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Abstract
Abstract
The gray wolf and the domestic dog are closely related species that can interbreed and produce fertile offspring. In settings where unrestrained dogs are present in the wild, hybridization can happen naturally. However, the behavior of the resulting hybrids and their ecological impact is largely understudied. In September–November 2018, a putative gray wolf was repeatedly camera-trapped in a group of 10 presumably feral dogs in a remote mountainous area (the Osogovo Mountain) along the border between Bulgaria and North Macedonia. The most feasible explanation for this individual’s atypical behavior is that it is of hybrid origin (assumption based on phenotype). To the best of our knowledge, this is the first documented observation of such a kind. A discussion of its recruitment and position in the group is presented, setting the basis for further investigation of the complex interaction between wolves, dogs and hybrids in the wild.
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Justyn NM, Callaghan CT, Hill GE. Birds rarely hybridize: A citizen science approach to estimating rates of hybridization in the wild*. Evolution 2020; 74:1216-1223. [DOI: 10.1111/evo.13943] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 01/24/2020] [Accepted: 02/04/2020] [Indexed: 01/09/2023]
Affiliation(s)
| | - Corey T. Callaghan
- Centre for Ecosystem Science, School of Biological, Earth and Environmental SciencesUNSW Sydney Sydney NSW 2052 Australia
| | - Geoffrey E. Hill
- Department of Biological SciencesAuburn University Auburn Alabama 36849
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Auliya M, Hofmann S, Segniagbeto GH, Assou D, Ronfot D, Astrin JJ, Forat S, Koffivi K. Ketoh G, D’Cruze N. The first genetic assessment of wild and farmed ball pythons (Reptilia, Serpentes, Pythonidae) in southern Togo. NATURE CONSERVATION 2020. [DOI: 10.3897/natureconservation.38.49478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The ball python (Python regius) is the world’s most commonly traded python species for the “exotic” pet industry. The majority of these live snakes are produced via a number of python farms in West Africa that have been in operation since the 1960s and involved with “ranching” operations since the 1990s. However, to date no thorough taxonomic review or genetic studies have been conducted within its range, despite the fact that the evaluation of a species’ genetic variability is generally considered mandatory for effective management. We used mtDNA sequence data and eight polymorphic microsatellite markers to assess the underlying population genetic structure and to test the potential of the nuclear markers to assign farm individuals to wild reference populations in southern Togo. Despite the relatively large distances between sample locations, no significant genetic population structure was found, either in mtDNA sequence data or in the microsatellite data. Instead, our data indicate considerable gene flow among the locations. The absence of a distinct population subdivision may have resulted from an anthropogenic driven admixture of populations associated with commercial wildlife trade activity in recent decades. Given the ongoing largely unregulated nature of the commercial ranching of ball pythons in West Africa, should a wild release component continue, as a first measure we recommend that the Management Authorities should develop an action plan with specific release protocols for python farms to minimise any potential negative conservation impacts resulting from admixture (genetic pollution) between farmed and wild individuals.
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Caniglia R, Galaverni M, Velli E, Mattucci F, Canu A, Apollonio M, Mucci N, Scandura M, Fabbri E. A standardized approach to empirically define reliable assignment thresholds and appropriate management categories in deeply introgressed populations. Sci Rep 2020; 10:2862. [PMID: 32071323 PMCID: PMC7028925 DOI: 10.1038/s41598-020-59521-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/28/2020] [Indexed: 11/09/2022] Open
Abstract
Anthropogenic hybridization is recognized as a major threat to the long-term survival of natural populations. While identifying F1 hybrids might be simple, the detection of older admixed individuals is far from trivial and it is still debated whether they should be targets of management. Examples of anthropogenic hybridization have been described between wolves and domestic dogs, with numerous cases detected in the Italian wolf population. After selecting appropriate wild and domestic reference populations, we used empirical and simulated 39-autosomal microsatellite genotypes, Bayesian assignment and performance analyses to develop a workflow to detect different levels of wolf x dog admixture. Membership proportions to the wild cluster (qiw) and performance indexes identified two q-thresholds which allowed to efficiently classify the analysed genotypes into three assignment classes: pure (with no or negligible domestic ancestry), older admixed (with a marginal domestic ancestry) and recent admixed (with a clearly detectable domestic ancestry) animals. Based on their potential to spread domestic variants, such classes were used to define three corresponding management categories: operational pure, introgressed and operational hybrid individuals. Our multiple-criteria approach can help wildlife managers and decision makers in more efficiently targeting the available resources for the long-term conservation of species threatened by anthropogenic hybridization.
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Affiliation(s)
- Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy.
| | | | - Edoardo Velli
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Federica Mattucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Antonio Canu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marco Apollonio
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Massimo Scandura
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
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McFarlane SE, Hunter DC, Senn HV, Smith SL, Holland R, Huisman J, Pemberton JM. Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland. Evol Appl 2020; 13:432-441. [PMID: 31993087 PMCID: PMC6976951 DOI: 10.1111/eva.12880] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/01/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date, many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here, we use 44,999 single nucleotide polymorphisms (SNPs) and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre, we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.
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Affiliation(s)
- S. Eryn McFarlane
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of BiologyLund UniversityLundSweden
| | - Darren C. Hunter
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Helen V. Senn
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- WildGenes LaboratoryRoyal Zoological Society of ScotlandEdinburghUK
| | - Stephanie L. Smith
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- The Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEaster Bush CampusMidlothian, EdinburghUK
| | - Rebecca Holland
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Jisca Huisman
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
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Tiesmeyer A, Ramos L, Manuel Lucas J, Steyer K, Alves PC, Astaras C, Brix M, Cragnolini M, Domokos C, Hegyeli Z, Janssen R, Kitchener AC, Lambinet C, Mestdagh X, Migli D, Monterroso P, Mulder JL, Schockert V, Youlatos D, Pfenninger M, Nowak C. Range-wide patterns of human-mediated hybridisation in European wildcats. CONSERV GENET 2020. [DOI: 10.1007/s10592-019-01247-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
AbstractHybridisation between wild taxa and their domestic congeners is a significant conservation issue. Domestic species frequently outnumber their wild relatives in population size and distribution and may therefore genetically swamp the native species. The European wildcat (Felis silvestris) has been shown to hybridise with domestic cats (Felis catus). Previously suggested spatially divergent introgression levels have not been confirmed on a European scale due to significant differences in the applied methods to assess hybridisation of the European wildcat. We analysed 926 Felis spp. samples from 13 European countries, using a set of 86 selected ancestry-informative SNPs, 14 microsatellites, and ten mitochondrial and Y-chromosome markers to study regional hybridisation and introgression patterns and population differentiation. We detected 51 hybrids (four F1 and 47 F2 or backcrosses) and 521 pure wildcats throughout Europe. The abundance of hybrids varied considerably among studied populations. All samples from Scotland were identified as F2 hybrids or backcrosses, supporting previous findings that the genetic integrity of that wildcat population has been seriously compromised. In other European populations, low to moderate levels of hybridisation were found, with the lowest levels being in Central and Southeast Europe. The occurrence of distinct maternal and paternal markers between wildcat and domestic cat suggests that there were no severe hybridisation episodes in the past. The overall low (< 1%) prevalence of F1 hybrids suggests a low risk of hybridisation for the long-term genetic integrity of the wildcat in most of Europe. However, regionally elevated introgression rates confirm that hybridisation poses a potential threat. We propose regional in-depth monitoring of hybridisation rates to identify factors driving hybridisation so as to develop effective strategies for conservation.
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Beugin M, Salvador O, Leblanc G, Queney G, Natoli E, Pontier D. Hybridization between Felis silvestris silvestris and Felis silvestris catus in two contrasted environments in France. Ecol Evol 2020; 10:263-276. [PMID: 31988727 PMCID: PMC6972816 DOI: 10.1002/ece3.5892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 11/30/2022] Open
Abstract
European wildcat (Felis silvestris silvestris) populations are fragmented throughout most of the whole range of the subspecies and may be threatened by hybridization with the domestic cat F.s. catus. The underlying ecological processes promoting hybridization remain largely unknown. In France, wildcats are mainly present in the northeast and signs of their presence in the Pyrenees have been recently provided. However, no studies have been carried out in the French Pyrenees to assess their exposure to hybridization. We compared two local populations of wildcats, one living in a continuous forest habitat in the French Pyrenees, the other living in a highly fragmented forest-agricultural landscape in northeastern France to get insights into the variability of hybridization rates. Strong evidence of hybridization was detected in northeastern France and not in the Pyrenees. Close kin in the Pyrenees were not found in the same geographic location contrary to what was previously reported for females in the northeastern wildcat population. The two wildcat populations were significantly differentiated (F ST = 0.072) to an extent close to what has been reported (F ST = 0.103) between the Iberian population, from which the Pyrenean population may originate, and the German population, which is connected to the northeastern population. The genetic diversity of the Pyrenean wildcats was lower than that of northeastern wildcat populations in France and in other parts of Europe. The lower hybridization in the Pyrenees may result from the continuity of natural forest habitats. Further investigations should focus on linking landscape features to hybridization rates working on local populations.
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Affiliation(s)
- Marie‐Pauline Beugin
- Laboratoire de Biométrie et Biologie Evolutive UMR5558CNRSUniv LyonUniversité Lyon 1VilleurbanneFrance
- Animal Genomics LaboratoryANTAGENELa tour de SalvagnyFrance
| | - Olivier Salvador
- Réserve naturelle nationale de Jujols et de NohèdesRéserves Naturelles CatalanesPradesFrance
| | | | | | | | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive UMR5558CNRSUniv LyonUniversité Lyon 1VilleurbanneFrance
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Mori E, Menchetti M, Camporesi A, Cavigioli L, Tabarelli de Fatis K, Girardello M. License to Kill? Domestic Cats Affect a Wide Range of Native Fauna in a Highly Biodiverse Mediterranean Country. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00477] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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Gering E, Incorvaia D, Henriksen R, Conner J, Getty T, Wright D. Getting Back to Nature: Feralization in Animals and Plants. Trends Ecol Evol 2019; 34:1137-1151. [PMID: 31488326 PMCID: PMC7479514 DOI: 10.1016/j.tree.2019.07.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022]
Abstract
Formerly domesticated organisms and artificially selected genes often escape controlled cultivation, but their subsequent evolution is not well studied. In this review, we examine plant and animal feralization through an evolutionary lens, including how natural selection, artificial selection, and gene flow shape feral genomes, traits, and fitness. Available evidence shows that feralization is not a mere reversal of domestication. Instead, it is shaped by the varied and complex histories of feral populations, and by novel selection pressures. To stimulate further insight we outline several future directions. These include testing how 'domestication genes' act in wild settings, studying the brains and behaviors of feral animals, and comparative analyses of feral populations and taxa. This work offers feasible and exciting research opportunities with both theoretical and practical applications.
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Affiliation(s)
- Eben Gering
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Davie, FL, USA.
| | - Darren Incorvaia
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Rie Henriksen
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jeffrey Conner
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Kellogg Biological Station and Dept. of Plant Biology, Michigan State University, Hickory Corners, MI, USA
| | - Thomas Getty
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Dominic Wright
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
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Päckert M, Ait Belkacem A, Wolfgramm H, Gast O, Canal D, Giacalone G, Lo Valvo M, Vamberger M, Wink M, Martens J, Stuckas H. Genetic admixture despite ecological segregation in a North African sparrow hybrid zone (Aves, Passeriformes, Passer domesticus × Passer hispaniolensis). Ecol Evol 2019; 9:12710-12726. [PMID: 31788209 PMCID: PMC6875665 DOI: 10.1002/ece3.5744] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 11/29/2022] Open
Abstract
Under different environmental conditions, hybridization between the same species might result in different patterns of genetic admixture. Particularly, species pairs with large distribution ranges and long evolutionary history may have experienced several independent hybridization events over time in different zones of overlap. In birds, the diverse hybrid populations of the house sparrow (Passer domesticus) and the Spanish sparrow (Passer hispaniolensis) provide a striking example. Throughout their range of sympatry, these two species do not regularly interbreed; however, a stabilized hybrid form (Passer italiae) exists on the Italian Peninsula and on several Mediterranean islands. The spatial distribution pattern on the Eurasian continent strongly contrasts the situation in North Africa, where house sparrows and Spanish sparrows occur in close vicinity of phenotypically intermediate populations across a broad mosaic hybrid zone. In this study, we investigate patterns of divergence and admixture among the two parental species, stabilized and nonstabilized hybrid populations in Italy and Algeria based on a mitochondrial marker, a sex chromosomal marker, and 12 microsatellite loci. In Algeria, despite strong spatial and temporal separation of urban early-breeding house sparrows and hybrids and rural late-breeding Spanish sparrows, we found strong genetic admixture of mitochondrial and nuclear markers across all study populations and phenotypes. That pattern of admixture in the North African hybrid zone is strikingly different from i) the Iberian area of sympatry where we observed only weak asymmetrical introgression of Spanish sparrow nuclear alleles into local house sparrow populations and ii) the very homogenous Italian sparrow population where the mitogenome of one parent (P. domesticus) and the Z-chromosomal marker of the other parent (P. hispaniolensis) are fixed. The North African sparrow hybrids provide a further example of enhanced hybridization along with recent urbanization and anthropogenic land-use changes in a mosaic landscape.
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Affiliation(s)
- Martin Päckert
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
| | - Abdelkrim Ait Belkacem
- Laboratoire d'Exploration et de Valorisation des Écosystèmes SteppiquesFaculté des Sciences de la nature et de la vieUniversité de DjelfaDjelfaAlgeria
| | - Hannes Wolfgramm
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
| | - Oliver Gast
- Institute of Vertebrate Biology Brno & Masaryk University BrnoBrnoCzech Republic
| | - David Canal
- Department of Evolutionary EcologyEstación Biológica de Doñana—CSICSevilleSpain
- Centro para el Estudio y Conservación de las Aves Rapaces en Argentina (CECARA‐UNLPam) & Instituto de las Ciencias de la Tierra y Ambientales de La Pampa (INCITAP)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Santa RosaArgentina
| | | | - Mario Lo Valvo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e FarmaceuticheUniversità degli Studi di PalermoPalermoItaly
| | - Melita Vamberger
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
| | - Michael Wink
- Department of BiologyInstitute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityHeidelbergGermany
| | - Jochen Martens
- Institute of Organismic and Molecular EvolutionJohannes Gutenberg UniversityMainzGermany
| | - Heiko Stuckas
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
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Leitwein M, Cayuela H, Ferchaud AL, Normandeau É, Gagnaire PA, Bernatchez L. The role of recombination on genome-wide patterns of local ancestry exemplified by supplemented brook charr populations. Mol Ecol 2019; 28:4755-4769. [PMID: 31579957 DOI: 10.1111/mec.15256] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022]
Abstract
Assessing the immediate and long-term evolutionary consequences of human-mediated hybridization is of major concern for conservation biology. Several studies have documented how selection in interaction with recombination modulates introgression at a genome-wide scale, but few have considered the dynamics of this process within and among chromosomes. Here, we used an exploited freshwater fish, the brook charr (Salvelinus fontinalis), for which decades of stocking practices have resulted in admixture between wild populations and an introduced domestic strain, to assess both the temporal dynamics and local chromosomal variation in domestic ancestry. We provide a detailed picture of the domestic ancestry patterns across the genome using about 33,000 mapped single nucleotide polymorphisms genotyped in 611 individuals from 24 supplemented populations. For each lake, we distinguished early- and late-generation hybrids using information regarding admixture tracts. To assess the selective outcomes following admixture we then evaluated the relationship between recombination and admixture proportions at three different scales: the whole genome, chromosomes and within 2-Mb windows. This allowed us to detect a wide range of evolutionary mechanisms varying along the genome, as reflected by the finding of favoured or disfavoured introgression of domestic haplotypes. Among these, the main factor modulating local ancestry was probably the presence of deleterious recessive mutations in the wild populations, which can be efficiently hidden to selection in the presence of long admixture tracts. Overall, our results emphasize the relevance of taking into consideration local ancestry information to assess both the temporal and the chromosomal variation in local admixture ancestry toward better understanding post-hybridization evolutionary outcomes.
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Affiliation(s)
- Maeva Leitwein
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | | | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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Assessing introgressive hybridization in roan antelope (Hippotragus equinus): Lessons from South Africa. PLoS One 2019; 14:e0213961. [PMID: 31626669 PMCID: PMC6799913 DOI: 10.1371/journal.pone.0213961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/06/2019] [Indexed: 12/02/2022] Open
Abstract
Biological diversity is being lost at unprecedented rates, with genetic admixture and introgression presenting major threats to biodiversity. Our ability to accurately identify introgression is critical to manage species, obtain insights into evolutionary processes, and ultimately contribute to the Aichi Targets developed under the Convention on Biological Diversity. The current study concerns roan antelope, the second largest antelope in Africa. Despite their large size, these antelope are sensitive to habitat disturbance and interspecific competition, leading to the species being listed as Least Concern but with decreasing population trends, and as extinct over parts of its range. Molecular research identified the presence of two evolutionary significant units across their sub-Saharan range, corresponding to a West African lineage and a second larger group which includes animals from East, Central and Southern Africa. Within South Africa, one of the remaining bastions with increasing population sizes, there are a number of West African roan antelope populations on private farms, and concerns are that these animals hybridize with roan that naturally occur in the southern African region. We used a suite of 27 microsatellite markers to conduct admixture analysis. Our results indicate evidence of hybridization, with our developed tests using a simulated dataset being able to accurately identify F1, F2 and non-admixed individuals at threshold values of qi > 0.80 and qi > 0.85. However, further backcrosses were not always detectable with backcrossed-Western roan individuals (46.7–60%), backcrossed-East, Central and Southern African roan individuals (28.3–45%) and double backcrossed (83.3–98.3%) being incorrectly classified as non-admixed. Our study is the first to confirm ongoing hybridization in this within this iconic African antelope, and we provide recommendations for the future conservation and management of this species.
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Salvatori V, Godinho R, Braschi C, Boitani L, Ciucci P. High levels of recent wolf × dog introgressive hybridization in agricultural landscapes of central Italy. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1313-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mattucci F, Galaverni M, Lyons LA, Alves PC, Randi E, Velli E, Pagani L, Caniglia R. Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations. Sci Rep 2019; 9:11612. [PMID: 31406125 PMCID: PMC6691104 DOI: 10.1038/s41598-019-48002-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 07/25/2019] [Indexed: 12/22/2022] Open
Abstract
The survival of indigenous European wildcat (Felis silvestris silvestris) populations can be locally threatened by introgressive hybridization with free-ranging domestic cats. Identifying pure wildcats and investigating the ancestry of admixed individuals becomes thus a conservation priority. We analyzed 63k cat Single Nucleotide Polymorphisms (SNPs) with multivariate, Bayesian and gene-search tools to better evaluate admixture levels between domestic and wild cats collected in Europe, timing and ancestry proportions of their hybrids and backcrosses, and track the origin (wild or domestic) of the genomic blocks carried by admixed cats, also looking for possible deviations from neutrality in their inheritance patterns. Small domestic ancestry blocks were detected in the genomes of most admixed cats, which likely originated from hybridization events occurring from 6 to 22 generations in the past. We identified about 1,900 outlier coding genes with excess of wild or domestic ancestry compared to random expectations in the admixed individuals. More than 600 outlier genes were significantly enriched for Gene Ontology (GO) categories mainly related to social behavior, functional and metabolic adaptive processes (wild-like genes), involved in cognition and neural crest development (domestic-like genes), or associated with immune system functions and lipid metabolism (parental-like genes). These kinds of genomic ancestry analyses could be reliably applied to unravel the admixture dynamics in European wildcats, as well as in other hybridizing populations, in order to design more efficient conservation plans.
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Affiliation(s)
- Federica Mattucci
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy.
| | | | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, USA
| | - Paulo C Alves
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBio - Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, USA
| | - Ettore Randi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Edoardo Velli
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy
| | - Luca Pagani
- Dipartimento di Biologia, Università degli Studi di Padova, Padua, Italy
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Romolo Caniglia
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy
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Anderson D, Toma R, Negishi Y, Okuda K, Ishiniwa H, Hinton TG, Nanba K, Tamate HB, Kaneko S. Mating of escaped domestic pigs with wild boar and possibility of their offspring migration after the Fukushima Daiichi Nuclear Power Plant accident. Sci Rep 2019; 9:11537. [PMID: 31395920 PMCID: PMC6687819 DOI: 10.1038/s41598-019-47982-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/25/2019] [Indexed: 12/03/2022] Open
Abstract
The 2011 Tohoku earthquake drastically changed human activities in some regions of Fukushima Prefecture, Japan. The subsequent tsunami damage and radioactive pollution from the Fukushima Daiichi nuclear power plant resulted in the evacuation of humans, and abandonment of agricultural lands, allowing population expansion of wildlife into areas formally inhabited by domesticated livestock. Unintentional escape of domesticated pigs into wildlife inhabited environments also occurred. In this study, we tested the possibility of introgression between wild boar and domesticated pigs in Fukushima and neighboring prefectures. We analyzed mitochondrial DNA sequences of 338 wild boar collected from populations in the Tohoku region between 2006 and 2018. Although most boar exhibited Asian boar mitochondrial haplotypes, 18 boar, phenotypically identified as wild boar, had a European domesticated pig haplotype. Frequencies of this haplotype have remained stable since first detection in 2015. This result infers ongoing genetic pollution in wild boar populations from released domesticated pigs. In 2018, this haplotype was detected outside of evacuated areas, suggesting migration and successful adaptation. The natural and anthropocentric disasters at Fukushima gave us the rare opportunity to study introgression processes of domestic genes into populations of wild boar. The present findings suggest a need for additional genetic monitoring to document the dispersal of domestic genes within wild boar stock.
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Affiliation(s)
- Donovan Anderson
- Fukushima University, Symbiotic Systems Science and Technology, Fukushima, 960-1248, Japan
| | - Rio Toma
- Fukushima University, Symbiotic Systems Science and Technology, Fukushima, 960-1248, Japan
| | - Yuki Negishi
- Fukushima University, Symbiotic Systems Science and Technology, Fukushima, 960-1248, Japan
| | - Kei Okuda
- Hiroshima Shudo University, Faculty of Human Environmental Studies, Hiroshima, 731-3195, Japan
| | - Hiroko Ishiniwa
- Fukushima University, Institute of Environmental Radioactivity, Fukushima, 960-1248, Japan
| | - Thomas G Hinton
- Fukushima University, Institute of Environmental Radioactivity, Fukushima, 960-1248, Japan
| | - Kenji Nanba
- Fukushima University, Symbiotic Systems Science and Technology, Fukushima, 960-1248, Japan.,Fukushima University, Institute of Environmental Radioactivity, Fukushima, 960-1248, Japan
| | | | - Shingo Kaneko
- Fukushima University, Symbiotic Systems Science and Technology, Fukushima, 960-1248, Japan. .,Fukushima University, Institute of Environmental Radioactivity, Fukushima, 960-1248, Japan.
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66
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Centeno‐Cuadros A, Razgour O, García‐Mudarra JL, Mingo‐Casas P, Sandonís V, Redondo A, Ibáñez C, Paz O, Martinez‐Alós S, Pérez Suarez G, Echevarría JE, Juste J. Comparative phylogeography and asymmetric hybridization between cryptic bat species. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12318] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | - Orly Razgour
- Biological Sciences University of Southampton Southampton UK
| | | | | | | | - Adrián Redondo
- Departmento de Ecología Evolutiva Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Carlos Ibáñez
- Departmento de Ecología Evolutiva Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Oscar Paz
- Departamento de Ciencias de la Vida, Facultad de Ciencias Universidad de Alcalá Alcalá de Henares, Madrid Spain
| | - Susana Martinez‐Alós
- Departamento de Ciencias de la Vida, Facultad de Ciencias Universidad de Alcalá Alcalá de Henares, Madrid Spain
| | - Gonzalo Pérez Suarez
- Departamento de Ciencias de la Vida, Facultad de Ciencias Universidad de Alcalá Alcalá de Henares, Madrid Spain
| | - Juan E. Echevarría
- Instituto de Salud Carlos III Majadahonda, Madrid Spain
- CIBER de Epidemiología y Salud Pública, CIBERESP Madrid Spain
| | - Javier Juste
- Departmento de Ecología Evolutiva Estación Biológica de Doñana (CSIC) Sevilla Spain
- CIBER de Epidemiología y Salud Pública, CIBERESP Madrid Spain
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67
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Cordonnier M, Gayet T, Escarguel G, Kaufmann B. From hybridization to introgression between two closely related sympatric ant species. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Marion Cordonnier
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, CNRS, Université Lyon 1, ENTPE Université Lyon Lyon France
| | - Thibault Gayet
- UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Lyon 1 Université de Lyon Lyon France
- Unité Cervidés Sangliers Office National de la Chasse et de la Faune Sauvage Birieux France
| | - Gilles Escarguel
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, CNRS, Université Lyon 1, ENTPE Université Lyon Lyon France
| | - Bernard Kaufmann
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, CNRS, Université Lyon 1, ENTPE Université Lyon Lyon France
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68
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Kelt DA, Heske EJ, Lambin X, Oli MK, Orrock JL, Ozgul A, Pauli JN, Prugh LR, Sollmann R, Sommer S. Advances in population ecology and species interactions in mammals. J Mammal 2019. [DOI: 10.1093/jmammal/gyz017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
AbstractThe study of mammals has promoted the development and testing of many ideas in contemporary ecology. Here we address recent developments in foraging and habitat selection, source–sink dynamics, competition (both within and between species), population cycles, predation (including apparent competition), mutualism, and biological invasions. Because mammals are appealing to the public, ecological insight gleaned from the study of mammals has disproportionate potential in educating the public about ecological principles and their application to wise management. Mammals have been central to many computational and statistical developments in recent years, including refinements to traditional approaches and metrics (e.g., capture-recapture) as well as advancements of novel and developing fields (e.g., spatial capture-recapture, occupancy modeling, integrated population models). The study of mammals also poses challenges in terms of fully characterizing dynamics in natural conditions. Ongoing climate change threatens to affect global ecosystems, and mammals provide visible and charismatic subjects for research on local and regional effects of such change as well as predictive modeling of the long-term effects on ecosystem function and stability. Although much remains to be done, the population ecology of mammals continues to be a vibrant and rapidly developing field. We anticipate that the next quarter century will prove as exciting and productive for the study of mammals as has the recent one.
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Affiliation(s)
- Douglas A Kelt
- Department of Wildlife, Fish, & Conservation Biology, University of California, Davis, CA, USA
| | - Edward J Heske
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Xavier Lambin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Madan K Oli
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - John L Orrock
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA
| | - Arpat Ozgul
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Jonathan N Pauli
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, WI, USA
| | - Laura R Prugh
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA
| | - Rahel Sollmann
- Department of Wildlife, Fish, & Conservation Biology, University of California, Davis, CA, USA
| | - Stefan Sommer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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69
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Donfrancesco V, Ciucci P, Salvatori V, Benson D, Andersen LW, Bassi E, Blanco JC, Boitani L, Caniglia R, Canu A, Capitani C, Chapron G, Czarnomska SD, Fabbri E, Galaverni M, Galov A, Gimenez O, Godinho R, Greco C, Hindrikson M, Huber D, Hulva P, Jedrzejewski W, Kusak J, Linnell JDC, Llaneza L, López-Bao JV, Männil P, Marucco F, Mattioli L, Milanesi P, Milleret C, Mysłajek RW, Ordiz A, Palacios V, Pedersen HC, Pertoldi C, Pilot M, Randi E, Rodríguez A, Saarma U, Sand H, Scandura M, Stronen AV, Tsingarska E, Mukherjee N. Unravelling the Scientific Debate on How to Address Wolf-Dog Hybridization in Europe. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00175] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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McFarlane SE, Pemberton JM. Detecting the True Extent of Introgression during Anthropogenic Hybridization. Trends Ecol Evol 2019; 34:315-326. [DOI: 10.1016/j.tree.2018.12.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/10/2018] [Accepted: 12/18/2018] [Indexed: 10/27/2022]
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72
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Senn HV, Ghazali M, Kaden J, Barclay D, Harrower B, Campbell RD, Macdonald DW, Kitchener AC. Distinguishing the victim from the threat: SNP-based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration. Evol Appl 2019; 12:399-414. [PMID: 30828363 PMCID: PMC6383845 DOI: 10.1111/eva.12720] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/15/2018] [Accepted: 09/18/2018] [Indexed: 02/06/2023] Open
Abstract
The degree of introgressive hybridization between the Scottish wildcat and domestic cat has long been suspected to be advanced. Here, we use a 35-SNP-marker test, designed to assess hybridization between wildcat and domestic cat populations in Scotland, to assess a database of 295 wild-living and captive cat samples, and test the assumptions of the test using 3,097 SNP markers generated independently in a subset of the data using ddRAD. We discovered that despite increased genetic resolution provided by these methods, wild-living cats in Scotland show a complete genetic continuum or hybrid swarm structure when judged against reference data. The historical population of wildcats, although hybridized, clearly groups at one end of this continuum, as does the captive population of wildcats. The interpretation of pelage scores against nuclear genetic data continues to be problematic. This is probably because of a breakdown in linkage equilibrium between wildcat pelage genes as the two populations have become increasingly mixed, meaning that pelage score or SNP score alone is poor diagnostic predictors of hybrid status. Until better tools become available, both should be used jointly, where possible, when making management decisions about individual cats. We recommend that the conservation community in Scotland must now define clearly what measures are to be used to diagnose a wildcat in the wild in Scotland, if future conservation action is to be effective.
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Affiliation(s)
- Helen V. Senn
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Muhammad Ghazali
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Jennifer Kaden
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - David Barclay
- Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Ben Harrower
- Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | | | - David W. Macdonald
- Wildlife Conservation Research Unit, Zoology, Recanati Kaplan Centre, Zoology DepartmentOxford UniversityOxfordUK
| | - Andrew C. Kitchener
- Department Natural SciencesNational Museums ScotlandEdinburghUK
- Institute of Geography, School of GeosciencesUniversity of EdinburghEdinburghUK
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73
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74
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Lavretsky P, Janzen T, McCracken KG. Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America. Ecol Evol 2019; 9:3470-3490. [PMID: 30962906 PMCID: PMC6434578 DOI: 10.1002/ece3.4981] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/15/2019] [Accepted: 01/17/2019] [Indexed: 01/04/2023] Open
Abstract
Resolving evolutionary relationships and establishing population structure depends on molecular diagnosability that is often limited for closely related taxa. Here, we use 3,200 ddRAD-seq loci across 290 mallards, American black ducks, and putative hybrids to establish population structure and estimate hybridization rates. We test between traditional assignment probability and accumulated recombination events based analyses to assign hybrids to generational classes. For hybrid identification, we report the distribution of recombination events complements ADMIXTURE simulation by extending resolution past F4 hybrid status; however, caution against hybrid assignment based on accumulated recombination events due to an inability to resolve F1 hybrids. Nevertheless, both analyses suggest that there are relatively few backcrossed stages before a lineage's hybrid ancestry is lost and the offspring are effectively parental again. We conclude that despite high rates of observed interspecific hybridization between mallards and black ducks in the middle part of the 20th century, our results do not support the predicted hybrid swarm. Conversely, we report that mallard samples genetically assigned to western and non-western clusters. We indicate that these non-western mallards likely originated from game-farm stock, suggesting landscape level gene flow between domestic and wild conspecifics.
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Affiliation(s)
- Philip Lavretsky
- Department of Biological SciencesUniversity of Texas at El PasoEl PasoTexas
- Department of BiologyUniversity of MiamiCoral GablesFlorida
| | - Thijs Janzen
- Department of Ecological Genomics, Institute for Biology and Environmental SciencesCarl von Ossietzky Universität OldenburgOldenburgGermany
| | - Kevin G. McCracken
- Department of BiologyUniversity of MiamiCoral GablesFlorida
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric SciencesUniversity of MiamiMiamiFlorida
- Human Genetics and GenomicsHussman Institute for Human Genomics, University of Miami Miller School of MedicineMiamiFlorida
- Institute of Arctic Biology and University of Alaska MuseumUniversity of Alaska FairbanksFairbanksAlaska
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75
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Two decades of non-invasive genetic monitoring of the grey wolves recolonizing the Alps support very limited dog introgression. Sci Rep 2019; 9:148. [PMID: 30651571 PMCID: PMC6335406 DOI: 10.1038/s41598-018-37331-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/30/2018] [Indexed: 02/07/2023] Open
Abstract
Potential hybridization between wolves and dogs has fueled the sensitive conservation and political debate underlying the recovery of the grey wolf throughout Europe. Here we provide the first genetic analysis of wolf-dog admixture in an area entirely recolonized, the northwestern Alps. As part of a long-term monitoring program, we performed genetic screening of thousands of non-invasive samples collected in Switzerland and adjacent territories since the return of the wolf in the mid-1990s. We identified a total of 115 individuals, only 2 of them showing significant signs of admixture stemming from past interbreeding with dogs, followed by backcrossing. This low rate of introgression (<2% accounting for all wolves ever detected over 1998–2017) parallels those from other European populations, especially in Western Europe (<7%). Despite potential hybridization with stray dogs, few founders and strong anthropogenic pressures, the genetic integrity of the Alpine population has remained intact throughout the entire recolonization process. In a context of widespread misinformation, this finding should reduce conflicts among the different actors involved and facilitate wolf conservation. Real-time genetic monitoring will be necessary to identify potential hybrids and support an effective management of this emblematic population.
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76
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Spitzweg C, Hofmeyr MD, Fritz U, Vamberger M. Leopard tortoises in southern Africa have greater genetic diversity in the north than in the south (Testudinidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cäcilia Spitzweg
- Museum of Zoology (Museum für Tierkunde) Senckenberg Dresden Dresden Germany
| | - Margaretha D. Hofmeyr
- Chelonian Biodiversity and Conservation, Department of Biodiversity and Conservation Biology University of the Western Cape Bellville South Africa
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde) Senckenberg Dresden Dresden Germany
| | - Melita Vamberger
- Museum of Zoology (Museum für Tierkunde) Senckenberg Dresden Dresden Germany
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77
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Thakur M, Fernandes M, Sathyakumar S, Singh SK, Vijh RK, Han J, Wu DD, Zhang YP. Understanding the cryptic introgression and mixed ancestry of Red Junglefowl in India. PLoS One 2018; 13:e0204351. [PMID: 30307994 PMCID: PMC6188471 DOI: 10.1371/journal.pone.0204351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/06/2018] [Indexed: 11/19/2022] Open
Abstract
Red Junglefowls (RJFs), the wild progenitor of modern day chickens (DCs), are
believed to be in genetic endangerment due to introgression of domestic genes
through opportunistic matings with domestic or feral chickens. Previous studies
from India reported rare hybridization of RJFs in the wild. However, RJF
population genetic structure, pattern of gene flow and their admixture with DC
populations are poorly understood at the landscape level. We conducted this
study with a large sample size, covering the predicted natural distribution
range of RJFs in India. We documented strong evidence of directional gene flow
from DCs to free-ranging wild RJFs, with the Northeastern RJF population
exhibiting the most genetic variants in their nuclear and mitochondrial genomes,
indicating it to be the ancestral population from which early radiation may have
occurred. The results provide evidence that landscape features do not act as a
barrier to gene flow and the distribution pattern could not be explored due to
physical sharing or exchange of wild birds in the past when forests were
continuous across RJF range in India.
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Affiliation(s)
- Mukesh Thakur
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
- State Key Laboratory of Genetic Resources and Evolution and Yunnan
Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of
Zoology, Chinese Academy of Sciences, Kunming, Yunnan, P.R.
China
- * E-mail: (MT); (SS)
| | - Merwyn Fernandes
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
| | - Sambandam Sathyakumar
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
- * E-mail: (MT); (SS)
| | - Sujeet K. Singh
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
| | - Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), G.T. Road Bye
Pass, Near Basant Vihar, Karnal, Haryana, India
| | - Jianlin Han
- CAAS—ILRI Joint Laboratory on Livestock and Forage Genetic Resources,
Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS),
Beijing, P.R. China
- International Livestock Research Institute (ILRI), Nairobi,
Kenya
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan
Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of
Zoology, Chinese Academy of Sciences, Kunming, Yunnan, P.R.
China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan
Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of
Zoology, Chinese Academy of Sciences, Kunming, Yunnan, P.R.
China
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78
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Forcina G, Guerrini M, Khaliq I, Khan AA, Barbanera F. Human-modified biogeographic patterns and conservation in game birds: The dilemma of the black francolin (Francolinus francolinus, Phasianidae) in Pakistan. PLoS One 2018; 13:e0205059. [PMID: 30289901 PMCID: PMC6173408 DOI: 10.1371/journal.pone.0205059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/19/2018] [Indexed: 11/18/2022] Open
Abstract
The ever-increasing human-mediated wildlife reshuffling is raising concern for the conservation of biodiversity. The loss of biological distinctiveness among regions lessens the genetic diversity and consequently the evolutionary potential of local biotas to tackle present-day global change and human disturbance. This process may be sometimes cryptic unless investigated by means of a molecular approach. In this respect, game birds are a paradigmatic case. The black francolin (Francolinus francolinus, Phasianidae) is a medium-sized galliform whose distribution range stretches from Cyprus to the Gulf of Bengal. Six morphologic subspecies are known, with three of which occurring in Pakistan, where the species is heavily hunted and used as pet for chirping competitions. We genotyped 98 samples (feathers) at both the entire mitochondrial DNA Control Region gene and nine microsatellite loci to get a deeper insight into the genetic diversity of the black francolin in Pakistan in order to offer cogent recommendations for its conservation management. We identified several mtDNA lineages that were consistent with the currently described subspecies/taxonomy whose pattern of co-occurrence is compatible with the geological history and the faunal movement routes of the region under study. However, the biparentally inherited microsatellites returned a quite discordant picture of an extensive, sex-biased genetic mixing due to the intensive relocations of already overharvested male individuals for chirping competitions. Our results indicated that the genetic integrity of the black francolin in Pakistan could be seriously at risk and call for monitoring and limiting its trade other than enhancing the public awareness of the importance of local biodiversity resources.
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Affiliation(s)
| | | | - Imran Khaliq
- Department of Zoology, Ghazi University, Dera Ghazi Khan, Punjab, Pakistan
| | - Aleem Ahmed Khan
- Department of Zoology, Ghazi University, Dera Ghazi Khan, Punjab, Pakistan
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Modesto P, Biolatti C, Favaro L, Colussi S, Peletto S, Piga S, Riina MV, Pessani D, Trincas E, Isaja V, Acutis PL. Molecular Genetics Unveiled Unknown Family Relationships and Hybrids in an Ex-Situ Colony of African Penguins (Spheniscus demersus). J Hered 2018; 109:653-662. [PMID: 30010804 DOI: 10.1093/jhered/esy032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 07/10/2018] [Indexed: 12/11/2022] Open
Abstract
Genealogical relationships among colony members, inbreeding status, and presence of hybrids are crucial data that can assist zoo curators in captive colony management and decision-making on relocation for reproduction. This study employed molecular markers to study a large colony (n = 56) of African Penguin hosted in an Italian biopark. A panel of 15 STRs (single tandem repeats) was selected, and genotype data were analyzed using COLONY software to determine parentage relationships and compare the existing studbook information to a pedigree built from genetic analyses. The existence of extra-pair mating and the presence of hybrids were investigated: discrepancies in kinship relationships emerged following molecular parentage analysis and 10 unknown genetic relationships were revealed. Infidelity of one member of the pair was observed in 6 cases and extra-pair copulation was assessed by genetic analysis in 2 episodes. One member of the colony was found to be a hybrid (S. demersus × S. humboldti); his progeny, derived by extra-pair copulation, was traced. Three other hidden hybrids were discovered and assessed using the identified candidate private alleles. Overall, our results demonstrate that molecular methods to confirm parentage and analyze relatedness among colony members are a valuable tool to complement studbook-based genetic management of African penguin captive populations. Because a variety of behavioral dynamics (e.g., extra-pair mating) can make observations ineffective in some species and because molecular markers outperform studbook in identifying the presence of hybrids, reliance on studbook information alone is not recommended.
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Affiliation(s)
- Paola Modesto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d1Aosta, Turin, Italy
| | - Cristina Biolatti
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d1Aosta, Turin, Italy
| | - Livio Favaro
- Laboratorio di Zoologia e Biologia Marina, Dipartimento Scienze della Vita e Biologia dei Sistemi, Turin, Italy
| | - Silvia Colussi
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d1Aosta, Turin, Italy
| | - Simone Peletto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d1Aosta, Turin, Italy
| | - Sara Piga
- Zoom Torino, Strada Piscina, Cumiana, Turin, Italy
| | - Maria Vittoria Riina
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d1Aosta, Turin, Italy
| | - Daniela Pessani
- Laboratorio di Zoologia e Biologia Marina, Dipartimento Scienze della Vita e Biologia dei Sistemi, Turin, Italy
| | - Egle Trincas
- Laboratorio di Zoologia e Biologia Marina, Dipartimento Scienze della Vita e Biologia dei Sistemi, Turin, Italy
| | | | - Pier Luigi Acutis
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d1Aosta, Turin, Italy
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80
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Leitwein M, Gagnaire PA, Desmarais E, Berrebi P, Guinand B. Genomic consequences of a recent three-way admixture in supplemented wild brown trout populations revealed by local ancestry tracts. Mol Ecol 2018; 27:3466-3483. [PMID: 30054960 DOI: 10.1111/mec.14816] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 12/20/2022]
Abstract
Understanding the evolutionary consequences of human-mediated introductions of domesticated strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. However, the genomic impacts of stocking from distinct sources (locally derived vs. divergent) on the genetic integrity of wild populations remain poorly understood. We designed an approach based on estimating local ancestry along individual chromosomes to provide a detailed picture of genomic admixture in supplemented populations. We used this approach to document admixture consequences in the brown trout Salmo trutta, for which decades of stocking practices have profoundly impacted the genetic make-up of wild populations. In southern France, small local Mediterranean populations have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. To address the impact of stocking, we evaluate the extent of admixture from both domestic strains within populations, using 75,684 mapped SNPs obtained from double-digested restriction site-associated DNA sequencing. Then, the chromosomal ancestry profiles of admixed individuals reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigrees. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple-way admixture with population genomic data.
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Affiliation(s)
- Maeva Leitwein
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | | | - Erick Desmarais
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Patrick Berrebi
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Bruno Guinand
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.,Département Biologie-Ecologie, Université de Montpellier, Montpellier Cedex 5, France
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81
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Saint-Pé K, Blanchet S, Tissot L, Poulet N, Plasseraud O, Loot G, Veyssière C, Prunier JG. Genetic admixture between captive-bred and wild individuals affects patterns of dispersal in a brown trout (Salmo trutta) population. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1095-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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82
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Tritsch C, Stuckas H, Martens J, Pentzold S, Kvist L, Lo Valvo M, Giacalone G, Tietze DT, Nazarenko AA, PÄckert M. Gene flow in the European coal tit, Periparus ater (Aves: Passeriformes): low among Mediterranean populations but high in a continental contact zone. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Christian Tritsch
- Senckenberg Natural History Collections, Königsbrücker Landstraße, Dresden, Germany
- Institute of Biology, Molecular Evolution & Animal Systematics, University of Leipzig, Leipzig, Germany
| | - Heiko Stuckas
- Senckenberg Natural History Collections, Königsbrücker Landstraße, Dresden, Germany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Stefan Pentzold
- Institute of Biology, Molecular Evolution & Animal Systematics, University of Leipzig, Leipzig, Germany
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Mario Lo Valvo
- Dipartimento di Scienze e Tecnologie biologiche, chimiche e farmaceutiche, Via Archirafi, Palermo, Italy
| | | | | | - Alexander A Nazarenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Martin PÄckert
- Senckenberg Natural History Collections, Königsbrücker Landstraße, Dresden, Germany
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83
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Ouchia-Benissad S, Ladjali-Mohammedi K. Banding cytogenetics of the Barbary partridge Alectoris barbara and the Chukar partridge Alectoris chukar (Phasianidae): a large conservation with Domestic fowl Gallus domesticus revealed by high resolution chromosomes. COMPARATIVE CYTOGENETICS 2018; 12:171-199. [PMID: 29896323 PMCID: PMC5995975 DOI: 10.3897/compcytogen.v12i2.23743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/16/2018] [Indexed: 06/08/2023]
Abstract
The development of avian cytogenetics is significantly behind that of mammals. In fact, since the advent of cytogenetic techniques, fewer than 1500 karyotypes have been established. The Barbary partridge Alectoris barbara Bonnaterre, 1790 is a bird of economic interest but its genome has not been studied so far. This species is endemic to North Africa and globally declining. The Chukar partridge Alectoris chukar Gray, 1830 is an introduced species which shares the same habitat area as the Barbary partridge and so there could be introgressive hybridisation. A cytogenetic study has been initiated in order to contribute to the Barbary partridge and the Chukar partridge genome analyses. The GTG, RBG and RHG-banded karyotypes of these species have been described. Primary fibroblast cell lines obtained from embryos were harvested after simple and double thymidine synchronisation. The first eight autosomal pairs and Z sex chromosome have been described at high resolution and compared to those of the domestic fowl Gallus domesticus Linnaeus, 1758. The diploid number was established as 2n = 78 for both partridges, as well as for most species belonging to the Galliformes order, underlying the stability of chromosome number in avian karyotypes. Wide homologies were observed for macrochromosomes and gonosome except for chromosome 4, 7, 8 and Z which present differences in morphology and/or banding pattern. Neocentromere occurrence was suggested for both partridges chromosome 4 with an assumed paracentric inversion in the Chukar partridge chromosome 4. Terminal inversion in the long arm of the Barbary partridge chromosome Z was also found. These rearrangements confirm that the avian karyotypes structure is conserved interchromosomally, but not at the intrachromosomal scale.
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Affiliation(s)
- Siham Ouchia-Benissad
- University of Sciences and Technology Houari Boumediene, Faculty of Biological Sciences, LBCM lab., Team: Genetics of Development. USTHB, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, Algeria
| | - Kafia Ladjali-Mohammedi
- University of Sciences and Technology Houari Boumediene, Faculty of Biological Sciences, LBCM lab., Team: Genetics of Development. USTHB, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, Algeria
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84
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Pilot M, Greco C, vonHoldt BM, Randi E, Jędrzejewski W, Sidorovich VE, Konopiński MK, Ostrander EA, Wayne RK. Widespread, long-term admixture between grey wolves and domestic dogs across Eurasia and its implications for the conservation status of hybrids. Evol Appl 2018; 11:662-680. [PMID: 29875809 PMCID: PMC5978975 DOI: 10.1111/eva.12595] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/03/2018] [Indexed: 01/05/2023] Open
Abstract
Hybridisation between a domesticated species and its wild ancestor is an important conservation problem, especially if it results in the introgression of domestic gene variants into wild species. Nevertheless, the legal status of hybrids remains unregulated, partially because of the limited understanding of the hybridisation process and its consequences. The occurrence of hybridisation between grey wolves and domestic dogs is well documented from different parts of the wolf geographic range, but little is known about the frequency of hybridisation events, their causes and the genetic impact on wolf populations. We analysed 61K SNPs spanning the canid genome in wolves from across Eurasia and North America and compared that data to similar data from dogs to identify signatures of admixture. The haplotype block analysis, which included 38 autosomes and the X chromosome, indicated the presence of individuals of mixed wolf-dog ancestry in most Eurasian wolf populations, but less admixture was present in North American populations. We found evidence for male-biased introgression of dog alleles into wolf populations, but also identified a first-generation hybrid resulting from mating between a female dog and a male wolf. We found small blocks of dog ancestry in the genomes of 62% Eurasian wolves studied and melanistic individuals with no signs of recent admixed ancestry, but with a dog-derived allele at a locus linked to melanism. Consequently, these results suggest that hybridisation has been occurring in different parts of Eurasia on multiple timescales and is not solely a recent phenomenon. Nevertheless, wolf populations have maintained genetic differentiation from dogs, suggesting that hybridisation at a low frequency does not diminish distinctiveness of the wolf gene pool. However, increased hybridisation frequency may be detrimental for wolf populations, stressing the need for genetic monitoring to assess the frequency and distribution of individuals resulting from recent admixture.
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Affiliation(s)
| | - Claudia Greco
- Department of Environmental Monitoring and Biodiversity ConservationItalian National Institute for Environmental Protection and ResearchBolognaItaly
| | - Bridgett M. vonHoldt
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
| | - Ettore Randi
- Department of Environmental Monitoring and Biodiversity ConservationItalian National Institute for Environmental Protection and ResearchBolognaItaly
- Department 18/Section of Environmental EngineeringAalborg UniversityAalborgDenmark
| | - Włodzimierz Jędrzejewski
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
- Present address:
Instituto Venezolano de Investigaciones Cientificas (IVIC)Centro de EcologiaCaracasVenezuela
| | | | | | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCAUSA
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85
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Yu HJ, Kim JK. Upwelling and eddies affect connectivity among local populations of the goldeye rockfish, Sebastes thompsoni (Pisces, Scorpaenoidei). Ecol Evol 2018; 8:4387-4402. [PMID: 29760881 PMCID: PMC5938445 DOI: 10.1002/ece3.3993] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/13/2018] [Accepted: 02/28/2018] [Indexed: 11/09/2022] Open
Abstract
The goldeye rockfish, Sebastes thompsoni, commercial rockfish catch in the Northwest Pacific Ocean, may influence its population structure. To clarify the population genetic structure of Korean S. thompsoni and its degree of hybridization with the most close species, Sebastes joyneri, we analyzed a mitochondrial (mt) DNA control region and eleven polymorphic microsatellite (ms) loci. S. joyneri individuals were clearly distinguished from S. thompsoni by the mtDNA control region and ms loci results, with single interspecific hybridization between two species suggesting no impact on genetic structure of S. thompsoni. Analysis of mtDNA revealed no population structure within S. thompsoni, suggesting the survival of a single population in southern refugia during the glacial period. The ms loci results, in contrast, showed two genetically distinct clusters within S. thompsoni: One was predominant throughout Korean coasts (from the Yellow Sea, via the Korea Strait to the East Sea); the other was predominant at Dokdo Island in the East Sea; and both occurred in similar ratios at Wangdolcho Reef in the East Sea. A possible factor that restricts gene flow between Korean coastal and offshore populations in the East Sea may be related to the complex oceanic current patterns such as eddies and upwelling, which represent impermeable barriers to population connectivity for this species. Our findings highlight that these two populations might be representative of two separate stock within Korean waters and maintain their geographically related genetic structure.
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Affiliation(s)
- Hyo Jae Yu
- Department of Marine Biology Pukyong National University Busan Korea
| | - Jin-Koo Kim
- Department of Marine Biology Pukyong National University Busan Korea
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86
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Steyer K, Tiesmeyer A, Muñoz‐Fuentes V, Nowak C. Low rates of hybridization between European wildcats and domestic cats in a human-dominated landscape. Ecol Evol 2018; 8:2290-2304. [PMID: 29468044 PMCID: PMC5817136 DOI: 10.1002/ece3.3650] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 10/18/2017] [Accepted: 10/27/2017] [Indexed: 01/07/2023] Open
Abstract
Hybridization between wild species and their domestic congeners is considered a major threat for wildlife conservation. Genetic integrity of the European wildcat, for instance, is a concern as they are outnumbered by domestic cats by several orders of magnitude throughout its range. We genotyped 1,071 individual wildcat samples obtained from hair traps and roadkills collected across the highly fragmented forests of western Central Europe, in Germany and Luxembourg, to assess domestic cat introgression in wildcats in human-dominated landscapes. Analyses using a panel of 75 autosomal SNPs suggested a low hybridization rate, with 3.5% of wildcat individuals being categorized as F1, F2, or backcrosses to either parental taxon. We report that results based on a set of SNPs were more consistent than on a set of 14 microsatellite markers, showed higher accuracy to detect hybrids and their class in simulation analyses, and were less affected by underlying population structure. Our results strongly suggest that very high hybridization rates previously reported for Central Europe may be partly due to inadequate choice of markers and/or sampling design. Our study documents that an adequately selected SNP panel for hybrid detection may be used as an alternative to commonly applied microsatellite markers, including studies relying on noninvasively collected samples. In addition, our finding of overall low hybridization rates in Central European wildcats provides an example of successful wildlife coexistence in human-dominated, fragmented landscapes.
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Affiliation(s)
- Katharina Steyer
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Institute of Ecology, Evolution and DiversityGoethe‐University FrankfurtFrankfurt am MainGermany
| | - Annika Tiesmeyer
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Institute of Ecology, Evolution and DiversityGoethe‐University FrankfurtFrankfurt am MainGermany
| | - Violeta Muñoz‐Fuentes
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteWellcome Trust Genome Campus, HinxtonCambridgeUK
| | - Carsten Nowak
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
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87
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Schüttler E, Saavedra-Aracena L, Jiménez JE. Domestic carnivore interactions with wildlife in the Cape Horn Biosphere Reserve, Chile: husbandry and perceptions of impact from a community perspective. PeerJ 2018; 6:e4124. [PMID: 29312813 PMCID: PMC5756619 DOI: 10.7717/peerj.4124] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/12/2017] [Indexed: 11/20/2022] Open
Abstract
Background Hundreds of millions of domestic carnivores worldwide have diverse positive affiliations with humans, but can provoke serious socio-ecological impacts when free-roaming. Unconfined dogs (Canis familiaris) and cats (Felis catus) interact with wildlife as predators, competitors, and disease-transmitters; their access to wildlife depends on husbandry, perceptions, attitudes, and behaviors of pet owners and non-owners. Methods To better understand husbandry and perceptions of impacts by unconfined, domestic carnivores, we administered questionnaires (n = 244) to pet owners and non-owners living in one of the last wilderness areas of the world, the Cape Horn Biosphere Reserve, located in southern Chile. We used descriptive statistics to provide demographic pet and husbandry information, quantify free-roaming dogs and cats, map their sightings in nature, and report experiences and perceptions of the impact of free-roaming dogs and cats on wildlife. We corroborated our results with an analysis of prey remains in dog feces (n = 53). With generalized linear models, we examined which factors (i.e., food provisioning, reproductive state, rural/village households, sex, and size) predicted that owned dogs and cats bring wildlife prey home. Results Thirty-one percent of village dogs (n = 121) and 60% of dogs in rural areas (n = 47) roamed freely day and/or night. Free-roaming dog packs were frequently observed (64% of participants) in the wild, including a feral dog population on Navarino Island. Dogs (31 of 168) brought home invasive muskrats (Ondatra zibethicus) and avian prey, and over half of all cats (27 of 51) brought home mainly avian prey. Birds were also the most harassed wildlife category, affected by one third of all dogs and cats. Nevertheless, dog-wildlife conflicts were hardly recognized (<9% of observed conflicts and suspected problems), and only 34% of the participants thought that cats might impact birds. Diet analysis revealed that dogs consumed livestock (64% of 59 prey occurrences), beavers (Castor canadensis, 14%), and birds (10%). The probability that dogs brought prey to owners’ homes was higher in rural locations and with larger dogs. There was also evidence that cats from rural households and with an inadequate food supply brought more prey home than village cats. Discussion Although muskrat, beavers, and birds were brought home, harassed, or found in dog feces, free-roaming dogs and, to a lesser extent, cats are perceived predominantly in an anthropogenic context (i.e., as pets) and not as carnivores interacting with wildlife. Therefore, technical and legal measures should be applied to encourage neutering, increase confinement, particularly in rural areas, and stimulate social change via environmental education that draws attention to the possibility and consequences of unconfined pet interaction with wildlife in the southernmost protected forest ecoregion of the globe.
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Affiliation(s)
- Elke Schüttler
- Sub-Antarctic Biocultural Conservation Program, Universidad de Magallanes, Punta Arenas, Región de Magallanes y Antártica Chilena, Chile
| | - Lorena Saavedra-Aracena
- Sub-Antarctic Biocultural Conservation Program, Universidad de Magallanes, Punta Arenas, Región de Magallanes y Antártica Chilena, Chile
| | - Jaime E Jiménez
- Sub-Antarctic Biocultural Conservation Program, Universidad de Magallanes, Punta Arenas, Región de Magallanes y Antártica Chilena, Chile.,Department of Biological Sciences, University of North Texas, Denton, TX, United States of America.,Department of Philosophy and Religion, University of North Texas, Denton, TX, United States of America.,Institute of Ecology and Biodiversity (IEB), Santiago, Chile
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88
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Söderquist P, Elmberg J, Gunnarsson G, Thulin CG, Champagnon J, Guillemain M, Kreisinger J, Prins HHT, Crooijmans RPMA, Kraus RHS. Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos). EUR J WILDLIFE RES 2017. [DOI: 10.1007/s10344-017-1156-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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89
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Miyazaki M, Nishimura T, Hojo W, Miyazaki T, Laine RA, Yamashita T. Potential use of domestic cat ( Felis catus ) urinary extracts for manipulating the behavior of free-roaming cats and wild small felids. Appl Anim Behav Sci 2017. [DOI: 10.1016/j.applanim.2017.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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90
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Bangs MR, Oswald KJ, Greig TW, Leitner JK, Rankin DM, Quattro JM. Introgressive hybridization and species turnover in reservoirs: a case study involving endemic and invasive basses (Centrarchidae: Micropterus) in southeastern North America. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1018-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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91
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Miller MP, Mullins TD, Forsman ED, Haig SM. Genetic differentiation and inferred dynamics of a hybrid zone between Northern Spotted Owls ( Strix occidentalis caurina) and California Spotted Owls ( S. o. occidentalis) in northern California. Ecol Evol 2017; 7:6871-6883. [PMID: 28904767 PMCID: PMC5587499 DOI: 10.1002/ece3.3260] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/05/2017] [Accepted: 06/28/2017] [Indexed: 12/04/2022] Open
Abstract
Genetic differentiation among Spotted Owl (Strix occidentalis) subspecies has been established in prior studies. These investigations also provided evidence for introgression and hybridization among taxa but were limited by a lack of samples from geographic regions where subspecies came into close contact. We analyzed new sets of samples from Northern Spotted Owls (NSO: S. o. caurina) and California Spotted Owls (CSO: S. o. occidentalis) in northern California using mitochondrial DNA sequences (mtDNA) and 10 nuclear microsatellite loci to obtain a clearer depiction of genetic differentiation and hybridization in the region. Our analyses revealed that a NSO population close to the northern edge of the CSO range in northern California (the NSO Contact Zone population) is highly differentiated relative to other NSO populations throughout the remainder of their range. Phylogenetic analyses identified a unique lineage of mtDNA in the NSO Contact Zone, and Bayesian clustering analyses of the microsatellite data identified the Contact Zone as a third distinct population that is differentiated from CSO and NSO found in the remainder of the subspecies' range. Hybridization between NSO and CSO was readily detected in the NSO Contact Zone, with over 50% of individuals showing evidence of hybrid ancestry. Hybridization was also identified among 14% of CSO samples, which were dispersed across the subspecies' range in the Sierra Nevada Mountains. The asymmetry of hybridization suggested that the hybrid zone may be dynamic and moving. Although evidence of hybridization existed, we identified no F1 generation hybrid individuals. We instead found evidence for F2 or backcrossed individuals among our samples. The absence of F1 hybrids may indicate that (1) our 10 microsatellites were unable to distinguish hybrid types, (2) primary interactions between subspecies are occurring elsewhere on the landscape, or (3) dispersal between the subspecies' ranges is reduced relative to historical levels, potentially as a consequence of recent regional fires.
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Affiliation(s)
- Mark P Miller
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
| | - Thomas D Mullins
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
| | - Eric D Forsman
- USDA Forest ServicePacific Northwest Research Station Corvallis OR USA
| | - Susan M Haig
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
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92
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Galaverni M, Caniglia R, Pagani L, Fabbri E, Boattini A, Randi E. Disentangling Timing of Admixture, Patterns of Introgression, and Phenotypic Indicators in a Hybridizing Wolf Population. Mol Biol Evol 2017; 34:2324-2339. [PMID: 28549194 PMCID: PMC5850710 DOI: 10.1093/molbev/msx169] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hybridization is a natural or anthropogenic process that can deeply affect the genetic make-up of populations, possibly decreasing individual fitness but sometimes favoring local adaptations. The population of Italian wolves (Canis lupus), after protracted demographic declines and isolation, is currently expanding in anthropic areas, with documented cases of hybridization with stray domestic dogs. However, identifying admixture patterns in deeply introgressed populations is far from trivial. In this study, we used a panel of 170,000 SNPs analyzed with multivariate, Bayesian and local ancestry reconstruction methods to identify hybrids, estimate their ancestry proportions and timing since admixture. Moreover, we carried out preliminary genotype-phenotype association analyses to identify the genetic bases of three phenotypic traits (black coat, white claws, and spur on the hind legs) putative indicators of hybridization. Results showed no sharp subdivisions between nonadmixed wolves and hybrids, indicating that recurrent hybridization and deep introgression might have started mostly at the beginning of the population reexpansion. In hybrids, we identified a number of genomic regions with excess of ancestry in one of the parental populations, and regions with excess or resistance to introgression compared with neutral expectations. The three morphological traits showed significant genotype-phenotype associations, with a single genomic region for black coats and white claws, and with multiple genomic regions for the spur. In all cases the associated haplotypes were likely derived from dogs. In conclusion, we show that the use of multiple genome-wide ancestry reconstructions allows clarifying the admixture dynamics even in highly introgressed populations, and supports their conservation management.
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Affiliation(s)
- Marco Galaverni
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
- Area Conservazione, WWF Italia, Rome, Italy
| | - Romolo Caniglia
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Luca Pagani
- Dipartimento di Biologia, Universita degli Studi di Padova, Padua, Italy
- Estonian Biocentre, Tartu, Estonia
| | - Elena Fabbri
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Ettore Randi
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
- Department 18/Section of Environmental Engineering, Aalborg Universitet, Aalborg, Denmark
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93
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Dzialuk A, Zastempowska E, Skórzewski R, Twarużek M, Grajewski J. High domestic pig contribution to the local gene pool of free-living European wild boar: a case study in Poland. MAMMAL RES 2017. [DOI: 10.1007/s13364-017-0331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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94
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Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic. Heredity (Edinb) 2017; 119:154-165. [PMID: 28422135 DOI: 10.1038/hdy.2017.22] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 02/20/2017] [Accepted: 03/02/2017] [Indexed: 12/20/2022] Open
Abstract
Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolutionary impacts of invasions yet has rarely been studied in marine invasive species. The European green crab (Carcinus maenas) invaded eastern North America twice from northern and southern locations in its native range. Here we examine the frequency of hybridization among these two distinct invasions at locations from New Jersey, USA to Newfoundland, Canada using restriction-site-associated DNA sequencing (RAD-seq), microsatellite loci and cytochrome c oxidase subunit I mitochondrial DNA (mtDNA) sequences. We used Bayesian clustering and hybrid assignment analyses to investigate hybridization between the northern and southern populations. Of the samples analyzed, six locations contained at least one hybrid individual, while two locations were characterized by extensive hybridization, with 95% of individuals collected from Placentia Bay, Newfoundland being hybrids (mostly F2) and 90% of individuals from Kejimkujik, Nova Scotia being classified as hybrids, mostly backcrosses to the northern ecotype. The presence of both F2 hybrids and backcrossed individuals suggests that these hybrids are viable and introgression is occurring between invasions. Our results provide insight into the demographic and evolutionary consequences of hybridization between independent invasions, and will inform the management of green crabs in eastern North America.
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95
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Spatial assessment of wolf-dog hybridization in a single breeding period. Sci Rep 2017; 7:42475. [PMID: 28195213 PMCID: PMC5307949 DOI: 10.1038/srep42475] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/11/2017] [Indexed: 11/17/2022] Open
Abstract
Understanding the dynamics of wolf-dog hybridization and delineating evidence-based conservation strategies requires information on the spatial extent of wolf-dog hybridization in real-time, which remains largely unknown. We collected 332 wolf-like scats over ca. 5,000km2 in the NW Iberian Peninsula to evaluate wolf-dog hybridization at population level in a single breeding/pup-rearing season. Mitochondrial DNA (MtDNA) and 18 ancestry informative markers were used for species and individual identification, and to detect wolf-dog hybrids. Genetic relatedness was assessed between hybrids and wolves. We identified 130 genotypes, including 67 wolves and 7 hybrids. Three of the hybrids were backcrosses to dog whereas the others were backcrosses to wolf, the latter accounting for a 5.6% rate of introgression into the wolf population. Our results show a previously undocumented scenario of multiple and widespread wolf-dog hybridization events at the population level. However, there is a clear maintenance of wolf genetic identity, as evidenced by the sharp genetic identification of pure individuals, suggesting the resilience of wolf populations to a small amount of hybridization. We consider that real-time population level assessments of hybridization provide a new perspective into the debate on wolf conservation, with particular focus on current management guidelines applied in wolf-dog hybridization events.
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96
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Temporal shifts in the saltmarsh–Nelson’s sparrow hybrid zone revealed by replicated demographic and genetic surveys. CONSERV GENET 2017. [DOI: 10.1007/s10592-016-0920-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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97
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Poglayen G, Gori F, Morandi B, Galuppi R, Fabbri E, Caniglia R, Milanesi P, Galaverni M, Randi E, Marchesi B, Deplazes P. Italian wolves ( Canis lupus italicus Altobello, 1921) and molecular detection of taeniids in the Foreste Casentinesi National Park, Northern Italian Apennines. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2017; 6:1-7. [PMID: 28180084 PMCID: PMC5284487 DOI: 10.1016/j.ijppaw.2017.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/21/2016] [Accepted: 01/16/2017] [Indexed: 01/22/2023]
Abstract
After centuries of massive decline, the recovery of the wolf (Canis lupus italicus) in Italy is a typical conservation success story. To learn more about the possible role of parasites in the wolves' individual and population health and conservation we used non-invasive molecular approaches on fecal samples to identify individual wolves, pack membership, and the taeniids present, some of which are zoonotic. A total of 130 specimens belonging to 54 wolves from eight packs were collected and examined. Taeniid eggs were isolated using a sieving/flotation technique, and the species level was identified by PCR (gene target: 12S rRNA and nad1). Taeniid prevalence was 40.7% for Taenia hydatigena, 22.2% for T. krabbei, 1.8% for T. polyachanta and 5.5% for Echinococcus granulosus. The prevalence of E. granulosus is discussed. Our results show that the taeniid fauna found in wolves from the Foreste Casentinesi National Park is comparable to that described for other domestic and wild Italian canids and provides insights into the wolves’ diet and their relationship with the environment. Non-invasive techniques were used to identify individual wolves and their taeniids. The taeniids detected could be linked to individual wolves and to packs. The taeniids detected provided information on the wolves' diet and on zoonotic risk.
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Affiliation(s)
- Giovanni Poglayen
- Alma Mater Studiorum, Department of Veterinary Medical Science, Via Tolara di Sopra, 50-40064, Ozzano dell'Emilia, Bologna, Italy
| | - Francesca Gori
- Institute of Parasitology, University of Zurich, Winterthurerstrasse 266a, CH-8057 Zurich, Switzerland
| | - Benedetto Morandi
- Alma Mater Studiorum, Department of Veterinary Medical Science, Via Tolara di Sopra, 50-40064, Ozzano dell'Emilia, Bologna, Italy
| | - Roberta Galuppi
- Alma Mater Studiorum, Department of Veterinary Medical Science, Via Tolara di Sopra, 50-40064, Ozzano dell'Emilia, Bologna, Italy
| | - Elena Fabbri
- Genetics Laboratory, Institute for Environmental Protection and Research (ISPRA), Ozzano dell'Emilia, Bologna, Italy
| | - Romolo Caniglia
- Genetics Laboratory, Institute for Environmental Protection and Research (ISPRA), Ozzano dell'Emilia, Bologna, Italy
| | - Pietro Milanesi
- Genetics Laboratory, Institute for Environmental Protection and Research (ISPRA), Ozzano dell'Emilia, Bologna, Italy
| | - Marco Galaverni
- Genetics Laboratory, Institute for Environmental Protection and Research (ISPRA), Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Genetics Laboratory, Institute for Environmental Protection and Research (ISPRA), Ozzano dell'Emilia, Bologna, Italy
| | - Barbara Marchesi
- Alma Mater Studiorum, Department of Veterinary Medical Science, Via Tolara di Sopra, 50-40064, Ozzano dell'Emilia, Bologna, Italy
| | - Peter Deplazes
- Institute of Parasitology, University of Zurich, Winterthurerstrasse 266a, CH-8057 Zurich, Switzerland
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Canu A, Mattioli L, Santini A, Apollonio M, Scandura M. ‘Video-scats’: combining camera trapping and non-invasive genotyping to assess individual identity and hybrid status in gray wolf. WILDLIFE BIOLOGY 2017. [DOI: 10.2981/wlb.00355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Antonio Canu
- A. Canu, M. Apollonio and M. Scandura , Dept. of Science for Nature and Environmental Resources, Univ. of Sassari, Via Muroni 25, IT-07100 Sassari, Italy. AC also at: C.I.R.Se.M.A.F. Firenze, Italy
| | - Luca Mattioli
- L. Mattioli, Regione Toscana, Settore Attività Faunistico Venatoria, Pesca Dilettantistica, Pesca in Mare, Arezzo, Italy
| | | | - Marco Apollonio
- A. Canu, M. Apollonio and M. Scandura , Dept. of Science for Nature and Environmental Resources, Univ. of Sassari, Via Muroni 25, IT-07100 Sassari, Italy. AC also at: C.I.R.Se.M.A.F. Firenze, Italy
| | - Massimo Scandura
- A. Canu, M. Apollonio and M. Scandura , Dept. of Science for Nature and Environmental Resources, Univ. of Sassari, Via Muroni 25, IT-07100 Sassari, Italy. AC also at: C.I.R.Se.M.A.F. Firenze, Italy
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99
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Trophic overlap between wolves and free-ranging wolf×dog hybrids in the Apennine Mountains, Italy. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2016.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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100
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Shiga T, Yokogawa M, Kaneko S, Isagi Y. Genetic diversity and population structure of Nuphar submersa (Nymphaeaceae), a critically endangered aquatic plant endemic to Japan, and implications for its conservation. JOURNAL OF PLANT RESEARCH 2017; 130:83-93. [PMID: 27878469 DOI: 10.1007/s10265-016-0869-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 07/20/2016] [Indexed: 06/06/2023]
Abstract
Nuphar submersa (Nymphaeaceae) is a critically endangered freshwater macrophyte indigenous to central Japan, with only four small extant populations represented across its entire range. We investigated the genotypic and genetic diversity as well as the genetic structure of all extant individuals of N. submersa based on analysis of 15 microsatellite loci. Among 278 individual ramets, 52 multilocus genotypes were detected: 30 genotypes in Nikko City (NIK), 18 in Nasukarasuyama City (NAS), 3 in Mooka City (MOK), and 1 in Sakura City (SAK). The average number of alleles per locus ranged from 1.20 to 1.93, whereas the observed and expected heterozygosities ranged from 0.11 to 0.33 and from 0.10 to 0.24, respectively. With the exception of SAK, all populations contained multiple clones, but our results indicated low levels of within-population genetic diversity. The populations NIK and NAS comprised few large or middle-sized genets and many small genets. The populations NIK and NAS were suggested to comprise large old, old fragmented, and/or young small genets resulting from seedling establishment. All four populations were differentiated, and gene flow between the populations was restricted (average level of gene flow (Nm) = 0.122, G' ST = 0.639). Of the total genetic diversity, 67.20 and 9.13% were attributable to inter- and intra-population diversity, respectively. STRUCTURE analysis revealed two or three well-differentiated groups of populations. Cluster I comprised one population (NIK) and cluster II comprised the remaining populations at K = 2. The populations NIK, NAS, and the remaining populations were assigned to clusters I, II, and III, respectively, at K = 3. For conservation practices, we recommend that each cluster be regarded as a different management unit. We further suggest that artificial gene flow among MOK and SAK populations is an appropriate option, whereas NIK should not be reinforced with genotypes from the remaining populations.
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Affiliation(s)
- Takashi Shiga
- Faculty of Education, Niigata University, Ikarashi-Ninocho, Nishi-ku, Niigata, 950-2181, Japan.
| | - Masashi Yokogawa
- Osaka Museum of Natural History, Nagai Park, Higashisumiyoshi-ku, Osaka, 546-0034, Japan
| | - Shingo Kaneko
- Faculty of Symbiotic Systems Science, Fukushima University, Kanayagawa, Fukushima, 960-1296, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
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