Nubian Ibex Research Articles

Species behavioral characteristics lead to unique fragmentation threats: The Nubian ibex as a case study

AbstractThe behavioral characteristics of species may result in certain populations being inherently more susceptible to fragmentation. For example, species exhibiting spatial sexual segregation or those constrained to elongated and narrow habitats. We studied the fragmentation threats, spatial dynamics, resource utilization, and movement ecology of a particularly vulnerable species that is both sexually segregated and constrained to elongated and narrow habitat—the north Judean Desert population of Nubian ibex (Capra nubiana). From 2016‒2020 we tracked 48 marked ibex (27 male, 21 female), of which 38 (20 male, 18 female) also had global position system (GPS) collars. Using GPS‐collar and camera‐trap data in zones delineated around perennial water sources (PWSs), we calculated ibex drinking frequencies and individual utilization distributions by season and sex, focusing on their overall (95% isopleth) and core (50% isopleth) home ranges. We quantified joint space use between sexes using a utilization distribution overlap index (UDOI) and ibex daily movements and space use via movement indices. Female groups formed philopatric activity centers that were anchored around PWSs year‐round and arranged in a metapopulation‐like structure, with no female movement detected between them. Conversely, movement of adult males changed seasonally, with the cores of male groups anchored around PWSs only during the dry season, and long‐range movement between female activity centers during the rut. Female groups also spent more time at steeper terrain and higher elevations compared with male groups. Outside the rut, groups of males and groups of females exhibited minimal joint space use (i.e., average dry season UDOI was 0.06). These patterns indicate high sensitivity of this population to intersexual fragmentation by obstacles (physical or virtual). Management strategies to mitigate fragmentation threats for such populations should be sex‐specific and landscape‐oriented.

Implications of newly developed SNPs for conservation programmes for the threatened Nubian ibex (Capra nubiana) in Oman

Conservation of elusive species affected by habitat degradation, population fragmentation and poaching is challenging. The remaining wild populations of a desert-adapted ungulate, Nubian ibex (Capra nubiana), within Oman are small and fragmented. The appropriateness of captive insurance populations for reinforcing existing, or establishing new, wild populations remains uncertain for Oman due to ambiguity regarding their genetic provenance. For effective management of this threatened species, it is essential to assess the genetic relationships between the wild and captive populations, and to investigate hybridisation with domestic goats (Capra hircus). We identified 5,775 high-quality SNPs using double digest restriction-site associated DNA (ddRAD), to assess genetic structure, gene flow and divergence between Oman’s wild populations of Nubian ibex and in captivity, which are likely of North African provenance. We detected hybridisation with goats in captivity and recommend that genetic assessments of captive individuals are routinely used to evaluate their suitability for conservation programs. Building on previous mitochondrial evidence, substantial nuclear divergence (FST = 0.540) was found between wild Oman and captive populations, providing further evidence that Nubian ibex may be composed of multiple species and urgently needs a taxonomic review. Additionally, an appropriate insurance population should be established for Oman’s threatened wild population. The data provided here will be invaluable for developing marker systems to assess wild populations using low-quality DNA from non-invasive sampling. Consequently, it will support further research into Nubian ibex throughout their range and highlights the need to integrate genetic information for effective conservation management of Nubian ibex.

Palaeodietary reconstruction of wild and domestic goats using dental microwear texture analysis. A case study from two early Neolithic sites in the southern Levant

ABSTRACT Dental microwear (DMA) is a tool used for the palaeodiet reconstruction of animals in Archaeology. The use of this proxy on domestic ungulates provides valuable information to reconstruct livestock strategies, yet it presents several methodological limitations. Most studies have been carried out using low-magnification DMA and the interpretations often relied on comparisons with databases of extant wild ungulates. In addition, several studies have highlighted challenges in discerning diets in extant domestic caprines. In parallel, dental microwear texture analysis (DMTA) – a quantitative methodology based on 3D micro-texture height maps – has shown better discrimination. In this paper, we explore the capacity to distinguish four different management strategies of domestic goats (Capra hircus) and three species of wild ibexes (Capra nubiana, C. pyrenaica and C. ibex) using DMTA. Results revealed good discrimination among extant domestic goat populations and between wild and domestic goats. This new dataset was subsequently used to characterise the palaeodiet of archaeological goats from two Pre-Pottery Neolithic B sites in the southern Levant. Preliminary findings suggest evidence of human intervention in goats at least during the early 8th millennium BCE. In addition, incorporating various current management strategies has enhanced our understanding of early goat domestication in southern Levant.

Exposure of Nubian ibex (Capra nubiana) to humans reduces behavioural responses to potential threats

Abstract The spatial expansion of human populations has increased the overlap between humans and wildlife, leading to the greater tolerance of many wildlife species to humans. However, our current understanding of the consequences of such tolerance is limited. In particular, we lack information on whether reduced behavioural responses to humans are indicative of reduced responses to other potential threats. We made use of a unique natural system comprising geographically adjacent, but nevertheless separate, populations of the threatened Nubian ibex (Capra nubiana) that are exposed to different levels of human disturbance to test the effects of exposure to humans on ibex behavioural responses to other stimuli. We measured flight initiation distance (FID) and alert distance (AD) in males approached by four different stimuli: a human, a human with a dog, a novel object, and a leopard model. Both FID and AD decreased for all stimuli as the human exposure level increased. Ibex in areas that are highly exposed to humans reduced their behavioural responses to humans more strongly compared to other stimuli. These findings suggest that tolerance for humans may be the product of several complementary behavioural mechanisms (such as habituation and non‐random dispersal). Policy implications. Our findings align with the concern that animals highly exposed to human beings may be less capable of surviving in the wild. Our results also emphasize that the interactions between people and wild animals (such as feeding them) determine the behavioural responses of wild animals, shaping patterns of human–wildlife conflict and co‐existence. Read the free Plain Language Summary for this article on the Journal blog.

Discriminating dietary behaviour between wild and domestic goats using dental microwear texture: first results from a modern reference set and early Neolithic goat exploitation in the southern Levant

Current evidence supports the idea that animal domestication occurred in multiple loci and at different time periods throughout the Near East rather than according to a single origin. In this scenario, the southern Levant is being increasingly considered as another presumed primary centre of goat domestication, alongside eastern Anatolia and the Zagros. Assessing the status (i.e. wild or domestic) of this animal in this region, however, is hampered by the difficulty of morphologically distinguishing domestic goats from their wild relatives. Diet reconstruction is a powerful approach to address this issue since the feeding of managed animals is partially controlled by their owners, unlike free-ranging wild populations. For the first time, we propose to contribute to this question through dental microwear texture analysis (DMTA) using confocal microscopy.Characterising how the dietary behaviour of extant wild and domestic goats is reflected in DMTA is critical. For this purpose, we constructed a reference collection composed of three wild goat species (19 Capra pyrenaica from the southern Iberian Peninsula, 12 Capra ibex from the Alps and 12 Capra nubiana from the Near East) and 15 domestic goats (Capra hircus) reared in an extensive system in Mediterranean scrubland areas.The preliminary results indicate that DMTA allows discrimination of the groups of extant goats. The results obtained were used to characterise the palaeodiet of 16 goats (Capra format aegagrus) from two key Early and Middle Pre-Pottery Neolithic B sites in the southern Levant: Kharaysin (Zarqa, Jordan, ca. 8800-7500 cal BC) and Qarassa (As-Suweyda, Syria, 8700-8200 cal BCE). The higher variability in archaeological goats could be an indicator of controlled feedings. It could also support the hypothesis about diverse and experimental management systems at the first steps of animal domestication.This paper shows the potential of this tool to address the process of early animal domestication. Following this initial work, the reference collection will include a broader spectrum of livestock management strategies and the archaeological corpus will be expanded through new samples during upcoming excavations and the integration of additional sites.

Foot-and mouth disease and peste des petits ruminants – the role of wildlife in the epidemiology and control of diseases

Foot-and mouth disease (FMD) and peste des petits ruminants (PPR) are highly contagious and an economically devastating diseases, currently endemic to the African and Asian continents. The aim of this paper was to present the role of wildlife in the epidemiology of both diseases. There are more than 100 species of wild, feral, laboratory, or domesticated animals that have been infected naturally or experimentally with FMD or PPR viruses. Experimental infections of several African wild ruminants can result in clinical FMD. African buffalo represents the best known FMD wild host reservoir in Sub-Saharan Africa. North American mule deer were found susceptible to FMDV infection with significant mortality. Other wild ruminants such as impala can also contribute to FMDV maintenance. In Europe several deer species and the Eurasian wild boar are susceptible to FMDV. PPRV has been reported to have infected some wildlife, such as African buffalo, saiga antelope, dorcas gazelles, gemsbok, Nubian ibex and some other ungulate species. The role of wildlife in FMD and PPR epidemiology may concern wildlife as indicators, victims, bridge hosts or maintenance hosts for both diseases. In addition, they are occasionally victims of disease outbreaks, and they are often relevant for disease management as either bridge or maintenance hosts. Wildlife deserves to become a key component of future integrated surveillance and disease control strategies in an ever-changing world. However, it must be stated that efforts to control FMD and PPR in wildlife may not be successful when the diseases are endemic in livestock and may cause more harm to wildlife, human livelihoods, and domestic animals.

Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate.

Understanding how evolutionary pressures related to climate change have shaped the current genetic background of domestic animals is a fundamental pursuit of biology. Here, we generated whole-genome sequencing data from native goat populations in Iraq and Pakistan. Combined with previously published data on modern, ancient (Late Neolithic to Medieval periods), and wild Capra species worldwide, we explored the genetic population structure, ancestry components, and signatures of natural positive selection in native goat populations in Southwest Asia (SWA). Results revealed that the genetic structure of SWA goats was deeply influenced by gene flow from the eastern Mediterranean during the Chalcolithic period, which may reflect adaptation to gradual warming and aridity in the region. Furthermore, comparative genomic analysis revealed adaptive introgression of the KITLG locus from the Nubian ibex ( C. nubiana) into African and SWA goats. The frequency of the selected allele at this locus was significantly higher among goat populations located near northeastern Africa. These results provide new insights into the genetic composition and history of goat populations in the SWA region.

Population dynamics and the effect of drought in the threatened Nubian ibex

AbstractEstimating key state variables such as abundance, survival, and recruitment of wild populations, and their interaction with local conditions such as precipitation, is essential for state‐dependent decision making and management. Estimation of state variables remains challenging, especially in species such as mountain ungulates inhabiting rugged and remote terrains. Camera traps present a technological advance that can mitigate some of the challenges in state estimation and can be used to enhance existing methods. Here, we combined camera traps, individual markings, and GPS tracking to estimate abundance and survival for the threatened Nubian ibex (Capra nubiana) population of the Judean Desert, Israel. Since precipitation is a key determinant for recruitment in desert ungulates, we complemented our estimates with kid‐female ratios and regional precipitation records. Between 2016 and 2019, we individually marked 48 ibex of which 38 were also fitted with GPS collars within the Judean Desert. We performed 6 days of camera‐trap surveys each year to estimate abundance for the north Judean Desert population using mark‐resight in a robust‐design framework. Weight‐averaged abundance estimates for 2017–2019, respectively, were as follows: = 267 (95% CI = 117–418, SE = 51.27), 201 (95% CI = 115–288, SE = 36.85), and 226 (95% CI = 154–299, SE = 36.94) for females, and = 291 (95% CI = 154–299, SE = 36.94), 160 (95% CI = 108–212, SE = 25.19), and 283 (95% CI = 181–384, SE = 29.76) for males. By augmenting data from telemetry with camera traps, we estimated survival via known fates for the entire Judean Desert (north, mid, and south populations). Weight‐averaged survival estimates for 2016–2019, respectively, were: = 0.99 (95% CI = 0.97–1.00, SE = 0.012), 0.90 (95% CI = 0.24–0.99, SE = 0.153), 0.87 (95% CI = 0.62–0.97, SE = 0.081), and 0.88 (95% CI = 0.69–0.96, SE = 0.062) for females, and = 0.77 (95% CI = 0.26–0.97, SE = 0.203), 0.64 (95% CI = 0.33–0.86, SE = 0.151), 0.85 (95% CI = 0.60–0.96, SE = 0.087), and 0.88 (95% CI = 0.69–0.96, SE = 0.062) for males. The interannual trends of abundance and survival estimates corresponded with observed kid‐female ratios and the regional precipitation records, reflecting a population decline following 2017's drought and an increase following the increased precipitation in 2018. Our findings substantiate the efficacy of using camera traps to estimate Nubian ibex's key state variables, as well as detecting population trends driven by environmental conditions. Despite being costly, the capacity of statistically‐robust methods to estimate key state variables is indispensable, and camera traps make similar methods increasingly more feasible in remote and inaccessible populations.

Bringing the Dead Sea to Life: Art and Nature at the Lowest Place on Earth

Bringing the Dead Sea to Life: Art and Nature at the Lowest Place on Earth

The use of demographic data to monitor population trends of the Nubian Ibex, Capra nubiana in Jordan (Mammalia: Bovidae)

The population status of the IUCN vulnerable Nubian Ibex Capra nubiana is largely unknown in the Middle East because of difficulties conducting intensive surveys. We tested the utility of camera-trapping at permanent water sites to estimate demographics and population trend of the species in the Dana Biosphere Reserve, Jordan. We also studied the relationship between precipitation and the Normalized Difference Vegetation Index NDVI on water site use by the Nubian Ibex, demographics, and population trend. The Nubian Ibex showed a mean annual productivity of 0.81 neonate/female and an adult female survival of 0.87 which is a lower survival rate than found in other ibex species. The mean potential annual rate of increase of this population (λ=1.14) was similar to those reported from other ibex species and indicated a viable population. The capture rate of camera traps (number of photographed animals/camera day) was found not to be a reliable index to monitor population trends because water site use was related to environmental conditions that could not be standardized or predicted a priori. Quantifying population demographic ratios using camera trapping allowed for monitoring the status of key population parameters and growth potential of Nubian Ibex populations in the Dana Reserve, and likely can be used to monitor population status and facilitate informed management of similar populations in the Middle East.

Cave paleozoology in the Judean Desert: assembling records of Holocene wild mammal communities

ABSTRACTLong temporal records of Holocene wild mammal communities are essential to examine the role of human impacts and climatic fluctuations in the configuration of modern ecosystems. We show that such records can be assembled through extensive radiocarbon dating of faunal remains obtained from biogenic cave deposits. We dated 110 mammalian remains from 19 different cave sites in the Judean Desert. We use the dates in combination with archaeological survey data and bone collagen/apatite δ13C values to study faunal succession in the context of Holocene climate change and human settlement history in the region. Our results suggest a change in the late Holocene, expressed in fewer observations of Arabian leopard (Panthera pardus nimr) and gazelle (Gazellaspp.), and an increase of Syrian striped hyena (Hyaena hyaena syriaca), fox (Vulpesspp.), Nubian ibex (Capra nubiana) and rock hyrax (Procavia capensis); suids (Sus scrofa) appear for the first time. According to the data distribution, however, the probability of finding a bone diminishes exponentially with time, which implies that the Judean Desert cave paleozoological record is temporally biased. The weight of evidence ultimately favors an explanation of the observed patterns as the consequence of a combined anthropogenic and climatic impact on local food webs.

COVID-19 Restrictions in a Nature Reserve Reveal the Costs of Human Presence for the Threatened Nubian Ibex (Capra nubiana)

The increasing pressure of ecotourism on wildlife in their natural habitats leads many wild animals to alter their behaviors. The restrictions issued in many places due to COVID-19 provide a rare opportunity to examine wildlife behavior in nature reserves with reduced human presence, and to reveal the impact of human visitation on the behaviors and fitness of local wildlife species. In 2019 and 2020 we placed trail cameras next to two natural springs in the Israeli Negev Desert, Ein-Avdat and Ein-Shaviv, located 9 km apart. Both sites serve as the main water source for local Nubian ibex (Capra nubiana) populations, but Ein-Avdat is situated within a popular national park into which visitors’ entrance was restricted due to COVID-19 regulations in 2020, while Ein-Shaviv is more remote and thus attracts only few visitors regardless of COVID-19 regulations. Our study revealed that during 2020, ibex in Ein-Avdat arrived to drink earlier in the day and the population’s Female:Kids ratio more than doubled. These changes were not observed in Ein-Shaviv. We found that the daily number of visitors in Ein-Avdat affected the arrival time of ibex to the water pool. We conclude that the reduced number of visitors to Ein-Avdat in 2020 compared to 2019 may have allowed ibex to arrive in preferred hours, and may have contributed to the increased kid-to-females ratio. Our study shows that behavioral adaptions to human visitation in nature reserves might carry a high fitness cost.

Survivorship in a heavily hunted population of Nubian ibex (Capra nubiana)

Survivorship in a heavily hunted population of Nubian ibex (<i>Capra nubiana</i>)

Anti Covid-19 face-masks increases vigilance in Nubian ibex (Capra nubiana)

Changes in ecosystems resulting from anthropause caused by Covid-19 relate to both abiotic and biotic factors which have both a positive or negative effect on wildlife. The lockdown was manifested by reduced air and water pollution, lower mortality of animals on the roads, an increase in animals' body condition and reproduction success. On the other hand, the closures lead to an increase in the populations of invasive species or poaching. We studied the behavioural reaction of natural, desert-dwelling Nubian ibex (Capra nubiana) on the appearance of a new element in the environment – the facial-masks. We hypothesized that the mask would trigger a response expressed through differences in the vigilance towards a potentially new threat. We applied the flight initiation distance (FID) technique to check the reaction at the approach of a human with a facial-mask and without it. The average FID was 8.8 m and was longer when the observer was wearing a mask (10.7 m) as compared to trials without the mask (6.9 m). Our study indicates that wildlife, even if habituated to human silhouette at a distance, appear to notice unusual accessories when up-close and respond by increased vigilance and what may affect their overall fitness.

Wild ungulates in Jordan: past, present, and forthcoming opportunities

Twelve species of ungulates are reported from the wild in Jordan. Three of these, Addax nasomaculatus (Addax), Bos primigenius (Aurochs), and Cervus elaphus (Red Deer) are known only from archaeological excavations. Dama mesopotamica (Mesopotamian Fallow Deer), Oryx leucoryx (Arabian Oryx) and Equus hemionus hemippus (Syrian Wild Ass) have been regionally extirpated in the wild. A semi-captive population of Persian Onager (E. h. hemionus) is held in Shumari Wildlife Reserve. The Arabian Oryx is also managed in semi-captive conditions in two reserves. Except the commonly occurring Wild Boar (Sus scrofa), other surviving ungulate species continue to be under serious threat. Gazella gazella (Palestinian Mountain Gazelle), Capreolus capreolus (European Roe Deer), Gazella marica (Arabian Sand Gazelle), and Gazella dorcas (Dorcas Gazelle) are Critically Endangered, and Capra nubiana (Nubian Ibex) is Endangered in the region. This paper provides a review of the historical and current status of wild ungulates in Jordan, listing the threats and conservation measures and provides recommendations for management and conservation in the future.

Genome Scan for Variable Genes Involved in Environmental Adaptations of Nubian Ibex

The Nubian ibex (Capra nubiana) is a wild goat species that inhabits the Sahara and Arabian deserts and is adapted to extreme ambient temperatures, intense solar radiation, and scarcity of food and water resources. To investigate desert adaptation, we explored the possible role of copy number variations (CNVs) in the evolution of Capra species with a specific focus on the environment of Capra nubiana. CNVs are structural genomic variations that have been implicated in phenotypic differences between species and could play a role in species adaptation. CNVs were inferred from Capra nubiana sequence data relative to the domestic goat reference genome using read-depth approach. We identified 191 CNVs overlapping with protein-coding genes mainly involved in biological processes such as innate immune response, xenobiotic metabolisms, and energy metabolisms. We found copy number variable genes involved in defense response to viral infections (Cluster of Differentiation 48, UL16 binding protein 3, Natural Killer Group 2D ligand 1-like, and Interferon-induced transmembrane protein 3), possibly suggesting their roles in Nubian ibex adaptations to viral infections. Additionally, we found copy number variable xenobiotic metabolism genes (carboxylesterase 1, Cytochrome P450 2D6, Glutathione S-transferase Mu 4, and UDP Glucuronosyltransferase-2B7), which are probably an adaptation of Nubian ibex to desert diets that are rich in plant secondary metabolites. Collectively, this study's results advance our understanding of CNVs and their possible roles in the adaptation of Nubian ibex to its environment. The copy number variable genes identified in Nubian ibex could be considered as subjects for further functional characterizations.

Horn growth patterns of Nubian ibex from the Sinai, Egypt

Abstract Documenting patterns of horn growth and horn-age relationships of Nubian ibex (Capra nubiana) can contribute to a more comprehensive understanding of their natural history, horn development in ibex in general, and future conservation of the species. Our specific objectives included (1) documenting age-horn growth patterns; (2) contrasting horn growth patterns of Nubian ibex with other ibex species; and (3) determining whether horn development accurately reflects age of Nubian ibex in Sinai, Egypt. As expected, all male and female horn measurements had significant relationships with age. Horn growth in males started plateauing at ca. age 7–8, whereas female horn growth started plateauing at ca. age 4–6. The extremely arid environment of Nubian ibex in the Sinai may account for the slowing of horn growth at a younger age than seen in populations of some other ibex species. We found a significant relationship between the number of horn ridges and age, indicating that counting horn ridges provides a viable method of aging males to within ±1 y. Thus counting horn ridges may be a useful and non-invasive method to determine age or age class, which can further our understanding of age structure, the natural history, and management of Nubian ibex populations.

Genetic diversity of the Nubian ibex in Oman as revealed by mitochondrial DNA.

The Nubian ibex (Capra nubiana) is patchily distributed across parts of Africa and Arabia. In Oman, it is one of the few free-ranging wild mammals found in the central and southern regions. Its population is declining due to habitat degradation, human expansion, poaching and fragmentation. Here, we investigated the population's genetic diversity using mitochondrial DNA (D-loop 186 bp and cytochrome b 487 bp). We found that the Nubian ibex in the southern region of Oman was more diverse (D-loop HD; 0.838) compared with the central region (0.511) and gene flow between them was restricted. We compared the genetic profiles of wild Nubian ibex from Oman with captive ibex. A Bayesian phylogenetic tree showed that wild Nubian ibex form a distinct clade independent from captive animals. This divergence was supported by high mean distances (D-loop 0.126, cytochrome b 0.0528) and high FST statistics (D-loop 0.725, cytochrome b 0.968). These results indicate that captive ibex are highly unlikely to have originated from the wild population in Oman and the considerable divergence suggests that the wild population in Oman should be treated as a distinct taxonomic unit. Further nuclear genetic work will be required to fully elucidate the degree of global taxonomic divergence of Nubian ibex populations.

Capture Sequencing to Explore and Map Rare Casein Variants in Goats.

Genetic variations in the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3 have obtained substantial attention since they affect the milk protein yield, milk composition, cheese processing properties, and digestibility as well as tolerance in human nutrition. Furthermore, milk protein variants are used for breed characterization, biodiversity, and phylogenetic studies. The current study aimed at the identification of casein protein variants in five domestic goat breeds from Sudan (Nubian, Desert, Nilotic, Taggar, and Saanen) and three wild goat species [Capra aegagrus aegagrus (Bezoar ibex), Capra nubiana (Nubian ibex), and Capra ibex (Alpine ibex)]. High-density capture sequencing of 33 goats identified in total 22 non-synonymous and 13 synonymous single nucleotide polymorphisms (SNPs), of which nine non-synonymous and seven synonymous SNPs are new. In the CSN1S1 gene, the new non-synonymous SNP ss7213522403 segregated in Alpine ibex. In the CSN2 gene, the new non-synonymous SNPs ss7213522526, ss7213522558, and ss7213522487 were found exclusively in Nubian and Alpine ibex. In the CSN1S2 gene, the new non-synonymous SNPs ss7213522477, ss7213522549, and ss7213522575 were found in Nubian ibex only. In the CSN3 gene, the non-synonymous SNPs ss7213522604 and ss7213522610 were found in Alpine ibex. The identified DNA sequence variants led to the detection of nine new casein protein variants. New variants were detected for alpha S1 casein in Saanen goats (CSN1S1∗C1), Bezoar ibex (CSN1S1∗J), and Alpine ibex (CSN1S1∗K), for beta and kappa caseins in Alpine ibex (CSN2∗F and CSN3∗X), and for alpha S2 casein in all domesticated and wild goats (CSN1S2∗H), in Nubian and Desert goats (CSN1S2∗I), or in Nubian ibex only (CSN1S2∗J and CSN1S2∗K). The results show that most novel SNPs and protein variants occur in the critically endangered Nubian ibex. This highlights the importance of the preservation of this endangered breed. Furthermore, we suggest validating and further characterizing the new casein protein variants.

Genome-Wide Analysis of Nubian Ibex Reveals Candidate Positively Selected Genes That Contribute to Its Adaptation to the Desert Environment.

Simple SummaryThe Nubian ibex is a wild relative of the domestic goat found in hot deserts of Northern Africa and Arabia. The domestic goat is an important livestock species that is mainly found in arid and semi-arid regions of Africa and Asia. The Nubian ibex is well adapted to challenging environments in hot deserts characterized by high diurnal temperatures, intense solar radiation, and scarce water resources. It is therefore important to understand the genetic basis of its adaptation for scientific and economic importance. To identify genes with adaptive traits, the Nubian ibex genome was sequenced and compared with that of related mammals. We identified twenty-five genes under selection in the Nubian ibex that play diverse biological roles such as immune response, visual development, signal transduction, and reproduction. Three other genes under adaptive evolution involved in protective functions of the skin against damaging solar radiation in the desert were identified in Nubian ibex genome. Our finding provides valuable genomic insights into the adaptation of Nubian ibex to desert environments. The genomic information generated in this study can be used in developing appropriate breeding programs aimed at enhancing adaptation of local goats to less favorable habitats in response to changing climates.The domestic goat (Capra hircus) is an important livestock species with a geographic range spanning all continents, including arid and semi-arid regions of Africa and Asia. The Nubian ibex (Capra nubiana), a wild relative of the domestic goat inhabiting the hot deserts of Northern Africa and the Arabian Peninsula, is well-adapted to challenging environments in hot deserts characterized by intense solar radiation, thermal extremes, and scarce water resources. The economic importance of C. hircus breeds, as well as the current trends of global warming, highlights the need to understand the genetic basis of adaptation of C. nubiana to the desert environments. In this study, the genome of a C. nubiana individual was sequenced at an average of 37x coverage. Positively selected genes were identified by comparing protein-coding DNA sequences of C. nubiana and related species using dN/dS statistics. A total of twenty-two positively selected genes involved in diverse biological functions such as immune response, protein ubiquitination, olfactory transduction, and visual development were identified. In total, three of the twenty-two positively selected genes are involved in skin barrier development and function (ATP binding cassette subfamily A member 12, Achaete-scute family bHLH transcription factor 4, and UV stimulated scaffold protein A), suggesting that C. nubiana has evolved skin protection strategies against the damaging solar radiations that prevail in deserts. The positive selection signatures identified here provide new insights into the potential adaptive mechanisms to hot deserts in C. nubiana.