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Werhahn G, Senn H, Macdonald DW, Sillero-Zubiri C. The Diversity in the Genus Canis Challenges Conservation Biology: A Review of Available Data on Asian Wolves. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.782528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Taxa belonging to the Genus Canis can challenge taxonomists because species boundaries and distribution ranges are often gradual. Species delineation within Canis is currently not based on consistent criteria, and is hampered by geographical bias and lack of taxonomic research. But a consistent taxonomy is critical, given its importance for assigning legal protection, conservation priorities, and financial resources. We carried out a qualitative review of the major wolf lineages so far identified from Asia from historical to contemporary time and considered relevant morphological, ecological, and genetic evidence. We present full mitochondrial phylogenies and genetic distances between these lineages. This review aims to summarize the available data on contemporary Asian wolf lineages within the context of the larger phylogenetic Canis group and to work toward a taxonomy that is consistent within the Canidae. We found support for the presence and taxon eligibility of Holarctic gray, Himalayan/Tibetan, Indian, and Arabian wolves in Asia and recommend their recognition at the taxonomic levels consistent within the group.
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Yang X, Sun G, Xia T, Cha M, Zhang L, Pang B, Tang Q, Dou H, Zhang H. Transcriptome analysis provides new insights into cold adaptation of corsac fox (
Vulpes Corsac
). Ecol Evol 2022; 12:e8866. [PMID: 35462974 PMCID: PMC9019142 DOI: 10.1002/ece3.8866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/10/2021] [Accepted: 04/06/2022] [Indexed: 11/11/2022] Open
Abstract
Vulpesare widely distributed throughout the world and have undergone drastic physiological and phenotypic changes in response to their environment. However, little is known about the underlying genetic causes of these traits, especially Vulpes corsac. In this study, RNA‐Seq was used to obtain a comprehensive dataset for multiple pooled tissues of corsac fox, and selection analysis of orthologous genes was performed to identify the genes that may be influenced by the low‐temperature environment. More than 6.32 Gb clean reads were obtained and assembled into a total of 173,353 unigenes with an average length of 557 bp for corsac fox. Selective pressure analysis showed that 16 positively selected genes (PSGs) were identified in corsac fox, red fox, and arctic fox. Enrichment analysis of PSGs showed that the LRP11 gene was enriched in several pathways related to the low‐temperature response and might play a key role in response to environmental stimuli of foxes. In addition, several positively selected genes were related to DNA damage repair (ELP2 and CHAF1A), innate immunity (ARRDC4 and S100A12), and the respiratory chain (NDUFA5), and these positively selected genes might play a role in adaptation to harsh wild fox environments. The results of common orthologous gene analysis showed that gene flow or convergent evolution might be an important factor in promoting regional differentiation of foxes. Our study provides a valuable transcriptomic resource for the evolutionary history of the corsac fox and the adaptations to the extreme environments.
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Affiliation(s)
- Xiufeng Yang
- College of Life Science Qufu Normal University Qufu China
| | - Guolei Sun
- College of Life Science Qufu Normal University Qufu China
| | - Tian Xia
- College of Life Science Qufu Normal University Qufu China
| | - Muha Cha
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas Hulunbuir China
| | - Lei Zhang
- College of Life Science Qufu Normal University Qufu China
| | - Bo Pang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas Hulunbuir China
| | - Qingming Tang
- Hulun Buir Forestry and Grassland Business Development Center Hulunbuir China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas Hulunbuir China
| | - Honghai Zhang
- College of Life Science Qufu Normal University Qufu China
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Krofel M, Hatlauf J, Bogdanowicz W, Campbell LAD, Godinho R, Jhala YV, Kitchener AC, Koepfli K, Moehlman P, Senn H, Sillero‐Zubiri C, Viranta S, Werhahn G, Alvares F. Towards resolving taxonomic uncertainties in wolf, dog and jackal lineages of Africa, Eurasia and Australasia. J Zool (1987) 2021. [DOI: 10.1111/jzo.12946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- M. Krofel
- Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
| | - J. Hatlauf
- University of Natural Resources and Life Sciences Vienna, Department of Integrative Biology and Biodiversity Research Institute of Wildlife Biology and Game Management Vienna Austria
| | - W. Bogdanowicz
- Museum and Institute of Zoology Polish Academy of Sciences Warszawa Poland
| | - L. A. D. Campbell
- Department of Zoology Recanati‐Kaplan Centre; Tubney University of Oxford Wildlife Conservation Research Unit Oxfordshire UK
| | - R. Godinho
- InBIO Laboratório Associado, Campus de Vairão CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
- BIOPOLIS Program in Genomics Biodiversity and Land Planning, CIBIO Vairão Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Y. V. Jhala
- Animal Ecology & Conservation Biology Wildlife Institute of India Dehradun India
| | - A. C. Kitchener
- Department of Natural Sciences National Museums Scotland Edinburgh UK
| | - K.‐P. Koepfli
- Smithsonian‐Mason School of Conservation George Mason University Front Royal VA USA
- Smithsonian Conservation Biology Institute Center for Species Survival National Zoological Park Front Royal VA USA
- Computer Technologies Laboratory ITMO University St. Petersburg Russia
| | - P. Moehlman
- IUCN/SSC Equid Specialist Group Tanzania Wildlife Research Institute (TAWIRI) EcoHealth Alliance and The Earth Institute Columbia University Arusha Tanzania
| | - H. Senn
- WildGenes Laboratory Conservation and Science Programmes Royal Zoological Society of Scotland, RZSS Edinburgh UK
| | - C. Sillero‐Zubiri
- Wildlife Conservation Research Unit, Zoology University of Oxford Tubney UK
- IUCN SSC Canid Specialist Group Oxford UK
- Born Free Foundation Horsham UK
| | - S. Viranta
- Faculty of Medicine University of Helsinki Helsinki Finland
| | - G. Werhahn
- IUCN SSC Canid Specialist Group Oxford UK
- Wildlife Conservation Research Unit, Zoology University of Oxford Tubney UK
| | - F. Alvares
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal
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Hennelly LM, Habib B, Modi S, Rueness EK, Gaubert P, Sacks BN. Ancient divergence of Indian and Tibetan wolves revealed by recombination-aware phylogenomics. Mol Ecol 2021; 30:6687-6700. [PMID: 34398980 DOI: 10.1111/mec.16127] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/24/2021] [Accepted: 08/13/2021] [Indexed: 12/29/2022]
Abstract
The grey wolf (Canis lupus) expanded its range across Holarctic regions during the late Pleistocene. Consequently, most grey wolves share recent (<100,000 years ago) maternal origins corresponding to a widespread Holarctic clade. However, two deeply divergent (200,000-700,000 years ago) mitochondrial clades are restricted, respectively, to the Indian subcontinent and the Tibetan Plateau, where remaining wolves are endangered. No genome-wide analysis had previously included wolves corresponding to the mitochondrial Indian clade or attempted to parse gene flow and phylogeny. We sequenced four Indian and two Tibetan wolves and included 31 additional canid genomes to resolve the phylogenomic history of grey wolves. Genomic analyses revealed Indian and Tibetan wolves to be distinct from each other and from broadly distributed wolf populations corresponding to the mitochondrial Holarctic clade. Despite gene flow, which was reflected disproportionately in high-recombination regions of the genome, analyses revealed Indian and Tibetan wolves to be basal to Holarctic grey wolves, in agreement with the mitochondrial phylogeny. In contrast to mitochondrial DNA, however, genomic findings suggest the possibility that the Indian wolf could be basal to the Tibetan wolf, a discordance potentially reflecting selection on the mitochondrial genome. Together, these findings imply that southern regions of Asia have been important centers for grey wolf evolution and that Indian and Tibetan wolves represent evolutionary significant units (ESUs). Further study is needed to assess whether these ESUs warrant recognition as distinct species. This question is especially urgent regarding the Indian wolf, which represents one of the world's most endangered wolf populations.
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Affiliation(s)
- Lauren M Hennelly
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Bilal Habib
- Department of Animal Ecology and Conservation, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Shrushti Modi
- Department of Animal Ecology and Conservation, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Eli K Rueness
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), CNRS/UPS/IRD, Université Toulouse III Paul Sabatier - Bâtiment 4R1, Toulouse cedex 9, France
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
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