Evolutionary systematics and biogeography of endemic gerbils (Rodentia, Muridae) from Morocco: an integrative approach

Unraveling phylogenetic relationships and species boundaries in the arid adapted Gerbillus rodents (Muridae: Gerbillinae) by RAD-seq data

Gerbillus is one of the most speciose genera among rodents, with ca. 51 recognized species. Previous attempts to reconstruct the evolutionary history of Gerbillus mainly relied on the mitochondrial cyt-b marker as a source of phylogenetic information. In this study, we utilize RAD-seq genomic data from 37 specimens representing 11 species to reconstruct the phylogenetic tree for Gerbillus, applying concatenation and coalescence methods. We identified four highly supported clades corresponding to the traditionally recognized subgenera: Dipodillus, Gerbillus, Hendecapleura and Monodia. Only two uncertain branches were detected in the resulting trees, with one leading to diversification of the main lineages in the genus, recognized by quartet sampling analysis as uncertain due to possible introgression. We also examined species boundaries for four pairs of sister taxa, including potentially new species from Morocco, using SNAPP. The results strongly supported a speciation model in which all taxa are treated as separate species. The dating analyses confirmed the Plio-Pleistocene diversification of the genus, with the uncertain branch coinciding with the beginning of aridification of the Sahara at the the Plio-Pleistocene boundary. This study aligns well with the earlier analyses based on the cyt-b marker, reaffirming its suitability as an adequate marker for estimating genetic diversity in Gerbillus.

High level of daily heterothermy in desert gerbils

Daily heterothermy is a strategy employed by endothermic birds and mammals to reduce their energetic costs by lowering their metabolic rate. We recorded nocturnal and diurnal rectal temperatures in three Moroccan Gerbillus rodent species to determine the level of heterothermy. A decrease in body temperature from night to day was observed by an average (±SD) of 8.7 (±4.2) in G. gerbillus, 11.1 (±3.0) in G. amoenus, and 7.7 (±3.3)°C in G. sp.1, the first records of heterothermy in the three species. The findings support a prediction that daily heterothermy is found in mammals from arid and semi-arid regions, contributing to further knowledge of thermoregulation in desert rodents.

Advances in research on the biology of the desert rodent Gerbillus tarabuli: a review

Selection of the appropriate species and strain of laboratory animals are among the scientist's major concerns. Tarabul's gerbil (Gerbillus tarabuli) is a small, seasonally breeding, desert rodent native to Africa. Despite its unique biological features, which make it an ideal model candidate for biomedical research, only a few reports have used it in research. Hence, the present review aims to provide more data about this species, covering all aspects of its biology, such as taxonomy, morphology, anatomy, ecology, wildlife biology, molecular biology, physiology, neurobiology, genetics, reproduction, development, evolutionary biology, and conservation biology, and covers current progress in exploration of G. tarabuli, discussing its valuable characteristics, which are widely useful for research in various fields. This review paper is destined for biologists, scientists, mammologists, zoologists, academics, and students.

Diversity, distribution and conservation of land mammals in Mauritania, North-West Africa

Detailed knowledge about biodiversity distribution is critical for monitoring the biological effects of global change processes. Biodiversity knowledge gaps hamper the monitoring of conservation trends and they are especially evident in the desert biome. Mauritania constitutes a remarkable example on how remoteness and regional insecurity affect current knowledge gaps. Mammals remain one of the least studied groups in this country, without a concerted species checklist, the mapping of regions concentrating mammal diversity, or a national assessment of their conservation status. This work assessed the diversity, distribution, and conservation of land mammals in Mauritania. A total of 6,718 published and original observations were assembled in a spatial database and used to update the occurrence status, distribution area, and conservation status. The updated taxonomic list comprises 107 species, including 93 extant, 12 Regionally Extinct, and 2 Extinct in the Wild. Mapping of species distributions allowed locating concentrations of extant mammal species richness in coastal areas, along the Senegal River valley, and in mountain plateaus. Recent regional extinction of large-sized Artiodactyla and Carnivora has been very high (11% extinct species). From the extant mammals, 11% are threatened, including flagship species (e.g., Addax nasomaculatus and Panthera pardus). Species richness is poorly represented by the current protected areas. Despite the strong advances made, 23% of species categorise as Data Deficient. Persisting systematics and distribution uncertainties require further research. Field surveys in currently unexplored areas (northern and south-eastern regions) are urgently needed to increase knowledge about threatened mammals. The long-term conservation of land mammals in Mauritania is embedded in a complex web of socioeconomic and environmental factors that call for collaborative action and investment in sustainable human development. The current work sets the baseline for the future development of detailed research studies and to address the general challenges faced by mammals and biodiversity in the country.

Pleistocene climate fluctuations drove demographic history of African golden wolves (Canis lupaster)

Pleistocene climate change impacted entire ecosystems throughout the world. In the northern hemisphere, the distribution of Arctic species expanded during glacial periods, while more temperate and mesic species contracted into climatic refugia, where isolation drove genetic divergence. Cycles of local cooling and warming in the Sahara region of northern Africa caused repeated contractions and expansions of savannah-like environments which connected mesic species isolated in refugia during interglacial times, possibly driving population expansions and contractions; divergence and geneflow in the associated fauna. Here, we use whole genome sequences of African golden wolves (Canis lupaster), a generalist mesopredator with a wide distribution in northern Africa to estimate their demographic history and past episodes of geneflow. We detect a correlation between divergence times and cycles of increased aridity-associated Pleistocene glacial cycles. A complex demographic history with responses to local climate change in different lineages was found, including a relict lineage north of the High Atlas Mountains of Morocco that has been isolated for more than 18,000 years, possibly a distinct ecotype.

BRC4Env, a network of Biological Resource Centres for research in environmental and agricultural sciences

The Biological Resource Centre for the Environment BRC4Env is a network of Biological Resource Centres (BRCs) and collections whose leading objectives are to improve the visibility of genetic and biological resources maintained by its BRCs and collections and to facilitate their use by a large research community, from agriculture research to life sciences and environmental sciences. Its added value relies on sharing skills, harmonizing practices, triggering projects in comparative biology, and ultimately proposing a single-entry portal to facilitate access to documented samples, taking into account the partnership policies of research institutions as well as the legal frame which varies with the biological nature of resources. BRC4Env currently includes three BRCs: the Centre for Soil Genetic Resources of the platform GenoSol, in partnership with the European Conservatory of Soil Samples; the Egg Parasitoids Collection (EP-Coll); and the collection of ichthyological samples, Colisa. BRC4Env is also associated to several biological collections: microbial consortia (entomopathogenic bacteria, freshwater microalgae…), terrestrial arthropods, nematodes (plant parasitic, entomopathogenic, animal parasitic...), and small mammals. The BRCs and collections of BRC4Env are involved in partnership with academic scientists, as well as private companies, in the fields of medicinal mining, biocontrol, sustainable agriculture, and additional sectors. Moreover, the staff of the BRCs is involved in many training courses for students from French licence degree to Ph.D, engineers, as well as ongoing training.

Notes on the distribution and phylogeography of two rare small Gerbillinae (Rodentia, Muridae) in Morocco: Gerbillus simoni and Gerbillus henleyi

Even though Gerbillinae rodents represent an important part of the mammalian fauna in North Africa, many gaps remain in our understanding of the distribution, ecology, evolution, and systematics of some lesser known species in this family. We present in this study the most recent findings on two of these species. The first species, Gerbillus simoni Lataste, 1881, is a short-tailed, small gerbil, endemic to North Africa. In Morocco, it is present only in a small area in the northeast, where it has not been caught since 1970. In 2014, we captured a small gerbil in this region that was identified as G. simoni based on morphology and molecular data (cytochrome b gene sequencing). This study represents the first genetic characterization of G. simoni in Morocco and the first one outside Tunisia. Populations from Morocco and Tunisia (mainland and Kerkennah Islands) show very little genetic differentiation. The second species, Gerbillus henleyi de Winton, 1903, is a long-tailed small gerbil that lives in the Sahel and North Africa with an extension to the Middle East. In Morocco, this species was only known in the southwest. Between 2014 and 2015, we have captured four gerbils in the northeast of the country, which were confirmed genetically and morphologically as belonging to this species. This represents an extension of its known distribution of about 370km to the northeast of the country. These new Moroccan specimens form a distinct lineage. High genetic diversity is observed throughout the geographic range of G. henleyi, suggesting the existence of several cryptic species.

Taxonomic hypotheses regarding the genus Gerbillus (Rodentia, Muridae, Gerbillinae) based on molecular analyses of museum specimens

Methodological improvements now allow routine analyses of highly degraded DNA samples as found in museum specimens. Using these methods could be useful in studying such groups as rodents of the genus Gerbillus for which i) the taxonomy is still highly debated, ii) collection of fresh specimens may prove difficult. Here we address precise taxonomic questions using a small portion of the cytochrome b gene obtained from 45 dry skin/skull museum samples (from 1913 to 1974) originating from two African and three Asian countries. The specimens were labelled Gerbillusgerbillus, Gerbillusandersoni, Gerbillusnanus, Gerbillusamoenus, Gerbillusperpallidus and Gerbilluspyramidum, and molecular results mostly confirmed these assignations. The close relationship between Gerbillusnanus (Asian origin) and Gerbillusamoenus (African origin) confirmed that they represent vicariant sibling species which differentiated in allopatry on either side of the Red Sea. In the closely related Gerbillusperpallidus and Gerbilluspyramidum, specimens considered as belonging to one Gerbilluspyramidum subspecies (Gerbilluspyramidumfloweri) appeared closer to Gerbillusperpallidus suggesting that they (Gerbilluspyramidumfloweri and Gerbillusperpallidus) may represent a unique species, distributed on both sides of the Nile River, for which the correct name should be Gerbillusfloweri. Furthermore, the three other Gerbilluspyramidum subspecies grouped together with no apparent genetic structure suggesting that they may not yet represent genetically differentiated lineages. This study confirms the importance of using these methods on museum samples, which can open new perspectives in this particular group as well as in other groups of interest.

Borrelia infection in small mammals in West Africa and its relationship with tick occurrence inside burrows

Tick-borne relapsing fever (TBRF) is a zoonotic disease caused by several Borrelia species transmitted to humans by Ornithodoros tick vectors. In West Africa, Borrelia crocidurae is a common cause of disease in many rural populations. Small mammals act as reservoirs of infection. We report here the results of surveys that investigated the occurrence of B. crocidurae infection in rodents and insectivores from eight countries of West and Central Africa. Animals were identified at the species level and tested for Borrelia either by examination of thick blood film, intra-peritoneal inoculation of blood or brain tissues into laboratory mice, or by molecular techniques. A total of 4358 small mammals belonging to 38 species and 7 families were collected, including 3225 specimens collected in areas where the occurrence of Ornithodoros sonrai tick in rodent burrows was documented, and 1133 in areas where this tick was absent. In areas with O. sonrai, Borrelia infection was demonstrated in 287 of 3109 (9.2%) small mammals tested, and none was documented in 1004 animals tested from other areas. There was no relationship between the occurrence of Rhipicephalus, Hyaloma and Argas ticks in burrows and the distribution of Borrelia infection in small mammals. The 287 specimens infected by Borrelia belonged to 15 rodent and shrew species, including three Saharo-Sahelian species - Gerbillus gerbillus, Gerbillus occiduus and Gerbillus tarabuli - identified as reservoirs for TBRF with a distribution restricted to this area. In Sudan and Sudano-Sahelian areas, Arvicanthis niloticus, Mastomys erythroleucus and Mastomys huberti were the main reservoir of infection. Although most small mammals species collected had a large distribution in West and Central Africa, the fact that only animals collected in areas with O. sonrai were found infected suggest that this tick is the only vector of TBRF in rodents and insectivores in this part of Africa.

Chromosomal polymorphism in mammals: an evolutionary perspective

Although chromosome rearrangements (CRs) are central to studies of genome evolution, our understanding of the evolutionary consequences of the early stages of karyotypic differentiation (i.e. polymorphism), especially the non-meiotic impacts, is surprisingly limited. We review the available data on chromosomal polymorphisms in mammals so as to identify taxa that hold promise for developing a more comprehensive understanding of chromosomal change. In doing so, we address several key questions: (i) to what extent are mammalian karyotypes polymorphic, and what types of rearrangements are principally involved? (ii) Are some mammalian lineages more prone to chromosomal polymorphism than others? More specifically, do (karyotypically) polymorphic mammalian species belong to lineages that are also characterized by past, extensive karyotype repatterning? (iii) How long can chromosomal polymorphisms persist in mammals? We discuss the evolutionary implications of these questions and propose several research avenues that may shed light on the role of chromosome change in the diversification of mammalian populations and species.

Dynamics of green Sahara periods and their role in hominin evolution

Astronomically forced insolation changes have driven monsoon dynamics and recurrent humid episodes in North Africa, resulting in green Sahara Periods (GSPs) with savannah expansion throughout most of the desert. Despite their potential for expanding the area of prime hominin habitats and favouring out-of-Africa dispersals, GSPs have not been incorporated into the narrative of hominin evolution due to poor knowledge of their timing, dynamics and landscape composition at evolutionary timescales. We present a compilation of continental and marine paleoenvironmental records from within and around North Africa, which enables identification of over 230 GSPs within the last 8 million years. By combining the main climatological determinants of woody cover in tropical Africa with paleoenvironmental and paleoclimatic data for representative (Holocene and Eemian) GSPs, we estimate precipitation regimes and habitat distributions during GSPs. Their chronology is consistent with the ages of Saharan archeological and fossil hominin sites. Each GSP took 2–3 kyr to develop, peaked over 4–8 kyr, biogeographically connected the African tropics to African and Eurasian mid latitudes, and ended within 2–3 kyr, which resulted in rapid habitat fragmentation. We argue that the well-dated succession of GSPs presented here may have played an important role in migration and evolution of hominins.

Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples

Rodentia is the most diverse order among mammals, with more than 2,000 species currently described. Most of the time, species assignation is so difficult based on morphological data solely that identifying rodents at the specific level corresponds to a real challenge. In this study, we compared the applicability of 100 bp mini-barcodes from cytochrome b and cytochrome c oxidase 1 genes to enable rodent species identification. Based on GenBank sequence datasets of 115 rodent species, a 136 bp fragment of cytochrome b was selected as the most discriminatory mini-barcode, and rodent universal primers surrounding this fragment were designed. The efficacy of this new molecular tool was assessed on 946 samples including rodent tissues, feces, museum samples and feces/pellets from predators known to ingest rodents. Utilizing next-generation sequencing technologies able to sequence mixes of DNA, 1,140 amplicons were tagged, multiplexed and sequenced together in one single 454 GS-FLX run. Our method was initially validated on a reference sample set including 265 clearly identified rodent tissues, corresponding to 103 different species. Following validation, 85.6% of 555 rodent samples from Europe, Asia and Africa whose species identity was unknown were able to be identified using the BLASTN program and GenBank reference sequences. In addition, our method proved effective even on degraded rodent DNA samples: 91.8% and 75.9% of samples from feces and museum specimens respectively were correctly identified. Finally, we succeeded in determining the diet of 66.7% of the investigated carnivores from their feces and 81.8% of owls from their pellets. Non-rodent species were also identified, suggesting that our method is sensitive enough to investigate complete predator diets. This study demonstrates how this molecular identification method combined with high-throughput sequencing can open new realms of possibilities in achieving fast, accurate and inexpensive species identification.