocus phylogeny based on four genetic markers shows presence of five major groups of Acomys called here subspinosus, spinosissimus, russatus, wilsoni and cahirinus groups. Three of these major groups ( spinosissimus, wilsoni and cahirinus ) are further sub-structured to phylogenetic lineages with predominantly parapatric distributions. Combination of alternative species delimitation methods suggests the existence of 26 molecular operational taxonomic units (MOTUs), potentially corresponding to separate species. The highest genetic diversity was found in Eastern Africa. The origin of the genus Acomys is dated to late Miocene ( ca. 8.7 Ma), when the first split occurred between spiny mice of eastern (Somali-Masai) and south-eastern (Zambezian) savannas. Further diversification, mostly in Plio-Pleistocene, and the current distribution of Acomys were influenced by the interplay of global climatic factors (e.g. , Messinian salinity crisis, intensification of Northern Hemisphere glaciation) with local geomorphology (mountain chains, aridity belts, water bodies). Combination of divergence dating, species distribution modelling and historical biogeography analysis suggests repeated “out-of-East-Africa” dispersal events into western Africa, the Mediterranean region and Arabia. Conclusions The genus Acomys is very suitable model for historical phylogeographic and biogeographic reconstructions of dry non-forested environments in Afro-Arabia. We provide the most thorough phylogenetic reconstruction of the genus and identify major factors that influenced its evolutionary history since the late Miocene. We also highlight the urgent need of integrative taxonomic revision of e...

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Section: Discussionsupporting

confidence: 81%

Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny

et al. 2019

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“…for several species of rodents strongly associated with miombo landscapes (e.g. Bryja et al, 2018;Mazoch et al, 2018). However, this remains surprising as the two subclades are nowadays forming contiguous wooded landscapes.…”

Section: Miombo and Rain Forest Lineagesmentioning

confidence: 99%

Plastid introgression and evolution of African miombo woodlands: New insights from the plastome‐based phylogeny of Brachystegia trees

Boom

Migliore

Kaymak

et al. 2021

Journal of Biogeography

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Aim Miombo woodlands form a characteristic vegetation type covering 2.7 million km2 in southern and eastern Africa. Despite their wide geographical extent, their origin, floristic and spatial evolution through time remain understudied. To fill this gap, we studied the evolution of Brachystegia trees, one of the most representative genera of these woodlands (20 species), also represented in Guineo‐Congolian rain forests (8 species). Location Tropical Africa, Guineo‐Congolian forests and Zambezian savannas. Taxon Brachystegia genus. Methods We used a genome skimming approach to sequence the plastomes of 45 Brachystegia samples, covering 25 of the 29 existing species, and one outgroup (Julbernardia paniculata). The phylogeny of the plastomes was reconstructed and time‐calibrated. We tested if the genetic divergence between lineages reflected taxonomic and/or geographical distances using Mantel tests. Finally, we inferred the evolutionary history of Brachystegia based on the age and spatial distribution of its lineages. Results Surprisingly, species represented by multiple specimens appear rarely monophyletic while plastid clades display strong geographical structuring, independently of the species. Two main clades separate woodland and rain forest species, which diverged during the late Miocene–Pliocene (95% HPD = 2.78–8.59 Ma). In miombo woodlands, three subclades occur in parapatry along an East–West axis, ranging from Angola to East Africa. Their divergence started from the Plio‐Pleistocene (95% HPD = 1.17–3.69 Ma). Divergence dates (TMRCA) within miombo subclades decrease from East Africa (1.53 Ma) to Angola (0.76 Ma). Main conclusions Brachystegia plastomes appear unreliable to identify species, probably due to species introgression leading to recurrent chloroplast captures. However, they prove very informative for tracking the past dynamics of the genus, and suggest a historical westwards expansion of miombo Brachystegia, and possibly of miombo vegetation, during the Plio‐Pleistocene. Further investigations using nuclear DNA are needed to assess the species tree as well as speciation and hybridization events between species.

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“…Recently, African rodents have been used as biogeographical models for reconstruction of the evolutionary history of savannas (e.g. Aghová et al, 2017;Mazoch et al, 2018), as well as various types of forests (e.g. Bohoussou et al, 2015;Bryja, Mikula, Patzenhauerová, et al, 2014).…”

mentioning

confidence: 99%

Genetic variation of the most abundant forest‐dwelling rodents in Central Africa (Praomys jacksoni complex): Evidence for Pleistocene refugia in both montane and lowland forests

Mizerovská

Nicolas

Demos

et al. 2019

Journal of Biogeography

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Aim We investigate the Plio‐Pleistocene evolutionary history of one of the most abundant rodents in Afrotropical forests. Specifically, we ask how their diversification was influenced by climate change, topography and major rivers. Location Tropical Africa: Lower Guinea (including Cameroon volcanic line; CVL), Congolia, Albertine Rift (AR), Kenyan highlands (KH). Taxon Murine rodents of the Praomys jacksoni complex. Methods We used 849 genotyped individuals to describe the overall diversity and spatial genetic structure across a majority of their known distribution area. The combination of one mitochondrial and three nuclear markers was used to infer dated phylogenies using Bayesian and maximum likelihood approaches. Genetic structure was further assessed by multispecies coalescent species delimitation. Current and past distributions of particular taxa were predicted using environmental niche modelling. Results The complex is composed of five major genetic clades (proposed species). Two of them are restricted to specific habitat types (either montane forests of AR or wetlands in lowland forests along the Congo River), three others have wide geographic distributions and lower levels of ecological specialization. The earliest divergence is dated to the Plio‐Pleistocene boundary and is in accordance with the separation of AR forests and Guineo‐Congolian forests. Further diversification of the complex is associated with Pleistocene climate changes. Relatively stable refugia of suitable climatic conditions were identified in lowland Congolia (for two species currently distributed only in lowland forests) as well as in montane forests of CVL, AR, KH (playing the role of reservoirs of diversity). Large rivers, especially the Congo River, are important barriers to gene flow for most taxa, but probably were not the primary cause of differentiation. Main conclusions The evolutionary history of the complex was primarily affected by Pleistocene climate changes and diversification in forest refugia. There is little support for ecological parapatric speciation or the riverine barrier hypothesis.

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Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion

Cited by 20 publications

References 85 publications

Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny

Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny

Plastid introgression and evolution of African miombo woodlands: New insights from the plastome‐based phylogeny of Brachystegia trees

Genetic variation of the most abundant forest‐dwelling rodents in Central Africa (Praomys jacksoni complex): Evidence for Pleistocene refugia in both montane and lowland forests

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