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Jourdan J, Bundschuh M, Copilaș-Ciocianu D, Fišer C, Grabowski M, Hupało K, Jemec Kokalj A, Kabus J, Römbke J, Soose LJ, Oehlmann J. Cryptic Species in Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1889-1914. [PMID: 37314101 DOI: 10.1002/etc.5696] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/20/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023]
Abstract
The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Jonas Jourdan
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau, Germany
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Denis Copilaș-Ciocianu
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michał Grabowski
- Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Kamil Hupało
- Department of Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Kabus
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie, Flörsheim am Main, Germany
| | - Laura J Soose
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
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Kaya S, Kabasakal B, Erdoğan A. Geographic Genetic Structure of Alectoris chukar in Türkiye: Post-LGM-Induced Hybridization and Human-Mediated Contaminations. BIOLOGY 2023; 12:biology12030401. [PMID: 36979093 PMCID: PMC10045126 DOI: 10.3390/biology12030401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/19/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Türkiye is considered an important evolutionary area for Chukar partridge (Alectoris chukar), since it is both a potential ancestral area and a diversification center for the species. Using 2 mitochondrial (Cty-b and D-loop) and 13 polymorphic microsatellite markers, we investigated the geographic genetic structure of A. chukar populations to determine how past climatic fluctuations and human activities have shaped the gene pool of this species in Türkiye. Our results indicate, firstly, that only A. chukar of the genus Alectoris is present in Türkiye (Anatolia and Thrace), with no natural or artificial gene flow from congenerics. Secondly, the geographic genetic structure of the species in Türkiye has been shaped by topographic heterogeneity, Pleistocene climatic fluctuations, and artificial transport by humans. Third, there appears to be three genetic clusters: Thracian, Eastern, and Western. Fourth, the post-LGM demographic expansion of the Eastern and Western populations has formed a hybrid zone in Central Anatolia (~8 kyBP). Fifth, the rate of China clade-B contamination in Türkiye is about 8% in mtDNA and about 12% in nuDNA, with the Southeastern Anatolian population having the highest contamination. Sixth, the Thracian population was the most genetically distinct, with the lowest genetic diversity and highest level of inbreeding and no China clad-B contamination. These results can contribute to the conservation regarding A. chukar populations, especially the Thracian population.
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Affiliation(s)
- Sarp Kaya
- First and Emergency Aid Programme, Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur 15030, Turkey
| | - Bekir Kabasakal
- Department of Biology, Akdeniz University, Antalya 07058, Turkey
- Anesthesia Programme, Department of Medical Services and Techniques, Vocational School of Health Services, Antalya Bilim University, Antalya 07190, Turkey
- Correspondence:
| | - Ali Erdoğan
- Department of Biology, Akdeniz University, Antalya 07058, Turkey
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Spatial genetic structure of European wild boar, with inferences on late-Pleistocene and Holocene demographic history. Heredity (Edinb) 2023; 130:135-144. [PMID: 36639700 PMCID: PMC9981775 DOI: 10.1038/s41437-022-00587-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023] Open
Abstract
European wildlife has been subjected to intensifying levels of anthropogenic impact throughout the Holocene, yet the main genetic partitioning of many species is thought to still reflect the late-Pleistocene glacial refugia. We analyzed 26,342 nuclear SNPs of 464 wild boar (Sus scrofa) across the European continent to infer demographic history and reassess the genetic consequences of natural and anthropogenic forces. We found that population fragmentation, inbreeding and recent hybridization with domestic pigs have caused the spatial genetic structure to be heterogeneous at the local scale. Underlying local anthropogenic signatures, we found a deep genetic structure in the form of an arch-shaped cline extending from the Dinaric Alps, via Southeastern Europe and the Baltic states, to Western Europe and, finally, to the genetically diverged Iberian peninsula. These findings indicate that, despite considerable anthropogenic influence, the deeper, natural continental structure is still intact. Regarding the glacial refugia, our findings show a weaker signal than generally assumed, but are nevertheless suggestive of two main recolonization routes, with important roles for Southern France and the Balkans. Our results highlight the importance of applying genomic resources and framing genetic results within a species' demographic history and geographic distribution for a better understanding of the complex mixture of underlying processes.
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Griciuvienė L, Janeliūnas Ž, Pilevičienė S, Jurgelevičius V, Paulauskas A. Changes in the Genetic Structure of Lithuania's Wild Boar ( Sus scrofa) Population Following the Outbreak of African Swine Fever. Genes (Basel) 2022; 13:1561. [PMID: 36140730 PMCID: PMC9498859 DOI: 10.3390/genes13091561] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
The emergence of African swine fever (ASF) in Lithuania and its subsequent persistence has led to a decline in the population of wild boar (Sus scrofa). ASF has been spreading in Lithuania since its introduction, therefore it is important to understand any genetic impact of ASF outbreaks on wild boar populations. The aim of this study was to assess how the propensity for an outbreak has shaped genetic variation in the wild boar population. A total of 491 wild boar samples were collected and genotyped using 16 STR markers. Allele richness varied between 15 and 51, and all SSR loci revealed a significant deviation from the Hardy-Weinberg equilibrium. Fixation indices indicated a significant reduction in heterozygosity within and between subpopulations. PCoA and STRUCTURE analysis demonstrated genetic differences between the western region which had had no outbreaks (restricted zone I) and the region with ASF infection (restricted zones II and III). It is concluded that environmental factors may play a particular role in shaping the regional gene flow and influence the genetic structure of the wild boar population in the region with ASF outbreaks.
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Affiliation(s)
- Loreta Griciuvienė
- Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio 58, 44248 Kaunas, Lithuania
| | - Žygimantas Janeliūnas
- Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio 58, 44248 Kaunas, Lithuania
- National Food and Veterinary Risk Assessment Institute, J. Kairiūkščio 10, 08409 Vilnius, Lithuania
| | - Simona Pilevičienė
- National Food and Veterinary Risk Assessment Institute, J. Kairiūkščio 10, 08409 Vilnius, Lithuania
| | - Vaclovas Jurgelevičius
- Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio 58, 44248 Kaunas, Lithuania
| | - Algimantas Paulauskas
- Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio 58, 44248 Kaunas, Lithuania
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Gong Y, Zhang HY, Yuan Y, He Y, Zhang W, Han Y, Na R, Zeng Y, Luo J, Yang H, Huang Y, Zhao Y, Zhao Z, E GX. Genome-Wide Selection Sweep between Wild and Local Pigs from Europe for the Investigation of the Hereditary Characteristics of Domestication in Sus Scrofa. Animals (Basel) 2022; 12:ani12081037. [PMID: 35454283 PMCID: PMC9030587 DOI: 10.3390/ani12081037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/23/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
The phenotypic characteristics of existing domestic pigs (DPs) greatly differ from those of wild boar (WB) populations thousands of years ago. After thousands of years of human domestication, WB and DP have diverged greatly in terms of genetics. Theoretically, worldwide local pigs have independent contributions from their local WBs at the beginning of Sus scrofa domestication. The investigation of the vicissitude of the heredity material between domestic populations and their wild ancestors will help in further understanding the domestication history of domestic animals. In the present study, we performed a genome-wide association scan (GWSA) and phylogeny estimation with a total of 1098 public European Illumina 60K single nucleotide polymorphism data, which included 650 local DPs and 448 WBs. The results revealed that the phylogenetic relationship of WBs corresponds to their geographical distribution and carries large divergence with DPs, and all WB breeds (e.g., HRWB, SBWB, and TIWB) presents a closely linkage with the middle WB (e.g., HRWB, and PLWB). In addition, 64 selected candidate genes (e.g., IDH2, PIP5K1B, SMARCA2, KIF5C, and TJP2) were identified from GWSA. A total of 63 known multiple biological functional pathways were annotated by 22 genes, and ubiquinone and other terpenoid-quinone biosynthesis pathways that belong to the metabolism of cofactors and vitamins were significantly enriched (p < 0.05). The most frequent (28.57%) pathways were classified under metabolism. We confirmed that the middle European WB has made an important genetic contribution to the entire European WB populations. A series of selected genes discovered from this study provides the scientific community with a deeper understanding of the heredity performance of metabolism and emotion and the real purpose behind domestication.
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Scandura M, Fabbri G, Caniglia R, Iacolina L, Mattucci F, Mengoni C, Pante G, Apollonio M, Mucci N. Resilience to Historical Human Manipulations in the Genomic Variation of Italian Wild Boar Populations. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.833081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human activities can globally modify natural ecosystems determining ecological, demographic and range perturbations for several animal species. These changes can jeopardize native gene pools in different ways, leading either to genetic homogenization, or conversely, to the split into genetically divergent demes. In the past decades, most European wild boar (Sus scrofa) populations were heavily managed by humans. Anthropic manipulations have strongly affected also Italian populations through heavy hunting, translocations and reintroductions that might have deeply modified their original gene pools. In this study, exploiting the availability of the well-mapped porcine genome, we applied genomic tools to explore genome-wide variability in Italian wild boar populations, investigate their genetic structure and detect signatures of possible introgression from domestic pigs and non-native wild boar. Genomic data from 134 wild boar sampled in six areas of peninsular Italy and in Sardinia were gathered using the Illumina Porcine SNP60 BeadChip (60k Single Nucleotide Polymorphisms – SNPs) and compared with reference genotypes from European specimens and from domestic pigs (both commercial and Italian local breeds), using multivariate and maximum-likelihood approaches. Pairwise FST values, multivariate analysis and assignment procedures indicated that Italian populations were highly differentiated from all the other analyzed European wild boar populations. Overall, a lower heterozygosity was found in the Italian population than in the other European regions. The most diverging populations in Castelporziano Presidential Estate and Maremma Regional Park can be the result of long-lasting isolation, reduced population size and genetic drift. Conversely, an unexpected similarity was found among Apennine populations, even at high distances. Signatures of introgression from both non-Italian wild boar and domestic breeds were very limited. To summarize, we successfully applied genome-wide procedures to explore, for the first time, the genomic diversity of Italian wild boar, demonstrating that they represent a strongly heterogeneous assemblage of demes with different demographic and manipulation histories. Nonetheless, our results suggest that a native component of genomic variation is predominant over exogenous ones in most populations.
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Snegin EA, Makeeva VM, Kaledin AP, Ostapchuk AM, Alazneli ID, Smurov AV. Genetic diversity of the Central European wild boar (Sus scrofa scrofa) population and domestic pig (Sus scrofa domesticus) breeds based on a microsatellite DNA locus. Vavilovskii Zhurnal Genet Selektsii 2022; 25:822-830. [PMID: 35083403 PMCID: PMC8755522 DOI: 10.18699/vj21.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 09/18/2021] [Accepted: 09/27/2021] [Indexed: 11/23/2022] Open
Abstract
The results of studies of the genetic structure of the Central European wild boar (Sus scrofa scrofa) population
and four breeds of domestic pigs (Duroc, Yorkshire, Large White and Landrace) bred in the Central Black Earth
region of Russia are presented in this work. Based on 12 microsatellite loci, a significant ( p <0.05) decrease in the
level of genetic variability in bred breeds was shown. The expected heterozygosity and Shannon index were as follows:
in the wild boar, Ho = 0.763 ± 0.026, I = 1.717 ± 0.091; in the Duroc breed, Ho = 0.569 ± 0.068, I = 1.191 ± 0.157;
in the Landrace, Ho = 0.618 ± 0.062, I = 1.201 ± 0.147; in the Large White, Ho = 0.680 ± 0.029, I = 1.362 ± 0.074; and in
the Yorkshire, Ho = 0.642 ± 0.065, I = 1.287 ± 0.156. The results of checking genotypic Hardy–Weinberg equilibrium
based on the G-test of maximum likelihood demonstrated that the overwhelming majority of loci in the wild boar
population were in the state of said equilibrium. By contrast, in pig breed populations, some loci demonstrated a
significant deviation from the indicated equilibrium. In addition, the Yorkshire, Large White, and Landrace populations
had loci, for which the hypothesis of neutrality was reliably rejected based on the results of the Ewens–Watterson
test. The revealed private alleles, characteristic of the wild boar and breeds, can later be used to identify
them. The ordination of the centroids of different herds in the space of the first two principal coordinates based on
the matrix of pairwise estimates of Nei’s genetic distances showed that the most distant populations are the Duroc
and Boar breeds, and the most genetically close are the Yorkshire and Landrace breeds. The closest to the wild boar
population was the Large White breed. The assessment of the effective size, carried out using the method based
on the linkage disequilibrium and the molecular coancestry method, showed that in all studied groups, including
the wild boar population, the effective size was less than 100 individuals. The low effective size of the wild boar
population (Ne = 21.8, Neb = 4.0) is probably caused by the death and shooting of animals due to Pestis africana
suum.
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Affiliation(s)
| | | | - A. P. Kaledin
- Russian State Agrarian University – Moscow Timiryazev Agricultural Academy
| | - A. M. Ostapchuk
- Russian State Agrarian University – Moscow Timiryazev Agricultural Academy
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Griciuvienė L, Janeliūnas Ž, Jurgelevičius V, Paulauskas A. The effects of habitat fragmentation on the genetic structure of wild boar (Sus scrofa) population in Lithuania. BMC Genom Data 2021; 22:53. [PMID: 34837959 PMCID: PMC8626901 DOI: 10.1186/s12863-021-01008-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/03/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Wild boar (Sus scrofa) is a widely distributed ungulate whose success can be attributed to a variety of ecological features. The genetic variation and population structure of Lithuania's wild boar population have not yet been thoroughly studied. The purposes of this study were to investigate the genetic diversity of S. scrofa and assess the effects of habitat fragmentation on the population structure of wild boar in Lithuania. A total of 96 S. scrofa individuals collected from different regions of Lithuania were genotyped using fifteen microsatellite loci. RESULTS The microsatellite analysis of the wild boars indicated high levels of genetic diversity within the population. Microsatellite markers showed evidence of a single panmictic wild boar population in Lithuania according to STRUCTURE's highest average likelihood, which was K = 1. This was supported by pairwise Fst values and AMOVA, which indicated no differentiation between the four sampling areas. The results of the Mantel test revealed a weak isolation by distance and geographic diversity gradients that persisted between locations. Motorway fencing and heavy traffic were not an effective barrier to wild boar movement. CONCLUSIONS There was limited evidence of population genetic structure among the wild boar, supporting the presence of a single population across the study area and indicating that there may be no barriers hindering wild boar dispersal across the landscape. The widespread wild boar population in Lithuania, the high level of genetic variation observed within subpopulations, and the low level of variation identified between subpopulations suggest migration and gene flow between locations. The results of this study should provide valuable information in future for understanding and comparing the detailed structure of wild boar population in Lithuania following the outbreak of African swine fever.
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Affiliation(s)
| | - Žygimantas Janeliūnas
- Vytautas Magnus University, K. Donelaičio 58, 44248, Kaunas, Lithuania
- Molecular Biology and GMO Department, National Food and Veterinary Risk Assessment Institute, J. Kairiūkščio 10, 08409, Vilnius, Lithuania
| | - Vaclovas Jurgelevičius
- Vytautas Magnus University, K. Donelaičio 58, 44248, Kaunas, Lithuania
- Molecular Biology and GMO Department, National Food and Veterinary Risk Assessment Institute, J. Kairiūkščio 10, 08409, Vilnius, Lithuania
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Schneemann H, De Sanctis B, Roze D, Bierne N, Welch JJ. The geometry and genetics of hybridization. Evolution 2020; 74:2575-2590. [PMID: 33150956 PMCID: PMC7839769 DOI: 10.1111/evo.14116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/26/2020] [Accepted: 10/12/2020] [Indexed: 11/30/2022]
Abstract
When divergent populations form hybrids, hybrid fitness can vary with genome composition, current environmental conditions, and the divergence history of the populations. We develop analytical predictions for hybrid fitness, which incorporate all three factors. The predictions are based on Fisher's geometric model, and apply to a wide range of population genetic parameter regimes and divergence conditions, including allopatry and parapatry, local adaptation, and drift. Results show that hybrid fitness can be decomposed into intrinsic effects of admixture and heterozygosity, and extrinsic effects of the (local) adaptedness of the parental lines. Effect sizes are determined by a handful of geometric distances, which have a simple biological interpretation. These distances also reflect the mode and amount of divergence, such that there is convergence toward a characteristic pattern of intrinsic isolation. We next connect our results to the quantitative genetics of line crosses in variable or patchy environments. This means that the geometrical distances can be estimated from cross data, and provides a simple interpretation of the "composite effects." Finally, we develop extensions to the model, involving selectively induced disequilibria, and variable phenotypic dominance. The geometry of fitness landscapes provides a unifying framework for understanding speciation, and wider patterns of hybrid fitness.
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Affiliation(s)
- Hilde Schneemann
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeUnited Kingdom
- Institut des Sciences de l'ÉvolutionUniversité MontpellierUMR 5554, Montpellier Cedex 05France
| | - Bianca De Sanctis
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeUnited Kingdom
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeUnited Kingdom
| | - Denis Roze
- CNRS, UMI 3614Evolutionary Biology and Ecology of AlgaeRoscoffFrance
- Station Biologique de RoscoffSorbonne UniversitéRoscoff29688France
| | - Nicolas Bierne
- ISEM Université Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | - John J. Welch
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeUnited Kingdom
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Mihalik B, Frank K, Astuti PK, Szemethy D, Szendrei L, Szemethy L, Kusza S, Stéger V. Population Genetic Structure of the Wild Boar ( Sus scrofa) in the Carpathian Basin. Genes (Basel) 2020; 11:genes11101194. [PMID: 33066463 PMCID: PMC7602151 DOI: 10.3390/genes11101194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 12/05/2022] Open
Abstract
In the Carpathian Basin the wild boar (Sus scrofa) belongs among the most important game species both ecologically and economically, therefore knowing more about the basics of the genetics of the species is a key factor for accurate and sustainable management of its population. The aim of this study was to estimate the genetic diversity and to elucidate the genetic structure and location of wild boar populations in the Carpathian Basin. A total of 486 samples were collected and genotyped using 13 STR markers. The number of alleles varied between 4 and 14, at 9 of the 13 loci the observed heterozygosity was significantly different (p < 0.05) from the expected value, showing remarkable introgression in the population. The population was separated into two groups, with an Fst value of 0.03, suggesting the presence of two subpopulations. The first group included 147 individuals from the north-eastern part of Hungary, whereas the second group included 339 samples collected west and south of the first group. The two subpopulations’ genetic indices are roughly similar. The lack of physical barriers between the two groups indicates that the genetic difference is most likely caused by the high reproduction rate and large home range of the wild boars, or by some genetic traces’ having been preserved from both the last ice age and the period before the Hungarian water regulation.
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Affiliation(s)
- Bendegúz Mihalik
- Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032 Debrecen, Hungary; (B.M.); (K.F.); (P.K.A.)
- NARIC Agricultural Biotechnological Institute, 2100 Gödöllő, Hungary;
- Doctoral School of Animal Science, University of Debrecen, 4032 Debrecen, Hungary
| | - Krisztián Frank
- Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032 Debrecen, Hungary; (B.M.); (K.F.); (P.K.A.)
| | - Putri Kusuma Astuti
- Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032 Debrecen, Hungary; (B.M.); (K.F.); (P.K.A.)
| | - Dániel Szemethy
- NARIC Agricultural Biotechnological Institute, 2100 Gödöllő, Hungary;
| | - László Szendrei
- Department of Nature Conservation Zoology and Game Management, University of Debrecen, 4032 Debrecen, Hungary;
| | - László Szemethy
- Faculty of Regional Development, University of Pécs, 7100 Szekszárd, Hungary;
| | - Szilvia Kusza
- Animal Genetics Laboratory, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (S.K.); (V.S.)
| | - Viktor Stéger
- NARIC Agricultural Biotechnological Institute, 2100 Gödöllő, Hungary;
- Correspondence: (S.K.); (V.S.)
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Phylogeography and epidemiology of Brucella suis biovar 2 in wildlife and domestic swine. Vet Microbiol 2019; 233:68-77. [PMID: 31176415 DOI: 10.1016/j.vetmic.2019.04.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 11/22/2022]
Abstract
Swine brucellosis due to Brucella suis biovar 2 (bv2) is enzootic in wild boar and hare in continental Europe and may cause major economic losses to the pig industry, mainly in free-ranged pig farms. The high nucleotide identity found among the B. suis biovar 2 isolates has long hindered the full understanding of the epidemiology and the phylogeography of the disease. Here, we used multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) and whole-genome analysis to identify single-nucleotide polymorphisms (SNPs) in order to gain insights from the largest B. suis bv2 dataset analyzed so far composed of domestic pigs and wildlife isolates collected throughout Europe since the 1970s. We found four major clades with a specific phylogeographic pattern. The Iberian clade contains isolates exclusively from the Iberian Peninsula. The Central European clade includes most isolates from France, Northern Italy, Switzerland and an important proportion of those of Northern Spain. The Eastern European clade clustered isolates from Croatia and Hungary mainly but also from areas of France, Germany, Italy and Poland. Finally, a separated Sardinian clade grouped three isolates from this island. At fine scale, MLVA demonstrated an endemic status of the infection in Europe and it allowed tracking a large outbreak formed by different farms from Spain linked to the same infection source. The whole genome SNP analysis showed that the strains form genetically distinct clades, shared between wild boar and pigs, in agreement with the MLVA clades. Interestingly, all hare isolates clustered together within two groups composed exclusively of wildlife isolates. Our results support the hypothesis that maintenance and spread of B. suis bv2 in Europe is a dynamic process linked to the natural expansion of wild boar as the main wild reservoir of the infection, while spread over long distances is found largely dependent on anthropogenic activities.
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Iacolina L, Corlatti L, Buzan E, Safner T, Šprem N. Hybridisation in European ungulates: an overview of the current status, causes, and consequences. Mamm Rev 2018. [DOI: 10.1111/mam.12140] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Laura Iacolina
- Department of Chemistry and Bioscience; Aalborg University; Frederik Bajers Vej 7H 9220 Aalborg Denmark
- Aalborg Zoo; Mølleparkvej 63 9000 Aalborg Denmark
| | - Luca Corlatti
- Wildlife Ecology and Management; University of Freiburg; Tennenbacher Straße 4 79106 Freiburg Germany
- Institute of Wildlife Biology and Game Management; University of Natural Resources and Life Sciences Vienna; Gregor-Mendel-Straße 33 1180 Vienna Austria
| | - Elena Buzan
- Department of Biodiversity; Faculty of Mathematics, Natural Sciences and Information Technologies; University of Primorska; Glagoljaška 8 6000 Koper Slovenia
| | - Toni Safner
- Faculty of Agriculture; Department of Plant Breeding, Genetics and Biometrics; University of Zagreb; Svetošimunska cesta 25 10000 Zagreb Croatia
| | - Nikica Šprem
- Faculty of Agriculture; Department of Fisheries, Beekeeping, Game Management and Special Zoology; University of Zagreb; Svetošimunska cesta 25 10000 Zagreb Croatia
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Tajchman K, Drozd L, Karpiński M, Czyżowski P, Goleman M. Population Genetic Structure of Wild Boars in Poland. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418050101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Wild boar (Sus scrofa L.) in the north of Western Siberia: history of expansion and modern distribution. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0378-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Invasion ecology of wild pigs (Sus scrofa) in Florida, USA: the role of humans in the expansion and colonization of an invasive wild ungulate. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1667-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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16
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Hillman TL, Keenlance P, Moore JA, Swanson BJ, Jacquot JJ, Witt JC, Cornman A. Genetic diversity of reintroduced American martens in Michigan’s Lower Peninsula. J Mammal 2017. [DOI: 10.1093/jmammal/gyx075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Beugin MP, Baubet E, Dufaure De Citres C, Kaerle C, Muselet L, Klein F, Queney G. A set of 20 multiplexed single nucleotide polymorphism (SNP) markers specifically selected for the identification of the wild boar (Sus scrofa scrofa) and the domestic pig (Sus scrofa domesticus). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0738-9] [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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18
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Veličković N, Ferreira E, Djan M, Ernst M, Obreht Vidaković D, Monaco A, Fonseca C. Demographic history, current expansion and future management challenges of wild boar populations in the Balkans and Europe. Heredity (Edinb) 2016; 117:348-357. [PMID: 27436523 PMCID: PMC5061920 DOI: 10.1038/hdy.2016.53] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 05/31/2016] [Accepted: 06/08/2016] [Indexed: 02/01/2023] Open
Abstract
Wild boar (Sus scrofa), one of the most widespread wildlife species, has entered a stage of continuous growth in Europe, and could even be considered a pest species. We analysed microsatellite variability in 723 wild boars from across Europe, including the northern Dinaric Balkans. Our aims were: (1) to define the population structure of wild boars in the Balkans and its relation with other European populations; (2) to estimate effective populations sizes, levels of intra- and inter-population diversity, inbreeding migration and gene flow patterns; (3) to test subpopulations for bottlenecks; (4) to interpret these results in light of current knowledge about the demographic history of wild boars in Europe; and (5) to discuss the relevance of these findings for management and conservation. Strong population structuring was observed and 14 subpopulations were revealed. High genetic diversity was found, and besides the well-known identity of the Italian populations of Sardinia and Castelporziano, we bring new insights into other potential relevant, refugial populations such as Littoral Slovenia, South Portugal, North-western Iberia and an entire cluster in the Balkans. There was evidence of gene flow going from these refugial subpopulations towards less peripheral and more admixed subpopulations. Recent population bottlenecks and expansions were detected, mostly in the peninsular refuge subpopulations. The results are consistent with the fluctuations of wild boar numbers in Europe since the beginning of the twentieth century. These results should be taken into account in future conservation and management plans for wild boar populations in Europe.
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Affiliation(s)
- N Veličković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - E Ferreira
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - M Djan
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - M Ernst
- Department of Forest Protection and Wildlife Management, Mendel University in Brno, Brno, Czech Republic
| | - D Obreht Vidaković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - A Monaco
- Regional Parks Agency–Lazio Region, Rome, Italy
| | - C Fonseca
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
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Yamazaki Y, Adachi F, Sawamura A. Multiple Origins and Admixture of Recently Expanding Japanese Wild Boar (Sus scrofa leucomystax) Populations in Toyama Prefecture of Japan. Zoolog Sci 2016; 33:38-43. [PMID: 26853867 DOI: 10.2108/zs150092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Japanese wild boar (Sus scrofa leucomystax) populations have expanded drastically throughout the Japanese Archipelago in recent decades. To elucidate the dispersal patterns of Japanese wild boar in Toyama Prefecture in central Japan, we used a multi-locus microsatellite DNA analysis to determine its population structure and the degree of admixture. The deviation from Hardy-Weinberg equilibrium was detected in either total or separate regional wild boar samples from Toyama Prefecture. This result could be explained by the Wahlund effect resulting from the mixture of samples from different sources. Bayesian structure analysis, assignment test, and factorial correspondence analysis suggested that wild boars around Toyama Prefecture derive from at least two ancestral sources. The migration and possible mating of each individual may have occurred recently and continued in each geographically neighboring region. The present genetic results may be useful for prediction of future dispersal patterns of Japanese wild boar, as well as other animals in expansion.
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Affiliation(s)
- Yuji Yamazaki
- Graduate School of Science and Engineering for Research, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Fuminari Adachi
- Graduate School of Science and Engineering for Research, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Akira Sawamura
- Graduate School of Science and Engineering for Research, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
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20
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Vetter SG, Brandstätter C, Macheiner M, Suchentrunk F, Gerritsmann H, Bieber C. Shy is sometimes better: personality and juvenile body mass affect adult reproductive success in wild boars, Sus scrofa. Anim Behav 2016. [DOI: 10.1016/j.anbehav.2016.03.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Are the dinaric mountains a boundary between continental and mediterranean wild boar populations in Croatia? EUR J WILDLIFE RES 2016. [DOI: 10.1007/s10344-016-0989-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Murase K, Horie R, Saito M, Koganezawa M, Sato T, Kaji K. Integrating Analyses of Population Genetics and Space-Time Information for Wildlife Management: An Empirical Study on Japanese Wild Boar Populations. MAMMAL STUDY 2015. [DOI: 10.3106/041.040.0202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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23
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24
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A parameter to quantify the degree of genetic mixing among individuals in hybrid populations. Heredity (Edinb) 2014; 114:249-54. [PMID: 25388141 DOI: 10.1038/hdy.2014.93] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 11/08/2022] Open
Abstract
Hybridization between genetically distinct taxa is a complex evolutionary process. One challenge to studying hybrid populations is quantifying the degree to which non-native genes have become evenly mixed among individuals in the population. In this paper, we present a variance-based parameter, md, that measures the degree to which non-native genes are evenly distributed among individuals in a population. The parameter has a minimum value of 0 for populations in which individuals from multiple taxa are present but have not interbred, and a maximum value of 1 for populations in which all individuals have the same amount of non-native ancestry. A recurrence equation showed that relatively few generations of random mating are required for md to approach 1 (indicating a well-mixed population), and that md is independent of initial amounts of non-native ancestry. The parameter is mathematically equivalent to FST and we show how existing formulae for FST can be used to estimate md when diagnostic loci are available. Computer simulations showed this estimator to have very little bias for realistic amounts of data.
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25
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Podgórski T, Lusseau D, Scandura M, Sönnichsen L, Jędrzejewska B. Long-lasting, kin-directed female interactions in a spatially structured wild boar social network. PLoS One 2014; 9:e99875. [PMID: 24919178 PMCID: PMC4053407 DOI: 10.1371/journal.pone.0099875] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/20/2014] [Indexed: 11/27/2022] Open
Abstract
Individuals can increase inclusive fitness benefits through a complex network of social interactions directed towards kin. Preferential relationships with relatives lead to the emergence of kin structures in the social system. Cohesive social groups of related individuals and female philopatry of wild boar create conditions for cooperation through kin selection and make the species a good biological model for studying kin structures. Yet, the role of kinship in shaping the social structure of wild boar populations is still poorly understood. In the present study, we investigated spatio-temporal patterns of associations and the social network structure of the wild boar Sus scrofa population in Białowieża National Park, Poland, which offered a unique opportunity to understand wild boar social interactions away from anthropogenic factors. We used a combination of telemetry data and genetic information to examine the impact of kinship on network cohesion and the strength of social bonds. Relatedness and spatial proximity between individuals were positively related to the strength of social bond. Consequently, the social network was spatially and genetically structured with well-defined and cohesive social units. However, spatial proximity between individuals could not entirely explain the association patterns and network structure. Genuine, kin-targeted, and temporarily stable relationships of females extended beyond spatial proximity between individuals while males interactions were short-lived and not shaped by relatedness. The findings of this study confirm the matrilineal nature of wild boar social structure and show how social preferences of individuals translate into an emergent socio-genetic population structure.
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Affiliation(s)
- Tomasz Podgórski
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - David Lusseau
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Massimo Scandura
- Department of Science for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | - Leif Sönnichsen
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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26
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Are captive wild boar more introgressed than free-ranging wild boar? Two case studies in Italy. EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0804-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Karaiskou N, Tsakogiannis A, Gkagkavouzis K, Papika S, Latsoudis P, Kavakiotis I, Pantis J, Abatzopoulos TJ, Triantaphyllidis C, Triantafyllidis A. Greece: a Balkan subrefuge for a remnant red deer (cervus elaphus) population. J Hered 2014; 105:334-44. [PMID: 24558101 DOI: 10.1093/jhered/esu007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A number of phylogeographic studies have revealed the existence of multiple ice age refugia within the Balkan Peninsula, marking it as a biodiversity hotspot. Greece has been reported to harbor genetically differentiated lineages from the rest of Balkans for a number of mammal species. We therefore searched for distinct red deer lineages in Greece, by analyzing 78 samples originating from its last population in Parnitha Mountain (Central Greece). Additionally, we tested the impact of human-induced practices on this population. The presence of 2 discrete mtDNA lineages was inferred: 1) an abundant one not previously sampled in the Balkans and 2) a more restricted one shared with other Balkan populations, possibly the result of successful translocations of Eastern European individuals. Microsatellite-based analyses of 14 loci strongly support the existence of 2 subpopulations with relative frequencies similar to mitochondrial analyses. This study stresses the biogeographic importance of Central Greece as a separate Last Glacial Maximum period refugium within the Balkans. It also delineates the possible effects that recent translocations of red deer populations had on the genetic structuring within Parnitha. We suggest that the Greek red deer population of Parnitha is genetically distinct, and restocking programs should take this genetic evidence into consideration.
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Affiliation(s)
- Nikoleta Karaiskou
- the Department of Genetics, Developmental and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Tsubono K, Taniguchi Y, Matsuda H, Yamada T, Sugiyama T, Homma K, Kaneko Y, Yamagishi S, Iwaisaki H. Identification of novel genetic markers and evaluation of genetic structure in a population of Japanese crested ibis. Anim Sci J 2013; 85:356-64. [PMID: 24330458 DOI: 10.1111/asj.12155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/03/2013] [Indexed: 11/28/2022]
Abstract
Japanese population of the Japanese crested ibis Nipponia nippon was founded by five individuals gifted from the People's Republic of China. In order to exactly evaluate genetic structure, we first performed development of novel genetic makers using 89 microsatellite primer pairs of related species for cross-amplification. Of these, only three primer pairs were useful for the genetic markers. Additionally, we sequenced allelic PCR products of these three markers together with 10 markers previously identified. Most markers showed typical microsatellite repeat units, but two markers were not simple microsatellites. Moreover, over half of the markers did not have the same repeat units as those of the original species. These results suggested that development of novel genetic markers in this population by cross-amplification is not efficient, partly because of low genetic diversity. Furthermore, the cluster analysis by STRUCTURE program using 17 markers showed that the five founders were divided into two clusters. However, the genetic relationships among the founders indicated by the clustering seemed to be questionable, because the analysis relied largely on a small number of triallelic markers, in spite of the addition of the three useful markers. Therefore, more efficient methods for identifying large numbers of single nucleotide polymorphisms are desirable.
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Affiliation(s)
- Kanako Tsubono
- Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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29
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Krtinić B, Francuski L, Petrić D, Milankov V. Genetic diversity and differentiation between Palearctic and Nearctic populations of Aedimorphus (=Aedes) vexans (Meigen, 1830) (Diptera, Culicidae). JOURNAL OF VECTOR ECOLOGY : JOURNAL OF THE SOCIETY FOR VECTOR ECOLOGY 2013; 38:154-162. [PMID: 23701620 DOI: 10.1111/j.1948-7134.2013.12021.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Genetic diversity was studied at allozyme loci in two Palearctic and one Nearctic population of Aedimorphus (=Aedes) vexans, a species of public health and veterinary importance. The population from Serbia was the most polymorphic (P= 35%) with the highest observed heterozygosity (H(o) = 0.027). The lowest observed heterozygosity (H(o) = 0.010) was obtained for the Nearctic population. All analyses based on individual (STRUCTURE analysis) and population level (pairwise F(ST), Nm values, AMOVA, Nei's D value) revealed significant structuring between Nearctic and Palearctic populations, indicating a lack of gene flow and thus, the presence of independent gene pools. Taxon-specific alleles at the diagnostic Ao, Hk-2, Hk-3, Hk-4, Idh-1, and Idh-2 loci were used for identification and separation of Nearctic and Palearctic populations. Population genetics study provided valuable information on the correct distinction of Am. vexans populations and their adaptive potential that could find a future use in the studies of vector competence and development of vector-control strategies.
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30
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Frantz AC, Zachos FE, Kirschning J, Cellina S, Bertouille S, Mamuris Z, Koutsogiannouli EA, Burke T. Genetic evidence for introgression between domestic pigs and wild boars (Sus scrofa) in Belgium and Luxembourg: a comparative approach with multiple marker systems. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12111] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Julia Kirschning
- Christian-Albrechts-Universitaet zu Kiel; Zoological Institute; Am Botanischen Garten 3-9; 24118; Kiel; Germany
| | - Sandra Cellina
- Département de l'Environnement; Ministère du Développement durable et des Infrastructures; 18; Montée de la Pétrusse; L-2918; Luxembourg; Luxembourg
| | - Sabine Bertouille
- Département de l'Etude du Milieu Naturel et Agricole; Service Public de Wallonie; B-5030; Gembloux; Belgium
| | - Zissis Mamuris
- Department of Biochemistry and Biotechnology; University of Thessaly; 26; Ploutonos Street; 41221; Larissa; Greece
| | - Evagelia A. Koutsogiannouli
- Department of Biochemistry and Biotechnology; University of Thessaly; 26; Ploutonos Street; 41221; Larissa; Greece
| | - Terry Burke
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Sheffield; S10 2TN; UK
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Goedbloed DJ, van Hooft P, Megens HJ, Langenbeck K, Lutz W, Crooijmans RPMA, van Wieren SE, Ydenberg RC, Prins HHT. Reintroductions and genetic introgression from domestic pigs have shaped the genetic population structure of Northwest European wild boar. BMC Genet 2013; 14:43. [PMID: 23688182 PMCID: PMC3663677 DOI: 10.1186/1471-2156-14-43] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/10/2013] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Population genetic studies focus on natural dispersal and isolation by landscape barriers as the main drivers of genetic population structure. However, anthropogenic factors such as reintroductions, translocations and wild x domestic hybridization may also have strong effects on genetic population structure. In this study we genotyped 351 Single Nucleotide Polymorphism markers evenly spread across the genome in 645 wild boar (Sus scrofa) from Northwest Europe to evaluate determinants of genetic population structure. RESULTS We show that wild boar genetic population structure is influenced by historical reintroductions and by genetic introgression from domestic pigs. Six genetically distinct and geographically coherent wild boar clusters were identified in the Netherlands and Western Germany. The Dutch Veluwe cluster is known to be reintroduced, and three adjacent Dutch and German clusters are suspected to be a result of reintroduction, based on clustering results, low levels of heterozygosity and relatively high genetic distances to nearby populations. Recent wild x domestic hybrids were found geographically widespread across clusters and at low frequencies (average 3.9%). The relationship between pairwise kinship coefficients and geographic distance showed male-biased dispersal at the population genetic level. CONCLUSIONS Our results demonstrate that wildlife and landscape management by humans are shaping the genetic diversity of an iconic wildlife species. Historical reintroductions, translocation and recent restocking activities with farmed wild boar have all influenced wild boar genetic population structure. The current trend of wild boar population growth and range expansion has recently led to a number of contact zones between clusters, and further admixture between the different wild boar clusters is to be expected.
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Affiliation(s)
- Daniel J Goedbloed
- Resource Ecology Group, Wageningen UR, P.O. Box 47, Wageningen 6700AA, the Netherlands
| | - Pim van Hooft
- Resource Ecology Group, Wageningen UR, P.O. Box 47, Wageningen 6700AA, the Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen UR, P.O. Box 338, Wageningen 6700AH, the Netherlands
| | - Katharina Langenbeck
- Resource Ecology Group, Wageningen UR, P.O. Box 47, Wageningen 6700AA, the Netherlands
| | - Walburga Lutz
- Wildlife Research Institute, Pützchens Chaussee 228, Bonn 53229, Germany
| | - Richard PMA Crooijmans
- Animal Breeding and Genomics Centre, Wageningen UR, P.O. Box 338, Wageningen 6700AH, the Netherlands
| | - Sip E van Wieren
- Resource Ecology Group, Wageningen UR, P.O. Box 47, Wageningen 6700AA, the Netherlands
| | - Ron C Ydenberg
- Resource Ecology Group, Wageningen UR, P.O. Box 47, Wageningen 6700AA, the Netherlands
| | - Herbert HT Prins
- Resource Ecology Group, Wageningen UR, P.O. Box 47, Wageningen 6700AA, the Netherlands
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Domestication does not narrow MHC diversity in Sus scrofa. Immunogenetics 2012; 65:195-209. [PMID: 23239371 DOI: 10.1007/s00251-012-0671-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 11/21/2012] [Indexed: 10/27/2022]
Abstract
The Major Histocompatibility Complex (MHC) is a multigene family of outstanding polymorphism. MHC molecules bind antigenic peptides in the peptide-binding region (PBR) that consists of five binding pockets (P). In this study, we compared the genetic diversity of domestic pigs to that of the modern representatives of their wild ancestors, the wild boar, in two MHC loci, the oligomorphic DQA and the polymorphic DRB1. MHC nucleotide polymorphism was compared with the actual functional polymorphism in the PBR and the binding pockets P1, P4, P6, P7, and P9. The analysis of approximately 200 wild boars collected throughout Europe and 120 domestic pigs from four breeds (three pureblood, Pietrain, Leicoma, and Landrace, and one mixed Danbred) revealed that wild boars and domestic pigs share the same levels of nucleotide and amino acid polymorphism, allelic richness, and heterozygosity. Domestication did not appear to act as a bottleneck that would narrow MHC diversity. Although the pattern of polymorphism was uniform between the two loci, the magnitude of polymorphism was different. For both loci, most of the polymorphism was located in the PBR region and the presence of positive selection was supported by a statistically significant excess of nonsynonymous substitutions over synonymous substitutions in the PBR. P4 and P6 were the most polymorphic binding pockets. Functional polymorphism, i.e., the number and the distribution of pocket variants within and among populations, was significantly narrower than genetic polymorphism, indicative of a hierarchical action of selection pressures on MHC loci.
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Velickovic N, Djan M, Obreht D, Vapa L. Population genetic structure of wild boars in the West Balkan region. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412080078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Kanthaswamy S, Ng J, Penedo MCT, Ward T, Smith DG, Ha JC. Population genetics of the Washington National Primate Research Center's (WaNPRC) captive pigtailed macaque (Macaca nemestrina) population. Am J Primatol 2012; 74:1017-27. [PMID: 22851336 DOI: 10.1002/ajp.22055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 05/31/2012] [Accepted: 06/17/2012] [Indexed: 01/03/2023]
Abstract
Pigtailed macaques (Macaca nemestrina) provide an important model for biomedical research on human disease and for studying the evolution of primate behavior. The genetic structure of captive populations of pigtailed macaques is not as well described as that of captive rhesus (M. mulatta) or cynomolgus (M. fascicularis) macaques. The Washington National Primate Research Center houses the largest captive colony of pigtailed macaques located in several different housing facilities. Based on genotypes of 18 microsatellite (short tandem repeat [STR]) loci, these pigtailed macaques are more genetically diverse than captive rhesus macaques and exhibit relatively low levels of inbreeding. Colony genetic management facilitates the maintenance of genetic variability without compromising production goals of a breeding facility. The periodic introduction of new founders from specific sources to separate housing facilities at different times influenced the colony's genetic structure over time and space markedly but did not alter its genetic diversity significantly. Changes in genetic structure over time were predominantly due to the inclusion of animals from the Yerkes National Primate Research Center in the original colony and after 2005. Strategies to equalize founder representation in the colony have maximized the representation of the founders' genomes in the extant population. Were exchange of animals among the facilities increased, further differentiation could be avoided. The use of highly differentiated animals may confound interpretations of phenotypic differences due to the inflation of the genetic contribution to phenotypic variance of heritable traits.
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Affiliation(s)
- Sree Kanthaswamy
- California National Primate Research Center, University of California, Davis, USA.
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37
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Sanchez-Donoso I, Vilà C, Puigcerver M, Butkauskas D, Caballero de la Calle JR, Morales-Rodríguez PA, Rodríguez-Teijeiro JD. Are farm-reared quails for game restocking really common quails (Coturnix coturnix)?: a genetic approach. PLoS One 2012; 7:e39031. [PMID: 22701745 PMCID: PMC3373495 DOI: 10.1371/journal.pone.0039031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 05/15/2012] [Indexed: 11/20/2022] Open
Abstract
The common quail (Coturnix coturnix) is a popular game species for which restocking with farm-reared individuals is a common practice. In some areas, the number of released quails greatly surpasses the number of wild breeding common quail. However, common quail are difficult to raise in captivity and this casts suspicion about a possible hybrid origin of the farmed individuals from crosses with domestic Japanese quail (C. japonica). In this study we used a panel of autosomal microsatellite markers to characterize the genetic origin of quails reared for hunting purposes in game farms in Spain and of quails from an experimental game farm which was founded with hybrids that have been systematically backcrossed with wild common quails. The genotypes of these quail were compared to those of wild common quail and domestic strains of Japanese quail. Our results show that more than 85% of the game farm birds were not common quail but had domestic Japanese quail ancestry. In the experimental farm a larger proportion of individuals could not be clearly separated from pure common quails. We conclude that the majority of quail sold for restocking purposes were not common quail. Genetic monitoring of individuals raised for restocking is indispensable as the massive release of farm-reared hybrids could represent a severe threat for the long term survival of the native species.
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Affiliation(s)
- Ines Sanchez-Donoso
- Conservation and Evolutionary Genetics Group, Doñana Biological Station, EBD-CSIC, Seville, Spain.
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Conyers CM, Allnutt TR, Hird HJ, Kaye J, Chisholm J. Development of a microsatellite-based method for the differentiation of European wild boar (Sus scrofa scrofa) from domestic pig breeds (Sus scrofa domestica) in food. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:3341-3347. [PMID: 22409233 DOI: 10.1021/jf205109b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Twenty microsatellites (simple sequence repeats, SSR) were used to discriminate wild boar from domestic pig and to identify mixtures of the two. Reference groups of wild boar and pig samples were collected from the UK and Europe for genetic assignment tests. Bayesian Analysis of Populations software (BAPs) gave 100% correct assignment for blind wild boar and pig samples and correctly identified mixed samples. DNA was extracted from 12 commercial food samples (11 labeled as containing wild boar) including patés, salamis, and sausage, and good SSR profiles were obtained. Eleven samples were correctly assigned as pig, and two as mixed meats. One sample sold as wild boar meat was clearly assigned as pig. A further 10 blind samples of meat cuts were analyzed, eight wild boar and two pig, and all were correctly assigned.
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Affiliation(s)
- Christine M Conyers
- The Food and Environment Research Agency, Sand Hutton, York, United Kingdom.
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Kolodziej K, Theissinger K, Brün J, Schulz HK, Schulz R. Determination of the minimum number of microsatellite markers for individual genotyping in wild boar (Sus scrofa) using a test with close relatives. EUR J WILDLIFE RES 2011. [DOI: 10.1007/s10344-011-0588-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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40
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Genetic diversity of Dinaric brown bears (Ursus arctos) in Croatia with implications for bear conservation in Europe. Mamm Biol 2011. [DOI: 10.1016/j.mambio.2010.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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García G, Vergara J, Lombardi R. Genetic characterization and phylogeography of the wild boar Sus scrofa introduced into Uruguay. Genet Mol Biol 2011; 34:329-37. [PMID: 21734838 PMCID: PMC3115331 DOI: 10.1590/s1415-47572011005000015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 12/01/2010] [Indexed: 11/22/2022] Open
Abstract
The European wild boar Sus scrofa was first introduced into Uruguay, in southern South America during the early decades of the last century. Subsequently, and starting from founder populations, its range spread throughout the country and into the neighbouring Brazilian state Rio Grande do Sul. Due to the subsequent negative impact, it was officially declared a national pest. The main aim in the present study was to provide a more comprehensive scenario of wild boar differentiation in Uruguay, by using mtDNA markers to access the genetic characterization of populations at present undergoing rapid expansion. A high level of haplotype diversity, intermediate levels of nucleotide diversity and considerable population differentiation, were detected among sampled localities throughout major watercourses and catchment dams countrywide. Phylogenetic analysis revealed the existence of two different phylogroups, thereby reflecting two deliberate introduction events forming distantly genetic lineages in local wild boar populations. Our analysis lends support to the hypothesis that the invasive potential of populations emerge from introgressive hybridization with domestic pigs. On taking into account the appreciable differentiation and reduced migration between locales in wild boar populations, management strategies could be effective if each population were to be considered as a single management unit.
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Affiliation(s)
- Graciela García
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República Uruguay, Montevideo, Uruguay
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SCANDURA M, IACOLINA L, APOLLONIO M. Genetic diversity in the European wild boar Sus scrofa: phylogeography, population structure and wild x domestic hybridization. Mamm Rev 2011. [DOI: 10.1111/j.1365-2907.2010.00182.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Scandura M, Iacolina L, Cossu A, Apollonio M. Effects of human perturbation on the genetic make-up of an island population: the case of the Sardinian wild boar. Heredity (Edinb) 2010; 106:1012-20. [PMID: 21179064 DOI: 10.1038/hdy.2010.155] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Game species are often manipulated by human beings, whose activities can deeply affect their genetic make-up and population structure. We focused on a geographically isolated wild boar population (Sardinia, Italy), which is classified, together with the Corsican population, as a separate subspecies (Sus scrofa meridionalis). Two hundred and ten wild boars collected across Sardinia were analysed with a set of 10 microsatellites and compared with 296 reference genotypes from continental wild populations and to a sample of domestic pigs. The Sardinian population showed remarkable diversity and a high proportion of private alleles, and strongly deviated from the equilibrium. A Bayesian cluster analysis of only the Sardinian sample revealed a partition into five subpopulations. However, two different Bayesian approaches to the assignment of individuals, accounting for different possible source populations, produced consistent results and proved the admixed nature of the Sardinian population. Indeed, introgressive hybridization with boars from multiple sources (Italian peninsula, central Europe, domestic stocks) was detected, although poor evidence of crossbreeding with free-ranging domestic pigs was unexpectedly found. After excluding individuals who carried exotic genes, the population re-entered Hardy-Weinberg proportions and a clear population structure with three subpopulations emerged. Therefore, the inclusion of introgressed animals in the Bayesian analysis implied an overestimation of the number of clusters. Nonetheless, two of them were consistent between analyses and corresponded to highly pure stocks, located, respectively, in north-west and south-west Sardinia. This work shows the critical importance of including adequate reference samples when studying the genetic structure of managed wild populations.
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Affiliation(s)
- M Scandura
- Department of Zoology and Evolutionary Genetics, University of Sassari, Sassari, Italy.
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Johnson JA, Talbot SL, Sage GK, Burnham KK, Brown JW, Maechtle TL, Seegar WS, Yates MA, Anderson B, Mindell DP. The use of genetics for the management of a recovering population: temporal assessment of migratory peregrine falcons in North America. PLoS One 2010; 5:e14042. [PMID: 21124969 PMCID: PMC2987794 DOI: 10.1371/journal.pone.0014042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 10/26/2010] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Our ability to monitor populations or species that were once threatened or endangered and in the process of recovery is enhanced by using genetic methods to assess overall population stability and size over time. This can be accomplished most directly by obtaining genetic measures from temporally-spaced samples that reflect the overall stability of the population as given by changes in genetic diversity levels (allelic richness and heterozygosity), degree of population differentiation (F(ST) and D(EST)), and effective population size (N(e)). The primary goal of any recovery effort is to produce a long-term self-sustaining population, and these genetic measures provide a metric by which we can gauge our progress and help make important management decisions. METHODOLOGY/PRINCIPAL FINDINGS The peregrine falcon in North America (Falco peregrinus tundrius and anatum) was delisted in 1994 and 1999, respectively, and its abundance will be monitored by the species Recovery Team every three years until 2015. Although the United States Fish and Wildlife Service makes a distinction between tundrius and anatum subspecies, our genetic results based on eleven microsatellite loci suggest limited differentiation that can be attributed to an isolation by distance relationship and warrant no delineation of these two subspecies in its northern latitudinal distribution from Alaska through Canada into Greenland. Using temporal samples collected at Padre Island, Texas during migration (seven temporal time periods between 1985-2007), no significant differences in genetic diversity or significant population differentiation in allele frequencies between time periods were observed and were indistinguishable from those obtained from tundrius/anatum breeding locations throughout their northern distribution. Estimates of harmonic mean N(e) were variable and imprecise, but always greater than 500 when employing multiple temporal genetic methods. CONCLUSIONS/SIGNIFICANCE These results, including those from simulations to assess the power of each method to estimate N(e), suggest a stable or growing population, which is consistent with ongoing field-based monitoring surveys. Therefore, historic and continuing efforts to prevent the extinction of the peregrine falcon in North America appear successful with no indication of recent decline, at least from the northern latitude range-wide perspective. The results also further highlight the importance of archiving samples and their use for continual assessment of population recovery and long-term viability.
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Affiliation(s)
- Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, Texas, USA.
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WILLIAMS BRONWYNW, SCRIBNER KIMT. Effects of multiple founder populations on spatial genetic structure of reintroduced American martens. Mol Ecol 2010; 19:227-40. [DOI: 10.1111/j.1365-294x.2009.04455.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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CÉLIO ALVES PAULO, PINHEIRO IRIS, GODINHO RAQUEL, VICENTE JOAQUIN, GORTÁZAR CHRISTIAN, SCANDURA MASSIMO. Genetic diversity of wild boar populations and domestic pig breeds (Sus scrofa) in South-western Europe. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01530.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Mitochondrial and nuclear DNA analyses reveal pronounced genetic structuring in Tunisian wild boar Sus scrofa. EUR J WILDLIFE RES 2010. [DOI: 10.1007/s10344-010-0452-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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48
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Analysis of 11 tetrameric STRs in wild boars for forensic purposes. Forensic Sci Int Genet 2010; 4:339-42. [DOI: 10.1016/j.fsigen.2010.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 06/22/2010] [Accepted: 07/06/2010] [Indexed: 11/22/2022]
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49
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Haanes H, Røed KH, Mysterud A, Langvatn R, Rosef O. Consequences for genetic diversity and population performance of introducing continental red deer into the northern distribution range. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0048-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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McMahon CR, Brook BW, Collier N, Bradshaw CJA. Spatially explicit spreadsheet modelling for optimising the efficiency of reducing invasive animal density. Methods Ecol Evol 2010. [DOI: 10.1111/j.2041-210x.2009.00002.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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