1
|
Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines. Genes (Basel) 2022; 14:genes14010075. [PMID: 36672816 PMCID: PMC9858670 DOI: 10.3390/genes14010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.
Collapse
|
2
|
Kazimirov PA, Leontyev SV, Nechaeva AV, Belokon MM, Belokon YS, Bondarev AY, Davydov AV, Politov DV. Population Genetic Structure of the Steppe Wolf of Russia and Kazakhstan by Microsatellite Loci. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422110047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
3
|
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.
Collapse
|
4
|
Reshamwala HS, Bhattacharya A, Khan S, Shrotriya S, Lyngdoh SB, Goyal SP, Kanagaraj R, Habib B. Modeling Potential Impacts of Climate Change on the Distribution of Wooly Wolf (Canis lupus chanco). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.815621] [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
The Central Asian wolves form a cohort within the wolf-dog clade known as the wooly wolf (Canis lupus chanco). These wolves are poorly studied and their current extent and distribution remain unknown. Apex predators already existing at higher elevations like wooly wolves can be severely affected by climate change because of the absence of suitable refuge. Concomitantly, in the era of Anthropocene, the change in land use land cover (LULC) is rapidly increasing. Even the most adaptable species occurring in human-dominated landscapes may fail to survive under the combined impact of both climate change and human pressure. We collected 3,776 presence locations of the wooly wolf across its range from published literature and compiled 39 predictor variables for species distribution modeling, which included anthropogenic factors, climatic, vegetation, and topographic features. We predicted the change in their distribution under different anthropogenic factors, climate change, and land-use land-cover change scenarios. Wolf showed affinity toward areas with low to moderately warm temperatures and higher precipitations. It showed negative relationships with forests and farmlands. Our future projections showed an expansion of wolf distribution and habitat suitability under the combined effects of future climate and LULC change. Myanmar and Russia had the introduction of high and medium suitability areas for the wooly wolf in future scenarios. Uzbekistan and Kazakhstan showed the consistent loss in high suitability areas while Mongolia and Bhutan had the largest gain in high suitability areas. The study holds great significance for the protection and management of this species and also provides opportunities to explore the impact on associated species.
Collapse
|
5
|
Khan S, Shrotriya S, Sadhukhan S, Lyngdoh S, Goyal SP, Habib B. Comparative Ecological Perspectives of Two Ancient Lineages of Gray Wolves: Woolly Wolf (Canis lupus chanco) and Indian Wolf (Canis lupus pallipes). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.775612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Geographical isolation can often lead to speciation, and two disconnected populations of the same species living in drastically different bioclimatic regions provide an opportunity to understand the process of speciation. The Woolly wolf is found in the cold-arid, Trans-Himalayan landscape, while the Indian wolf inhabits the semi-arid grasslands of Central India. Both the lineages of wolves from India have generated scientific debate on their taxonomic status in recent years. In this study, we collected data and reviewed published literature to document the ecological and behavioral differences between the Woolly wolf and the Indian wolf. Most studies have used genetic data; hence we discuss variation in spatial ecology, habitat preferences, vocalization, diet diversity and cranial measurements of these two subspecies. The spatial ecology of two lineages was compared from the data on three Woolly and ten Indian wolves tagged with GPS collars. The telemetry data shows that there has been no difference in the day-night movement of Woolly wolves, whereas Indian wolves show significant high displacement during the night. The BBMM method indicated that Woolly wolf home ranges were three times larger than the Indian wolf. The Woolly wolf diet is comprised of 20 different types of food items, whereas the Indian wolf diet consists of 17 types. The Woolly and Indian wolf largely depend upon domestic prey base, i.e., 48.44 and 40.34%, respectively. We found no differences in the howling parameters of these subspecies. Moreover, the Woolly wolf skull was significantly longer and broader than the Indian wolf. Wolves of India are ancient and diverged from the main clade about 200,000–1,000,000 years ago. Their genetic and ecological evolution in different bioclimatic zones has resulted in considerable differences as distinct subspecies. The present study is a step in understanding ecological differences between two important, genetically unique subspecies of wolves.
Collapse
|
6
|
Pal R, Panwar A, Goyal SP, Sathyakumar S. Space Use by Woolly Wolf Canis lupus chanco in Gangotri National Park, Western Himalaya, India. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.782339] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The woolly wolf Canis lupus chanco is increasingly being accepted as a unique taxon that needs immediate protection and management; however, information on its ecology remains limited across its range. We used camera trapping data set of 4 years (2015–2019) to investigate seasonal activity patterns and space use and assessed woolly wolf food habits in the Gangotri National Park, western Himalaya, India. We used generalized linear mixed models to assess the distribution of the wolf about prey, seasonal livestock grazing, human presence, habitat, and seasons. We observed a positive association with elevation and a negative response to an increase in ruggedness. The capture of wolves increased in winters, indicating a possible effect of snow on the ranging pattern. Spatial avoidance to anthropogenic pressure was not evident in our study; however, temporal avoidance was observed. The activity pattern of the wolf varied among seasons. Wolves were mostly active in the morning and late evening hours in summer and showed a diurnal activity pattern in winter. A less diverse diet was observed where the mean percentage frequency of occurrence and relative biomass was highest for bharal, followed by livestock. Himalayan marmot Marmota himalayana, birds, and rodents also form minor constituents to the diet. Synthesizing all three factors (space, diet, and activity), it may be stated that the wolf presence in the region is influenced by both wild prey availability and seasonality. Therefore, conservation of woolly wolves would require securing a vast landscape with optimal wild prey.
Collapse
|
7
|
Wang MS, Thakur M, Jhala Y, Wang S, Srinivas Y, Dai SS, Liu ZX, Chen HM, Green RE, Koepfli KP, Shapiro B. OUP accepted manuscript. Genome Biol Evol 2022; 14:6524629. [PMID: 35137061 PMCID: PMC8841465 DOI: 10.1093/gbe/evac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, USA
- Corresponding authors: E-mails: ; ; ;
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, India
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Corresponding authors: E-mails: ; ; ;
| | | | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yellapu Srinivas
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, India
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zheng-Xi Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Hong-Man Chen
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia
- Corresponding authors: E-mails: ; ; ;
| | - Beth Shapiro
- Howard Hughes Medical Institute, University of California Santa Cruz, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, USA
- Corresponding authors: E-mails: ; ; ;
| |
Collapse
|
8
|
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
| |
Collapse
|
9
|
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: 12] [Impact Index Per Article: 4.0] [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.
Collapse
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
| |
Collapse
|
10
|
Pandey BP, Thami SM, Shrestha R, Chalise MK. On the occurrence of the Himalayan Wolf Canis lupus, L. 1758 (Mammalia: Carnivora: Canidae) in the Gaurishankar Conservation Area, Nepal; its existence confirmed through sign and visual evidence in Rolwaling Valley. JOURNAL OF THREATENED TAXA 2021. [DOI: 10.11609/jott.6216.13.8.18967-18974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The Himalayan Wolf Canis lupus L., a top predator of the Third Pole, is proposed to be of a distinct wolf lineage (C. himalayensis) relative to the Holarctic Grey Wolf as described by mtDNA analyses. A biodiversity survey organized by the Gaurishankar Conservation Area Project (GCAP) has captured images of wolves in three different regions, and the study team has observed wolf scats in five additional regions above the tree line in Rolwaling Valley. Further, interviews with local herders provided evidence of wolf depredation of livestock in the area. The Rolwaling Valley in the Gaurishankar Conservation Area was the study area which was divided into 12, 4 x 4 km (16 km2) grid cells, each supplied with one camera trap operated continuously from June to November 2019 (only 6 out of 12 cameras functioned for the duration of our study). Wolf detections were recorded by camera traps from Yalung Pass (4,956 m), Tsho-Rolpa glacial Lake (4,536 m) and the Dudhkunda ridgeline (5,091 m). The photo capture rate index (PCRI) for wolves was 0.71. Our study reports the first photographic evidence of the Himalayan Wolf in the Rolwaling Valley.
Collapse
|
11
|
Rehman EU, Din JU, Ahmad S, Hameed S, Shah KA, Mehmood T, Nawaz MA. Insight into occupancy determinants and conflict dynamics of grey wolf (Canis lupus) in the dry temperate zone of Hindukush Range. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2020.e01402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
|
12
|
|
13
|
Jiang HH, Li B, Ma Y, Bai SY, Dahmer TD, Linacre A, Xu YC. Forensic validation of a panel of 12 SNPs for identification of Mongolian wolf and dog. Sci Rep 2020; 10:13249. [PMID: 32764603 PMCID: PMC7413520 DOI: 10.1038/s41598-020-70225-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/24/2020] [Indexed: 11/26/2022] Open
Abstract
Wolf (Canis lupus) is a species included in appendices of CITES and is often encountered in cases of alleged poaching and trafficking of their products. When such crimes are suspected, those involved may attempt to evade legal action by claiming that the animals involved are domestic dogs (C. l. familiaris). To respond effectively to such claims, law enforcement agencies require reliable and robust methods to distinguish wolves from dogs. Reported molecular genetic methods are either unreliable (mitogenome sequence based), or operationally cumbersome and require much DNA (un-multiplexed microsatellites), or financially expensive (genome wide SNP genotyping). We report on the validation of a panel of 12 ancestral informative single nucleotide polymorphism (SNP) markers for discriminating wolves from dogs. A SNaPshot multiplex genotyping system was developed for the panel, and 97 Mongolian wolves (C. l. chanco) and 108 domestic dogs were used for validation. Results showed this panel had high genotyping success (0.991), reproducibility (1.00) and origin assignment accuracy (0.97 ± 0.05 for dogs and 1.00 ± 0.03 for wolves). Species-specificity testing suggested strong tolerance to DNA contamination across species, except for Canidae. The minimum DNA required for reliable genotyping was 6.25 pg/μl. The method and established gene frequency database are available to support identification of wolves and dogs by law enforcement agencies.
Collapse
Affiliation(s)
- Hong Hui Jiang
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Bo Li
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Detecting Center of Wildlife, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
| | - Yue Ma
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Su Ying Bai
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China
| | | | - Adrian Linacre
- College of Science and Engineering, Flinders University, Adelaide, SA, 5042, Australia
| | - Yan Chun Xu
- College of Wildlife and Protected Areas, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
- National Forestry and Grassland Administration Detecting Center of Wildlife, No. 26, Hexing Road, Xiangfang District, Harbin, 150040, China.
| |
Collapse
|
14
|
Joshi B, Lyngdoh S, Singh SK, Sharma R, Kumar V, Tiwari VP, Dar SA, Maheswari A, Pal R, Bashir T, Reshamwala HS, Shrotriya S, Sathyakumar S, Habib B, Kvist L, Goyal SP. Revisiting the Woolly wolf (Canis lupus chanco) phylogeny in Himalaya: Addressing taxonomy, spatial extent and distribution of an ancient lineage in Asia. PLoS One 2020; 15:e0231621. [PMID: 32298359 PMCID: PMC7162449 DOI: 10.1371/journal.pone.0231621] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/27/2020] [Indexed: 11/23/2022] Open
Abstract
Of the sub-species of Holarctic wolf, the Woolly wolf (Canis lupus chanco) is uniquely adapted to atmospheric hypoxia and widely distributed across the Himalaya, Qinghai Tibetan Plateau (QTP) and Mongolia. Taxonomic ambiguity still exists for this sub-species because of complex evolutionary history anduse of limited wild samples across its range in Himalaya. We document for the first time population genetic structure and taxonomic affinity of the wolves across western and eastern Himalayan regions from samples collected from the wild (n = 19) using mitochondrial control region (225bp). We found two haplotypes in our data, one widely distributed in the Himalaya that was shared with QTP and the other confined to Himachal Pradesh and Uttarakhand in the western Himalaya, India. After combining our data withpublished sequences (n = 83), we observed 15 haplotypes. Some of these were shared among different locations from India to QTP and a few were private to geographic locations. A phylogenetic tree indicated that Woolly wolves from India, Nepal, QTP and Mongolia are basal to other wolves with shallow divergence (K2P; 0.000-0.044) and high bootstrap values. Demographic analyses based on mismatch distribution and Bayesian skyline plots (BSP) suggested a stable population over a long time (~million years) with signs of recent declines. Regional dominance of private haplotypes across its distribution range may indicate allopatric divergence. This may be due to differences in habitat characteristics, availability of different wild prey species and differential deglaciation within the range of the Woolly wolf during historic time. Presence of basal and shallow divergence within-clade along with unique ecological requirements and adaptation to hypoxia, the Woolly wolf of Himalaya, QTP, and Mongolian regions may be considered as a distinct an Evolutionary Significant Unit (ESU). Identifying management units (MUs) is needed within its distribution range using harmonized multiple genetic data for effective conservation planning.
Collapse
Affiliation(s)
| | | | | | - Reeta Sharma
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Vinay Kumar
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | | - S. A. Dar
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | | - Ranjana Pal
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Tawqir Bashir
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | | | | - S. Sathyakumar
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Bilal Habib
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Laura Kvist
- Department of Biology, University of Oulu, Oulu, Finland
| | | |
Collapse
|
15
|
Loog L, Thalmann O, Sinding MHS, Schuenemann VJ, Perri A, Germonpré M, Bocherens H, Witt KE, Samaniego Castruita JA, Velasco MS, Lundstrøm IKC, Wales N, Sonet G, Frantz L, Schroeder H, Budd J, Jimenez EL, Fedorov S, Gasparyan B, Kandel AW, Lázničková-Galetová M, Napierala H, Uerpmann HP, Nikolskiy PA, Pavlova EY, Pitulko VV, Herzig KH, Malhi RS, Willerslev E, Hansen AJ, Dobney K, Gilbert MTP, Krause J, Larson G, Eriksson A, Manica A. Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia. Mol Ecol 2020; 29:1596-1610. [PMID: 31840921 PMCID: PMC7317801 DOI: 10.1111/mec.15329] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/16/2019] [Accepted: 12/03/2019] [Indexed: 01/21/2023]
Abstract
Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long‐range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog. see also the Perspective by Rena M. Schweizer and Robert K. Wayne.
Collapse
Affiliation(s)
- Liisa Loog
- Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Department of Zoology, University of Cambridge, Cambridge, UK.,Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, UK.,Department of Genetics, University of Cambridge, Cambridge, UK
| | - Olaf Thalmann
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Mikkel-Holger S Sinding
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Natural History Museum, University of Oslo, Oslo, Norway.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Angela Perri
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mietje Germonpré
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Herve Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany
| | - Kelsey E Witt
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Marcela S Velasco
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Inge K C Lundstrøm
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nathan Wales
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,BioArch, Department of Archaeology, University of York, York, UK, USA
| | - Gontran Sonet
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Laurent Frantz
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Hannes Schroeder
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jane Budd
- Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
| | - Elodie-Laure Jimenez
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Sergey Fedorov
- Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, Yakutsk, Russia
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Republic of Armenia
| | - Andrew W Kandel
- Heidelberg Academy of Sciences and Humanities: The Role of Culture in Early Expansions of Humans, Tübingen, Germany
| | - Martina Lázničková-Galetová
- Department of Anthropology, University of West Bohemia, Pilzen, Czech Republic.,Moravian museum, Brno, Czech Republic.,Hrdlička Museum of Man, Faculty of Science, Charles University, Praha, Czech Republic
| | - Hannes Napierala
- Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Hans-Peter Uerpmann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Pavel A Nikolskiy
- Geological Institute, Russian Academy of Sciences, Moscow, Russia.,Institute for Material Culture History, Russian Academy of Sciences, St Petersburg, Russia
| | - Elena Y Pavlova
- Institute for Material Culture History, Russian Academy of Sciences, St Petersburg, Russia.,Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Vladimir V Pitulko
- Institute for Material Culture History, Russian Academy of Sciences, St Petersburg, Russia
| | - Karl-Heinz Herzig
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Biomedicine and Biocenter of Oulu, Medical Research Center and University Hospital, University of Oulu, Oulu, Finland
| | - Ripan S Malhi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eske Willerslev
- Department of Zoology, University of Cambridge, Cambridge, UK.,Centre for GeoGenetics Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Wellcome Trust Sanger Institute, Cambridge, UK
| | - Anders J Hansen
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Centre for GeoGenetics Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada
| | - M Thomas P Gilbert
- EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Greger Larson
- Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Medical & Molecular Genetics, King's College London, Guys Hospital, London, UK.,cGEM, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
| |
Collapse
|
16
|
Sadhukhan S, Hennelly L, Habib B. Characterising the harmonic vocal repertoire of the Indian wolf (Canis lupus pallipes). PLoS One 2019; 14:e0216186. [PMID: 31671161 PMCID: PMC6822943 DOI: 10.1371/journal.pone.0216186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/21/2019] [Indexed: 11/18/2022] Open
Abstract
Vocal communication in social animals plays a crucial role in mate choice, maintaining social structure, and foraging strategy. The Indian grey wolf, among the least studied subspecies, is a social carnivore that lives in groups called packs and has many types of vocal communication. In this study, we characterise harmonic vocalisation types of the Indian wolf using howl survey responses and opportunistic recordings from captive and nine packs (each pack contains 2–9 individuals) of free-ranging Indian wolves. Using principal component analysis, hierarchical clustering, and discriminant function analysis, we found four distinct vocalisations using 270 recorded vocalisations (Average Silhouette width Si = 0.598) which include howls and howl-barks (N = 238), whimper (N = 2), social squeak (N = 28), and whine (N = 2). Although having a smaller body size compared to other wolf subspecies, Indian wolf howls have an average mean fundamental frequency of 422 Hz (±126), which is similar to other wolf subspecies. The whimper showed the highest frequency modulation (37.296±4.601) and the highest mean fundamental frequency (1708±524 Hz) compared to other call types. Less information is available on the third vocalisation type, i.e. ‘Social squeak’ or ‘talking’ (Mean fundamental frequency = 461±83 Hz), which is highly variable (coefficient of frequency variation = 18.778±3.587). Lastly, we identified the whine, which had a mean fundamental frequency of 906Hz (±242) and is similar to the Italian wolf (979±109 Hz). Our study’s characterisation of the Indian wolf’s harmonic vocal repertoire provides a first step in understanding the function and contextual use of vocalisations in this social mammal.
Collapse
Affiliation(s)
- Sougata Sadhukhan
- Department of Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, India;
| | - Lauren Hennelly
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America
| | - Bilal Habib
- Department of Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, India;
- * E-mail:
| |
Collapse
|
17
|
Werhahn G, Kusi N, Li X, Chen C, Zhi L, Lázaro Martín R, Sillero-Zubiri C, Macdonald DW. Himalayan wolf foraging ecology and the importance of wild prey. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00780] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
18
|
Reale S, Randi E, Cumbo V, Sammarco I, Bonanno F, Spinnato A, Seminara S. Biodiversity lost: The phylogenetic relationships of a complete mitochondrial DNA genome sequenced from the extinct wolf population of Sicily. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
19
|
Balajeid Lyngdoh S, Habib B, Shrotriya S. Dietary spectrum in Himalayan wolves: comparative analysis of prey choice in conspecifics across high‐elevation rangelands of Asia. J Zool (1987) 2019. [DOI: 10.1111/jzo.12724] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. Balajeid Lyngdoh
- Department of Animal Ecology & Conservation Biology Wildlife Institute of India Dehradun Uttarakhand India
| | - B. Habib
- Department of Animal Ecology & Conservation Biology Wildlife Institute of India Dehradun Uttarakhand India
| | - S. Shrotriya
- Department of Animal Ecology & Conservation Biology Wildlife Institute of India Dehradun Uttarakhand India
| |
Collapse
|
20
|
|
21
|
Werhahn G, Senn H, Ghazali M, Karmacharya D, Sherchan AM, Joshi J, Kusi N, López-Bao JV, Rosen T, Kachel S, Sillero-Zubiri C, Macdonald DW. The unique genetic adaptation of the Himalayan wolf to high-altitudes and consequences for conservation. Glob Ecol Conserv 2018. [DOI: 10.1016/j.gecco.2018.e00455] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
|
22
|
Dufresnes C, Miquel C, Remollino N, Biollaz F, Salamin N, Taberlet P, Fumagalli L. Howling from the past: historical phylogeography and diversity losses in European grey wolves. Proc Biol Sci 2018; 285:rspb.2018.1148. [PMID: 30068681 DOI: 10.1098/rspb.2018.1148] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022] Open
Abstract
Genetic bottlenecks resulting from human-induced population declines make alarming symbols for the irreversible loss of our natural legacy worldwide. The grey wolf (Canis lupus) is an iconic example of extreme declines driven by anthropogenic factors. Here, we assessed the genetic signatures of 150 years of wolf persecution throughout the Western Palaearctic by high-throughput mitochondrial DNA sequencing of historical specimens in an unprecedented spatio-temporal framework. Despite Late Pleistocene bottlenecks, we show that historical genetic variation had remained high throughout Europe until the last several hundred years. In Western Europe, where wolves nearly got fully exterminated, diversity dramatically collapsed at the turn of the twentieth century and recolonization from few homogeneous relict populations induced drastic shifts of genetic composition. By contrast, little genetic displacement and steady levels of diversity were maintained in Eastern European regions, where human persecution had lesser effects on wolf demography. By comparing prehistoric, historic and modern patterns of genetic diversity, our study hence traces the timeframe and the active human role in the decline of the grey wolf, an emblematic yet controversial animal which symbolizes the complex relationship between human societies and nature conservation.
Collapse
Affiliation(s)
- Christophe Dufresnes
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Christian Miquel
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Nadège Remollino
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - François Biollaz
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Route Pra de Louetse 32, 1968 Mase, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Computational Biology University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Pierre Taberlet
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| |
Collapse
|
23
|
Conservation implications for the Himalayan wolf Canis (lupus) himalayensis based on observations of packs and home sites in Nepal. ORYX 2017. [DOI: 10.1017/s0030605317001077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractWe provide insights into pack composition and den site parameters of the Himalayan wolf Canis (lupus) himalayensis based on observations of free-ranging wolves in three study areas in Nepal. We combine this with a social survey of the local Buddhist communities regarding human–carnivore conflict, to draw inferences for conservation practice in the Nepalese Himalayas. We recorded eight wolf packs (with an average composition of two adults and three pups), and found five home sites in high-altitude shrubland patches within alpine grasslands at 4,270–4,940 m altitude. There was a spatial–temporal overlap of wolf home sites and livestock herding during spring and summer, which facilitated human–wolf conflict. The litters of three out of five wolf packs found in Dolpa during 2016 were killed by local people in the same year. In Nepal compensation is offered for depredation by snow leopards Panthera uncia, with associated lowering of negative attitudes, but not for depredation by wolves. We recommend the implementation of financial and educational conservation schemes for all conflict-causing carnivores across the Himalayan regions of Nepal.
Collapse
|
24
|
Thai QK, Chung DA, Tran HD. Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database. BMC Genet 2017; 18:60. [PMID: 28651548 PMCID: PMC5485557 DOI: 10.1186/s12863-017-0528-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes. DESCRIPTION The Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD. The CHD can be accessed at http://chd.vnbiology.com . It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download. CONCLUSIONS The Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582 bp sequences.
Collapse
Affiliation(s)
- Quan Ke Thai
- Saigon University, 273 An Duong Vuong street, District 5, Ho Chi Minh city, Vietnam
| | - Dung Anh Chung
- Institute of Agricultural science for Southern Vietnam, 121 Nguyen Binh Khiem street, District 1, Ho Chi Minh city, Vietnam
| | - Hoang-Dung Tran
- Nguyen Tat Thanh University, 300A Nguyen Tat Thanh street, District 4, Ho Chi Minh city, Vietnam
| |
Collapse
|
25
|
Werhahn G, Senn H, Kaden J, Joshi J, Bhattarai S, Kusi N, Sillero-Zubiri C, Macdonald DW. Phylogenetic evidence for the ancient Himalayan wolf: towards a clarification of its taxonomic status based on genetic sampling from western Nepal. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170186. [PMID: 28680672 PMCID: PMC5493914 DOI: 10.1098/rsos.170186] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/10/2017] [Indexed: 06/07/2023]
Abstract
Wolves in the Himalayan region form a monophyletic lineage distinct from the present-day Holarctic grey wolf Canis lupus spp. (Linnaeus 1758) found across Eurasia and North America. Here, we analyse phylogenetic relationships and the geographic distribution of mitochondrial DNA haplotypes of the contemporary Himalayan wolf (proposed in previous studies as Canis himalayensis) found in Central Asia. We combine genetic data from a living Himalayan wolf population collected in northwestern Nepal in this study with already published genetic data, and confirm the Himalayan wolf lineage based on mitochondrial genomic data (508 bp cytochrome b and 242 bp D-loop), and X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences. We then compare the genetic profile of the Himalayan wolf lineage found in northwestern Nepal with canid reference sequences from around the globe with maximum likelihood and Bayesian phylogeny building methods to demonstrate that the Himalayan wolf forms a distinct monophyletic clade supported by posterior probabilities/bootstrap for D-loop of greater than 0.92/85 and cytochrome b greater than 0.99/93. The Himalayan wolf shows a unique Y-chromosome (ZFY) haplotype, and shares an X-chromosome haplotype (ZFX) with the newly postulated African wolf. Our results imply that the Himalayan wolf distribution range extends from the Himalayan range north across the Tibetan Plateau up to the Qinghai Lakes region in Qinghai Province in the People's Republic of China. Based on its phylogenetic distinction and its older age of divergence relative to the Holarctic grey wolf, the Himalayan wolf merits formal classification as a distinct taxon of special conservation concern.
Collapse
Affiliation(s)
- Geraldine Werhahn
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, The Recanati-Kaplan Centre, Tubney House, Tubney OX13 5QL, UK
| | - Helen Senn
- WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK
| | - Jennifer Kaden
- WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK
| | - Jyoti Joshi
- Centre for Molecular Dynamics Nepal CMDN, GPO Box 21049, Kathmandu, Nepal
| | - Susmita Bhattarai
- Centre for Molecular Dynamics Nepal CMDN, GPO Box 21049, Kathmandu, Nepal
| | - Naresh Kusi
- Resources Himalaya Foundation, Sanepa, Lalitpur, Nepal
| | - Claudio Sillero-Zubiri
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, The Recanati-Kaplan Centre, Tubney House, Tubney OX13 5QL, UK
- IUCN SSC Canid Specialist Group, Oxford, UK
| | - David W. Macdonald
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, The Recanati-Kaplan Centre, Tubney House, Tubney OX13 5QL, UK
| |
Collapse
|
26
|
|
27
|
Ersmark E, Klütsch CFC, Chan YL, Sinding MHS, Fain SR, Illarionova NA, Oskarsson M, Uhlén M, Zhang YP, Dalén L, Savolainen P. From the Past to the Present: Wolf Phylogeography and Demographic History Based on the Mitochondrial Control Region. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00134] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
|
28
|
Distribution of grey wolves Canis lupus lupus in the Nepalese Himalaya: implications for conservation management. ORYX 2016. [DOI: 10.1017/s0030605316000296] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractThe grey wolf Canis lupus lupus is Critically Endangered in Nepal, and is a protected species there. Understanding the species’ status and distribution is critical for its conservation in the Nepalese Himalaya. We assessed the distribution of the grey wolf in the Himalayan and Trans-Himalayan regions using data from faecal and camera trap surveys and published data sources. We recorded 40 instances of wolf presence. Using these data we estimated a distribution of 28,553 km2, which includes potential as well as known habitat and comprises 73% of the Nepalese Himalaya. There is evidence of recovery of the grey wolf population in Kanchenjunga Conservation Area in the eastern portion of the species’ range. A livestock insurance scheme has been shown to be a viable option to reduce retaliatory killing of wolves as a result of livestock depredation. The wolf plays an important ecological role in the Himalaya, and its conservation should not be delayed by the ongoing taxonomic debate about its subspecific status.
Collapse
|
29
|
Aksöyek E, İbiş O, Özcan S, Moradi M, Tez C. DNA barcoding of three species (Canis aureus, Canis lupus and Vulpes vulpes) of Canidae. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:747-755. [PMID: 27180732 DOI: 10.1080/24701394.2016.1180512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene have been used for DNA barcoding and determining the genetic diversity of mammal species. In the current study, our intention was to test the validity of COI barcodes for detecting genetic divergence and to reveal whether or not there is a genetic variation at this marker within canids. Three species (Canis aureus, Canis lupus and Vulpes vulpes) from the family Canidae were selected for DNA barcoding using samples collected from Iran and Turkey. All three species had unique barcoding sequences and none of the sequences were shared among these species. The mean sequence divergences within and among the species were 0.61% and 12.32%, respectively, which fell into the mean divergence ranges found in some mammal groups. The genetic diversity of these three canid species was relatively higher than that found in previously reported studies.
Collapse
Affiliation(s)
- Eren Aksöyek
- a Graduate School of Natural and Applied Sciences , Erciyes University , Kayseri , Turkey
| | - Osman İbiş
- b Department of Agricultural Biotechnology, Faculty of Agriculture , Erciyes University , Kayseri , Turkey.,c Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey
| | - Servet Özcan
- c Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey.,d Department of Biology, Faculty of Sciences , Erciyes University , Kayseri , Turkey
| | - Mohammad Moradi
- e Department of Biology, Faculty of Science , University of Zanjan , Zanjan , Iran
| | - Coşkun Tez
- d Department of Biology, Faculty of Sciences , Erciyes University , Kayseri , Turkey
| |
Collapse
|
30
|
Chetri M, Jhala YV, Jnawali SR, Subedi N, Dhakal M, Yumnam B. Ancient Himalayan wolf (Canis lupus chanco) lineage in Upper Mustang of the Annapurna Conservation Area, Nepal. Zookeys 2016:143-56. [PMID: 27199590 PMCID: PMC4857050 DOI: 10.3897/zookeys.582.5966] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 03/16/2016] [Indexed: 11/12/2022] Open
Abstract
The taxonomic status of the wolf (Canis lupus) in Nepal's Trans-Himalaya is poorly understood. Recent genetic studies have revealed the existence of three lineages of wolves in the Indian sub-continent. Of these, the Himalayan wolf, Canis lupus chanco, has been reported to be the most ancient lineage historically distributed within the Nepal Himalaya. These wolves residing in the Trans-Himalayan region have been suggested to be smaller and very different from the European wolf. During October 2011, six fecal samples suspected to have originated from wolves were collected from Upper Mustang in the Annapurna Conservation Area of Nepal. DNA extraction and amplification of the mitochondrial (mt) control region (CR) locus yielded sequences from five out of six samples. One sample matched domestic dog sequences in GenBank, while the remaining four samples were aligned within the monophyletic and ancient Himalayan wolf clade. These four sequences which matched each other, were new and represented a novel Himalayan wolf haplotype. This result confirms that the endangered ancient Himalayan wolf is extant in Nepal. Detailed genomic study covering Nepal's entire Himalayan landscape is recommended in order to understand their distribution, taxonomy and, genetic relatedness with other wolves potentially sharing the same landscape.
Collapse
Affiliation(s)
| | | | | | - Naresh Subedi
- National Trust for Nature Conservation, Khumaltar, Lalitpur, Kathmandu, Nepal
| | - Maheshwar Dhakal
- Department of National Parks and Wildlife Conservation, Babarmahal, Kathmandu, Nepal
| | - Bibek Yumnam
- Wildlife Institute of India, Chandrabani, Dehradun 248001, India
| |
Collapse
|
31
|
Rutkowski R, Krofel M, Giannatos G, Ćirović D, Männil P, Volokh AM, Lanszki J, Heltai M, Szabó L, Banea OC, Yavruyan E, Hayrapetyan V, Kopaliani N, Miliou A, Tryfonopoulos GA, Lymberakis P, Penezić A, Pakeltytė G, Suchecka E, Bogdanowicz W. A European Concern? Genetic Structure and Expansion of Golden Jackals (Canis aureus) in Europe and the Caucasus. PLoS One 2015; 10:e0141236. [PMID: 26540195 PMCID: PMC4634961 DOI: 10.1371/journal.pone.0141236] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 10/05/2015] [Indexed: 11/19/2022] Open
Abstract
In the first continent-wide study of the golden jackal (Canis aureus), we characterised its population genetic structure and attempted to identify the origin of European populations. This provided a unique insight into genetic characteristics of a native carnivore population with rapid large-scale expansion. We analysed 15 microsatellite markers and a 406 base-pair fragment of the mitochondrial control region. Bayesian-based and principal components methods were applied to evaluate whether the geographical grouping of samples corresponded with genetic groups. Our analysis revealed low levels of genetic diversity, reflecting the unique history of the golden jackal among Europe’s native carnivores. The results suggest ongoing gene flow between south-eastern Europe and the Caucasus, with both contributing to the Baltic population, which appeared only recently. The population from the Peloponnese Peninsula in southern Greece forms a common genetic cluster with samples from south-eastern Europe (ΔK approach in STRUCTURE, Principal Components Analysis [PCA]), although the results based on BAPS and the estimated likelihood in STRUCTURE indicate that Peloponnesian jackals may represent a distinct population. Moreover, analyses of population structure also suggest either genetic distinctiveness of the island population from Samos near the coast of Asia Minor (BAPS, most STRUCTURE, PCA), or possibly its connection with the Caucasus population (one analysis in STRUCTURE). We speculate from our results that ancient Mediterranean jackal populations have persisted to the present day, and have merged with jackals colonising from Asia. These data also suggest that new populations of the golden jackal may be founded by long-distance dispersal, and thus should not be treated as an invasive alien species, i.e. an organism that is “non-native to an ecosystem, and which may cause economic or environmental harm or adversely affect human health”. These insights into the genetic structure and ancestry of Baltic jackals have important implications for management and conservation of jackals in Europe. The golden jackal is listed as an Annex V species in the EU Habitats Directive and as such, considering also the results presented here, should be legally protected in all EU member states.
Collapse
Affiliation(s)
- Robert Rutkowski
- Museum and Institute of Zoology, Polish Academy of Sciences, Warszawa, Poland
| | - Miha Krofel
- Wildlife Ecology Research Group, Department of Forestry, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Giorgos Giannatos
- Department of Zoology - Marine Biology, School of Biology, University of Athens, Panepistimioupolis, Athens, Greece
| | - Duško Ćirović
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | | | - József Lanszki
- Department of Nature Conservation, University of Kaposvár, Kaposvár, Hungary
| | - Miklós Heltai
- Institute for Wildlife Conservation, Szent István University, Gödöllő, Hungary
| | - László Szabó
- Institute for Wildlife Conservation, Szent István University, Gödöllő, Hungary
| | | | - Eduard Yavruyan
- Scientific Centre of Zoology and Hydroecology, National Academy of Sciences of Armenia, Yerevan, Armenia
| | - Vahram Hayrapetyan
- Stepanakert Branch of the Armenian National Agrarian University, Stepanakert, Armenia
| | - Natia Kopaliani
- Institute of Ecology, Ilia State University, Tbilisi, Georgia
| | - Anastasia Miliou
- Archipelagos Institute of Marine Conservation, Mesokampos, Pythagorio, Samos, Greece
| | | | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Heraklion, Crete, Greece
| | - Aleksandra Penezić
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | - Ewa Suchecka
- Museum and Institute of Zoology, Polish Academy of Sciences, Warszawa, Poland
| | - Wiesław Bogdanowicz
- Museum and Institute of Zoology, Polish Academy of Sciences, Warszawa, Poland
- * E-mail:
| |
Collapse
|
32
|
Phylogeography of the Golden Jackal (Canis aureus) in India. PLoS One 2015; 10:e0138497. [PMID: 26414163 PMCID: PMC4586146 DOI: 10.1371/journal.pone.0138497] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 08/31/2015] [Indexed: 01/23/2023] Open
Abstract
The golden jackal (Canis aureus) is one of the most common and widely distributed carnivores in India but phylogeographic studies on the species have been limited across its range. Recent studies have observed absence of mitochondrial (mt) DNA diversity in European populations while some North African populations of golden jackal were found to carry gray wolf (Canis lupus lupaster) mtDNA lineages. In the present study, we sequenced 440 basepairs (bp) of control region (CR) and 412 bp of cytochrome b (cyt b) gene of mtDNA from 62 golden jackals sampled from India (n = 55), Israel (n = 2) and Bulgaria (n = 5), to obtain a total of eighteen haplotypes, comprising sixteen from India and one each from Israel and Bulgaria. Except for three previously described haplotypes represented by one cyt b and one CR haplotype both from India, and one CR haplotype from Bulgaria, all haplotypes identified in this study are new. Genetic diversity was high in golden jackals compared to that reported for other canids in India. Unlike the paraphyletic status of African conspecifics with the gray wolf, the Indian (and other Eurasian) golden jackal clustered in a distinct but shallow monophyletic clade, displaying no evidence of admixture with sympatric and related gray wolf and domestic dog clades in the region. Phylogeographic analyses indicated no clear pattern of genetic structuring of the golden jackal haplotypes and the median joining network revealed a star-shaped polytomy indicative of recent expansion of the species from India. Indian haplotypes were observed to be interior and thus ancestral compared to haplotypes from Europe and Israel, which were peripheral and hence more derived. Molecular tests for demographic expansion confirmed a recent event of expansion of golden jackals in the Indian subcontinent, which can be traced back ~ 37,000 years ago during the late Pleistocene. Our results suggest that golden jackals have had a potentially longer evolutionary history in India than in other parts of the world, although further sampling from Africa, the Middle East and south-east Asia is needed to test this hypothesis.
Collapse
|
33
|
Reconstructing the colonization history of lost wolf lineages by the analysis of the mitochondrial genome. Mol Phylogenet Evol 2014; 80:105-12. [PMID: 25132126 DOI: 10.1016/j.ympev.2014.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/29/2014] [Accepted: 08/03/2014] [Indexed: 11/27/2022]
Abstract
The grey wolves (Canis lupus) originally inhabited major parts of the Northern hemisphere, but many local populations became extinct. Two lineages of wolves in Japan, namely, Japanese or Honshu (C. l. hodophilax) and Ezo or Hokkaido (C. l. hattai) wolves, rapidly went extinct between 100 and 120years ago. Here we analyse the complete mitochondrial genome sequences from ancient specimens and reconstruct the colonization history of the two extinct subspecies. We show a unique status of Japanese wolves in wolf phylogeny, suggesting their long time separation from other grey wolf populations. Japanese wolves appeared to have colonized the Japanese archipelago in the Late Pleistocene (ca. 25,000-125,000years ago). By contrast, Ezo wolves, which are clearly separated from Japanese wolves in phylogeny, are likely to have arrived at Japan relatively recently (<14,000years ago). Interestingly, their colonization history to Japan tallies well with the dynamics of wolf populations in Europe and America during the last several millennia. Our analyses suggest that at least several thousands of wolves once inhabited in the Japanese archipelago. Our analyses also show that an enigmatic clade of domestic dogs is likely to have originated from rare admixture events between male dogs and female Japanese wolves.
Collapse
|
34
|
Aghbolaghi MA, Rezaei HR, Scandura M, Kaboli M. Low gene flow between Iranian Grey Wolves(Canis lupus)and dogs documented using uniparental genetic markers. ZOOLOGY IN THE MIDDLE EAST 2014. [DOI: 10.1080/09397140.2014.914708] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
35
|
Genetic variability of the grey wolf Canis lupus in the Caucasus in comparison with Europe and the Middle East: distinct or intermediary population? PLoS One 2014; 9:e93828. [PMID: 24714198 PMCID: PMC3979716 DOI: 10.1371/journal.pone.0093828] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/07/2014] [Indexed: 01/17/2023] Open
Abstract
Despite continuous historical distribution of the grey wolf (Canis lupus) throughout Eurasia, the species displays considerable morphological differentiation that resulted in delimitation of a number of subspecies. However, these morphological discontinuities are not always consistent with patterns of genetic differentiation. Here we assess genetic distinctiveness of grey wolves from the Caucasus (a region at the border between Europe and West Asia) that have been classified as a distinct subspecies C. l. cubanensis. We analysed their genetic variability based on mtDNA control region, microsatellite loci and genome-wide SNP genotypes (obtained for a subset of the samples), and found similar or higher levels of genetic diversity at all these types of loci as compared with other Eurasian populations. Although we found no evidence for a recent genetic bottleneck, genome-wide linkage disequilibrium patterns suggest a long-term demographic decline in the Caucasian population--a trend consistent with other Eurasian populations. Caucasian wolves share mtDNA haplotypes with both Eastern European and West Asian wolves, suggesting past or ongoing gene flow. Microsatellite data also suggest gene flow between the Caucasus and Eastern Europe. We found evidence for moderate admixture between the Caucasian wolves and domestic dogs, at a level comparable with other Eurasian populations. Taken together, our results show that Caucasian wolves are not genetically isolated from other Eurasian populations, share with them the same demographic trends, and are affected by similar conservation problems.
Collapse
|
36
|
Jansson E, Harmoinen J, Ruokonen M, Aspi J. Living on the edge: reconstructing the genetic history of the Finnish wolf population. BMC Evol Biol 2014; 14:64. [PMID: 24678616 PMCID: PMC4033686 DOI: 10.1186/1471-2148-14-64] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/05/2014] [Indexed: 11/19/2022] Open
Abstract
Background Many western European carnivore populations became almost or completely eradicated during the last ~200 years, but are now recovering. Extirpation of wolves started in Finland in the 19th century, and for more than 150 years the population size of wolves has remained small. To investigate historical patterns of genetic variation, we extracted DNA from 114 wolf samples collected in zoological museums over the last ~150 years. Fifteen microsatellite loci were used to look at genotypic variation in this historical sample. Additionally, we amplified a 430 bp sequence of mtDNA control region from the same samples. Contemporary wolf samples (N = 298) obtained after the population recovery in the mid-1990s, were used as a reference. Results Our analyses of mtDNA revealed reduced variation in the mtDNA control region through the loss of historical haplotypes observed prior to wolf declines. Heterozygosity at autosomal microsatellite loci did not decrease significantly. However, almost 20% of microsatellite alleles were unique to wolves collected before the 1960s. The genetic composition of the population changed gradually with the largest changes occurring prior to 1920. Half of the oldest historical samples formed a distinguishable genetic cluster not detected in the modern-day Finnish or Russian samples, and might therefore represent northern genetic variation lost from today’s gene pool. Point estimates of Ne were small (13.2 and 20.5) suggesting population fragmentation. Evidence of a genetic population bottleneck was also detected. Conclusions Our genetic analyses confirm changes in the genetic composition of the Finnish wolf population through time, despite the geographic interconnectivity to a much larger population in Russia. Our results emphasize the need for restoration of the historical connectivity between the present wolf populations to secure long-term viability. This might be challenging, however, because the management policies between Western and Eastern Europe often differ greatly. Additionally, wolf conservation is still a rather controversial issue, and anthropogenic pressure towards wolves remains strong.
Collapse
Affiliation(s)
| | | | | | - Jouni Aspi
- Department of Biology, University of Oulu, P,O, Box 3000, FIN-90014 Oulu, Finland.
| |
Collapse
|
37
|
Crowther MS, Fillios M, Colman N, Letnic M. An updated description of the
A
ustralian dingo (
C
anis dingo
M
eyer, 1793). J Zool (1987) 2014. [DOI: 10.1111/jzo.12134] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- M. S. Crowther
- School of Biological Sciences University of Sydney Sydney NSW Australia
| | - M. Fillios
- Department of Archaeology University of Sydney Sydney NSW Australia
| | - N. Colman
- Hawkesbury Institute for the Environment University of Western Sydney Penrith NSW Australia
| | - M. Letnic
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
| |
Collapse
|
38
|
Weckworth BV, Dawson NG, Talbot SL, Flamme MJ, Cook JA. Going coastal: shared evolutionary history between coastal British Columbia and Southeast Alaska wolves (Canis lupus). PLoS One 2011; 6:e19582. [PMID: 21573241 PMCID: PMC3087762 DOI: 10.1371/journal.pone.0019582] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 04/10/2011] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Many coastal species occupying the temperate rainforests of the Pacific Northwest in North America comprise endemic populations genetically and ecologically distinct from interior continental conspecifics. Morphological variation previously identified among wolf populations resulted in recognition of multiple subspecies of wolves in the Pacific Northwest. Recently, separate genetic studies have identified diverged populations of wolves in coastal British Columbia and coastal Southeast Alaska, providing support for hypotheses of distinct coastal subspecies. These two regions are geographically and ecologically contiguous, however, there is no comprehensive analysis across all wolf populations in this coastal rainforest. METHODOLOGY/PRINCIPAL FINDINGS By combining mitochondrial DNA datasets from throughout the Pacific Northwest, we examined the genetic relationship between coastal British Columbia and Southeast Alaska wolf populations and compared them with adjacent continental populations. Phylogenetic analysis indicates complete overlap in the genetic diversity of coastal British Columbia and Southeast Alaska wolves, but these populations are distinct from interior continental wolves. Analyses of molecular variation support the separation of all coastal wolves in a group divergent from continental populations, as predicted based on hypothesized subspecies designations. Two novel haplotypes also were uncovered in a newly assayed continental population of interior Alaska wolves. CONCLUSIONS/SIGNIFICANCE We found evidence that coastal wolves endemic to these temperate rainforests are diverged from neighbouring, interior continental wolves; a finding that necessitates new international strategies associated with the management of this species.
Collapse
Affiliation(s)
- Byron V Weckworth
- Faculty of Environmental Design, University of Calgary, Calgary, Alberta, Canada.
| | | | | | | | | |
Collapse
|
39
|
Klütsch CFC, Seppälä EH, Fall T, Uhlén M, Hedhammar A, Lohi H, Savolainen P. Regional occurrence, high frequency but low diversity of mitochondrial DNA haplogroup d1 suggests a recent dog-wolf hybridization in Scandinavia. Anim Genet 2011; 42:100-3. [PMID: 20497152 PMCID: PMC3040290 DOI: 10.1111/j.1365-2052.2010.02069.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The domestic dog mitochondrial DNA (mtDNA)-gene pool consists of a homogenous mix of haplogroups shared among all populations worldwide, indicating that the dog originated at a single time and place. However, one small haplogroup, subclade d1, found among North Scandinavian/Finnish spitz breeds at frequencies above 30%, has a clearly separate origin. We studied the genetic and geographical diversity for this phylogenetic group to investigate where and when it originated and whether through independent domestication of wolf or dog-wolf crossbreeding. We analysed 582 bp of the mtDNA control region for 514 dogs of breeds earlier shown to harbour d1 and possibly related northern spitz breeds. Subclade d1 occurred almost exclusively among Swedish/Finnish Sami reindeer-herding spitzes and some Swedish/Norwegian hunting spitzes, at a frequency of mostly 60–100%. Genetic diversity was low, with only four haplotypes: a central, most frequent, one surrounded by two haplotypes differing by an indel and one differing by a substitution. The substitution was found in a single lineage, as a heteroplasmic mix with the central haplotype. The data indicate that subclade d1 originated in northern Scandinavia, at most 480–3000 years ago and through dog-wolf crossbreeding rather than a separate domestication event. The high frequency of d1 suggests that the dog-wolf hybrid phenotype had a selective advantage.
Collapse
Affiliation(s)
- C F C Klütsch
- KTH-Royal Institute of Technology, Gene Technology, Roslagstullsbacken 21, 10691 Stockholm, Sweden
| | | | | | | | | | | | | |
Collapse
|
40
|
Rueness EK, Asmyhr MG, Sillero-Zubiri C, Macdonald DW, Bekele A, Atickem A, Stenseth NC. The cryptic African wolf: Canis aureus lupaster is not a golden jackal and is not endemic to Egypt. PLoS One 2011; 6:e16385. [PMID: 21298107 PMCID: PMC3027653 DOI: 10.1371/journal.pone.0016385] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Accepted: 12/14/2010] [Indexed: 11/18/2022] Open
Abstract
The Egyptian jackal (Canis aureus lupaster) has hitherto been considered a large, rare subspecies of the golden jackal (C. aureus). It has maintained its taxonomical status to date, despite studies demonstrating morphological similarities to the grey wolf (C. lupus). We have analyzed 2055 bp of mitochondrial DNA from C. a. lupaster and investigated the similarity to C. aureus and C. lupus. Through phylogenetic comparison with all wild wolf-like canids (based on 726 bp of the Cytochrome b gene) we conclusively (100% bootstrap support) place the Egyptian jackal within the grey wolf species complex, together with the Holarctic wolf, the Indian wolf and the Himalayan wolf. Like the two latter taxa, C. a. lupaster seems to represent an ancient wolf lineage which most likely colonized Africa prior to the northern hemisphere radiation. We thus refer to C. a. lupaster as the African wolf. Furthermore, we have detected C. a. lupaster individuals at two localities in the Ethiopian highlands, extending the distribution by at least 2,500 km southeast. The only grey wolf species to inhabit the African continent is a cryptic species for which the conservation status urgently needs assessment.
Collapse
Affiliation(s)
- Eli Knispel Rueness
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
| | - Maria Gulbrandsen Asmyhr
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
| | - Claudio Sillero-Zubiri
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - David W. Macdonald
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Afework Bekele
- Biology Department, Science Faculty, Addis Ababa University, Addis Ababa, Ethiopia
| | - Anagaw Atickem
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
| | - Nils Chr. Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
| |
Collapse
|
41
|
|
42
|
Weckworth BV, Talbot SL, Cook JA. Phylogeography of wolves (Canis lupus) in the Pacific Northwest. J Mammal 2010. [DOI: 10.1644/09-mamm-a-036.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
43
|
Singh L. Development and exploitation of DNA fingerprinting technology in India. Biotechnol J 2009; 4:335-41. [DOI: 10.1002/biot.200900015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|