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Yoshimura H, Hayakawa T, Kikuchi DM, Zhumabai Uulu K, Qi H, Sugimoto T, Sharma K, Kinoshita K. Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240132. [PMID: 39076800 PMCID: PMC11285773 DOI: 10.1098/rsos.240132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 07/31/2024]
Abstract
Species of the family Felidae are thought to be obligate carnivores. However, detection of plants in their faeces raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia). Our study aimed to comprehensively identify the prey and plants consumed by snow leopards. We applied DNA metabarcoding methods on 90 faecal samples of snow leopards collected in Kyrgyzstan, employing one vertebrate and four plant markers. We found that argali (Ovis ammon) was detected only from male snow leopards. Myricaraia sp. was the most consumed among 77 plant operational taxonomic units found in snow leopard samples. It frequently appeared in samples lacking any prey animal DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed differences in the patterns of plant consumption between male and female snow leopards. Our comprehensive overview of prey and plants detected in the faeces of snow leopards and other sympatric mammals will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behaviour in felids. This knowledge supports the enhancement of their captive environments and the conservation planning of their natural habitats.
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Affiliation(s)
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Japan Monkey Center, Inuyama, Aichi, Japan
| | - Dale M. Kikuchi
- Department of Bioresource Development, Tokyo University of Agriculture, Kanagawa, Japan
| | | | - Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Taro Sugimoto
- Institute of Natural and Environmental Sciences, University of Hyogo, Tamba, Hyogo, Japan
| | - Koustubh Sharma
- Snow Leopard Foundation in Kyrgyzstan, Bishkek, Kyrgyzstan
- Snow Leopard Trust, Seattle, WA, USA
| | - Kodzue Kinoshita
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, Japan
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Dong PP, Wang RR, Abduriyim S. Diversity and evolution of the MHC class II DRB gene in the Capra sibirica experienced a demographic fluctuation in China. Sci Rep 2023; 13:19352. [PMID: 37935954 PMCID: PMC10630338 DOI: 10.1038/s41598-023-46717-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
The major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, and their proteins play a critical role in adaptive immunity for defense against a variety of pathogens. MHC diversity was lost in many species after experiencing a decline in size. To understand the variation and evolution of MHC genes in the Siberian ibex, Capra sibirica, which has undergone a population decline, we analyzed the variation of the second exon of MHC class II DRB genes in samples collected from five geographic localities in Xinjiang, China, that belong to three diverged mitochondrial clades. Consequently, we identified a total of 26 putative functional alleles (PFAs) with 260 bp in length from 43 individuals, and found one (for 27 individuals) to three (for 5 individuals) PFAs per individual, indicating the presence of one or two DRB loci per haploid genome. The Casi-DRB1*16 was the most frequently occurring PFA, Casi-DRB1*22 was found in only seven individuals, 14 PFAs occurred once, 7 PFAs twice, implying high frequency of rare PFAs. Interestingly, more than half (15) of the PFAs were specific to clade I, only two and three PFAs were specific to clades II and III, respectively. So, we assume that the polygamy and sexual segregation nature of this species likely contributed to the allelic diversity of DRB genes. Genetic diversity indices showed that PFAs of clade II were lower in nucleotide, amino acid, and supertype diversity compared to those of the other two clades. The pattern of allele sharing and FST values between the three clades was to some extent in agreement with the pattern observed in mitochondrial DNA divergence. In addition, recombination analyses revealed no evidence for significant signatures of recombination events. Alleles shared by clades III and the other two clades diverged 6 million years ago, and systematic neighbor grids showed Trans-species polymorphism. Together with the PAML and MEME analyses, the results indicated that the DRB gene in C. sibirica evolved under balancing and positive selection. However, by comparison, it can be clearly seen that different populations were under different selective pressures. Our results are valuable in understanding the diversity and evolution of the DRB gene in a mountain living C. sibirica and in making decisions on future long-term protection strategies.
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Affiliation(s)
- Pei-Pei Dong
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Rui-Rui Wang
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Shamshidin Abduriyim
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University, Shihezi, 832003, Xinjiang, China.
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Garcia F, Alves da Silva A, Ruckstuhl K, Neuhaus P, Coelho C, Wang M, Sousa JP, Alves J. Differences in the Diets of Female and Male Red Deer: The Meaning for Sexual Segregation. BIOLOGY 2023; 12:biology12040540. [PMID: 37106741 PMCID: PMC10136149 DOI: 10.3390/biology12040540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023]
Abstract
Sexual segregation is a common phenomenon among animals, particularly dimorphic ones. Although widely addressed, the reasons and consequences of sexual segregation are still an important topic in need of better understanding. In this study, we mainly evaluate the diet composition and feeding behaviour of animals, which are related to the use of different habitats by the sexes, a special case of sexual segregation also termed habitat segregation. Sexually size dimorphic males and females often have different energetic and nutritional needs and, thus, different diets. We collected fresh faecal samples from wild Iberian red deer (Cervus elaphus L.) in Portugal. Samples were analysed in terms of diet composition and quality. As expected, both sexes differed in their diet composition, with males eating more arboreous species than females, but this difference was affected by sampling periods. Diet composition of both sexes had the biggest differences (and the lowest overlap) in spring, which corresponds to the end of gestation and beginning of birth. These differences might be a consequence of the sexual body size dimorphism characteristic of this species, as well as of different needs due to different reproductive costs. No differences regarding the quality of the excreted diet were observed. Our results may help to understand some patterns of sexual segregation observed in this red deer population. However, besides foraging ecology, other factors may also be contributing to sexual segregation in this Mediterranean population of red deer, and further studies focusing on sexual differences regarding feeding behaviour and digestibility are needed.
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Affiliation(s)
- Fernanda Garcia
- Centre for Functional Ecology (CFE), TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - António Alves da Silva
- Centre for Functional Ecology (CFE), TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Kathreen Ruckstuhl
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Peter Neuhaus
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Catarina Coelho
- Centre for Functional Ecology (CFE), TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Muyang Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Sino-Tajikistan Joint Laboratory for Conservation and Utilization of Biological Resources, Urumqi 830011, China
| | - José Paulo Sousa
- Centre for Functional Ecology (CFE), TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Joana Alves
- Centre for Functional Ecology (CFE), TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
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Jabin G, Dolker S, Joshi BD, Singh SK, Chandra K, Sharma LK, Thakur M. Lahaul–Zanskar–Sham Valley Corridor in Indian Trans Himalayan Region Facilitates Dispersal and Gene Flow in Himalayan Ibex. BIOLOGY 2023; 12:biology12030382. [PMID: 36979074 PMCID: PMC10045165 DOI: 10.3390/biology12030382] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
Wildlife corridors that connect mosaic habitats in heterogeneous mountainous landscapes can be of high significance as they facilitate the genetic and demographic stability of free-ranging populations. Peripheral populations of widespread species are usually ignored in conservation planning. However, these populations retain locally common alleles and are genetic reservoir under the changing climatic conditions. Capra sibirica has widespread distribution, and its southern peripheral population is distributed in the Indian trans-Himalayan region (ITR). In the present study, we studied the spatial distribution and genetic make-up of Himalayan ibex from the ITR following the landscape genetics approach. We obtained 16 haplotypes at the mitochondrial d-loop region and found a stable demography in the past with a recent decline. With 10 nuclear microsatellites, we ascertained 111 unique individuals assigned into two clusters following Bayesian and non-Bayesian clustering analysis with several admixed individuals. We also recorded 25 first-generation migrants that reflected relatively high dispersal and gene-flow across the range. We identified a 19,835 sq.km suitable area with 13,311 sq.km in Ladakh and 6524 sq.km in Lahaul-Spiti. We identified a novel movement corridor for Himalayan ibex across the Lahaul–Zanskar–Sham valley (L–Z–SV) that displayed a fairly good conductance with low genetic divergence among the samples collected on the L–Z–SV corridor. We propose declaring a protected area in the Lahaul and Kargil districts to prioritize dedicated conservation efforts for the Himalayan ibex and other sympatric ungulates that impart a major role in the diet of large carnivore and balancing ecosystem services in the trans-Himalayan region.
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Affiliation(s)
- Gul Jabin
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata 700019, West Bengal, India
| | - Stanzin Dolker
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata 700019, West Bengal, India
| | - Bheem Dutt Joshi
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Sujeet Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Kailash Chandra
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Lalit Kumar Sharma
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
- Correspondence:
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Ahmad S, Strelnikov II, Ahmad A, Rajpar MN, Khan MZ, Wanghe K, Ahmad IM, Nabi G, Li D. Recent advances in ecological research on Asiatic ibex (Capra sibirica): A critical ungulate species of highland landscapes. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Han L, Wang Z, Blank D, Wang M, Yang W. Different environmental requirements of female and male Siberian ibex, Capra sibirica. Sci Rep 2021; 11:6064. [PMID: 33727618 PMCID: PMC7966747 DOI: 10.1038/s41598-021-85550-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 03/03/2021] [Indexed: 11/16/2022] Open
Abstract
In sexually dimorphic species, males and females may select different habitat for greater fitness. However, the key factors that play a leading role between sexes in habitat selection are still poorly understood. In this paper, we investigated the possible causes of the differences in habitat preference between male and female Siberian ibex (Capra sibirica) living in the Tianshan Mountains (China). Using the Maximum entropy model, we found that the ruggedness and elevation of the terrain were the most important factors affecting habitat selection in Siberian ibex. Females preferred the most rugged terrain to increase the security of their young and themselves, while males favored moderately rugged terrain to provide sufficient safety from predators, and availability of suitable forage simultaneously. Females used a wider variety of elevations to search for newly emerged vegetation for its higher nutritional value, while males preferred more elevated slopes to avoid the higher temperatures and greater presence of biting insects found at the lower elevations. In addition, females were associated more with rivers due to their higher water demands. The differences in habitat selection between Siberian ibex males and females depend on multiple considerations, but only a limited number of key factors determine their actual distribution.
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Affiliation(s)
- Lei Han
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.,Mori Wildlife Monitoring and Experimentation Station, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Mori, 831900, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - David Blank
- Research Center for Ecology and Environment of Central Asia, Bishkek, 720001, Kyrgyzstan
| | - Muyang Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. .,Mori Wildlife Monitoring and Experimentation Station, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Mori, 831900, China.
| | - Weikang Yang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. .,Mori Wildlife Monitoring and Experimentation Station, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Mori, 831900, China.
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