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

Abstract

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...

Diversity and evolution of African Grass Rats (Muridae:Arvicanthis)—From radiation in East Africa to repeated colonization of northwestern and southeastern savannas

“…It has clear north–south intraspecific structure, separating mtDNA haplotypes into two subgroups. A similar phylogeographic pattern was found also in other rodents living in Ethiopian Somali‐Masai savannas, for example, gerbils (Aghová et al, ) or spiny mice (Aghová et al, ). Intraspecific divergence can be a result of a vicariance event caused by the African rift lakes forming important barriers to gene flow, especially during humid periods of Pleistocene (Trauth et al, ; see also discussion in Aghová et al, ).…”

Genetic diversity of the naked mole‐rat ( Heterocephalus glaber)

“…The suitable habitats have been found in the Afar lowlands and neighboring areas that corresponds to known paleontological data (Stoetzel et al., 2018). Such habitats may serve as refugiums that probably could be also relevant for others small mammals groups of the Somali–Masai bioregion, for example, Gerbilliscus , Acomys , and Arvicanthis genera (Aghová et al., 2017, 2019; Bryja et al., 2019). We, therefore, hypothesized that similar to LGM, general climate aridization and cooling after MPR may have led to range fragmentation and intraspecific divergence, which resulted in the main eastern and southern lineages of H. glaber .…”

“…There is a high level of endemism among plants (Thulin, 1993), reptiles (Burgess et al, 2007), and rodents (Varshavsky, Karimova, & Neronov, 2007). Recently, the phylogeographic structure of some rodents (Aghová et al, 2017(Aghová et al, , 2019Bryja et al, 2019) and reptiles (Šmíd et al, 2019) endemic to the Somali-Masai region was described. Park (##1080Park (## , 1081 were kindly donated to us by Prof. Radim Šumbera.…”

Multimammate mice of the genus Mastomys (Rodentia: Muridae) in Ethiopia – diversity and distribution assessed by genetic approaches and environmental niche modelling

“…Such a refugium may have been located at the margin of the Afar lowlands, where other endemic taxa of savannah rodents were recently found, e.g. the genera Gerbilliscus (Aghová et al 2017), Acomys (Aghová et al 2019) and Arvicanthis . Spreading deeper and higher into the highlands, especially along the river valleys, may have been facilitated by recent intensive deforestation of the landscape by humans.…”