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Hennelly LM, Sarwar G, Fatima H, Werhahn G, Abbas FI, Khan AM, Mahmood T, Kachel S, Kubanychbekov Z, Waseem MT, Zahra Naqvi R, Hamid A, Abbas Y, Aisha H, Waseem M, Farooq M, Sacks BN. Genomic analysis of wolves from Pakistan clarifies boundaries among three divergent wolf lineages. J Hered 2024; 115:339-348. [PMID: 37897187 DOI: 10.1093/jhered/esad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023] Open
Abstract
Among the three main divergent lineages of gray wolf (Canis lupus), the Holarctic lineage is the most widespread and best studied, particularly in North America and Europe. Less is known about Tibetan (also called Himalayan) and Indian wolf lineages in southern Asia, especially in areas surrounding Pakistan where all three lineages are thought to meet. Given the endangered status of the Indian wolf in neighboring India and unclear southwestern boundary of the Tibetan wolf range, we conducted mitochondrial and genome-wide sequencing of wolves from Pakistan and Kyrgyzstan. Sequences of the mitochondrial D-loop region of 81 wolves from Pakistan indicated contact zones between Holarctic and Indian lineages across the northern and western mountains of Pakistan. Reduced-representation genome sequencing of eight wolves indicated an east-to-west cline of Indian to Holarctic ancestry, consistent with a contact zone between these two lineages in Pakistan. The western boundary of the Tibetan lineage corresponded to the Ladakh region of India's Himalayas with a narrow zone of admixture spanning this boundary from the Karakoram Mountains of northern Pakistan into Ladakh, India. Our results highlight the conservation significance of Pakistan's wolf populations, especially the remaining populations in Sindh and Southern Punjab that represent the highly endangered Indian lineage.
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Affiliation(s)
- Lauren M Hennelly
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA, United States
| | - Ghulam Sarwar
- Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Hira Fatima
- Department of Zoology, University of Education, Lahore, Pakistan
| | - Geraldine Werhahn
- IUCN SCC Canid Specialist Group, Oxford, United Kingdom
- Wildlife Conservation Research Unit, Zoology, University of Oxford, Tubney, United Kingdom
| | | | - Abdul M Khan
- Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Tariq Mahmood
- Department of Zoology, Wildlife and Fisheries, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | | | | | - Muhammad T Waseem
- Zoological Science Division, Pakistan Museum of Natural History, Islamabad, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Abdul Hamid
- Department of Zoology, Wildlife and Fisheries, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Yasir Abbas
- Central Karakoram National Park, Skardu, Pakistan
| | - Hamera Aisha
- World Wildlife Fund, Pakistan, Islamabad, Pakistan
| | | | - Muhammad Farooq
- Department of Zoology, Wildlife and Fisheries, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA, United States
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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2
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Kunde MN, Barlow A, Klittich AM, Yakupova A, Patel RP, Fickel J, Förster DW. First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages. Ecol Evol 2023; 13:e9969. [PMID: 37082317 PMCID: PMC10111171 DOI: 10.1002/ece3.9969] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 03/04/2023] [Accepted: 03/14/2023] [Indexed: 04/22/2023] Open
Abstract
The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focussing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species' distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra, and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged ~295 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; "Mainland clade"), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand ("Sunda clade"). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbor a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.
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Affiliation(s)
- Miriam N. Kunde
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
- School of EnvironmentGriffith UniversityNathan Campus, 170 Kessels Road, NathanBrisbaneQueensland4111Australia
| | - Axel Barlow
- School of Natural SciencesBangor UniversityBangorGwyneddLL57 2DGUK
| | - Achim M. Klittich
- Institute for Biochemistry and BiologyUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476PotsdamGermany
| | - Aliya Yakupova
- Computer Technologies LaboratoryITMO University197101Saint PetersburgRussia
| | - Riddhi P. Patel
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
- Institute for Biochemistry and BiologyUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476PotsdamGermany
| | - Daniel W. Förster
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
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3
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Sosale MS, Songsasen N, İbiş O, Edwards CW, Figueiró HV, Koepfli KP. The complete mitochondrial genome and phylogenetic characterization of two putative subspecies of golden jackal (Canis aureus cruesemanni and Canis aureus moreotica). Gene 2023; 866:147303. [PMID: 36854348 DOI: 10.1016/j.gene.2023.147303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023]
Abstract
The golden jackal (Canis aureus) is a canid species found across southern Eurasia. Several subspecies of this animal have been genetically studied in regions such as Europe, the Middle East, and India. However, one subspecies that lacks current research is the Indochinese jackal (Canis aureus cruesemanni), which is primarily found in Southeast Asia. Using a genome skimming approach, we assembled the first complete mitochondrial genome for an Indochinese jackal from Thailand. To expand the number of available Canis aureus mitogenomes, we also assembled and sequenced the first complete mitochondrial genome of a golden jackal from Turkey, representing the C. a. moreotica subspecies. The mitogenomes contained 37 annotated genes and are 16,729 bps (C. a. cruesemanni) and 16,669 bps (C. a. moreotica) in length. Phylogenetic analysis with 26 additional canid mitogenomes and analyses of a cytochrome b gene-only data set together support the Indochinese jackal as a distinct and early-branching lineage among golden jackals, thereby supporting its recognition as a possible subspecies. These analyses also demonstrate that the golden jackal from Turkey is likely not a distinct lineage due to close genetic relationships with golden jackals from India and Israel.
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Affiliation(s)
- Medhini S Sosale
- Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, VA, USA; Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA.
| | - Nucharin Songsasen
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA
| | - Osman İbiş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey; Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey; Vectors and Vector-Borne Diseases Implementation and Research Center, Erciyes University, Kayseri, Turkey
| | - Cody W Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA; Department of Biology, George Mason University, Fairfax, VA, USA
| | - Henrique V Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA; Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA.
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Sacks BN. Evolutionary legacy of the extirpated red wolf clings to life in gulf-coast canids. Mol Ecol 2022; 31:5419-5422. [PMID: 36210646 DOI: 10.1111/mec.16725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/15/2022] [Accepted: 10/06/2022] [Indexed: 12/24/2022]
Abstract
Before Europeans colonized North America, a uniquely American wolf roamed the eastern forests of southern Canada to Florida and west to the Great Plains. Known today as "red wolf" (Canis rufus) in the south and "eastern wolf" (Canis lycaon) in the north, evidence suggests that these indigenous forest wolves shared a common evolutionary history until only a few centuries ago when they were extirpated from the intervening majority of their historical range. While the eastern wolf persists today primarily as a small population in Algonquin Provincial Park, Canada, the red wolf was ostensibly driven from its last stronghold in gulf-coastal Louisiana and Texas by 1980. The last-known red wolves were taken captive for propagation and reintroduction. Today, the red wolf exists as ~250 descendants of 12 founders and are distributed among 42 captive breeding facilities and one reintroduced population in coastal North Carolina. As red and eastern wolves declined in the 20th century, coyotes expanded from the west into the eastern forests, replacing them. Along with human persecution, coyote hybridization has been blamed for the late 20th century demise of the red wolf. However, rather than helping to drive the red wolf to extinction, coyote hybridization may have instead helped to preserve it. In this issue of Molecular Ecology, vonHoldt and colleagues provide the most comprehensive description yet of the substantial quantity and distribution of red wolf ancestry sequestered in southeastern coyote populations. They find the highest frequency of red wolf genes in coyotes from the gulf-coastal sites where the last known wild red wolves occurred, but also present evidence for a high prevalence of red wolf genes in coyotes throughout the southeastern expansion zone. Given the significant reduction in genetic diversity in extant red wolves owing to their late 20th century population bottleneck, this coyote-sequestered reservoir of red wolf genes could prove an important resource for red wolf conservation.
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Affiliation(s)
- Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics, Department of Population Health and Reproduction, University of California, Davis, California, USA
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Sacks BN, Statham MJ, Serieys LEK, Riley SPD. Population Genetics of California Gray Foxes Clarify Origins of the Island Fox. Genes (Basel) 2022; 13:genes13101859. [PMID: 36292742 PMCID: PMC9602142 DOI: 10.3390/genes13101859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 11/04/2022] Open
Abstract
We used mitochondrial sequences and nuclear microsatellites to investigate population structure of gray foxes (Urocyon cinereoargenteus) and the evolutionary origins of the endemic island fox (Urocyon littoralis), which first appeared in the northern Channel Islands <13,000 years ago and in the southern Channel Islands <6000 years ago. It is unclear whether island foxes evolved directly from mainland gray foxes transported to the islands one or more times or from a now-extinct mainland population, already diverged from the gray fox. Our 345 mitochondrial sequences, combined with previous data, confirmed island foxes to be monophyletic, tracing to a most recent common ancestor approximately 85,000 years ago. Our rooted nuclear DNA tree additionally indicated genome-wide monophyly of island foxes relative to western gray foxes, although we detected admixture in northern island foxes from adjacent mainland gray foxes, consistent with some historical gene flow. Southern California gray foxes also bore a genetic signature of admixture and connectivity to a desert population, consistent with partial replacement by a late-Holocene range expansion. Using our outgroup analysis to root previous nuclear sequence-based trees indicated reciprocal monophyly of northern versus southern island foxes. Results were most consistent with island fox origins through multiple introductions from a now-extirpated mainland population.
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Affiliation(s)
- Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA
- Correspondence:
| | - Mark J. Statham
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA
| | | | - Seth P. D. Riley
- National Park Service, Santa Monica Mountains National Recreation Area, 401 W Hillcrest Dr, Thousand Oaks, CA 91360, USA
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6
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Thompson CA, Benson JF, Patterson BR. A novel survey design for modeling species distribution of beavers in Algonquin Park, Canada. WILDLIFE SOC B 2022. [DOI: 10.1002/wsb.1322] [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]
Affiliation(s)
| | - John F. Benson
- School of Natural Resources University of Nebraska–Lincoln 3300 Holdrege Street Lincoln NE 68583 USA
| | - Brent R. Patterson
- Ontario Ministry of Natural Resources and Forestry 2140 East Bank Drive Peterborough ON K9L 1Z8 Canada
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Rocha JL, Vaz Pinto P, Siegismund HR, Meyer M, Jansen van Vuuren B, Veríssimo L, Ferrand N, Godinho R. African climate and geomorphology drive evolution and ghost introgression in sable antelope. Mol Ecol 2022; 31:2968-2984. [PMID: 35305042 DOI: 10.1111/mec.16427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 02/13/2022] [Accepted: 03/04/2022] [Indexed: 11/27/2022]
Abstract
The evolutionary history of African ungulates has been largely explained in the light of Pleistocene climatic oscillations and the way these influenced the distribution of vegetation types, leading to range expansions and/or isolation in refugia. In contrast, comparatively fewer studies have addressed the continent's environmental heterogeneity and the role played by its geomorphological barriers. In this study, we performed a range-wide analysis of complete mitogenomes of sable antelope (Hippotragus niger) to explore how these different factors may have contributed as drivers of evolution in South-Central Africa. Our results supported two sympatric and deeply divergent mitochondrial lineages in west Tanzanian sables, which can be explained as the result of introgressive hybridization of a mitochondrial ghost lineage from an archaic, as-yet-undefined, congener. Phylogeographic subdivisions into three main lineages suggest that sable diversification may not have been solely driven by climatic events affecting populations differently across a continental scale. Often in interplay with climate, geomorphological features have also clearly shaped the species' patterns of vicariance, where the East Africa Rift System and the Eastern Arc Mountains acted as geological barriers. Subsequent splits among southern populations may be linked to rearrangements in the Zambezi system, possibly framing the most recent time when the river attained its current drainage profile. This work underscores how the use of comprehensive mitogenomic datasets on a model species with a wide geographic distribution can contribute to a much-enhanced understanding of environmental, geomorphological, and evolutionary patterns in Africa throughout the Quaternary.
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Affiliation(s)
- Joana L Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Pedro Vaz Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Fundação Kissama, Rua Joaquim Capango 49, Luanda, Angola
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bettine Jansen van Vuuren
- Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Luís Veríssimo
- Fundação Kissama, Rua Joaquim Capango 49, Luanda, Angola
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
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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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