Modeling Siberian ibex (Capra sibirica) occupancy in Ikh Nart Nature Reserve, Mongolia

As the world becomes increasingly populated, humans continue to modify habitats to suit their needs. Mongolia is one of many Asian countries currently undergoing human-induced landscape change, namely in the form of increased grazing pressure on the land by domesticated animals. There is uncertainty as to how wildlife will be impacted by this change. The Siberian ibex (Capra sibirica) is an ungulate classified as IUCN Near Threatened in Mongolia and an important species for tourism. I developed an occupancy model for the species based on radio- telemetry locations (n = 920) collected in Ikh Nart Nature Reserve, then estimated the effect of habitat reductions as expected under increasing levels of grazing. I developed 13 candidate models that include combinations of habitat and human variables, and used model selection techniques to evaluate the best-supported model in the set. The model with the most support indicated that rocky outcrop, open plain, and their interaction best described ibex occupancy. Average occupancy was 5.7% across the northern Ikh Nart landscape, 7.4% within the borders of the reserve, and 17.4% within the reserve’s core protected area. Simulations showed that in the absence of open plain habitat, average occupancy declined to 1.9%, 2.1%, and 5.0% respectively in these areas. The results provide a description of how landscape factors shape the distribution of the species. Because livestock grazing is concentrated in open plain habitats, these results may be used to inform decision-making about ibex conservation in the region

Genetic analysis of mitochondrial ND5 gene of siberian ibex (Capra Sibirica, Pallas, 1776) population in Mongolia

The Siberian ibex (Capra sibirica) from Central Asia is believed to be the most ancient species of the genus Capra. In Mongolia, it is distributed in the areas of Mongolian Altai, Gobi-Altai, Dzungaria, Altai, Khan Khuhii, Khoridal Saridag and Ulaan Taiga as well as in the desert and semi-desert steppe zones of Dundgobi and Dornogobi aimags (provinces). In the current study, we investigated the mitochondrial ND5 gene fragments of the Siberian ibex population from different parts of Mongolia. Nine haplotypes, including 6 shared and 3 unique haplotypes were identified among these populations. Furthermore, Tajima’s statistics and Fu’s statistics did not reveal significant positive value across the population, indicating population decline and balancing selection.In the phylogenetic tree by 9 haplotypes, no separated clusters were generated. In addition, nucleotide diversity was 0.015, haplotype diversity was 0.86 and the average number of differences in nucleotides was 8.2 in the overall population. These results suggest that genetic diversity across all the populations was low, while haplotype diversity and the average number of differences in nucleotides were high

Using species distribution modelling to guide survey efforts of the Snow Leopard (Panthera uncia) in the Central Kyrgyz Ala-Too region

Listed as Vulnerable (IUCN 2017), the snow leopard is declining across much of its present range. One of the major reasons for the snow leopard population decline in the last two decades is a reduction in large prey species that are the cornerstone of the conservation of the snow leopard; in the Central Kyrgyz Ala-Too region such species is primarily the Siberian ibex (Capra sibirica). Understanding factors affecting basic requirement of ibex and shaping its distribution is essential for protecting the prey species snow leopards rely on the most. Using a niche modelling approach we explored which environmental features are best associated with ibex occurrence, how well do models predict ibex occurrence, and does the potential distribution of highly suitable ibex habitat correlate with records of snow leopard. A PC analysis was used to capture aspects of ibex ecology and niche. Results of such analysis agree with the herbivore character of the species and bioclimatic habitat requirements of the vegetation it feeds upon, richer in flatter areas, and where plants may benefit from more sunlight. The niche model based on maximum entropy (Maxent) had “useful” discrimination abilities (AUC = 0.746), enabling to produce a map, where a contour line is drawn around areas of highly predicted probability (> 0.5) of ibex occurrence. In terms of nature conservation planning and setting snow leopard research priorities these areas represent the most interest. With one outlier, most of snow leopard records made in the study area (n = 15) fell within the 10 percentile presence threshold (0.368). Predicted probability of ibex occurrence in places where records were made of snow leopard presence (pugmarks, scrapes etc.) was 0.559 expectedly suggesting areas of high ibex habitat suitability attract the predator.Сніговий барс є у списку вразливих видів (IUCN 2017) і його чисельність продовжує знижуватися на більшій площі його сучасного ареалу. Однією з основних причин цього за останні два десятиліття є зниження чисельності крупних видів-жертв, присутність яких є умовою збереження барса; в регіоні Центрального Киргизького Ала-Тоо таким видом є сибірський гірський козел (Capra sibirica). Розуміння факторів, що впливають на екологічні вимоги козла та формування його поширення, є важливим для захисту цих тварин, від яких барси є трофічно залежними. Використовуючи підхід, заснований на моделюванні ніш, ми намагалися з’ясувати, які екологічні особливості найкраще асоціюються з оселищами козлів, наскільки добре моделі прогнозують перебування козлів, та чи корелює розподіл територій, сприятливих для козлів, з розподілом реєстрацій барса. Для екологічного аналізу був застосований метод головних компонент. Його результати узгоджуються з травоїдним характером цього виду та біокліматичними вимогами рослинності, якими козли живляться. Ця рослинність є багатшою на плоскогір’ї та там, де рослини можуть отримати вигоду від більшої кількості сонячного світла. Модель ніші, що була побудована на принципах максимальній ентропії (Maxent), мала «корисні» дискримінаційні здібності (AUC = 0,746), що дало змогу створити карту, де контурна лінія окреслює території з високою прогнозованою ймовірністю (> 0,5) перебування козлів. З точки зору планування природоохоронної діяльності та встановлення пріоритетів досліджень барса ці території представляють найбільший інтерес. Майже всі реєстрації барса в досліджуваній зоні (n = 15) потрапили в межі 10 процентильного порогу (0,368). Прогнозована ймовірність перебування козлів в місцях, де були відмічені сліди барса (відбитки лап тощо), в середньому становила 0,559, тобто, як очікувалось, сприятливі для жертв місця є привабливими для хижака

Temporal Dynamics of Group Size and Sexual Segregation in Ibex

Group size is an important variable describing behavioral ecology of animals. A variety of factors such as habitat characteristics, life history, spatio-temporal resource dynamics, population density, predation risk, competition with kin, and social learning often determine group size in large mammals. We studied temporal dynamics of group size in Siberian ibex (Capra sibirica) in a protected area in Mongolia. We measured monthly and yearly variations in typical group size and used the sexual segregation and aggregation statistic to assess sexual segregation. Ibex formed the largest groups in November and smallest groups in July. However, group sizes did not significantly differ between the sexes. There was marked sexual segregation during the summer months and within all years segregation increased with temperature. We show that grouping behavior is a complex phenomenon and is probably determined by a combination of factors, such as species’ life history, habitat and environmental characteristics, and behavioral strategy against predation risk

Carbon and oxygen stable isotopic evidence for diverse sheep and goat husbandry strategies amid a Final Bronze Age farming milieu in the Kyrgyz Tian Shan

Abstract The mountains of Central Asia during the Bronze and Iron Ages are increasingly being reconceived as an important zone for intensive crop cultivation in combination with pastoralist herding. However, very little information is known about how farming practices intersected with livestock husbandry, especially at high-elevation sites. This paper presents the first insights to ancient animal management strategies in the Tian Shan through incremental carbon and oxygen stable isotope analysis of domesticated caprine teeth recovered from the Chap-1 farmstead located at 2000?m.a.s.l. in Kyrgyzstan (1065 to 825?cal?BCE). We implemented a fully reproducible analysis of time-series isotope data in the R programming language. Results show subtle but variable manipulation of domesticated caprine diets at subannual scales, suggesting mixed strategies of providing access to a small amount of C4 plant biomass, in addition to summer movements to high pastures where the overall carbon isotopic composition of graze was depleted in 13C compared with that of the environs of the site or lowland pastures. Nevertheless, caprine dietary intake was overwhelmingly dominated by C3 plants. Analysis of domesticated caprine birth seasonality reveals off-season fall and winter births, which represent a common strategy employed by ancient producers in Central Asia to improve herd security and extend meat and milk availability. This study illustrates a well-integrated system of agro-pastoralist production that can help clarify the social dynamics underlying food systems in the mountain regions of Central and Inner Asia in the Final Bronze Age. It further reveals the capability for more sedentary agro-pastoralist communities to facilitate wider interregional cultural connections, through limited seasonal herding mobility and investment in highland settlement.1 Introduction 2 Archaeology and enviroment of Chap-1 3 Material and methods 3.1 Study design and sample selection 3.2 Isotope mechanics 3.3 Isotopic analysis 3.4 Oxygen isotopic modelling and seasonal inference 4 Results 5 Discussion 5.1 Agricultural and pastoralist integration 5.2 Manipulation of animal births 5.3 Regional perspective 6 Conclusio

Ancient mitochondrial and modern whole genomes unravel massive genetic diversity loss during near extinction of Alpine ibex

Population bottlenecks can have dramatic consequences for the health and long-term survival of a species. Understanding of historic population size and standing genetic variation prior to a contraction allows estimating the impact of a bottleneck on the species' genetic diversity. Although historic population sizes can be modelled based on extant genomics, uncertainty is high for the last 10–20 millenia. Hence, integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern whole genomes. Coalescent demography simulations based on modern whole genomes indicate population fluctuations coinciding with the last major glaciation period. Using our ancient and historic mitogenomes, we investigate the more recent demographic history of the species and show that mitochondrial haplotype diversity was reduced to a fifth of the prebottleneck diversity with several highly differentiated mitochondrial lineages having coexisted historically. The main collapse of mitochondrial diversity coincides with elevated human population growth during the last 1–2 kya. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations from the emergence of a species through its near extinction up to the recent past

High mitochondrial diversity of domesticated goats persisted among Bronze and Iron Age pastoralists in the Inner Asian Mountain Corridor

Goats were initially managed in the Near East approximately 10,000 years ago and spread across Eurasia as economically productive and environmentally resilient herd animals. While the geographic origins of domesticated goats (Capra hircus) in the Near East have been long-established in the zooarchaeological record and, more recently, further revealed in ancient genomes, the precise pathways by which goats spread across Asia during the early Bronze Age (ca. 3000 to 2500 cal BC) and later remain unclear. We analyzed sequences of hypervariable region 1 and cytochrome b gene in the mitochondrial genome (mtDNA) of goats from archaeological sites along two proposed transmission pathways as well as geographically intermediary sites. Unexpectedly high genetic diversity was present in the Inner Asian Mountain Corridor (IAMC), indicated by mtDNA haplotypes representing common A lineages and rarer C and D lineages. High mtDNA diversity was also present in central Kazakhstan, while only mtDNA haplotypes of lineage A were observed from sites in the Northern Eurasian Steppe (NES). These findings suggest that herding communities living in montane ecosystems were drawing from genetically diverse goat populations, likely sourced from communities in the Iranian Plateau, that were sustained by repeated interaction and exchange. Notably, the mitochondrial genetic diversity associated with goats of the IAMC also extended into the semi-arid region of central Kazakhstan, while NES communities had goats reflecting an isolated founder population, possibly sourced via eastern Europe or the Caucasus region

Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae

Prey Preference of Snow Leopard (Panthera uncia) in South Gobi, Mongolia

International audienceAccurate information about the diet of large carnivores that are elusive and inhabit inaccessible terrain, is required to properly design conservation strategies. Predation on livestock and retaliatory killing of predators have become serious issues throughout the range of the snow leopard. Several feeding ecology studies of snow leopards have been conducted using classical approaches. These techniques have inherent limitations in their ability to properly identify both snow leopard feces and prey taxa. To examine the frequency of livestock prey and nearly-threatened argali in the diet of the snow leopard, we employed the recently developed DNA-based diet approach to study a snow leopard population located in the Tost Mountains, South Gobi, Mongolia. After DNA was extracted from the feces, a region of ~100 bp long from mitochondrial 12S rRNA gene was amplified, making use of universal primers for vertebrates and a blocking oligonucleotide specific to snow leopard DNA. The amplicons were then sequenced using a next-generation sequencing platform. We observed a total of five different prey items from 81 fecal samples. Siberian ibex predominated the diet (in 70.4% of the feces), followed by domestic goat (17.3%) and argali sheep (8.6%). The major part of the diet was comprised of large ungulates (in 98.8% of the feces) including wild ungulates (79%) and domestic livestock (19.7%). The findings of the present study will help to understand the feeding ecology of the snow leopard, as well as to address the conservation and management issues pertaining to this wild cat