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Aim: The Eastern Afromontane Biodiversity Hotspot (EABH) offers an ideal location to investigate the evolutionary mechanisms producing a high level of endemic biodiversity. We tested the hypothesis that the cradle of Eastern Afromontane diversity is in the largest sub‐region of the EABH montane archipelago, that is the Ethiopian Highlands. Further, we expected that climate oscillations followed by elevational shifts in montane habitats facilitated the dispersal of small mammal populations across unsuitable arid lowlands. Location: Mountains and highlands of East Africa. Taxon: Shrews of the genus Crocidura (Eastern Afromontane phylogenetic clade). Methods: We collected comprehensive genetic data from 511 (mitochondrial gene for cytochrome b) and 147 (double digest Restriction‐Associated DNA sequencing) samples of Crocidura shrews across the EABH. We estimated phylogenetic relationships with Bayesian and Maximum Likelihood approaches. Population genetic analyses were performed in STRUCTURE to evaluate the internal structure of species outside Ethiopia. Ancestral area and dispersal routes were analysed by the BioGeoBears package. Results: Six major phylogenomic clades were delimited based on concatenated nuclear loci. The mitochondrial phylogeny roughly matches nuclear phylogenies, but with poorer resolution. Five of the six revealed clades are restricted to the Ethiopian Highlands, which is unambiguously the cradle of the diversity of this group of mammals (also confirmed by the biogeographic analysis). All non‐Ethiopian and a single Ethiopian species fall into the sixth clade with poorly resolved internal relationships. Detailed population genetic analysis of SNP data revealed a pronounced structure with multiple gene pools in this clade; however, this structure only partly corresponds with the current taxonomy. Main Conclusions: Eastern Afromontane Crocidura shrews originated in the Ethiopian Highlands. They radiated there, and through a single southward dispersal event across the Turkana depression, they colonised the rest of the EABH in response to diverse geomorphology and climatic changes during the Plio‐Pleistocene. [ABSTRACT FROM AUTHOR]

RAD sequencing yields large amounts of genome‐wide data at a relatively low cost and without requiring previous taxon‐specific information, making it ideal for evolutionary studies of highly diversified and neglected organisms. However, concerns about information decay with phylogenetic distance have discouraged its use for assessing supraspecific relationships. Here, using Double Digest Restriction Associated DNA (ddRAD) data, we perform the first deep‐level approach to the phylogeny of Zodarion, a highly diversified spider genus. We explore the impact of loci and taxon filtering across concatenated and multispecies coalescent reconstruction methods and investigate the patterns of information dropout in reference to both the time of divergence and the mitochondrial divergence between taxa. We found that relaxed loci‐filtering and nested taxon‐filtering strategies maximized the amount of molecular information and improved phylogenetic inference. As expected, there was a clear pattern of allele dropout towards deeper time and mitochondrial divergences, but the phylogenetic signal remained strong throughout the phylogeny. Therefore, we inferred topologies that were almost fully resolved, highly supported, and noticeably congruent between setups and inference methods, which highlights overall inconsistency in the taxonomy of Zodarion. Because Zodarion appears to be among the oldest and most mitochondrially diversified spider genera, our results suggest that ddRAD data show high potential for inferring intra‐generic relationships across spiders and probably also in other taxonomic groups. [ABSTRACT FROM AUTHOR]

The libyan jird is one of the most widely distributed species among wild rodents, with its range extending from Morocco to China. Fifteen subspecies were described but their validity and the phylogenetic relationships among them are uncertain. Based on a comprehensive sampling, this study aims to define subspecies limits within Meriones libycus and to discuss the factors driving subspecific diversification. We used an integrative approach combining molecular (Cytochrome b and Cytochrome Oxidase Subunit 1 genes) and geometric morphometric data. Genetic data allowed us to identify three allopatric lineages within M. libycus: Western lineage in North Africa, Central lineage in Saudi Arabia, Jordan, and Syria, and Eastern lineage in Iran, Afghanistan, and China. These three lineages can also be differentiated based on skull morphology. Our results support the existence of at least three subspecies within the libyan jird: Meriones libycus libycus, M. l. syrius, and Meriones libycus erythrourus. Based on our divergence time estimates, all divergence events within M. libycus probably occurred during the Pleistocene, after 1.597 Ma. Quaternary climate fluctuations in the Sinai Peninsula explain the differentiation between the African M. l. libycus and the Levant‐Arabian M. l. syrius. The differentiation of M. l. syrius with respect to the eastern M. l. erythrourus is putatively linked to the climatic fluctuations and tectonic activity of the Zagros Mountains and/or the Mesopotamia Plain of Iraq during the Pleistocene. [ABSTRACT FROM AUTHOR]

The Persian Jird, Meriones persicus, is distributed from Eastern Anatolia to Afghanistan and western Pakistan. Six subspecies were described based on skull features and coat colours, but the validity of these subspecies is uncertain, and no molecular work has ever been conducted on this species. Iran appears to be a key geographical region in which to revise the systematic and evolutionary history of this species, because five of the six subspecies are present in this country. To evaluate the phylogeographical history and taxonomy of this species in Iran, we used a combination of genetic (cytochrome b gene sequences of 70 specimens) and geometric morphometric (2D landmarks on the ventral side of skull of 258 specimens) analyses. We also used ecological niche modelling to make inferences about the evolutionary history of these lineages. Our molecular data highlight the existence of four genetic lineages, but they only partly correspond to the previously described subspecies. Our molecular and morphometric data confirm the validity of M. p. rossicus and show that it has a wider geographical range than previously thought. M. p. gurganensis and M. p. baptistae are genetically very close. The skull of M. p. gurganensis is morphologically distinguishable from other subspecies. The subspecies M. p. persicus and M. p. baptistae are genetically distinct, but morphologically close. Meriones p. ambrosius is genetically close to M. p. persicus, and additional analyses with more specimens are needed to validate its subspecific status. The genetic structure observed in Iran seems to fit the topography and biogeography of the country and emphasize the role of the Abarkooh, Central and Lut deserts as barriers to gene flow. All intraspecific divergent events within the Persian Jird occurred during the last 1.4 My, suggesting that climatic changes probably trigger diversification within this species. Our genetic and species niche modelling results suggest that potential refugial areas persisted during glacial periods for this species in north-western Zagros Mountains, north-eastern Alborz Mountains and Kohrud Mountains. [ABSTRACT FROM AUTHOR]