North African fox genomes show signatures of repeated introgression and adaptation to life in deserts.

Elucidating the evolutionary process of animal adaptation to deserts is key to understanding adaptive responses to climate change. Here we generated 82 individual whole genomes of four fox species (genus Vulpes) inhabiting the Sahara Desert at different evolutionary times. We show that adaptation of new colonizing species to a hot arid environment has probably been facilitated by introgression and trans-species polymorphisms shared with older desert resident species, including a putatively adaptive 25 Mb genomic region. Scans for signatures of selection implicated genes affecting temperature perception, non-renal water loss and heat production in the recent adaptation of North African red foxes (Vulpes vulpes), after divergence from Eurasian populations approximately 78 thousand years ago. In the extreme desert specialists, Rueppell's fox (V. rueppellii) and fennec (V. zerda), we identified repeated signatures of selection in genes affecting renal water homeostasis supported by gene expression and physiological differences. Our study provides insights into the mechanisms and genetic underpinnings of a natural experiment of repeated adaptation to extreme conditions.

Feeding Ecology of the Cuvier's Gazelle (Gazella cuvieri, Ogilby, 1841) in the Sahara Desert.

Knowledge of the feeding ecology of ungulates in arid biomes offers an interesting model for understanding the drought resistance of large desert-adapted herbivores, a crucial issue in the face of increasing desertification due to climate change. To assess the feeding ecology of the endangered Cuvier's gazelle (Gazella cuvieri) in the Sahara desert, we used a multi-method approach combining faecal samples, direct observations, and the recording of indirect signs of feeding. We hypothesised that browser behaviour is the best foraging strategy for species living in hyper-arid environments, mainly due to long periods without grazing opportunities. Complementarily, we explored the effects of the main environmental descriptors (rainfalls and NDVI) on feeding patterns and diet quality. We found that Cuvier's diets are based mainly on acacias (Vachellia tortilis, V. flava) and occasionally on the annual forb Anastatica hierochuntica. In total, eighteen species (five trees, nine shrubs, three herbs, and one grass) belonging to fifteen families were recorded. Our result confirmed the browsers' characteristic of this species, reaffirming its ability to settle in a hostile environment. Acacias stand out as key species consumed at the southernmost limit of their range; hence, future conservation plans and strategies should take this into account for the survival of Cuvier's gazelle in desert environments.

Parasites of Moroccan desert Coptodon guineensis (Pisces, Cichlidae): transition and resilience in a simplified hypersaline ecosystem.

Sebkha Imlili (Atlantic Sahara) is a salt flat with over 160 permanent holes of hypersaline water generated in the Holocene and inhabited by euryhaline organisms that are considered to be relics of the past, including the cichlid fish Coptodon guineensis. We surveyed the fish parasites four times over one year, to i) identify the parasites, and ii) determine possible seasonality in infection patterns. Over 60% of the fish were infected by one to three helminths: an acanthocephalan in the intestine and two digenean metacercariae in the kidney, spleen, liver, muscle, and mesenteries. The acanthocephalan Acanthogyrus (Acanthosentis) cf. tilapiae was identified morphologically and molecularly; only one digenean (the heterophyid Pygidiopsis genata) could be identified molecularly. Both identified parasites were present throughout the sampling periods; the unidentified metacercariae were present only in summer and fall. Mean intensities, but not prevalence of infection by the acanthocephalan, reflected a biannual pattern of transmission. Infection accrued with fish size, possibly due to cannibalism. Because the water holes include only a few invertebrates, the intermediate hosts of these parasites can be inferred to be the gastropod Ecrobia ventrosa for the digeneans and either the copepod Cletocamtpus retrogressus or the ostracod Cyprideis torosa for the acanthocephalan. This ecosystem appears stable and provides a window into the past, as the acanthocephalan likely switched from freshwater tilapia to C. guineensis when the Sebkha formed. However, this is a vulnerable environment where the survival of these parasites depends on interactions maintained among only very few hosts.

Title: Parasites de Coptodon guineensis (Pisces, Cichlidae) du désert marocain : transition et résilience dans un écosystème hypersalin simplifié. Abstract: La Sebkha d'Imlili est une sebkha (étendue désertique sableuse et salée) dans le Sahara Atlantique caractérisée par la présence de plus de 160 poches permanentes d'eau hypersaline qui sont apparues à l'Holocène et qui sont habitées par des organismes considérés comme des reliques du passé, dont un poisson cichlidé, Coptodon guineensis. Nous avons fait l'inventaire des parasites de ce poisson au cours des quatre saisons d'une année pour 1) identifier les parasites et 2) déterminer une éventuelle transmission saisonnière. Plus de 60 % des poissons étaient infestés par un à trois helminthes : un Acanthocéphale dans l'intestin et des métacercaires de deux espèces de Digène dans le rein, la rate, les muscles et le mésentère. L'Acanthocéphale Acanthogyrus (Acanthosentis) cf. tilapiae a été identifié morphologiquement et génétiquement mais seul un des deux Digènes (l'hétérophyidé Pygidiopsis genata) a pu être identifié par séquençage. Ces deux parasites étaient présents à chaque période d'étude, mais la métacercaire non identifiée était présente seulement en été et en automne. L'intensité moyenne de l'infestation par l'Acanthocéphale, mais pas sa prévalence, reflète une transmission biannuelle. L'infestation augmente avec la taille du poisson, peut-être à cause du cannibalisme. L'identité des hôtes intermédiaires de ces parasites peut être avancée parce que cet écosystème est simplifié et inclut seulement quelques invertébrés : pour les Digènes, le Gastéropode Ecrobia ventrosa, et pour l'Acanthocéphale, le Copépode Cletocamtpus retrogressus ou l'Ostracode Cyprideis torosa. Cet écosystème apparait stable et offre une vue sur le passé étant donné que l'Acanthocéphale a sans doute été transféré d'un tilapia d'eau douce quand la sebkha s'est formée. Cependant, c'est un environnement vulnérable où la survie de ces parasites dépend d'interactions entre très peu d'espèces hôtes.

Publisher Correction: Identifying priority conservation areas in a Saharan environment by highlighting the endangered Cuvier's Gazelle as a flagship species.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Identifying priority conservation areas in a Saharan environment by highlighting the endangered Cuvier's Gazelle as a flagship species.

Monitoring populations and designing effective conservation actions for endangered species present significant challenges. An accurate understanding of current distribution, ecological traits and habitat requirements is imperative in formulating conservation strategies. Recent surveys on the southernmost Cuvier's Gazelle (Gazella cuvieri) population, an ungulate endemic to North Africa, showcase its importance in terms of numbers and genetic diversity. This population inhabits a remote region in the extreme north-western portion of the Sahara Desert and has not been well studied. Here, we examine the potential distribution of Cuvier's Gazelle and the environmental factors limiting the species in a Saharan environment, by combining broad-scale field survey data and species distribution models. Our objective was to identify high priority conservation areas in the southernmost known portion of the species' distribution by modelling habitat selection at the landscape scale using a predictive distribution map. Our results show that the distribution of Cuvier's Gazelle is strongly related to mountainous areas with heterogeneous terrain and remoteness from large human settlements over other ecological factors that had less impact on the species' presence and distribution. We also provide a quantitative estimate of the potential distribution range of Cuvier's Gazelle in southern Morocco, identifying two well-demarcated key areas. The two core areas currently contain enough rugged terrain isolated from human encroachment to support the endangered species in this harsh desert environment. We encourage the implementation of conservation planning for Cuvier's Gazelle as an "umbrella species", which will confer effective protection to higher-quality habitat zones and co-occurring species, leading to sustainable and ecologically responsible development in the region.

Unravelling population processes over the Late Pleistocene driving contemporary genetic divergence in Palearctic buzzards.

Population range expansions and contractions as a response to climate and habitat change throughout the Quaternary are known to have contributed to complex phylogenetic and population genetic events. Speciation patterns and processes in Palearctic buzzards (genus Buteo) are a long-standing example of morphological and genetic data incongruence, attributed to panmixia, habitat range shifts, contact zones, and climate change. Here we assess the systematics, phylogeography and population genetic structure of three nominal species of Palearctic buzzards, Buteo buteo (including B. b. vulpinus), B. rufinus (including B. r. cirtensis) and B. hemilasius. Phylogenetic analyses inferred from mitochondrial data recover B. hemilasius as sister to the sister clades B. r. rufinus and B. buteo complex (B. b. buteo, B. b. vulpinus, but also including B. r. cirtensis). In contrast, we find an unresolved genetic delimitation inferred from four nuclear loci, suggesting an ancestral genetic pool for all species. Time-trees suggest population contractions and expansions throughout the Pleistocene, which likely reflect habitat change and contrasting ecological niche requirements between species. Microsatellite-based extended Bayesian skyline plots reveal relatively constant population sizes for B. hemilasius, B. r. rufinus, and B. b. vulpinus, in contrast to a dramatic population expansion in B. r. cirtensis within the last 3 kya. Overall, our study illustrates how complex population processes over the Late Pleistocene have shaped the patterns of genetic divergence in Palearctic buzzards, due to the joint effects of shared ancestral polymorphisms, population expansions and contractions, with hybridization at contact zones leading to admixture and introgression.

A euryhaline fish, lost in the desert: The unexpected metapopulation structure of Coptodon guineensis (Günther, 1862) in the Sebkha of Imlili.

Euryhaline Cichlid fish of the species Coptodon guineensis are present in different water holes situated in a dried depression in the desert in the extreme South of Morocco, the Sebkha of Imlili. A genetic survey of this population, using complete sequences of the ND2 gene (mtDNA) and sixteen microsatellite loci, revealed that the fish in the sebkha did not form a single population, but rather a metapopulation. This metapopulational structure may be regarded as good news from the point of view of the conservation of fish in the sebkha. Although small individual populations may have short, finite life spans, the metapopulation as a whole is more stable, because immigrants from one population are likely to re-colonize the habitat, left open by the extinction of another.