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Cox DTC, Gaston KJ. Cathemerality: a key temporal niche. Biol Rev Camb Philos Soc 2024; 99:329-347. [PMID: 37839797 DOI: 10.1111/brv.13024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/01/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023]
Abstract
Given the marked variation in abiotic and biotic conditions between day and night, many species specialise their physical activity to being diurnal or nocturnal, and it was long thought that these strategies were commonly fairly fixed and invariant. The term 'cathemeral', was coined in 1987, when Tattersall noted activity in a Madagascan primate during the hours of both daylight and darkness. Initially thought to be rare, cathemerality is now known to be a quite widespread form of time partitioning amongst arthropods, fish, birds, and mammals. Herein we provide a synthesis of present understanding of cathemeral behaviour, arguing that it should routinely be included alongside diurnal and nocturnal strategies in schemes that distinguish and categorise species across taxa according to temporal niche. This synthesis is particularly timely because (i) the study of animal activity patterns is being revolutionised by new and improved technologies; (ii) it is becoming apparent that cathemerality covers a diverse range of obligate to facultative forms, each with their own common sets of functional traits, geographic ranges and evolutionary history; (iii) daytime and nighttime activity likely plays an important but currently neglected role in temporal niche partitioning and ecosystem functioning; and (iv) cathemerality may have an important role in the ability of species to adapt to human-mediated pressures.
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Affiliation(s)
- Daniel T C Cox
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Kevin J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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2
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Dorji J, Reverter A, Alexandre PA, Chamberlain AJ, Vander-Jagt CJ, Kijas J, Porto-Neto LR. Ancestral alleles defined for 70 million cattle variants using a population-based likelihood ratio test. Genet Sel Evol 2024; 56:11. [PMID: 38321371 PMCID: PMC10848479 DOI: 10.1186/s12711-024-00879-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/30/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND The study of ancestral alleles provides insights into the evolutionary history, selection, and genetic structures of a population. In cattle, ancestral alleles are widely used in genetic analyses, including the detection of signatures of selection, determination of breed ancestry, and identification of admixture. Having a comprehensive list of ancestral alleles is expected to improve the accuracy of these genetic analyses. However, the list of ancestral alleles in cattle, especially at the whole genome sequence level, is far from complete. In fact, the current largest list of ancestral alleles (~ 42 million) represents less than 28% of the total number of detected variants in cattle. To address this issue and develop a genomic resource for evolutionary studies, we determined ancestral alleles in cattle by comparing prior derived whole-genome sequence variants to an out-species group using a population-based likelihood ratio test. RESULTS Our study determined and makes available the largest list of ancestral alleles in cattle to date (70.1 million) and includes 2.3 million on the X chromosome. There was high concordance (97.6%) of the determined ancestral alleles with those from previous studies when only high-probability ancestral alleles were considered (29.8 million positions) and another 23.5 million high-confidence ancestral alleles were novel, expanding the available reference list to improve the accuracies of genetic analyses involving ancestral alleles. The high concordance of the results with previous studies implies that our approach using genomic sequence variants and a likelihood ratio test to determine ancestral alleles is appropriate. CONCLUSIONS Considering the high concordance of ancestral alleles across studies, the ancestral alleles determined in this study including those not previously listed, particularly those with high-probability estimates, may be used for further genetic analyses with reasonable accuracy. Our approach that used predetermined variants in species and the likelihood ratio test to determine ancestral alleles is applicable to other species for which sequence level genotypes are available.
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Affiliation(s)
- Jigme Dorji
- CSIRO, Agriculture & Food, St. Lucia, QLD, 4067, Australia.
| | | | | | - Amanda J Chamberlain
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| | - Christy J Vander-Jagt
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| | - James Kijas
- CSIRO, Agriculture & Food, St. Lucia, QLD, 4067, Australia
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3
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Lauer DA, Lawing AM, Short RA, Manthi FK, Müller J, Head JJ, McGuire JL. Disruption of trait-environment relationships in African megafauna occurred in the middle Pleistocene. Nat Commun 2023; 14:4016. [PMID: 37463920 DOI: 10.1038/s41467-023-39480-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/15/2023] [Indexed: 07/20/2023] Open
Abstract
Mammalian megafauna have been critical to the functioning of Earth's biosphere for millions of years. However, since the Plio-Pleistocene, their biodiversity has declined concurrently with dramatic environmental change and hominin evolution. While these biodiversity declines are well-documented, their implications for the ecological function of megafaunal communities remain uncertain. Here, we adapt ecometric methods to evaluate whether the functional link between communities of herbivorous, eastern African megafauna and their environments (i.e., functional trait-environment relationships) was disrupted as biodiversity losses occurred over the past 7.4 Ma. Herbivore taxonomic and functional diversity began to decline during the Pliocene as open grassland habitats emerged, persisted, and expanded. In the mid-Pleistocene, grassland expansion intensified, and climates became more variable and arid. It was then that phylogenetic diversity declined, and the trait-environment relationships of herbivore communities shifted significantly. Our results divulge the varying implications of different losses in megafaunal biodiversity. Only the losses that occurred since the mid-Pleistocene were coincident with a disturbance to community ecological function. Prior diversity losses, conversely, occurred as the megafaunal species and trait pool narrowed towards those adapted to grassland environments.
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Affiliation(s)
- Daniel A Lauer
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - A Michelle Lawing
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Rachel A Short
- Department of Natural Resource Management, South Dakota State University, Rapid City, SD, 57703, USA
| | - Fredrick K Manthi
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Johannes Müller
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde Berlin, 10115, Berlin, Germany
| | - Jason J Head
- Department of Zoology and University Museum of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Jenny L McGuire
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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4
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König MT, Frölich K, Jandowsky A, Knauf-Witzens T, Langner C, Dietrich R, Märtlbauer E, Didier A. First Insights into the Occurrence of Circular Single-Stranded DNA Genomes in Asian and African Cattle. Animals (Basel) 2023; 13:ani13091492. [PMID: 37174530 PMCID: PMC10177065 DOI: 10.3390/ani13091492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Circular replicase-encoding single-stranded (CRESS) DNA viruses and other circular DNA agents are increasingly found in various samples and animals. A specific class of these agents-termed bovine meat and milk factors (BMMF)-has been supposed to act as a factor in indirect carcinogenesis in humans. Initial observations attributed the BMMF to European cattle breeds and foodstuffs produced thereof. In the present study, blood and fecal samples from African and Asian cattle were examined. BMMF molecules and genomoviruses were detected in all bovids under study. The majority (79%) of the 29 circular elements could be assigned to BMMF groups 1 and 2, whereas CRESS viruses of the family Genomoviridae accounted for the smaller part (21%). Two genomoviruses belong to the genus Gemykibivirus and one to the genus Gemykrogvirus. The remaining three might be considered as novel species within the genus Gemycircularvirus. The majority of all isolated molecules originated from fecal samples, whereas only three derived from blood. The results from this study expand our knowledge on the diversity and presence of circular DNA in different ruminants that serve for food production in many countries over the world.
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Affiliation(s)
- Marie-Thérèse König
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
| | - Kai Frölich
- Tierpark Arche Warder, Zentrum für Seltene Nutztierrassen e. V., Langwedeler Weg 11, 24646 Warder, Germany
| | - Anabell Jandowsky
- Tierpark Arche Warder, Zentrum für Seltene Nutztierrassen e. V., Langwedeler Weg 11, 24646 Warder, Germany
| | - Tobias Knauf-Witzens
- Wilhelma Zoological-Botanical Gardens Stuttgart, Wilhelma 13, 70376 Stuttgart, Germany
| | - Christoph Langner
- Stralsund Zoological Garden, Grünhufer Bogen 2, 18437 Stralsund, Germany
| | - Richard Dietrich
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
| | - Andrea Didier
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
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Roy S, Naidu DGT, Bagchi S. Functional substitutability of native herbivores by livestock for soil carbon stock is mediated by microbial decomposers. GLOBAL CHANGE BIOLOGY 2023; 29:2141-2155. [PMID: 36732877 DOI: 10.1111/gcb.16600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 05/28/2023]
Abstract
Grazing by large mammalian herbivores impacts climate as it can favor the size and stability of a large carbon (C) pool in the soils of grazing ecosystems. As native herbivores in the world's grasslands, steppes, and savannas are progressively being displaced by livestock, it is important to ask whether livestock can emulate the functional roles of their native counterparts. While livestock and native herbivores can have remarkable similarity in their traits, they can differ greatly in their impacts on vegetation composition which can affect soil-C. It is uncertain how these similarities and differences impact soil-C via their influence on microbial decomposers. We test competing alternative hypotheses with a replicated, long-term, landscape-level, grazing-exclusion experiment to ask whether livestock in the Trans-Himalayan ecosystem of northern India can match decadal-scale (2005-2016) soil-C stocks under native herbivores. We evaluate multiple lines of evidence from 17 variables that influence soil-C (quantity and quality of C-input from plants, microbial biomass and metabolism, microbial community composition, eDNA, veterinary antibiotics in soil), and assess their inter-relationships. Livestock and native herbivores differed in their effects on several soil microbial processes. Microbial carbon use efficiency (CUE) was 19% lower in soils under livestock. Compared to native herbivores, areas used by livestock contained 1.5 kg C m-2 less soil-C. Structural equation models showed that alongside the effects arising from plants, livestock alter soil microbial communities which is detrimental for CUE, and ultimately also for soil-C. Supporting evidence pointed toward a link between veterinary antibiotics used on livestock, microbial communities, and soil-C. Overcoming the challenges of sequestering antibiotics to minimize their potential impacts on climate, alongside microbial rewilding under livestock, may reconcile the conflicting demands from food-security and ecosystem services. Conservation of native herbivores and alternative management of livestock is crucial for soil-C stewardship to envision and achieve natural climate solutions.
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Affiliation(s)
- Shamik Roy
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Dilip G T Naidu
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
- Divecha Centre for Climate Change, Indian Institute of Science, Bangalore, India
| | - Sumanta Bagchi
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
- Divecha Centre for Climate Change, Indian Institute of Science, Bangalore, India
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Zhou C, Liu Y, Zheng X, Shang K, Cheng M, Wang L, Yang N, Yue B. Characterization of olfactory receptor repertoires provides insights into the high-altitude adaptation of the yak based on the chromosome-level genome. Int J Biol Macromol 2022; 209:220-230. [PMID: 35378160 DOI: 10.1016/j.ijbiomac.2022.03.194] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/15/2022]
Abstract
Olfaction in vertebrates plays pivotal parts in many aspects, such as localizing prey or food, mating behavior, avoiding predators, and social communication. Yak (Bos grunniens) is the only Bos species that can thrive in high-altitude areas. In view of the critical role of olfactory receptors (ORs) in the specific recognition of diverse stimuli, investigating the evolutionary dynamics of ORs in the yak means a lot. In this study, we used the chromosome-level genome of the yak to identify the ORs genes and discussed the effects of high altitude on the yak's olfaction by comparing the yak with other low-altitude living Bos species (Bos frontalis (gayal), Bos gaurus (gaur), Bos indicus (zebu) and Bos taurus (cattle)). The yak had 400 OR genes, including 264 functional genes, 16 partial genes and 120 OR pseudo genes. There were 387 OR genes mapped to yak 31 chromosomes, and chromosomes 13 and 8 had the most OR genes and functional OR genes. Among these five Bos species, yak had the least number of OR gene subfamilies, OR genes and functional OR genes, while the total number of OR genes in gayal (n = 784) was almost twice as many as that of yak, indicating that the olfaction of yak may be less developed. In addition, the phylogenetic relationships of the functional Bos OR genes were illustrated, which comprised 79 families and 466 subfamilies distributed in two classes (Class I and Class II). There were 76 OR gene subfamilies shared by these five Bos species and 17 OR gene subfamilies were unique to the yak. The potential odor specificity of 44 yak OR genes was identified through the similarity to human OR protein sequences. Remarkably, yak lacks β-ionone and Isovaleric acid(IVA)-related ORs, which may be related to the decline of high-altitude herbaceous plant diversity and underdeveloped yak sweat glands. The conserved motifs of OR genes were highly conserved in Bos species. These results provided a solid foundation for further studies on the molecular mechanisms of the yak's adaptation to the high-altitude environment in olfaction.
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Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Yi Liu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Xiaofeng Zheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Ke Shang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Meiling Cheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Lei Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610064, PR China; Collaborative Innovation Center for Ecological Animal Husbandry of Qinghai- Tibetan plateau, Southwest Minzu University.
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China.
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Wan R, Zhao Z, Zhao M, Hu K, Zhai J, Yu H, Wei Q. Characteristics of pulmonary microvascular structure in postnatal yaks. Sci Rep 2021; 11:18265. [PMID: 34521949 PMCID: PMC8440534 DOI: 10.1038/s41598-021-97760-z] [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: 12/04/2020] [Accepted: 08/30/2021] [Indexed: 11/09/2022] Open
Abstract
Yaks are typical plateau-adapted animals, however the microvascular changes and characteristics in their lungs after birth are still unclear. Pulmonary microvasculature characteristics and changes across age groups were analysed using morphological observation and molecular biology detection in yaks aged 1, 30 and 180 days old in addition to adults. Results: Our experiments demonstrated that yaks have fully developed pulmonary alveolar at birth but that interalveolar thickness increased with age. Immunofluorescence observations showed that microvessel density within the interalveolar septum in the yak gradually increased with age. In addition, transmission electron microscopy (TEM) results showed that the blood–air barrier of 1-day old and 30-days old yaks was significantly thicker than that observed at 180-days old and in adults (P < 0.05), which was caused by the thinning of the membrane of alveolar epithelial cells. Furthermore, Vegfa and Epas1 expression levels in 30-day old yaks were the highest in comparison to the other age groups (P < 0.05), whilst levels in adult yaks were the lowest (P < 0.05). The gradual increase in lung microvessel density can effectively satisfy the oxygen requirements of ageing yaks. In addition, these results suggest that the key period of yak lung development is from 30 to 180 days.
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Affiliation(s)
- Ruidong Wan
- Department of Veterinary Medicine, College of Agriculture and Animal Husbandry, Qinghai University, 251 Ningda Road, Xining, 810016, Qinghai, China
| | - Ziqi Zhao
- College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, Qinghai, China
| | - Min Zhao
- College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, Qinghai, China
| | - Ke Hu
- College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, Qinghai, China
| | - Jiaxin Zhai
- College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, Qinghai, China
| | - Hongxian Yu
- Department of Veterinary Medicine, College of Agriculture and Animal Husbandry, Qinghai University, 251 Ningda Road, Xining, 810016, Qinghai, China. .,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251 Ningda Road, Xining, 810016, Qinghai, China.
| | - Qing Wei
- College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, Qinghai, China. .,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251 Ningda Road, Xining, 810016, Qinghai, China.
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8
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Xiong L, Pei J, Chu M, Wu X, Kalwar Q, Yan P, Guo X. Fat Deposition in the Muscle of Female and Male Yak and the Correlation of Yak Meat Quality with Fat. Animals (Basel) 2021; 11:ani11072142. [PMID: 34359275 PMCID: PMC8300776 DOI: 10.3390/ani11072142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 02/06/2023] Open
Abstract
This study aimed to explore the differences in fat deposition between female (FYs) and male yaks (MYs). Compared with MYs, the tenderness, L*, marbling, absolute content of fat, and most fatty acids (FAs) of longissimus dorsi (LD) in FYs were higher or better (p < 0.05), whereas the relative content of polyunsaturated fatty acids (PUFAs) and n-3 PUFAs were lower (p < 0.01). The absolute content of fat, C18:0, cis-C18:2, cis-C18:1, and C24:0 were positively correlated with L*45 min, b*24 h, tenderness, and marbling score of LD in FYs and MYs (p < 0.05), respectively. LPL, FATP2, ELOVL6, HADH, HACD, and PLINS genes play a crucial role in improving the marbling score and tenderness of yak meat. The results of gene expression and protein synthesis showed the effect of gender to FA biosynthesis, FA transport, lipolysis, and FA oxidation in the adipose tissue of yak was realized by the expressions of ME1, SCD, ACSL5, LPL, FABP1, PLIN4, and PLIN2 in peroxisome proliferators-activated receptor (PPAR) signaling. This study established a theoretical basis for the improvement of the meat quality of yak and molecular breeding.
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Affiliation(s)
- Lin Xiong
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (L.X.); (J.P.); (M.C.); (X.W.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China
| | - Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (L.X.); (J.P.); (M.C.); (X.W.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (L.X.); (J.P.); (M.C.); (X.W.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (L.X.); (J.P.); (M.C.); (X.W.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China
| | - Qudratullah Kalwar
- Department of Animal Reproduction, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand 67210, Pakistan;
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (L.X.); (J.P.); (M.C.); (X.W.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China
- Correspondence: (P.Y.); (X.G.); Tel.: +86-0931-2115288 (P.Y.); +86-0931-2115271 (X.G.)
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (L.X.); (J.P.); (M.C.); (X.W.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China
- Correspondence: (P.Y.); (X.G.); Tel.: +86-0931-2115288 (P.Y.); +86-0931-2115271 (X.G.)
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Guo S, Wu X, Song R, Za X, Zhao Q, Li J, Ma H, Wu F, Liang C, Pei J, Guo X. The complete mitochondrial genome and phylogenetic analysis of Yanglong yak ( Bos grunniens). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1392-1394. [PMID: 33948491 PMCID: PMC8057086 DOI: 10.1080/23802359.2021.1910086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this study, we assembled the complete mitochondrial genome of Yanglong yak (Bos grunniens) from Illumina sequencing reads. The mitochondrial genome is 16,323 bp long with an A + T-biased nucleotide composition, and encodes 13 protein-coding, 22 tRNA, and two rRNA genes along with a noncoding control region. In addition, its gene order is identical to those of the previously published mitochondrial genomes of its congeners. Phylogenetic analysis indicates that this breed is closely related to Datong yak, Pamir yak, Tianjun yak, polled yak, Seron yak, Sunnan yak, a series of Domestic Yak and wild yak, followed by Jinchuan yak and Gannan yak, and slightly far away from Bison and Bos taurus.
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Affiliation(s)
- Shaoke Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Rende Song
- Animal Disease Prevention and Control, Center of Yushu Tibetan Autonomous Prefecture in Qinghai Province, Yushu, People's Republic of China
| | - Xita Za
- Animal Husbandry and Veterinary Station of Qilian County in Qinghai Province, Qilian, People's Republic of China
| | - Qingzhang Zhao
- Animal Husbandry and Veterinary Station of Xitan Township in Menyuan County in Qinghai Province, Menyuan, People's Republic of China
| | - Jiye Li
- Datong Cattle Farm in Qinghai Province, Xining, People's Republic of China
| | - Haiqing Ma
- Animal Husbandry and Veterinary Station of Qilian County in Qinghai Province, Qilian, People's Republic of China
| | - Fude Wu
- Datong Cattle Farm in Qinghai Province, Xining, People's Republic of China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
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10
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Buttar I, Solounias N. Specialized Position of the Horns, and Frontal and Parietal Bones in Bos taurus (Bovini, Artiodactyla), and Notes on the Evolution of Bos. ANN ZOOL FENN 2021. [DOI: 10.5735/086.058.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Irvind Buttar
- Department of Anatomy, New York Institute of Technology, College of Osteopathic Medicine, Old Westbury, NY 11568, USA
| | - Nikos Solounias
- Department of Anatomy, New York Institute of Technology, College of Osteopathic Medicine, Old Westbury, NY 11568, USA
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11
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Lundgren EJ, Schowanek SD, Rowan J, Middleton O, Pedersen RØ, Wallach AD, Ramp D, Davis M, Sandom CJ, Svenning JC. Functional traits of the world's late Quaternary large-bodied avian and mammalian herbivores. Sci Data 2021; 8:17. [PMID: 33473149 PMCID: PMC7817692 DOI: 10.1038/s41597-020-00788-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023] Open
Abstract
Prehistoric and recent extinctions of large-bodied terrestrial herbivores had significant and lasting impacts on Earth's ecosystems due to the loss of their distinct trait combinations. The world's surviving large-bodied avian and mammalian herbivores remain among the most threatened taxa. As such, a greater understanding of the ecological impacts of large herbivore losses is increasingly important. However, comprehensive and ecologically-relevant trait datasets for extinct and extant herbivores are lacking. Here, we present HerbiTraits, a comprehensive functional trait dataset for all late Quaternary terrestrial avian and mammalian herbivores ≥10 kg (545 species). HerbiTraits includes key traits that influence how herbivores interact with ecosystems, namely body mass, diet, fermentation type, habitat use, and limb morphology. Trait data were compiled from 557 sources and comprise the best available knowledge on late Quaternary large-bodied herbivores. HerbiTraits provides a tool for the analysis of herbivore functional diversity both past and present and its effects on Earth's ecosystems.
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Affiliation(s)
- Erick J Lundgren
- Centre for Compassionate Conservation, School of Life Sciences, University of Technology Sydney, Ultimo, Australia.
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, Denmark.
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark.
| | - Simon D Schowanek
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, Denmark.
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark.
| | - John Rowan
- Department of Anthropology, University at Albany, Albany, NY, 12222, USA
| | - Owen Middleton
- School of Life Sciences, University of Sussex, Sussex, UK
| | - Rasmus Ø Pedersen
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Arian D Wallach
- Centre for Compassionate Conservation, School of Life Sciences, University of Technology Sydney, Ultimo, Australia
| | - Daniel Ramp
- Centre for Compassionate Conservation, School of Life Sciences, University of Technology Sydney, Ultimo, Australia
| | - Matt Davis
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
- Natural History Museum of Los Angeles County, Los Angeles, CA, 90007, USA
| | | | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
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12
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Iqbal Yatoo M, Shabir M, Kubrevi SS, Dar RA, Angmo K, Kanwar MS, Bhat RA, Muheet, Parray OR. A study on biological rhythms of Himalayan yaks. BIOL RHYTHM RES 2020. [DOI: 10.1080/09291016.2019.1579883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Mohd Iqbal Yatoo
- Faculty of Veterinary Sciences and Animal Husbandary, Division of Veterinary Clinical Complex, Srinagar, India
| | - Mir Shabir
- Farm Science Centre, Krishi Vigyan Kendra, Ladakh, India
| | | | | | - Kunzes Angmo
- Farm Science Centre, Krishi Vigyan Kendra, Ladakh, India
| | | | - Riyaz Ahmad Bhat
- Faculty of Veterinary Sciences and Animal Husbandary, Division of Veterinary Clinical Complex, Srinagar, India
| | - Muheet
- Faculty of Veterinary Sciences and Animal Husbandary, Division of Veterinary Clinical Complex, Srinagar, India
| | - Oveas Raffiq Parray
- Faculty of Veterinary Sciences and Animal Husbandary, Division of Veterinary Clinical Complex, Srinagar, India
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13
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Reproduction in female wild cattle: Influence of seasonality on ARTs. Theriogenology 2020; 150:396-404. [PMID: 32081408 DOI: 10.1016/j.theriogenology.2020.02.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/08/2020] [Indexed: 12/31/2022]
Abstract
Wild cattle species, often considered less alluring than certain conservation-dependent species, have not attracted the same level of interest as the charismatic megafauna from the general public, private or corporate donors, and other funding agencies. Currently, most wild cattle populations are vulnerable or threatened with extinction. The implementation of reproductive technologies to maintain genetically healthy cattle populations in situ and ex situ has been considered for more than 30 years. Protocols developed for domestic cattle breeds have been used with some success in various wild cattle species. However, inherent differences in the natural life history of these species makes extrapolation of domestic cattle protocols difficult, and in some cases, minimally effective. Reproductive seasonality, driven by either photoperiod or nutritional resource availability, has significant influence on the success of assisted reproductive technologies (ARTs). This review focuses on the physiological processes that differ in breeding (ovulatory) and non-breeding (anovulatory) seasons in female cattle, and the potential methods used to overcome these challenges. Techniques to be discussed within the context of seasonality include: estrus synchronization and ovulation induction, ovarian superstimulation, artificial insemination (AI), multiple ovulation embryo transfer (MOET), and ovum pick-up (OPU) with in vitro fertilization (IVF) and embryo transfer (ET).
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14
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Sánchez-Hernández C, Gourichon L, Pubert E, Rendu W, Montes R, Rivals F. Combined dental wear and cementum analyses in ungulates reveal the seasonality of Neanderthal occupations in Covalejos Cave (Northern Iberia). Sci Rep 2019; 9:14335. [PMID: 31586143 PMCID: PMC6778078 DOI: 10.1038/s41598-019-50719-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 09/17/2019] [Indexed: 11/09/2022] Open
Abstract
We propose for the first time the use of the combination of two high-resolution techniques, dental wear (meso- and microwear) and dental cementum analyses, to gain a better understanding of Neanderthal subsistence strategies and occupational patterns. Dental wear analysis provides information not only on ungulate palaeodiet and palaeoenvironments but also on hunting time and seasons. Dental cementum analysis allows the accurate determination of the age and season at death of a prey. Our study has focused on the Cantabrian region and has applied both methods to investigate the Mousterian faunal assemblages in Covalejos Cave. Identification of the ungulate palaeodiet reveals information on the environmental conditions of the studied region. Moreover, it may facilitate observation on the evolution of both palaeodiet and palaeoenvironment throughout the site sequence. Results show a general stability in the palaeoenvironmental conditions and in the ungulate palaeodiet throughout the Mousterian sequence; this finding may be attributed to the role of the area as a climate refuge, and slight differences in levels 8, 7 and 4 suggest long- or short-term but repeated Neanderthal occupations at different seasons in the annual cycle.
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Affiliation(s)
- Carlos Sánchez-Hernández
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Zona Educacional 4, Campus Sescelades URV (Edifici W3), 43007, Tarragona, Spain. .,Universitat Rovira i Virgili (URV), Àrea de Prehistòria, Avinguda de Catalunya 35, 43002, Tarragona, Spain. .,Université Côte d'Azur, CNRS, CEPAM, Nice, France.
| | | | - Eric Pubert
- PACEA (CNRS-UMR 5199), Université de Bordeaux, Bâtiment B2, Allée Geoffroy Saint Hilaire, Pessac, France
| | - William Rendu
- PACEA (CNRS-UMR 5199), Université de Bordeaux, Bâtiment B2, Allée Geoffroy Saint Hilaire, Pessac, France
| | - Ramón Montes
- Itinerario Cultural del Consejo de Europa Prehistoric Rock Art, Madrid, Spain
| | - Florent Rivals
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Zona Educacional 4, Campus Sescelades URV (Edifici W3), 43007, Tarragona, Spain.,Universitat Rovira i Virgili (URV), Àrea de Prehistòria, Avinguda de Catalunya 35, 43002, Tarragona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
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15
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Guo X, Wu X, Bao P, Zhao S, Za X, Liang C, Chu M, Pei J, Yan P. Characterization of the mitochondrial genome of the Qilian yak ( Bos grunniens) with a phylogenetic analysis of the family Bovidae (Artiodactyla). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2687-2689. [PMID: 33365684 PMCID: PMC7706800 DOI: 10.1080/23802359.2019.1644553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/29/2022]
Abstract
Qilian yak (Bos grunniens) is a local breed of yak with high adaptation to the high-elevation, cold, and anoxic environments. In this study, its complete mitochondrial genome was assembled from high-throughput sequencing reads. The mitogenome is 16,324 bp long with an A + T-biased nucleotide composition and has the typical set of 37 animal mitochondrial genes and the noncoding control region. Phylogenetic analysis supported the monophyly of the subfamilies Aepycerotinae, Alcelaphinae, Bovinae, Caprinae, and Cephalophinae, confirmed the polyphyly of the family Antilopinae within the family Bovidae, and indicated the close relatedness between domestic yaks (Bos grunniens) and wild yaks (Bos mutus).
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Affiliation(s)
- Xian Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Suonan Zhao
- Institute of Animal Husbandry and Veterinary Medicine, Haibei Tibetan Autonomous Prefecture, Xihai, People's Republic of China
| | - Xita Za
- Animal Husbandry and Veterinary Station of Qilian County, Qilian, People's Republic of China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
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16
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Wu X, Zhou X, Ding X, Liang C, Guo X, Chu M, Wang H, Pei J, Bao P, Yan P. Characterization of the complete mitochondrial genome of the hybrid of wild yak (♂) × domestic yak (♀). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1574659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuelan Zhou
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuezhi Ding
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hongbo Wang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
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17
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Oyun NY, Konorov EA, Urum AV, Artyushin IV, Svishcheva GR, Cendsuren C, Stolpovsky YA. Study of Genetic Diversity and Population Structure of the Yak (Bos grunniens) in the Sayan-Altai Region. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418100125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Affiliation(s)
- Farshid S Ahrestani
- Foundation for Ecological Research, Advocacy and Learning, Auroville Post, Tamil Nadu, India
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19
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Characterization of the complete mitochondrial genome of Kunlun Mountain type wild yak (Bos mutus). CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0776-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Leslie DM. Bovids of the World: Antelopes, Gazelles, Cattle, Goats, Sheep, and Relatives. José R.Castelló.
2016.
Princeton University Press,
Princeton, New Jersey, USA. 664 pp. $35.00 paperback. ISBN 978-0-691-16717-6. J Wildl Manage 2017. [DOI: 10.1002/jwmg.21197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- David M. Leslie
- U.S. Geological Survey, Oklahoma Cooperative Fish and Wildlife Research Unit, Department of Natural Resource Ecology and Management, 007 Ag Hall; Oklahoma State University; Stillwater OK USA
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21
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Wang X, Liu X, Groenewald JZ. Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China. Antonie van Leeuwenhoek 2016; 110:87-103. [PMID: 27734254 PMCID: PMC5222902 DOI: 10.1007/s10482-016-0779-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/30/2016] [Indexed: 11/30/2022]
Abstract
The phylum Neocallimastigomycota contains eight genera (about 20 species) of strictly anaerobic fungi. The evolutionary relationships of these genera are uncertain due to insufficient sequence data to infer their phylogenies. Based on morphology and molecular phylogeny, thirteen isolates obtained from yak faeces and rumen digesta in China were assigned to Neocallimastix frontalis (nine isolates), Orpinomyces joyonii (two isolates) and Caecomyces sp. (two isolates), respectively. The phylogenetic relationships of the eight genera were evaluated using complete ITS and partial LSU sequences, compared to the ITS1 region which has been widely used in this phylum in the past. Five monophyletic lineages corresponding to six of the eight genera were statistically supported. Isolates of Caecomyces and Cyllamyces were present in a single lineage and could not be separated properly. Members of Neocallimastigomycota with uniflagellate zoospores represented by Piromyces were polyphyletic. The Piromyces-like genus Oontomyces was consistently closely related to the traditional Anaeromyces, and separated the latter genus into two clades. The phylogenetic position of the Piromyces-like genus Buwchfawromyces remained unresolved. Orpinomyces and Neocallimastix, sharing polyflagellate zoospores, were supported as sister genera in the LSU phylogeny. Apparently ITS, specifically ITS1 alone, is not a good marker to resolve the generic affinities of the studied fungi. The LSU sequences are easier to align and appear to work well to resolve generic relationships. This study provides a comparative phylogenetic revision of Neocallimastigomycota isolates known from culture and sequence data.
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Affiliation(s)
- Xuewei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3, 1st Beichen West Road, Chaoyang District, Beijing, 100101, China.,CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3, 1st Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Johannes Z Groenewald
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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Shi Q, Guo Y, Engelhardt SC, Weladji RB, Zhou Y, Long M, Meng X. Endangered wild yak (Bos grunniens) in the Tibetan plateau and adjacent regions: Population size, distribution, conservation perspectives and its relation to the domestic subspecies. J Nat Conserv 2016. [DOI: 10.1016/j.jnc.2016.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
AbstractWe tested a series of hypotheses on drivers of habitat selection by the Vulnerable wild yak Bos mutus, combining distribution-wide sighting data with species distribution modelling approaches. The results indicate that climatic conditions are of paramount importance in shaping the wild yak's distribution on the Tibetan Plateau. Habitat selection patterns were seasonal, with yaks appearing to select areas closer to villages during the vegetation-growing season. Unexpectedly, our index of forage quantity had a limited effect in determining the distribution of the species. Overall, our results suggest that expected changes in climate for this region could have a significant impact on habitat availability for wild yaks, and we call for more attention to be focused on the unique wildlife in this ecosystem.
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24
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Deng F, Xia C, Jia X, Song T, Liu J, Lai SJ, Chen SY. Comparative Study on the Genetic Diversity ofGHRGene in Tibetan Cattle and Holstein Cows. Anim Biotechnol 2015; 26:217-21. [DOI: 10.1080/10495398.2014.993082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Berger J, Schaller GB, Cheng E, Kang A, Krebs M, Li L, Hebblewhite M. Legacies of past exploitation and climate affect mammalian sexes differently on the roof of the world - the case of wild yaks. Sci Rep 2015; 5:8676. [PMID: 25728642 PMCID: PMC4345326 DOI: 10.1038/srep08676] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/20/2015] [Indexed: 11/30/2022] Open
Abstract
In polar environments, a lack of empirical knowledge about biodiversity prompts reliance on species distribution models to predict future change, yet these ignore the role of biotic interactions including the role of long past human exploitation. To explore how mammals of extreme elevation respond to glacial recession and past harvest, we combined our fieldwork with remote sensing and used analyses of ~60 expeditions from 1850–1925 to represent baseline conditions for wildlife before heavy exploitation on the Tibetan Plateau. Focusing on endangered wild yaks (Bos mutus), we document female changes in habitat use across time whereupon they increasingly relied on steeper post-glacial terrain, and currently have a 20x greater dependence on winter snow patches than males. Our twin findings—that the sexes of a cold-adapted species respond differently to modern climate forcing and long-past exploitation—indicate that effective conservation planning will require knowledge of the interplay between past and future if we will assure persistence of the region's biodiversity.
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Affiliation(s)
- Joel Berger
- 1] Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA [2] Wildlife Conservation Society, Bronx, NY 10460, USA
| | | | - Ellen Cheng
- Ugyen Wangchuck Institute for Conservation and Environment, Lamai Goempa, Bumthang, Bhutan
| | - Aili Kang
- China Program, Wildlife Conservation Society, Beijing, China 10024
| | - Michael Krebs
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Lishu Li
- Rm. 1229, Blvd. 5, Wuliqiao 2nd Street, 1 SectionChaoyang District, Beijing, China 10002
| | - Mark Hebblewhite
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT 59812, USA
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26
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Na RS, Zhao YJ, Gao HJ, An TW, Huang YF, E GX. Complete mitochondrial genome of the Yakow (Bos primigenius taurus × Bos grunniens) in China. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:3826-3827. [PMID: 25186658 DOI: 10.3109/19401736.2014.953134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Chinese Yakow, Bos primigenius taurus × Bos grunniens, is a large and commercially important hybrid in family Bovidae. We first determined and annotated its complete mitochondrial genome. The mitogenome is 16,322 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.7%, T: 27.3%, C: 25.8% and G: 13.2%. The complete mitogenome of Yakow (B. p. taurus × B. grunniens) could provide an important data to further explore the taxonomic status of Yakow (B. p. taurus × B. grunniens) in B. grunniens and enrich the genetic information or evolutionary history of the Bovidae.
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Affiliation(s)
- Ri-Su Na
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University , Chongqing , P.R. China
| | - Yong-Ju Zhao
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University , Chongqing , P.R. China
| | - Hui-Jiang Gao
- b Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS) , Beijing , P.R. China , and
| | - Tian-Wu An
- c Yak Research Institute, National Beef Cattle Industry Technology System (CARS-38), Sichuan Academy of Grassland Science , Chengdu , P.R. China
| | - Yong-Fu Huang
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University , Chongqing , P.R. China
| | - Guang-Xin E
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University , Chongqing , P.R. China
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E G, Na RS, Zhao YJ, Gao HJ, An TW, Huang YF. Complete mitochondrial genome of the a rare subspecies of genus Bos, Tianzhu white yak from Tibetan area in China. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1443-4. [PMID: 25162469 DOI: 10.3109/19401736.2014.953084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The population of domestic yak, Tianzhu white yak, from Tibetan area in China is considered as a rare Bos grunniens species. We first determined and annotated its complete mitochondrial genome. The mitogenome is 16,319 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.7%, T: 27.2%, C: 25.8% and G: 13.2%. The complete mitogenome of the new subspecies of Bos grunniens could provide an important data to further explore the taxonomic status of the subspecies.
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Affiliation(s)
- Guangxin E
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University , Chongqing , P.R. China
| | - Ri-Su Na
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University , Chongqing , P.R. China
| | - Yong-Ju Zhao
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University , Chongqing , P.R. China
| | - Hui-Jiang Gao
- b Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS) , Beijing , P.R. China , and
| | - Tian-Wu An
- c Yak Research Institute, National Beef Cattle Industry Technology System (CARS-38), Sichuan Academy of Grassland Science , Chengdu , P.R. China
| | - Yong-Fu Huang
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University , Chongqing , P.R. China
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28
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Berger J, Cheng E, Kang A, Krebs M, Li L, Lu ZX, Buqiong, Buzhou, Schaller GB. Sex differences in ecology of wild yaks at high elevation in the Kekexili Reserve, Tibetan Qinghai Plateau, China. J Mammal 2014. [DOI: 10.1644/13-mamm-a-154] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Modeling trophic resource availability for the first human settlers of Europe: the case of Atapuerca TD6. J Hum Evol 2013; 64:645-57. [PMID: 23541385 DOI: 10.1016/j.jhevol.2013.02.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 02/18/2013] [Accepted: 02/24/2013] [Indexed: 11/22/2022]
Abstract
Food resource availability strongly influences the survival opportunities of all organisms. The effect of animal food resource availability on the survival and dispersal of hominin populations is hotly debated. In this article, we present a mathematical model that provides estimations of the maximum and minimum available resources for secondary consumers in a palaeocommunity. This model provides insights into the intensity of competition and the available niche space for hominins in Europe during the early Galerian (1.2-0.8 Ma). Published data from the Atapuerca TD6 assemblage were used in combination with the model to investigate trophic dynamics and resource availability for a Homo antecessor population 800,000 years ago. The effect on our results of the possible presence at Atapuerca of some large carnivores not recorded in the fossil assemblage is also evaluated. Results indicate the existence of a rich ecosystem at Atapuerca at the end of the Early Pleistocene. Secondary production was abundant enough to maintain a hunter-gatherer population and a rich carnivore guild more diverse than that recorded in the TD6 assemblage. Based on these results, the practice of cannibalism by H. antecessor cannot be explained by a long-term scarcity of resources. High food availability at TD6 implies a low to moderate level of competition for resources between carnivores and humans. According to this interpretation, an empty niche for a highly carnivorous omnivore existed in Europe during the early Galerian, and it was successfully exploited by Homo.
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Hassanin A, An J, Ropiquet A, Nguyen TT, Couloux A. Combining multiple autosomal introns for studying shallow phylogeny and taxonomy of Laurasiatherian mammals: Application to the tribe Bovini (Cetartiodactyla, Bovidae). Mol Phylogenet Evol 2012; 66:766-75. [PMID: 23159894 DOI: 10.1016/j.ympev.2012.11.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 09/27/2012] [Accepted: 11/01/2012] [Indexed: 12/26/2022]
Abstract
Mitochondrial sequences are widely used for species identification and for studying phylogenetic relationships among closely related species or populations of the same species. However, many studies of mammals have shown that the maternal history of the mitochondrial genome can be discordant with the true evolutionary history of the taxa. In such cases, the analyses of multiple nuclear genes can be more powerful for deciphering interspecific relationships. Here, we designed primers for amplifying 13 new exon-primed intron-crossing (EPIC) autosomal loci for studying shallow phylogeny and taxonomy of Laurasiatherian mammals. Three criteria were used for the selection of the markers: gene orthology, a PCR product length between 600 and 1200 nucleotides, and different chromosomal locations in the bovine genome. Positive PCRs were obtained from different species representing the orders Carnivora, Cetartiodactyla, Chiroptera, Perissodactyla and Pholidota. The newly developed markers were analyzed in a phylogenetic study of the tribe Bovini (the group containing domestic and wild cattle, bison, yak, African buffalo, Asian buffalo, and saola) based on 17 taxa and 18 nuclear genes, representing a total alignment of 13,095 nucleotides. The phylogenetic results were compared to those obtained from analyses of the complete mitochondrial genome and Y chromosomal genes. Our analyses support a basal divergence of the saola (Pseudoryx) and a sister-group relationship between yak and bison. These results contrast with recent molecular studies but are in better agreement with morphology. The comparison of pairwise nucleotide distances shows that our nuDNA dataset provides a good signal for identifying taxonomic levels, such as species, genera, subtribes, tribes and subfamilies, whereas the mtDNA genome fails because of mtDNA introgression and higher levels of homoplasy. Accordingly, we conclude that the genus Bison should be regarded as a synonym of Bos, with the European bison relegated to a subspecies rank within Bos bison. We compared our molecular dating estimates to the fossil record in order to propose a biogeographic scenario for the evolution of Bovini during the Neogene.
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Affiliation(s)
- Alexandre Hassanin
- Muséum national d'Histoire naturelle (MNHN), Département Systématique et Evolution, UMR 7205 - Origine, Structure et Evolution de la Biodiversité, 75005 Paris, France.
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Deng T, Wang X, Fortelius M, Li Q, Wang Y, Tseng ZJ, Takeuchi GT, Saylor JE, Säilä LK, Xie G. Out of Tibet: Pliocene woolly rhino suggests high-plateau origin of Ice Age megaherbivores. Science 2011; 333:1285-8. [PMID: 21885780 DOI: 10.1126/science.1206594] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Ice Age megafauna have long been known to be associated with global cooling during the Pleistocene, and their adaptations to cold environments, such as large body size, long hair, and snow-sweeping structures, are best exemplified by the woolly mammoths and woolly rhinos. These traits were assumed to have evolved as a response to the ice sheet expansion. We report a new Pliocene mammal assemblage from a high-altitude basin in the western Himalayas, including a primitive woolly rhino. These new Tibetan fossils suggest that some megaherbivores first evolved in Tibet before the beginning of the Ice Age. The cold winters in high Tibet served as a habituation ground for the megaherbivores, which became preadapted for the Ice Age, successfully expanding to the Eurasian mammoth steppe.
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Affiliation(s)
- Tao Deng
- Key Laboratory of Evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
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