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Hrebianchuk AE, Tsybovsky IS. A universal panel of STR loci for the study of polymorphism of the species Canis lupus and forensic identification of dog and wolf. Vavilovskii Zhurnal Genet Selektsii 2024; 28:98-107. [PMID: 38465248 PMCID: PMC10917668 DOI: 10.18699/vjgb-24-12] [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: 01/24/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 03/12/2024] Open
Abstract
Commercial panels of microsatellite (STR) loci are intended for DNA analysis of the domestic dog (Canis lupus familiaris) and, therefore, when genotyping the Grey wolf (Canis lupus lupus), most markers reveal significant deviations from the Hardy-Weinberg equilibrium and have a low informative value, which complicates their use in a forensic examination. The aim of this study was to select STR markers that equally effectively reflect population polymorphism in the wolf and the dog, and to create a universal panel for the identification of individuals in forensic science. Based on the study of polymorphisms of 34 STR loci, a CPlex panel of 15 autosomal loci and two sex loci was developed, which is equally suitable for identifying wolfs and dogs. Analysis of molecular variance (AMOVA) between samples revealed significant differentiation values (FST = 0.0828, p < 0.05), which allows the panel to be used for differentiating between wolf and dog samples. For the first time in the forensic examination of objects of animal origin in the Republic of Belarus, population subdivision coefficients (θ-values) were calculated for each of the 15 STR loci of the test system being reported. It was shown that the values of the genotype frequency, when averaged over all studied animals without and with considering the θ-value, differ by three orders of magnitude (3.39 · 10-17 and 4.71 · 10-14, respectively). The use of population subdivision coefficients will provide the researcher with the most relevant results of an expert identification study. The test system was validated in accordance with the protocol of the Scientific Working Group on DNA Analysis Methods. A computational tool was developed to automate the analysis of genetic data on the wolf and dog in the forensic examination; two guides were approved for practicing forensic experts. This methodology is being successfully used in expert practice in investigating cases of illegal hunting, animal abuse and other offenses in the Republic of Belarus.
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Affiliation(s)
- A E Hrebianchuk
- Forensic Examination Committee of the Republic of Belarus, Minsk, Belarus
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2
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Lapid R, Motro Y, Craddock H, Khalfin B, King R, Bar-Gal GK, Moran-Gilad J. Fecal microbiota of the synanthropic golden jackal (Canis aureus). Anim Microbiome 2023; 5:37. [PMID: 37542305 PMCID: PMC10403885 DOI: 10.1186/s42523-023-00259-3] [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: 03/25/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The golden jackal (Canis aureus), is a medium canid carnivore widespread throughout the Mediterranean region and expanding into Europe. This species thrives near human settlements and is implicated in zoonoses such as rabies. This study explores for the first time, the golden jackal fecal microbiota. We analyzed 111 fecal samples of wild golden jackals using 16S rRNA amplicon sequencing the connection of the microbiome to animal characteristics, burden of pathogens and geographic and climate characteristics. We further compared the fecal microbiota of the golden jackal to the black-backed jackal and domestic dog. We found that the golden jackal fecal microbiota is dominated by the phyla Bacteroidota, Fusobacteriota and Firmicutes. The golden jackal fecal microbiota was associated with different variables, including geographic region, age-class, exposure to rabies oral vaccine, fecal parasites and toxoplasmosis. A remarkable variation in the relative abundance of different taxa was also found associated with different variables, such as age-class. Linear discriminant analysis effect size (LEfSe) analysis found abundance of specific taxons in each region, Megasphaera genus in group 1, Megamonas genus in group 2 and Bacteroides coprocola species in group 3. We also found a different composition between the fecal microbiota of the golden jackal, blacked-backed jackal and the domestic dog. Furthermore, LEfSe analysis found abundance of Fusobacterium and Bacteroides genera in the golden jackal, Clostridia class in blacked-backed jackal and Megamonas genus in domestic dog. The golden jackal fecal microbiota is influenced by multiple factors including host traits and pathogen burden. The characterization of the microbiota of this thriving species may aid in mapping its spread and proximity to human settlements. Moreover, understanding the jackal microbiota could inform the study of potential animal and human health risks and inform control measures.
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Affiliation(s)
- Roi Lapid
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O.B. 12, 7610001, Rehovot, Israel
| | - Yair Motro
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Hillary Craddock
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Boris Khalfin
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Roni King
- Science and Conservation Division, Israel Nature and Parks Authority, 3 Am Ve'Olamo St., 95463, Jerusalem, Israel
| | - Gila Kahila Bar-Gal
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O.B. 12, 7610001, Rehovot, Israel
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel.
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3
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Barash A, Preiss-Bloom S, Machluf Y, Fabbri E, Malkinson D, Velli E, Mucci N, Barash A, Caniglia R, Dayan T, Dekel Y. Possible origins and implications of atypical morphologies and domestication-like traits in wild golden jackals (Canis aureus). Sci Rep 2023; 13:7388. [PMID: 37149712 PMCID: PMC10164184 DOI: 10.1038/s41598-023-34533-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
Deciphering the origins of phenotypic variations in natural animal populations is a challenging topic for evolutionary and conservation biologists. Atypical morphologies in mammals are usually attributed to interspecific hybridisation or de-novo mutations. Here we report the case of four golden jackals (Canis aureus), that were observed during a camera-trapping wildlife survey in Northern Israel, displaying anomalous morphological traits, such as white patches, an upturned tail, and long thick fur which resemble features of domesticated mammals. Another individual was culled under permit and was genetically and morphologically examined. Paternal and nuclear genetic profiles, as well as geometric morphometric data, identified this individual as a golden jackal rather than a recent dog/wolf-jackal hybrid. Its maternal haplotype suggested past introgression of African wolf (Canis lupaster) mitochondrial DNA, as previously documented in other jackals from Israel. When viewed in the context of the jackal as an overabundant species in Israel, the rural nature of the surveyed area, the abundance of anthropogenic waste, and molecular and morphological findings, the possibility of an individual presenting incipient stages of domestication should also be considered.
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Affiliation(s)
- Ayelet Barash
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel
| | - Shlomo Preiss-Bloom
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - Yossy Machluf
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Dan Malkinson
- Department of Geography and Environmental Studies, University of Haifa, 3498838, Haifa, Israel
| | - Edoardo Velli
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Alon Barash
- The Azrieli Faculty of Medicine, Bar Ilan University, 8 Henrietta Szold St, Safed, Israel
| | - Romolo Caniglia
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy.
| | - Tamar Dayan
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel.
| | - Yaron Dekel
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel.
- The Cheryl Spencer Department of Nursing and The Cheryl Spencer Institute of Nursing Research, University of Haifa, 3498838, Haifa, Israel.
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4
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Nikitović J, Djan M, Ćirović D, Antić M, Šnjegota D. The first report on genetic variability and population structure in jackals from Bosnia and Herzegovina. MAMMAL RES 2022. [DOI: 10.1007/s13364-022-00665-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Tolerance of wolves shapes desert canid communities in the Middle East. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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6
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Horecka B, Jakubczak A, Ślaska B, Jeżewska-Witkowska G. Raccoon dog ( Nyctereutes procyonoides) phylogeography including the Polish population: local and global aspects. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2070289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- B. Horecka
- Institute of Biological Basis of Animal Production, Faculty of Animal Science and Bioeconomy, University of Life Sciences in Lublin, Lublin
| | - A. Jakubczak
- Institute of Biological Basis of Animal Production, Faculty of Animal Science and Bioeconomy, University of Life Sciences in Lublin, Lublin
| | - B. Ślaska
- Institute of Biological Basis of Animal Production, Faculty of Animal Science and Bioeconomy, University of Life Sciences in Lublin, Lublin
| | - G. Jeżewska-Witkowska
- Institute of Biological Basis of Animal Production, Faculty of Animal Science and Bioeconomy, University of Life Sciences in Lublin, Lublin
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7
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Yusefi GH, Godinho R, Khalatbari L, Broomand S, Fahimi H, Martínez‐Freiría F, Alvares F. Habitat use and population genetics of golden jackals in Iran: Insights from a generalist species in a highly heterogeneous landscape. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gholam Hosein Yusefi
- CIBIO/InBIO ‐ Centro de Investigação em Biodiversidade e Recursos Genéticos University of PortoVairão Vairão Portugal
- Mohitban Society Tehran Iran
| | - Raquel Godinho
- CIBIO/InBIO ‐ Centro de Investigação em Biodiversidade e Recursos Genéticos University of PortoVairão Vairão Portugal
- Department of Biology Faculty of Sciences University of Porto Porto Portugal
- Department of Zoology University of Johannesburg Johannesburg South Africa
| | - Leili Khalatbari
- CIBIO/InBIO ‐ Centro de Investigação em Biodiversidade e Recursos Genéticos University of PortoVairão Vairão Portugal
- Mohitban Society Tehran Iran
- Department of Biology Faculty of Sciences University of Porto Porto Portugal
| | | | | | - Fernando Martínez‐Freiría
- CIBIO/InBIO ‐ Centro de Investigação em Biodiversidade e Recursos Genéticos University of PortoVairão Vairão Portugal
| | - Francisco Alvares
- CIBIO/InBIO ‐ Centro de Investigação em Biodiversidade e Recursos Genéticos University of PortoVairão Vairão Portugal
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Transmission of the Human Relapsing Fever Spirochete Borrelia persica by the Argasid Tick Ornithodoros tholozani Involves Blood Meals from Wildlife Animal Reservoirs and Mainly Transstadial Transfer. Appl Environ Microbiol 2021; 87:AEM.03117-20. [PMID: 33741637 DOI: 10.1128/aem.03117-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/14/2021] [Indexed: 11/20/2022] Open
Abstract
Borrelia persica, transmitted by the argasid tick Ornithodoros tholozani, causes human tick-borne relapsing fever in the Middle East and Central Asia. Infection is acquired often when visiting tick-infested caves and reported to be transmitted mainly transovarially between ticks, occasionally infecting humans. To study the epidemiology of this infection, ticks were trapped in 24 caves in 12 geographic zones covering all of Israel and identified morphologically. DNA was extracted from larvae, nymphs, and adult stages from each location and PCR followed by DNA sequencing was performed to identify Borrelia infection, tick species, and tick blood meal sources. We collected 51,472 argasid ticks from 16 of 24 caves surveyed. We analyzed 2,774 O. tholozani ticks, and 72 (2.6%) from nine caves were PCR positive for B. persica Infection rates in male, female, and nymphal ticks (4.4%, 3%, and 3.2%, respectively) were higher than in larva (P < 0.001), with only 3 (0.04%) positive larvae. Presence of blood meal was associated with B. persica infection in ticks (P = 0.003), and blood meals of golden jackals, red foxes, and Cairo spiny mouse were associated with infection (P ≤ 0.043). PCR survey of 402 wild mammals revealed B. persica infection with the highest rates in social voles (22%), red foxes (16%), golden jackals (8%), and Cairo spiny mice (3%). In conclusion, although transovarial tick transmission of B. persica occurs at low levels, ticks apparently acquire infection mainly from wildlife canid and rodents and may eventually transmit relapsing fever borreliosis to humans who enter their habitat.IMPORTANCE Borrelia persica is a spirochete that causes tick-borne relapsing fever in humans in an area that spans from India to the Mediterranean. Until now, it was thought that the soft tick vector of this infection, Ornithodoros tholozani, is also its main reservoir and it transmits B. persica mostly transovarially between tick generations. This study showed that tick infection with B. persica is associated with feeding blood from wild jackals, foxes, and rodents and that transovarial transmission is minimal. Since O. tholozani ticks are found in isolated caves and ruins, it is assumed that wild canids who migrate over long distances have a major role in the transmission of B. persica between remote tick populations, and it is then maintained locally also by rodents and eventually transferred to humans during tick bites. Prevention of human infection could be achieved by restricting entrance of canines and humans to habitats with O. tholozani populations.
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Abd Rabou AFN, Elkahlout KE, Almabhouh FA, Mohamed WF, Khalaf NA, Al-Sadek MA, Alfarra RN, Al-Moqayed LT, Shafei AA, Fayyad NA, Adeem BS, Dardona AW, Awad AS, Al-Agha MR, Abd Rabou MA. Occurrence and Some Ecological Aspects of the Golden Jackal (<i>Canis aureus</i> Linnaeus, 1758) in the Gaza Strip, Palestine. OPEN JOURNAL OF ECOLOGY 2021; 11:105-125. [DOI: 10.4236/oje.2021.112010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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10
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Shakarashvili M, Kopaliani N, Gurielidze Z, Dekanoidze D, Ninua L, Tarkhnishvili D. Population genetic structure and dispersal patterns of grey wolfs (
Canis lupus
) and golden jackals (
Canis aureus
) in Georgia, the Caucasus. J Zool (1987) 2020. [DOI: 10.1111/jzo.12831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - N. Kopaliani
- Institute of Ecology Ilia State University Tbilisi Georgia
| | - Z. Gurielidze
- Institute of Ecology Ilia State University Tbilisi Georgia
- Tbilisi Zoo Tbilisi Georgia
| | - D. Dekanoidze
- Institute of Ecology Ilia State University Tbilisi Georgia
| | - L. Ninua
- Institute of Ecology Ilia State University Tbilisi Georgia
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11
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MacLeod N, Kolska Horwitz L. Machine-learning strategies for testing patterns of morphological variation in small samples: sexual dimorphism in gray wolf (Canis lupus) crania. BMC Biol 2020; 18:113. [PMID: 32883273 PMCID: PMC7470621 DOI: 10.1186/s12915-020-00832-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 07/20/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Studies of mammalian sexual dimorphism have traditionally involved the measurement of selected dimensions of particular skeletal elements and use of single data-analysis procedures. Consequently, such studies have been limited by a variety of both practical and conceptual constraints. To compare and contrast what might be gained from a more exploratory, multifactorial approach to the quantitative assessment of form-variation, images of a small sample of modern Israeli gray wolf (Canis lupus) crania were analyzed via elliptical Fourier analysis of cranial outlines, a Naïve Bayes machine-learning approach to the analysis of these same outline data, and a deep-learning analysis of whole images in which all aspects of these cranial morphologies were represented. The statistical significance and stability of each discriminant result were tested using bootstrap and jackknife procedures. RESULTS Our results reveal no evidence for statistically significant sexual size dimorphism, but significant sex-mediated shape dimorphism. These are consistent with the findings of prior wolf sexual dimorphism studies and extend these studies by identifying new aspects of dimorphic variation. Additionally, our results suggest that shape-based sexual dimorphism in the C. lupus cranial complex may be more widespread morphologically than had been appreciated by previous researchers. CONCLUSION Our results suggest that size and shape dimorphism can be detected in small samples and may be dissociated in mammalian morphologies. This result is particularly noteworthy in that it implies there may be a need to refine allometric hypothesis tests that seek to account for phenotypic sexual dimorphism. The methods we employed in this investigation are fully generalizable and can be applied to a wide range of biological materials and could facilitate the rapid evaluation of a diverse array of morphological/phenomic hypotheses.
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Affiliation(s)
- Norman MacLeod
- School of Earth Science and Engineering, Zhu Gongshan Building, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023 Jiangsu China
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus - Givat Ram, 9190401 Jerusalem, Israel
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12
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Hong Y, Kim KS, Kimura J, Kauhala K, Voloshina I, Goncharuk MS, Yu L, Zhang YP, Sashika M, Lee H, Min MS. Genetic Diversity and Population Structure of East Asian Raccoon Dog (Nyctereutes procyonoides): Genetic Features in Central and Marginal Populations. Zoolog Sci 2019; 35:249-259. [PMID: 29882500 DOI: 10.2108/zs170140] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The raccoon dog (Nyctereutes procyonoides) is endemic to East Asia but has been introduced in Europe. Its high adaptability enabled its rapid colonization of European countries, where population growth has been raising concerns regarding ecosystem disturbance and the spread of zoonotic diseases. The genetic diversity and structure of endemic, source, and introduced populations from seven locations across South Korea, China, Russian Far East, Finland (spread to Finland after introduction to European part of Russia from Russian Far East), Vietnam, and Japan (Honshu and Hokkaido) were examined based on 16 microsatellite loci. Two major and significantly different (FST = 0.236) genetic clusters were found: continental (South Korean, Chinese, Russian, Finnish, and Vietnamese) and island (Japanese) populations. The continental raccoon dog population comprises three subpopulations (Chinese_Russian_Finnish, South Korean, and Vietnamese) and the Japanese population consists of Honshu and Hokkaido subpopulations. The genetic diversity and geographic structure of raccoon dogs in East Asia has been influenced by natural barriers to gene flow and reveals a typical central-marginal trend in genetic diversity (continental vs. island, and central vs. marginal or source vs. introduced within continental populations). The detected differences between continental and island populations agree with those reported in previous studies that considered these populations as different species.
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Affiliation(s)
- YoonJee Hong
- 1 Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Kyung Seok Kim
- 2 Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA 50011, USA
| | - Junpei Kimura
- 3 Laboratory of Anatomy and Cell Biology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Kaarina Kauhala
- 4 Luonnonvarakeskus (Luke)/Natural Resources Institute Finland, Itäinen Pitkäkatu 3 A, FI-20520 Turku, Finland
| | - Inna Voloshina
- 5 Lazovsky State Nature Reserve, Lazo, Primorsky Krai 692980, Russia
| | - Mikhail S Goncharuk
- 6 Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom
| | - Li Yu
- 7 State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Ya-Ping Zhang
- 8 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| | - Mariko Sashika
- 9 Laboratory of Wildlife Biology and Medicine, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Hang Lee
- 1 Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Mi-Sook Min
- 1 Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
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Zecchin B, De Nardi M, Nouvellet P, Vernesi C, Babbucci M, Crestanello B, Bagó Z, Bedeković T, Hostnik P, Milani A, Donnelly CA, Bargelloni L, Lorenzetto M, Citterio C, Obber F, De Benedictis P, Cattoli G. Genetic and spatial characterization of the red fox (Vulpes vulpes) population in the area stretching between the Eastern and Dinaric Alps and its relationship with rabies and canine distemper dynamics. PLoS One 2019; 14:e0213515. [PMID: 30861028 PMCID: PMC6413928 DOI: 10.1371/journal.pone.0213515] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/24/2019] [Indexed: 01/02/2023] Open
Abstract
Information on the population dynamics of a reservoir species have been increasingly adopted to understand and eventually predict the dispersal patterns of infectious diseases throughout an area. Although potentially relevant, to date there are no studies which have investigated the genetic structure of the red fox population in relation to infectious disease dynamics. Therefore, we genetically and spatially characterised the red fox population in the area stretching between the Eastern and Dinaric Alps, which has been affected by both distemper and rabies at different time intervals. Red foxes collected from north-eastern Italy, Austria, Slovenia and Croatia between 2006–2012, were studied using a set of 21 microsatellite markers. We confirmed a weak genetic differentiation within the fox population using Bayesian clustering analyses, and we were able to differentiate the fox population into geographically segregated groups. Our finding might be due to the presence of geographical barriers that have likely influenced the distribution of the fox population, limiting in turn gene flow and spread of infectious diseases. Focusing on the Italian red fox population, we observed interesting variations in the prevalence of both diseases among distinct fox clusters, with the previously identified Italy 1 and Italy 2 rabies as well as distemper viruses preferentially affecting different sub-groups identified in the study. Knowledge of the regional-scale population structure can improve understanding of the epidemiology and spread of diseases. Our study paves the way for an integrated approach for disease control coupling pathogen, host and environmental data to inform targeted control programs in the future.
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Affiliation(s)
- Bianca Zecchin
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
- * E-mail:
| | - Marco De Nardi
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Pierre Nouvellet
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Barbara Crestanello
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Zoltán Bagó
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control, Mödling, Austria
| | | | - Peter Hostnik
- Virology Unit, Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Adelaide Milani
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Christl Ann Donnelly
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, London, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Monica Lorenzetto
- Department of Veterinary Epidemiology, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Carlo Citterio
- SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Belluno, Italy
| | - Federica Obber
- SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Belluno, Italy
| | - Paola De Benedictis
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Giovanni Cattoli
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
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Kusza S, Nagy K, Lanszki J, Heltai M, Szabó C, Czarnomska SD. Moderate genetic variability and no genetic structure within the European golden jackal (Canis aureus) population in Hungary. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0390-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Canis aureus (Linnaeus, 1758), the golden jackal, is a medium-sized, wide spread, terrestrial carnivore. It is 1 of 7 species found in the genus Canis. It ranges from Africa to Europe, the Middle East, Central Asia, and Southeast Asia. Due to its tolerance of dry habitats and its omnivorous diet, C. aureus can live in a wide variety of habitats. It normally lives in open grassland habitat but also occurs in deserts, woodlands, mangroves, and agricultural and rural habitats in India and Bangladesh. It ranges from sea level in Eritrea to 3,500 m in the Bale Mountains of Ethiopia and 2,000 m in India. C. aureus is listed as “Least Concern” by the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species version 2016.1.
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Affiliation(s)
| | - Virginia Hayssen
- Department of Biological Sciences, Smith College, Northampton, MA, USA
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16
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Hanke D, Freuling CM, Fischer S, Hueffer K, Hundertmark K, Nadin-Davis S, Marston D, Fooks AR, Bøtner A, Mettenleiter TC, Beer M, Rasmussen TB, Müller TF, Höper D. Spatio-temporal Analysis of the Genetic Diversity of Arctic Rabies Viruses and Their Reservoir Hosts in Greenland. PLoS Negl Trop Dis 2016; 10:e0004779. [PMID: 27459154 PMCID: PMC4961414 DOI: 10.1371/journal.pntd.0004779] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 05/24/2016] [Indexed: 12/05/2022] Open
Abstract
There has been limited knowledge on spatio-temporal epidemiology of zoonotic arctic fox rabies among countries bordering the Arctic, in particular Greenland. Previous molecular epidemiological studies have suggested the occurrence of one particular arctic rabies virus (RABV) lineage (arctic-3), but have been limited by a low number of available samples preventing in-depth high resolution phylogenetic analysis of RABVs at that time. However, an improved knowledge of the evolution, at a molecular level, of the circulating RABVs and a better understanding of the historical perspective of the disease in Greenland is necessary for better direct control measures on the island. These issues have been addressed by investigating the spatio-temporal genetic diversity of arctic RABVs and their reservoir host, the arctic fox, in Greenland using both full and partial genome sequences. Using a unique set of 79 arctic RABV full genome sequences from Greenland, Canada, USA (Alaska) and Russia obtained between 1977 and 2014, a description of the historic context in relation to the genetic diversity of currently circulating RABV in Greenland and neighboring Canadian Northern territories has been provided. The phylogenetic analysis confirmed delineation into four major arctic RABV lineages (arctic 1–4) with viruses from Greenland exclusively grouping into the circumpolar arctic-3 lineage. High resolution analysis enabled distinction of seven geographically distinct subclades (3.I – 3.VII) with two subclades containing viruses from both Greenland and Canada. By combining analysis of full length RABV genome sequences and host derived sequences encoding mitochondrial proteins obtained simultaneously from brain tissues of 49 arctic foxes, the interaction of viruses and their hosts was explored in detail. Such an approach can serve as a blueprint for analysis of infectious disease dynamics and virus-host interdependencies. The results showed a fine-scale spatial population structure in Greenland arctic foxes based on mitochondrial sequences, but provided no evidence for independent isolated evolutionary development of RABV in different arctic fox lineages. These data are invaluable to support future initiatives for arctic fox rabies control and elimination in Greenland. Next to dog-mediated rabies, wildlife rabies continues to pose a public health problem, particularly in the northern hemisphere. Control of this zoonosis at the animal source has been proven the most efficient route to reduction of human rabies burden. Successful elimination of red fox-mediated rabies in Western Europe and parts of North America has demonstrated the viability of wildlife rabies control strategies. In some regions, the epidemiology of wildlife rabies is well understood; this is not the case for arctic rabies, particularly in Greenland. Previous molecular epidemiological studies demonstrated the occurrence of one particular arctic rabies virus (RABV) lineage (arctic-3) but were limited by low sample numbers and limited sequence length so as to preclude generation of high resolution phylogenetic analysis. Here, a unique set comprised of 79 complete genome sequences of RABVs from Greenland, Canada, USA (Alaska) and Russia collected over the past four decades was analysed. The use of next generation sequencing (NGS) allowed simultaneous determination of host derived sequences encoding mitochondrial proteins from the same brain tissue of 49 arctic foxes. These sequence data combined with geographical and temporal information permit the study of the genetic diversity and evolution of circulating RABVs in Greenland against the background of reservoir host genetics. The results reveal the existence of a single arctic RABV lineage (arctic-3) in Greenland, which has evolved into multiple distinct variants. These analyses provide an improved knowledge of the evolution of the circulating viruses at the molecular level and a better understanding of the historical perspective of the disease in Greenland compared to other parts of the Arctic. This knowledge will support policy on rabies control in mammalian wildlife reservoirs.
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Affiliation(s)
- Dennis Hanke
- Friedrich-Loeffler-Institut (FLI), Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Conrad M. Freuling
- FLI, Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, Germany
| | - Susanne Fischer
- FLI, Institute of Epidemiology, Greifswald-Insel Riems, Germany
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska, Fairbanks, Alaska, United States of America
| | - Kris Hundertmark
- Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska, United States of America
| | - Susan Nadin-Davis
- Animal Health Microbiology Research, Canadian Food Inspection Agency (CFIA), Centre of Expertise for Rabies, Ottawa Laboratory, Ottawa, Ontario, Canada
| | - Denise Marston
- Animal and Plant Health Agency (APHA), Wildlife Zoonoses and Vector-borne Diseases Research Group, Addlestone, Surrey, United Kingdom
| | - Anthony R. Fooks
- Animal and Plant Health Agency (APHA), Wildlife Zoonoses and Vector-borne Diseases Research Group, Addlestone, Surrey, United Kingdom
- University of Liverpool, Department of Clinical Infection, Microbiology and Immunology, Liverpool, United Kingdom
| | - Anette Bøtner
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, Denmark
| | | | - Martin Beer
- Friedrich-Loeffler-Institut (FLI), Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Thomas B. Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, Denmark
| | - Thomas F. Müller
- FLI, Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, Germany
- * E-mail:
| | - Dirk Höper
- Friedrich-Loeffler-Institut (FLI), Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
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Basto MP, Santos-Reis M, Simões L, Grilo C, Cardoso L, Cortes H, Bruford MW, Fernandes C. Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox. PLoS One 2016; 11:e0145165. [PMID: 26727497 PMCID: PMC4699814 DOI: 10.1371/journal.pone.0145165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 11/30/2015] [Indexed: 11/23/2022] Open
Abstract
The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.
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Affiliation(s)
- Mafalda P. Basto
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
- * E-mail:
| | - Margarida Santos-Reis
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Luciana Simões
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Clara Grilo
- Centro Brasileiro de Estudos em Ecologia de Estradas/Programa de Pós-graduação em Ecologia Aplicada, Universidade Federal de Lavras, Lavras, Minas Gerais, Brasil
| | - Luís Cardoso
- Departamento de Ciências Veterinárias, Escola de Ciências Agrárias e Veterinárias, Universidade de Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
| | - Helder Cortes
- Laboratório de Parasitologia Victor Caeiro, Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Michael W. Bruford
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Carlos Fernandes
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Galov A, Fabbri E, Caniglia R, Arbanasić H, Lapalombella S, Florijančić T, Bošković I, Galaverni M, Randi E. First evidence of hybridization between golden jackal (Canis aureus) and domestic dog (Canis familiaris) as revealed by genetic markers. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150450. [PMID: 27019731 PMCID: PMC4807452 DOI: 10.1098/rsos.150450] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/03/2015] [Indexed: 05/22/2023]
Abstract
Interspecific hybridization is relatively frequent in nature and numerous cases of hybridization between wild canids and domestic dogs have been recorded. However, hybrids between golden jackals (Canis aureus) and other canids have not been described before. In this study, we combined the use of biparental (15 autosomal microsatellites and three major histocompatibility complex (MHC) loci) and uniparental (mtDNA control region and a Y-linked Zfy intron) genetic markers to assess the admixed origin of three wild-living canids showing anomalous phenotypic traits. Results indicated that these canids were hybrids between golden jackals and domestic dogs. One of them was a backcross to jackal and another one was a backcross to dog, confirming that golden jackal-domestic dog hybrids are fertile. The uniparental markers showed that the direction of hybridization, namely females of the wild species hybridizing with male domestic dogs, was common to most cases of canid hybridization. A melanistic 3bp-deletion at the K locus (β-defensin CDB103 gene), that was absent in reference golden jackal samples, but was found in a backcross to jackal with anomalous black coat, suggested its introgression from dogs via hybridization. Moreover, we demonstrated that MHC sequences, although rarely used as markers of hybridization, can be also suitable for the identification of hybrids, as long as haplotypes are exclusive for the parental species.
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Affiliation(s)
- Ana Galov
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb 10000, Croatia
- Author for correspondence: Ana Galov e-mail:
| | - Elena Fabbri
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
| | - Romolo Caniglia
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
| | - Haidi Arbanasić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb 10000, Croatia
| | - Silvana Lapalombella
- Department of Biological, Geological and Environmental Sciences University of Bologna, Via Selmi 3, Bologna 40126, Italy
| | - Tihomir Florijančić
- Department for Hunting, Fishery and Beekeeping, Faculty of Agriculture in Osijek, Josip Juraj Strossmayer University of Osijek, Kralja Petra Svačića 1d, Osijek 31000, Croatia
| | - Ivica Bošković
- Department for Hunting, Fishery and Beekeeping, Faculty of Agriculture in Osijek, Josip Juraj Strossmayer University of Osijek, Kralja Petra Svačića 1d, Osijek 31000, Croatia
| | - Marco Galaverni
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
| | - Ettore Randi
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
- Department 18/Section of Environmental Engineering, Aalborg University, Sohngårdsholmsvej 57, Aalborg 9000, Denmark
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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.
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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:
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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.
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Koepfli KP, Pollinger J, Godinho R, Robinson J, Lea A, Hendricks S, Schweizer RM, Thalmann O, Silva P, Fan Z, Yurchenko AA, Dobrynin P, Makunin A, Cahill JA, Shapiro B, Álvares F, Brito JC, Geffen E, Leonard JA, Helgen KM, Johnson WE, O'Brien SJ, Van Valkenburgh B, Wayne RK. Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species. Curr Biol 2015; 25:2158-65. [PMID: 26234211 DOI: 10.1016/j.cub.2015.06.060] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 04/15/2015] [Accepted: 06/22/2015] [Indexed: 10/23/2022]
Abstract
The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a previously unrecognized phylogenetically distinct species despite a long history of taxonomic work on African canids. To test the distinct-species hypothesis and understand the evolutionary history that would account for this puzzling result, we analyzed extensive genomic data including mitochondrial genome sequences, sequences from 20 autosomal loci (17 introns and 3 exon segments), microsatellite loci, X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences, and whole-genome nuclear sequences in African and Eurasian golden jackals and gray wolves. Our results provide consistent and robust evidence that populations of golden jackals from Africa and Eurasia represent distinct monophyletic lineages separated for more than one million years, sufficient to merit formal recognition as different species: C. anthus (African golden wolf) and C. aureus (Eurasian golden jackal). Using morphologic data, we demonstrate a striking morphologic similarity between East African and Eurasian golden jackals, suggesting parallelism, which may have misled taxonomists and likely reflects uniquely intense interspecific competition in the East African carnivore guild. Our study shows how ecology can confound taxonomy if interspecific competition constrains size diversification.
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Affiliation(s)
- Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Prospekt, St. Petersburg 199034, Russia.
| | - John Pollinger
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles Young Drive East, Los Angeles, CA 90095-1606, USA
| | - Raquel Godinho
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, and Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s⁄n, 4169-007 Porto, Portugal; Department of Zoology, University of Johannesburg, PO Box 534, Auckland Park 2006, South Africa
| | - Jacqueline Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles Young Drive East, Los Angeles, CA 90095-1606, USA
| | - Amanda Lea
- Department of Biology, Duke University, PO Box 90388, Durham, NC 27708, USA
| | - Sarah Hendricks
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, 875 Perimeter MS 3051, Moscow, ID 83844, USA
| | - Rena M Schweizer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles Young Drive East, Los Angeles, CA 90095-1606, USA
| | - Olaf Thalmann
- Department of Biological Sciences, Division of Genetics and Physiology, University of Turku, Itäinen Pitkäkatu 4, 20014 Turku, Finland; Department of Biology, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Pedro Silva
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, and Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s⁄n, 4169-007 Porto, Portugal
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Andrey A Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Prospekt, St. Petersburg 199034, Russia
| | - Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Prospekt, St. Petersburg 199034, Russia
| | - Alexey Makunin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Prospekt, St. Petersburg 199034, Russia
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Francisco Álvares
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, and Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s⁄n, 4169-007 Porto, Portugal
| | - José C Brito
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, and Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s⁄n, 4169-007 Porto, Portugal
| | - Eli Geffen
- Department of Zoology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jennifer A Leonard
- Estación Biológica de Doñana, Conservation and Evolutionary Genetics Group (EBD-CSIC), Avenida Américo Vespucio s/n, 41092 Sevilla, Spain
| | - Kristofer M Helgen
- Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Prospekt, St. Petersburg 199034, Russia; Nova Southeastern University, Oceanographic Center, 8000 North Ocean Drive, Dania Beach, FL 33004 USA
| | - Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles Young Drive East, Los Angeles, CA 90095-1606, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles Young Drive East, Los Angeles, CA 90095-1606, USA.
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Atterby H, Allnutt TR, MacNicoll AD, Jones EP, Smith GC. Population genetic structure of the red fox (Vulpes vulpes) in the UK. MAMMAL RES 2014. [DOI: 10.1007/s13364-014-0209-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Mullins J, McDevitt AD, Kowalczyk R, Ruczyńska I, Górny M, Wójcik JM. The influence of habitat structure on genetic differentiation in red fox populations in north-eastern Poland. ACTA ACUST UNITED AC 2014; 59:367-376. [PMID: 24954926 PMCID: PMC4058057 DOI: 10.1007/s13364-014-0180-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 03/05/2014] [Indexed: 02/02/2023]
Abstract
The red fox (Vulpes vulpes) has the widest global distribution among terrestrial carnivore species, occupying most of the Northern Hemisphere in its native range. Because it carries diseases that can be transmitted to humans and domestic animals, it is important to gather information about their movements and dispersal in their natural habitat but it is difficult to do so at a broad scale with trapping and telemetry. In this study, we have described the genetic diversity and structure of red fox populations in six areas of north-eastern Poland, based on samples collected from 2002–2003. We tested 22 microsatellite loci isolated from the dog and the red fox genome to select a panel of nine polymorphic loci suitable for this study. Genetic differentiation between the six studied populations was low to moderate and analysis in Structure revealed a panmictic population in the region. Spatial autocorrelation among all individuals showed a pattern of decreasing relatedness with increasing distance and this was not significantly negative until 93 km, indicating a pattern of isolation-by-distance over a large area. However, there was no correlation between genetic distance and either Euclidean distance or least-cost path distance at the population level. There was a significant relationship between genetic distance and the proportion of large forests and water along the Euclidean distances. These types of habitats may influence dispersal paths taken by red foxes, which is useful information in terms of wildlife disease management.
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Affiliation(s)
- Jacinta Mullins
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - Allan D McDevitt
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland ; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - Iwona Ruczyńska
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - Marcin Górny
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - Jan M Wójcik
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
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Oro D, Genovart M, Tavecchia G, Fowler MS, Martínez-Abraín A. Ecological and evolutionary implications of food subsidies from humans. Ecol Lett 2013; 16:1501-14. [PMID: 24134225 DOI: 10.1111/ele.12187] [Citation(s) in RCA: 336] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/15/2013] [Accepted: 08/23/2013] [Indexed: 11/28/2022]
Abstract
Human activities are the main current driver of global change. From hunter-gatherers through to Neolithic societies-and particularly in contemporary industrialised countries-humans have (voluntarily or involuntarily) provided other animals with food, often with a high spatio-temporal predictability. Nowadays, as much as 30-40% of all food produced in Earth is wasted. We argue here that predictable anthropogenic food subsidies (PAFS) provided historically by humans to animals has shaped many communities and ecosystems as we see them nowadays. PAFS improve individual fitness triggering population increases of opportunistic species, which may affect communities, food webs and ecosystems by altering processes such as competition, predator-prey interactions and nutrient transfer between biotopes and ecosystems. We also show that PAFS decrease temporal population variability, increase resilience of opportunistic species and reduce community diversity. Recent environmental policies, such as the regulation of dumps or the ban of fishing discards, constitute natural experiments that should improve our understanding of the role of food supply in a range of ecological and evolutionary processes at the ecosystem level. Comparison of subsidised and non-subsidised ecosystems can help predict changes in diversity and the related ecosystem services that have suffered the impact of other global change agents.
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Affiliation(s)
- Daniel Oro
- Population Ecology Group, IMEDEA (CSIC-UIB), Esporles, 07190, Spain
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Genetic structure and expansion of golden jackals (Canis aureus) in the north-western distribution range (Croatia and eastern Italian Alps). CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0530-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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