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...

The Malaysian Giant Turtle (Orlitia borneensis) is a poorly known turtle with rapidly decreasing numbers in nature in spite of its strong protection on paper. Most individuals of this species kept in European zoos and included in captive breeding programs are confiscates from the illegal trade for food consumption and their geographic provenance is unknown. This study was aimed to assess genetic and phenotypic variation of the founders of this captive population. We sequenced the mitochondrial cytochrome b gene and found 23 haplotypes. We constructed a haplotype network and examined demographic changes by Bayesian skyline plots of the effective population size. The maximum sequence divergence was less than 1.5% and the phylogenetic structure of the haplotypes was supported poorly. A close genetic similarity among sampled turtles was further confirmed by sequencing the nuclear R35 gene, while the geometric morphometrics of the shell-shape were likewise similar. Thus, the examined captive population of O. borneensis may be further treated as a single conservation unit.

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Spiny mice belonging to the cahirinus-dimidiatus group of the genus Acomys have become a widely used model in physiology and behaviour. To improve current knowledge concerning the phylogeny of this taxon, we analysed 24 samples from Libya, Chad, Egypt, Jordan, Cyprus, Crete, Turkey, Yemen and Iran. We sequenced the whole mitochondrial control region and part of the flanking tRNA genes for a total length of 986 to 996 bp and described 22 haplotypes. Our results confirmed that the Afro-Mediterranean and Asian clades are clearly distinct (p-distance = 6-8.1%). The former clade corresponds to A. cahirinus sensu lato (i.e. including also the Cretan A. minous, Cypriot A. nesiotes and Turkish A. cilicicus). Haplotypes of A. cahirinus from the E Sahara (S Egypt, SW Libya, N Chad) grouped with those of A. cilicicus and A. minous (p-distance ≤ 2.2%), while haplotypes of A. nesiotes grouped with one haplotype representing the commensal A. cahirinus from Cairo (p-distance = 1.2%). Close similarity among haplotypes from mainland Africa and NE Mediterranean (clade A. cahirinus sensu stricto) support the hypothesis that ancestors of A. nesiotes, A. cilicicus and A. minous dispersed most probably as commensal populations, thus questioning their status of valid species. The most surprising finding was the considerable genetic variation in Asia. In addition to a haplogroup from Sinai and Jordan (corresponding to A. dimidiatus sensu stricto), we detected two previously unknown haplogroups, from Yemen and Iran + United Arab Emirates. These clades are fairly distinct and separate species/subspecies status of these animals might be further considered.

Distinguishing between species is an essential aspect of animal research and conservation. For turtles, morphology and genetic analysis are potentially valuable tools for identification. Shell shape is an important component of phenotypic variation in turtles and can be easily described and quantified by geometric morphometrics (GM). Here, we focus on carapace and plastron shape discrimination of immature Southeast Asian box turtles (Cuora amboinensis) from two of the Greater Sunda Islands with partially distinct faunas. GM analysis identified significant differences in carapace and plastron shape between turtles from Borneo and Sumatra. The discrimination success amounted to 90% and 83.7% for carapace and plastron, respectively. The correlations of carapace and plastron shapes were high for Sumatra (0.846), and less pronounced for Borneo (0.560). We detected no differences in the ontogenetic trajectories of the shell shape between the two islands. We conclude that shell shape can be used for reliable geographic assignment of C. amboinensis of unknown origin. In addition to the comparison of shell shapes, turtles from Borneo, Sumatra, Seram, and turtles of unknown origin from two Czech zoos were studied genetically. Analysis of the complete mitochondrial cytochrome b gene confirmed the distinctness of turtles from Borneo and Sumatra, with p-distance 2.68 – 4.09% sequence difference. Moreover, we discovered considerable genetic difference in Seram turtles of previously unknown haplogroup (p-distance 6.00 – 8.68%) revealing the need for the revision of the whole species complex of Cuora amboinensis.

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