45 results on '"Iacolina L"'
Search Results
2. 1. African swine fever (ASF), the pig health challenge of the century
- Author
-
Martins, C., primary, Boinas, F.S., additional, Iacolina, L., additional, Ruiz-Fons, F., additional, and Gavier-Widén, D., additional
- Published
- 2021
- Full Text
- View/download PDF
3. Main roads and land cover shaped the genetic structure of a Mediterranean island wild boar population
- Author
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Lecis, R, Dondina, O, Orioli, V, Biosa, D, Canu, A, Fabbri, G, Iacolina, L, Cossu, A, Bani, L, Apollonio, M, Scandura, M, Lecis, R, Dondina, O, Orioli, V, Biosa, D, Canu, A, Fabbri, G, Iacolina, L, Cossu, A, Bani, L, Apollonio, M, and Scandura, M
- Abstract
Patterns of genetic differentiation within and among animal populations might vary due to the simple effect of distance or landscape features hindering gene flow. An assessment of how landscape connectivity affects gene flow can help guide management, especially in fragmented landscapes. Our objective was to analyze population genetic structure and landscape genetics of the native wild boar (Sus scrofa meridionalis) population inhabiting the island of Sardinia (Italy), and test for the existence of Isolation-by-Distance (IBD), Isolation-by-Barrier (IBB), and Isolation-by-Resistance (IBR). A total of 393 Sardinian wild boar samples were analyzed using a set of 16 microsatellite loci. Signals of genetic introgression from introduced non-native wild boars or from domestic pigs were revealed by a Bayesian cluster analysis including 250 reference individuals belonging to European wild populations and domestic breeds. After removal of introgressed individuals, genetic structure in the population was investigated by different statistical approaches, supporting a partition into five discrete subpopulations, corresponding to five geographic areas on the island: north-west (NW), central west (CW), south-west (SW), north-central east (NCE), and south-east (SE). To test the IBD, IBB, and IBR hypotheses, we optimized resistance surfaces using genetic algorithms and linear mixed-effects models with a maximum likelihood population effects parameterization. Landscape genetics analyses revealed that genetic discontinuities between subpopulations can be explained by landscape elements, suggesting that main roads, urban settings, and intensively cultivated areas are hampering gene flow (and thus individual movements) within the Sardinian wild boar population. Our results reveal how human-transformed landscapes can affect genetic connectivity even in a large-sized and highly mobile mammal such as the wild boar, and provide crucial information to manage the spread of pathogens, includin
- Published
- 2022
4. Past, present and future of chamois science
- Author
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Corlatti, L., primary, Iacolina, L., additional, Safner, T., additional, Apollonio, M., additional, Buzan, E., additional, Ferretti, F., additional, Hammer, S. E., additional, Herrero, J., additional, Rossi, L., additional, Serrano, E., additional, Arnal, M. C., additional, Brivio, F., additional, Chirichella, R., additional, Cotza, A., additional, Crestanello, B., additional, Espunyes, J., additional, Fernández de Luco, D., additional, Friedrich, S., additional, Gačić, D., additional, Grassi, L., additional, Grignolio, S., additional, Hauffe, H. C., additional, Kavčić, K., additional, Kinser, A., additional, Lioce, F., additional, Malagnino, A., additional, Miller, C., additional, Peters, W., additional, Pokorny, B., additional, Reiner, R., additional, Rezić, A., additional, Stipoljev, S., additional, Tešija, T., additional, Yankov, Y., additional, Zwijacz‐Kozica, T., additional, and Šprem, N., additional
- Published
- 2022
- Full Text
- View/download PDF
5. Past, present and future of chamois science
- Author
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Corlatti, L., Iacolina, L., Safner, T., Apollonio, M., Buzan, E., Ferretti, F., Hammer, S. E., Herrero, J., Rossi, L., Serrano, E., Arnal, M. C., Brivio, F., Chirichella, R., Cotza, A., Crestanello, B., Espunyes, J., Fernández de Luco, D., Friedrich, S., Gačić, D., Grassi, L., Grignolio, S., Hauffe, H. C., Kavčić, K., Kinser, A., Lioce, F., Malagnino, A., Miller, C., Peters, W., Pokorny, B., Reiner, R., Rezić, A., Stipoljev, S., Tešija, T., Yankov, Y., and Šprem, T. Zwijacz-Kozica and N.
- Published
- 2022
6. Lack of polymorphism at the MC1R wild-type allele and evidence of domestic allele introgression across European wild boar populations
- Author
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Canu, A., Vilaça, S. T., Iacolina, L., Apollonio, M., Bertorelle, G., and Scandura, M.
- Published
- 2016
- Full Text
- View/download PDF
7. Genome-wide profiles indicate wolf population connectivity within the eastern Carpathian Mountains
- Author
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Ericson, H. S., primary, Fedorca, A., additional, Toderas, I., additional, Hegyeli, Z., additional, Plis, K., additional, Dykyy, I., additional, Jędrzejewska, B., additional, Ionescu, G., additional, Fedorca, M., additional, Iacolina, L., additional, and Stronen, A. V., additional
- Published
- 2019
- Full Text
- View/download PDF
8. Genome-wide profiles indicate wolf population connectivity within the eastern Carpathian Mountains.
- Author
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Ericson, H. S., Fedorca, A., Toderas, I., Hegyeli, Z., Plis, K., Dykyy, I., Jędrzejewska, B., Ionescu, G., Fedorca, M., Iacolina, L., and Stronen, A. V.
- Abstract
The Carpathian Mountains provide critical wildlife habitat in central Europe, and previous genome-wide studies have found western Carpathian Mountain wolves (Canis lupus) to be a separate population. Whereas differentiation to the north may be explained by a lowland-mountain transition and habitat fragmentation, the eastern Carpathian Mountains extending through Romania appear to offer continuous wildlife habitat southward. Our objective was to assess gene flow patterns and population connectivity among wolves in Romania, western Ukraine, and the Republic of Moldova. We sought to determine if the Carpathian Mountain region is best described by a north–south gradient in genetic profiles, or whether Romanian wolves show population structure with northern individuals clustering with western Ukraine. We genotyped 48 individuals with 170 000 single nucleotide polymorphism markers, and successful profiles from Romania (n = 27) and Moldova (n = 2) were merged with existing data from western Ukraine (n = 10). Expected heterozygosity was 0.234 (SE 0.001) for Romania and 0.229 (SE 0.001) for western Ukraine, whereas observed heterozygosity values were 0.230 (SE 0.001) versus 0.231 (SE 0.001). Population structure analyses with a maximum likelihood method supported K = 1 population, followed by K = 2 where Romania formed one cluster, and western Ukraine and Moldova formed another. Principal component analysis results were broadly consistent with K = 2. Pairwise F
ST between western Ukraine and Romania was 0.042 (p = 0.001). Our findings indicated weak population differentiation, and future research may clarify whether the spatial distribution of genetic diversity in the region is associated with environmental and ecological factors such as terrain ruggedness and the distribution of prey species. [ABSTRACT FROM AUTHOR]- Published
- 2020
- Full Text
- View/download PDF
9. Lack of polymorphism at MC1R wild-type allele and evidence of domestic allele introgression across European wild boar populations
- Author
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Canu, A., Vilaça, S. T., Iacolina, L., Apollonio, M., Bertorelle, Giorgio, Scandura, M., and TORRES VILACA, Sibelle
- Subjects
0106 biological sciences ,0301 basic medicine ,endocrine system ,QTL ,Sus scrofa, MC1R, NR6A1, QTL, Genetic introgression ,Sus scrofa ,NR6A1 ,Introgression ,Quantitative trait locus ,Genetic introgression ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Wild boar ,biology.animal ,MC1R ,Allele ,Domestication ,Ecology, Evolution, Behavior and Systematics ,Genetics ,Genetic diversity ,biology ,urogenital system ,Wild type ,Ambientale ,030104 developmental biology ,Animal ecology ,Animal Science and Zoology - Abstract
Domestication promotes the emergence of novel phenotypic and behavioural traits in domesticated animals compared to their wild ancestors. We analysed variation at the melanocortin receptor I (MC1R) and nuclear receptor subfamily 6, group A, member 1 (NR6A1) genes in European wild boar populations, two loci which have been under strong artificial selection during domestication. These loci influence coat colour and number of vertebrae, respectively. A total of 145 wild boars were sampled throughout Europe, to evaluate frequency and spatial distribution of domestic alleles and patterns of hybridization between wild and domestic forms. Most of the wild boars (94%) were homozygous for the European wild-type (E+) MC1R allele. We did not observe any synonymous substitution in the European E+ allele, confirming its monomorphism even in areas known to be hotspots of wild boar genetic diversity. The remaining wild boars (6%) showed genetic introgression of three different European domestic alleles. No Asian MC1R allele was found in our sample. Furthermore, domestic NR6A1 alleles were observed in 6% of wild boars. Considering jointly the two loci analyzed, 11% of boars, sampled all over Europe, showed signs of recent or past introgression in their genome. These data agree with previous investigations on other molecular markers, confirming that, compared to Asian conspecifics, European wild boars have a relatively low genetic diversity, which is locally increased by the introgression of allelic variants from the domestic counterpart.
- Published
- 2016
10. Genomic diversity and differentiation of a managed island wild boar population
- Author
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Iacolina, L., Scandura, M., Goedbloed, D.J., Alexandri, P., Crooijmans, R.P.M.A., Larson, G., Archibald, A., Apollonio, M., Schook, L.B., Groenen, M.A.M., Megens, H.J., Iacolina, L., Scandura, M., Goedbloed, D.J., Alexandri, P., Crooijmans, R.P.M.A., Larson, G., Archibald, A., Apollonio, M., Schook, L.B., Groenen, M.A.M., and Megens, H.J.
- Abstract
The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (F ST =0.126-0.138), and from DP (F ST =0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, F ST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status.
- Published
- 2016
11. Genetic peculiarities of the wild boar in Italy
- Author
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Lancioni, Hovirag, Vercillo, Francesca, Capodiferro, MARCO ROSARIO, Cardinali, Irene, Sabino, M, Biagetti, M, Vincenti, F, Sebastiani, Carla, Dionigi, F, Iacolina, L, Rizzi, E, Olivieri, A, Sergiacomi, U, Scandura, M, Torroni, Antonio, Ragni, Bernardino, and Achilli, Alessandro
- Subjects
mitochondrial DNA, Phylogeny ,mitochondrial DNA ,Phylogeny - Published
- 2014
12. Novel Y-chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations
- Author
-
Iacolina, L., primary, Brajković, V., additional, Canu, A., additional, Šprem, N., additional, Cubric-Curik, V., additional, Fontanesi, L., additional, Saarma, U., additional, Apollonio, M., additional, and Scandura, M., additional
- Published
- 2016
- Full Text
- View/download PDF
13. Data from: Genomic diversity and differentiation of a managed island wild boar population
- Author
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Iacolina, L., Scandura, M., Goedbloed, D.J., Alexandri, Panoraia, Crooijmans, R.P.M.A., Larson, G., Archibald, A.L., Apollonio, M., Schook, L.B., Groenen, M., Megens, H.J.W.C., Iacolina, L., Scandura, M., Goedbloed, D.J., Alexandri, Panoraia, Crooijmans, R.P.M.A., Larson, G., Archibald, A.L., Apollonio, M., Schook, L.B., Groenen, M., and Megens, H.J.W.C.
- Abstract
Structure input file. The four populations correspond to the "Group" column in the file Individuals_info.txt
- Published
- 2015
14. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025
- Author
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Bruford, Mw, Ginja, C, Hoffmann, I, Joost, S, Orozco Terwengel, P, Alberto, Fj, Amaral, Aj, Barbato, Mario, Biscarini, F, Colli, Licia, Costa, M, Curik, I, Duruz, S, Ferenčaković, M, Fischer, D, Fitak, R, Groeneveld, Lf, Hall, Sjg, Hanotte, O, Hassan, F, Helsen, P, Iacolina, L, Kantanen, J, Leempoel, K, Lenstra, Ja, Ajmone Marsan, Paolo, Masembe, C, Megens, H, Miele, M, Neuditschko, M, Nicolazzi, El, Pompanon, F, Roosen, J, Sevane, N, Smetko, A, Štambuk, A, Streeter, I, Stucki, S, Supakorn, C, Telo Da Gama, L, Tixier Boichard, M, Wegmann, D, Zhan, X., Barbato, M (ORCID:0000-0002-7203-1549), Colli, Licia (ORCID:0000-0002-7221-2905), Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Bruford, Mw, Ginja, C, Hoffmann, I, Joost, S, Orozco Terwengel, P, Alberto, Fj, Amaral, Aj, Barbato, Mario, Biscarini, F, Colli, Licia, Costa, M, Curik, I, Duruz, S, Ferenčaković, M, Fischer, D, Fitak, R, Groeneveld, Lf, Hall, Sjg, Hanotte, O, Hassan, F, Helsen, P, Iacolina, L, Kantanen, J, Leempoel, K, Lenstra, Ja, Ajmone Marsan, Paolo, Masembe, C, Megens, H, Miele, M, Neuditschko, M, Nicolazzi, El, Pompanon, F, Roosen, J, Sevane, N, Smetko, A, Štambuk, A, Streeter, I, Stucki, S, Supakorn, C, Telo Da Gama, L, Tixier Boichard, M, Wegmann, D, Zhan, X., Barbato, M (ORCID:0000-0002-7203-1549), Colli, Licia (ORCID:0000-0002-7221-2905), and Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579)
- Abstract
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that "...the genetic diversity of ...farmed and domesticated animals and of wild relatives ...is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity." However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societa
- Published
- 2015
15. Genomic diversity and differentiation of a managed island wild boar population
- Author
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Iacolina, L, primary, Scandura, M, additional, Goedbloed, D J, additional, Alexandri, P, additional, Crooijmans, R P M A, additional, Larson, G, additional, Archibald, A, additional, Apollonio, M, additional, Schook, L B, additional, Groenen, M A M, additional, and Megens, H-J, additional
- Published
- 2015
- Full Text
- View/download PDF
16. Ecologia e genetica per approfondire la conoscenza degli uccelli di maggiore interesse gestionale
- Author
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Baratti M., Iacolina L., and Dessì-Fulgheri
- Published
- 2010
17. Differenziamento genetico tra pernici (genere Alectoris) dell'area mediterranea
- Author
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Scandura M., Baratti M., Iacolina L., Bartali S., Apollonio M., and Dessi' Fulgheri F.
- Published
- 2006
18. Analisi della variabilità genetica del complesso di specie riferito a Pseudomonocelis ophiocephala (Platyhelminthes: Proseriata) tramite marcatori molecolari RAPD
- Author
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Casu, M, Maltagliati, F, Cossu, P, Meloni, M, Binelli, GIORGIO PIETRO MARIO, Castelli, A, CURINI GALLETTI, M, and Iacolina, L.
- Published
- 2002
19. Effects of human perturbation on the genetic make-up of an island population: the case of the Sardinian wild boar
- Author
-
Scandura, M, primary, Iacolina, L, additional, Cossu, A, additional, and Apollonio, M, additional
- Published
- 2010
- Full Text
- View/download PDF
20. Ancient vs. recent processes as factors shaping the genetic variation of the European wild boar: are the effects of the last glaciation still detectable?
- Author
-
SCANDURA, M., primary, IACOLINA, L., additional, CRESTANELLO, B., additional, PECCHIOLI, E., additional, DI BENEDETTO, M. F., additional, RUSSO, V., additional, DAVOLI, R., additional, APOLLONIO, M., additional, and BERTORELLE, G., additional
- Published
- 2008
- Full Text
- View/download PDF
21. Genomic diversity and differentiation of a managed island wild boar population
- Author
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Iacolina, L, Scandura, M, Goedbloed, D J, Alexandri, P, Crooijmans, R P M A, Larson, G, Archibald, A, Apollonio, M, Schook, L B, Groenen, M A M, and Megens, H-J
- Abstract
The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (FST=0.126–0.138), and from DP (FST=0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, FSTand ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status.
- Published
- 2016
- Full Text
- View/download PDF
22. Effects of human perturbation on the genetic make-up of an island population: the case of the Sardinian wild boar.
- Author
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Scandura, M., Iacolina, L., Cossu, A., and Apollonio, M.
- Subjects
- *
WILD boar , *MICROSATELLITE repeats , *SPECIES hybridization , *BAYESIAN analysis , *DOMESTIC animals , *HUMAN beings - 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. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
23. New developments in the field of genomic technologies and their relevance to conservation management
- Author
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Philippe Helsen, Carles Vilà, Samantha M. Wisely, Christina Hvilsom, Marina Nonić, Pamela Burger, Delphine Thizy, Mirte Bosse, Ivaylo Tsvetkov, Laura Iacolina, Peter Galbusera, Adla Kahric, Gernot Segelbacher, José A. Godoy, Elena Buzan, Chiara Manfrin, Nevena Veličković, Segelbacher, G., Bosse, M., Burger, P., Galbusera, P., Godoy, J. A., Helsen, P., Hvilsom, C., Iacolina, L., Kahric, A., Manfrin, C., Nonic, M., Thizy, D., Tsvetkov, I., Velickovic, N., Vila, C., Wisely, S. M., and Buzan, E.
- Subjects
Emerging technologies ,Ecology (disciplines) ,Biotechnology ,Gene editing ,Genetic rescue ,Genomic tools ,Management ,Animal Breeding and Genomics ,Biology ,Data science ,Field (computer science) ,Toolbox ,WIAS ,Genetics ,Fokkerij en Genomica ,Relevance (information retrieval) ,Population management ,Adaptation (computer science) ,Genomic tool ,Ecology, Evolution, Behavior and Systematics - Abstract
Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.
- Published
- 2021
24. Main roads and land cover shaped the genetic structure of a Mediterranean island wild boar population
- Author
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Roberta Lecis, Olivia Dondina, Valerio Orioli, Daniela Biosa, Antonio Canu, Giulia Fabbri, Laura Iacolina, Antonio Cossu, Luciano Bani, Marco Apollonio, Massimo Scandura, Lecis, R, Dondina, O, Orioli, V, Biosa, D, Canu, A, Fabbri, G, Iacolina, L, Cossu, A, Bani, L, Apollonio, M, and Scandura, M
- Subjects
microsatellite ,Ecology ,landscape genetic ,Sus scrofa meridionali ,population structure ,gene flow ,Sardinia ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Abstract
Patterns of genetic differentiation within and among animal populations might vary due to the simple effect of distance or landscape features hindering gene flow. An assessment of how landscape connectivity affects gene flow can help guide management, especially in fragmented landscapes. Our objective was to analyze population genetic structure and landscape genetics of the native wild boar (Sus scrofa meridionalis) population inhabiting the island of Sardinia (Italy), and test for the existence of Isolation-by-Distance (IBD), Isolation-by-Barrier (IBB), and Isolation-by-Resistance (IBR). A total of 393 Sardinian wild boar samples were analyzed using a set of 16 microsatellite loci. Signals of genetic introgression from introduced non-native wild boars or from domestic pigs were revealed by a Bayesian cluster analysis including 250 reference individuals belonging to European wild populations and domestic breeds. After removal of introgressed individuals, genetic structure in the population was investigated by different statistical approaches, supporting a partition into five discrete subpopulations, corresponding to five geographic areas on the island: north-west (NW), central west (CW), south-west (SW), north-central east (NCE), and south-east (SE). To test the IBD, IBB, and IBR hypotheses, we optimized resistance surfaces using genetic algorithms and linear mixed-effects models with a maximum likelihood population effects parameterization. Landscape genetics analyses revealed that genetic discontinuities between subpopulations can be explained by landscape elements, suggesting that main roads, urban settings, and intensively cultivated areas are hampering gene flow (and thus individual movements) within the Sardinian wild boar population. Our results reveal how human-transformed landscapes can affect genetic connectivity even in a large-sized and highly mobile mammal such as the wild boar, and provide crucial information to manage the spread of pathogens, including the African Swine Fever virus, endemic in Sardinia.
- Published
- 2022
25. Novel Y-chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations
- Author
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Marco Apollonio, Luca Fontanesi, Antonio Canu, Nikica Šprem, Massimo Scandura, Urmas Saarma, Vladimir Brajkovic, Laura Iacolina, Vlatka Cubric-Curik, Iacolina, L, Brajković, V, Canu, A, Šprem, N, Cubric-Curik, V, Fontanesi, L, Saarma, U, Apollonio, M, and Scandura, M.
- Subjects
0106 biological sciences ,0301 basic medicine ,Gene Flow ,Male ,microsatellite ,Sus scrofa ,Population genetics ,Locus (genetics) ,Breeding ,010603 evolutionary biology ,01 natural sciences ,Gene flow ,03 medical and health sciences ,Wild boar ,paternal DNA marker ,biology.animal ,Y Chromosome ,Genetics ,Animals ,Alleles ,biology ,Haplotype ,Genetic Variation ,General Medicine ,genetic diversity ,paternal DNA markers ,Y haplotype ,Europe ,Domestic pig ,030104 developmental biology ,Genetics, Population ,Haplotypes ,Genetic marker ,Microsatellite ,Animal Science and Zoology ,Microsatellite Repeats - Abstract
Summary Y-chromosome markers are important tools for studying male-specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non-human mammals is often hampered by the lack of Y-specific polymorphic markers. We identified new male-specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5–10 alleles per locus), falling in one duplicated and two single-copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (HD = 0.904 ± 0.011 and HD = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (FST = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y-chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.
- Published
- 2016
26. Molecular analysis of scats revealed diet and prey choice of grey wolves and Eurasian lynx in the contact zone between the Dinaric Mountains and the Alps.
- Author
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Buzan E, Potočnik H, Pokorny B, Potušek S, Iacolina L, Gerič U, Urzi F, and Kos I
- Abstract
A comprehensive understanding of the dietary habits of carnivores is essential to get ecological insights into their role in the ecosystem, potential competition with other carnivorous species, and their effect on prey populations. Genetic analysis of non-invasive samples, such as scats, can supplement behavioural or microscopic diet investigations. The objective of this study was to employ DNA metabarcoding to accurately determine the prey species in grey wolf (Canis lupus) and Eurasian lynx (Lynx lynx) scat samples collected in the Julian Alps and the Dinaric Mountains, Slovenia. The primary prey of wolves were red deer (Cervus elaphus) (detected in 96% scat samples), European roe deer (Capreolus capreolus) (68%), and wild boar (Sus scrofa) (45%). A smaller portion of their diet consisted of mesocarnivores, small mammals, and domestic animals. In contrast, the lynx diet mostly consisted of European roe deer (82%) and red deer (64%). However, small mammals and domestic animals were also present in lynx diet, albeit to a lesser extent. Our findings indicate that the dietary habits of wolves and lynx are influenced by geographical location. Snapshot dietary analyses using metabarcoding are valuable for comprehending the behaviour and ecology of predators, and for devising conservation measures aimed at sustainable management of both their natural habitats and prey populations. However, to gain a more detailed understanding of wolf and lynx dietary habits and ecological impact, it would be essential to conduct long-term genetic monitoring of their diet., (© 2024. The Author(s).)
- Published
- 2024
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27. Monitoring of species' genetic diversity in Europe varies greatly and overlooks potential climate change impacts.
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Pearman PB, Broennimann O, Aavik T, Albayrak T, Alves PC, Aravanopoulos FA, Bertola LD, Biedrzycka A, Buzan E, Cubric-Curik V, Djan M, Fedorca A, Fuentes-Pardo AP, Fussi B, Godoy JA, Gugerli F, Hoban S, Holderegger R, Hvilsom C, Iacolina L, Kalamujic Stroil B, Klinga P, Konopiński MK, Kopatz A, Laikre L, Lopes-Fernandes M, McMahon BJ, Mergeay J, Neophytou C, Pálsson S, Paz-Vinas I, Posledovich D, Primmer CR, Raeymaekers JAM, Rinkevich B, Rolečková B, Ruņģis D, Schuerz L, Segelbacher G, Kavčič Sonnenschein K, Stefanovic M, Thurfjell H, Träger S, Tsvetkov IN, Velickovic N, Vergeer P, Vernesi C, Vilà C, Westergren M, Zachos FE, Guisan A, and Bruford M
- Subjects
- Europe, Ecosystem, Genetic Variation, Climate Change, Conservation of Natural Resources methods
- Abstract
Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species' joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union's Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity., (© 2024. The Author(s).)
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- 2024
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28. Spatial genetic structure of European wild boar, with inferences on late-Pleistocene and Holocene demographic history.
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de Jong JF, Iacolina L, Prins HHT, van Hooft P, Crooijmans RPMA, van Wieren SE, Baños JV, Baubet E, Cahill S, Ferreira E, Fonseca C, Glazov PM, Jelenko Turinek I, Lizana Martín VM, Náhlik A, Pokorny B, Podgórski T, Šprem N, Veeroja R, Ydenberg RC, and Megens HJ
- Subjects
- Animals, Swine, Europe, Demography, Sus scrofa genetics, Phylogeny, DNA, Mitochondrial genetics, Genetic Variation, Genome
- 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., (© 2023. The Author(s).)
- Published
- 2023
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29. Traces of past reintroduction in genetic diversity: The case of the Balkan chamois (Mammalia, Artiodactyla).
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Rezić A, Safner T, Iacolina L, Bužan E, and Šprem N
- Abstract
The translocation of wild animal species became a common practice worldwide to re-establish local populations threatened with extinction. Archaeological data confirm that chamois once lived in the Biokovo Mountain but, prior to their reintroduction in the 1960s, there was no written evidence of their recent existence in the area. The population was reintroduced in the period 1964-1969, when 48 individuals of Balkan chamois from the neighbouring mountains in Bosnia and Herzegovina were released. The main objective of this study was to determine the accuracy of the existing historical data on the origin of the Balkan chamois population from the Biokovo Mountain and to assess the genetic diversity and population structure of the source and translocated populations 56 years after reintroduction. Sixteen microsatellite loci were used to analyse the genetic structure of three source chamois populations from Prenj, Čvrsnica and Čabulja Mountains and from Biokovo Mountain. Both STRUCTURE and GENELAND analyses showed a clear separation of the reintroduced population on Biokovo from Prenj's chamois and considerable genetic similarity between the Biokovo population and the Čvrsnica-Čabulja population. This suggests that the current genetic composition of the Biokovo population does not derive exclusively from Prenj, as suggested by the available literature and personal interviews, but also from Čvrsnica and Čabulja. GENELAND analysis recognised the Balkan chamois from Prenj as a separate cluster, distinct from the populations of Čvrsnica and Čabulja. Our results thus highlight the need to implement genetic monitoring of both reintroduced and source populations of endangered Balkan chamois to inform sustainable management and conservation strategies in order to maximise the chances of population persistence., (Andrea Rezić, Toni Safner, Laura Iacolina, Elena Bužan, Nikica Šprem.)
- Published
- 2022
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30. Main roads and land cover shaped the genetic structure of a Mediterranean island wild boar population.
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Lecis R, Dondina O, Orioli V, Biosa D, Canu A, Fabbri G, Iacolina L, Cossu A, Bani L, Apollonio M, and Scandura M
- Abstract
Patterns of genetic differentiation within and among animal populations might vary due to the simple effect of distance or landscape features hindering gene flow. An assessment of how landscape connectivity affects gene flow can help guide management, especially in fragmented landscapes. Our objective was to analyze population genetic structure and landscape genetics of the native wild boar ( Sus scrofa meridionalis ) population inhabiting the island of Sardinia (Italy), and test for the existence of Isolation-by-Distance (IBD), Isolation-by-Barrier (IBB), and Isolation-by-Resistance (IBR). A total of 393 Sardinian wild boar samples were analyzed using a set of 16 microsatellite loci. Signals of genetic introgression from introduced non-native wild boars or from domestic pigs were revealed by a Bayesian cluster analysis including 250 reference individuals belonging to European wild populations and domestic breeds. After removal of introgressed individuals, genetic structure in the population was investigated by different statistical approaches, supporting a partition into five discrete subpopulations, corresponding to five geographic areas on the island: north-west (NW), central west (CW), south-west (SW), north-central east (NCE), and south-east (SE). To test the IBD, IBB, and IBR hypotheses, we optimized resistance surfaces using genetic algorithms and linear mixed-effects models with a maximum likelihood population effects parameterization. Landscape genetics analyses revealed that genetic discontinuities between subpopulations can be explained by landscape elements, suggesting that main roads, urban settings, and intensively cultivated areas are hampering gene flow (and thus individual movements) within the Sardinian wild boar population. Our results reveal how human-transformed landscapes can affect genetic connectivity even in a large-sized and highly mobile mammal such as the wild boar, and provide crucial information to manage the spread of pathogens, including the African Swine Fever virus, endemic in Sardinia., Competing Interests: The authors have no conflicts of interest to declare., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)
- Published
- 2022
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31. Author Correction: eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants.
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Nørgaard L, Olesen CR, Trøjelsgaard K, Pertoldi C, Nielsen JL, Taberlet P, Ruiz-González A, De Barba M, and Iacolina L
- Published
- 2021
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32. A Mother's Story, Mitogenome Relationships in the Genus Rupicapra .
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Iacolina L, Buzan E, Safner T, Bašić N, Geric U, Tesija T, Lazar P, Arnal MC, Chen J, Han J, and Šprem N
- Abstract
Although the two species of chamois ( Rupicapra rupicapra and R. pyrenaica ) are currently classified as least-concern by the IUCN (International Union for Conservation of Nature), inconsistencies on the subspecies classification reported in literature make it challenging to assess the conservation status of the single subspecies. Previous studies relying on mitochondrial genes, sometimes in combination with nuclear or Y-chromosome markers, reported the presence of clusters corresponding to the geographic distribution but highlighting ambiguities in the genus phylogeny. Here we report novel de novo assembled sequences of the mitochondrial genome from nine individuals, including previously unpublished R. r. balcanica and R. r. tatrica subspecies, and use them to untangle the genus phylogeny. Our results based on the full mitogenome inferred phylogeny confirm the previously reported genus subdivision in three clades and its monophyletic positioning within the Caprinae. Phylogeny and taxonomy of Rupicapra species thus remain controversial prompting for the inclusion of archeological remains to solve the controversy.
- Published
- 2021
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33. eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants.
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Nørgaard L, Olesen CR, Trøjelsgaard K, Pertoldi C, Nielsen JL, Taberlet P, Ruiz-González A, De Barba M, and Iacolina L
- Subjects
- Animal Feed analysis, Animals, Denmark, Ecosystem, Feces chemistry, Geography, Biodiversity, DNA Barcoding, Taxonomic, DNA, Environmental analysis, Food Chain
- Abstract
With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as "biodiversity capsules" and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.
- Published
- 2021
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34. MHC Genotyping by SSCP and Amplicon-Based NGS Approach in Chamois.
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Stipoljev S, Bužan E, Rolečková B, Iacolina L, and Šprem N
- Abstract
Genes of the major histocompatibility complex (MHC) code for cell surface proteins essential for adaptive immunity. They show the most outstanding genetic diversity in vertebrates, which has been connected with various fitness traits and thus with the long-term persistence of populations. In this study, polymorphism of the MHC class II DRB locus was investigated in chamois with Single-Strand Conformation Polymorphism (SSCP)/Sanger genotyping and Ion Torrent S5 next-generation sequencing (NGS). From eight identified DRB variants in 28 individuals, five had already been described, and three were new, undescribed alleles. With conventional SSCP/Sanger sequencing, we were able to detect seven alleles, all of which were also detected with NGS. We found inconsistencies in the individual genotypes between the two methods, which were mainly caused by allelic dropout in the SSCP/Sanger method. Six out of 28 individuals were falsely classified as homozygous with SSCP/Sanger analysis. Overall, 25% of the individuals were identified as genotyping discrepancies between the two methods. Our results show that NGS technologies are better performing in sequencing highly variable regions such as the MHC, and they also have a higher detection capacity, thus allowing a more accurate description of the genetic composition, which is crucial for evolutionary and population genetic studies.
- Published
- 2020
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35. Correction to: Genome-wide SNP data unveils the globalization of domesticated pigs.
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Yang B, Cui L, Perez-Enciso M, Traspov A, Crooijmans RPMA, Zinovieva N, Schook LB, Archibald A, Gatphayak K, Knorr C, Triantafyllidis A, Alexandri P, Semiadi G, Hanotte O, Dias D, Dovč P, Uimari P, Iacolina L, Scandura M, Groenen MAM, Huang L, and Megens HJ
- Abstract
An amendment to this paper has been published and can be accessed via the original article.
- Published
- 2020
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36. Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds.
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Lukić B, Ferenčaković M, Šalamon D, Čačić M, Orehovački V, Iacolina L, Curik I, and Cubric-Curik V
- Abstract
The majority of the nearly 400 existing local pig breeds are adapted to specific environments and human needs. The demand for large production quantities and the industrialized pig production have caused a rapid decline of many local pig breeds in recent decades. Black Slavonian pig and Turopolje pig, the latter highly threatened, are the two Croatian local indigenous breeds typically grown in extensive or semi-intensive systems. In order to guide a long-term breeding program to prevent the disappearance of these breeds, we analyzed their genetic diversity, inbreeding level and relationship with other local breeds across the world, as well as modern breeds and several wild populations, using high throughput genomic data obtained using the Illumina Infinium PorcineSNP60 v2 BeadChip. Multidimensional scaling analysis positioned Black Slavonian pigs close to the UK/North American breeds, while the Turopolje pig clustered within the Mediterranean breeds. Turopolje pig showed a very high inbreeding level (F
ROH > 4 Mb = 0.400 and FROH > 8 Mb = 0.332) that considerably exceeded the level of full-sib mating, while Black Slavonian pig showed much lower inbreeding (FROH > 4 Mb = 0.098 and FROH > 8 Mb = 0.074), indicating a planned mating strategy. In Croatian local breeds we identified several genome regions showing adaptive selection signals that were not present in commercial breeds. The results obtained in this study reflect the current genetic status and breeding management of the two Croatian indigenous local breeds. Given the small populations of both breeds, a controlled management activity has been implemented in Black Slavonian pigs since their commercial value has been recognized. In contrast, the extremely high inbreeding level observed in Turopolje pig argues for an urgent conservation plan with a long-term, diversity-oriented breeding program., (Copyright © 2020 Lukić, Ferenčaković, Šalamon, Čačić, Orehovački, Iacolina, Curik and Cubric-Curik.)- Published
- 2020
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37. Microsatellite based assignment reveals history of extirpated mountain ungulate.
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Safner T, Buzan E, Iacolina L, Potušek S, Rezić A, Sindičić M, Kavčić K, and Šprem N
- Subjects
- Animals, Conservation of Natural Resources, Evolution, Molecular, Horns, Male, Phylogeny, Sequence Analysis, DNA methods, Skull, Microsatellite Repeats genetics, Rupicapra genetics
- Abstract
During the early 1900s, Northern chamois (Rupicapra rupicapra) populations in the northern Dinaric Mountains were extirpated. During the 1960s and 1970s there were several reintroductions of individuals from two Northern chamois subspecies (Alpine chamois, R. r. rupicapra and Balkan chamois, R. r. balcanica) from neighbouring areas in the attempt to re-establish the population. Accurate taxonomic classification, at subspecies level, of the autochthonous extirpated population was not known. To clarify which subspecies was present before reintroduction, we genotyped four male chamois skulls originating from Velebit Mountain, collected around 25 years before the population local extinction. DNA was successfully extracted from middle layer and outer sheath of horns. Assignment based on microsatellite loci, using both Bayesian clustering in STRUCTURE (with q values between 0.55 and 0.73) and DAPC (with individual membership probabilities of 0.99 and 1.00) indicated higher assessed likelihood for the Alpine subspecies.
- Published
- 2020
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38. Author Correction: Hotspots of recent hybridization between pigs and wild boars in Europe.
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Iacolina L, Pertoldi C, Amills M, Kusza S, Megens HJ, Bâlteanu VA, Bakan J, Cubric-Curik V, Oja R, Saarma U, Scandura M, Šprem N, and Stronen AV
- Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
- Published
- 2019
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39. Genomic analyses suggest adaptive differentiation of northern European native cattle breeds.
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Stronen AV, Pertoldi C, Iacolina L, Kadarmideen HN, and Kristensen TN
- Abstract
Native domestic breeds represent important cultural heritage and genetic diversity relevant for production traits, environmental adaptation and food security. However, risks associated with low effective population size, such as inbreeding and genetic drift, have elevated concerns over whether unique within-breed lineages should be kept separate or managed as one population. As a conservation genomic case study of the genetic diversity represented by native breeds, we examined native and commercial cattle ( Bos taurus ) breeds including the threatened Danish Jutland cattle. We examined population structure and genetic diversity within breeds and lineages genotyped across 770K single nucleotide polymorphism loci to determine (a) the amount and distribution of genetic diversity in native breeds, and (b) the role of genetic drift versus selection. We further investigated the presence of outlier loci to detect (c) signatures of environmental selection in native versus commercial breeds, and (d) native breed adaptation to various landscapes. Moreover, we included older cryopreserved samples to determine (e) whether cryopreservation allows (re)introduction of original genetic diversity. We investigated a final set of 195 individuals and 677K autosomal loci for genetic diversity within and among breeds, examined population structure with principal component analyses and a maximum-likelihood approach and searched for outlier loci suggesting artificial or natural selection. Our findings demonstrate the potential of genomics for identifying the uniqueness of native domestic breeds, and for maintaining their genetic diversity and long-term evolutionary potential through conservation plans balancing inbreeding with carefully designed outcrossing. One promising opportunity is the use of cryopreserved samples, which can provide important genetic diversity for populations with few individuals, while helping to preserve their traditional genetic characteristics. Outlier tests for native versus commercial breeds identified genes associated with climate adaptation, immunity and metabolism, and native breeds may carry genetic variation important for animal health and robustness in a changing climate., Competing Interests: None declared.
- Published
- 2019
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40. Hotspots of recent hybridization between pigs and wild boars in Europe.
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Iacolina L, Pertoldi C, Amills M, Kusza S, Megens HJ, Bâlteanu VA, Bakan J, Cubric-Curik V, Oja R, Saarma U, Scandura M, Šprem N, and Stronen AV
- Subjects
- Animals, Austria, Breeding methods, Ecosystem, Europe, Middle East, Nucleic Acid Hybridization genetics, Polymorphism, Single Nucleotide genetics, Hybridization, Genetic genetics, Sus scrofa genetics, Swine genetics
- Abstract
After a strong demographic decline before World War II, wild boar populations are expanding and the species is now the second-most abundant ungulate in Europe. This increase raises concerns due to wild boar impact on crops and natural ecosystems and as potential vector of diseases. Additionally, wild boar can hybridize with domestic pigs, which could increase health risks and alter wild boar adaptive potential. We analysed 47,148 Single Nucleotide Polymorphisms in wild boar from Europe (292) and the Near East (16), and commercial (44) and local (255) pig breeds, to discern patterns of hybridization across Europe. We identified 33 wild boars with more than 10% domestic ancestry in their genome, mostly concentrated in Austria, Bosnia and Herzegovina, Bulgaria and Serbia. This difference is probably due to contrasting practices, with free-ranging vs. industrial farming but more samples would be needed to investigate larger geographic patterns. Our results suggest hybridization has occurred over a long period and is still ongoing, as we observed recent hybrids. Although wild and domestic populations have maintained their genetic distinctiveness, potential health threats raise concerns and require implementation of management actions and farming practices aimed at reducing contact between wild and domestic pigs.
- Published
- 2018
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41. Genome-wide SNP data unveils the globalization of domesticated pigs.
- Author
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Yang B, Cui L, Perez-Enciso M, Traspov A, Crooijmans RPMA, Zinovieva N, Schook LB, Archibald A, Gatphayak K, Knorr C, Triantafyllidis A, Alexandri P, Semiadi G, Hanotte O, Dias D, Dovč P, Uimari P, Iacolina L, Scandura M, Groenen MAM, Huang L, and Megens HJ
- Subjects
- Animals, Asia, Australia, Europe, Internationality, Selection, Genetic, Sus scrofa classification, Swine, Breeding, Genome-Wide Association Study, Polymorphism, Single Nucleotide genetics, Sus scrofa genetics
- Abstract
Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection., Results: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection., Conclusions: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.
- Published
- 2017
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42. How much does it cost to look like a pig in a wild boar group?
- Author
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Battocchio D, Iacolina L, Canu A, and Mori E
- Subjects
- Aggression, Animals, Hybridization, Genetic, Skin Pigmentation, Social Behavior, Animals, Domestic psychology, Sus scrofa psychology, Swine psychology
- Abstract
Hybridization between domestic and wild species is known to widely occur and it is reported to be one of the major causes of the current biodiversity crisis. Despite this, poor attention has been deserved to the behavioural ecology of hybrids, in particular in relation to their social behaviour. We carried out a camera trap study to assess whether phenotypically anomalous colouration in wild boar, i.e. potentially introgressed with domestic pigs, affected the hierarchical structure of wild boar social groups. Chromatically anomalous wild boars (CAWs) were detected in 32 out of 531 wild boar videos. In most videos (75%) CAWs were the latest of the group, independently from their age class and group composition. Aggressions by their wild type fellows were recorded in 31.25% videos; by contrast, no aggression among wild type individuals was observed. The lack of camouflage may expose CAWs, and thus their group, to a higher predation risk, compared to wild type groups. This individual loss of local adaptation may increase predation risk by the wolf or detection by hunters, being maladaptive for the whole social group., (Copyright © 2017 Elsevier B.V. All rights reserved.)
- Published
- 2017
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43. Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds.
- Author
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Iacolina L, Stronen AV, Pertoldi C, Tokarska M, Nørgaard LS, Muñoz J, Kjærsgaard A, Ruiz-Gonzalez A, Kamiński S, and Purfield DC
- Abstract
Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle ( Bos taurus ) and the European bison ( Bison bonasus ) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5-15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation.
- Published
- 2016
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44. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025.
- Author
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Bruford MW, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferenčaković M, Fischer D, Fitak R, Groeneveld LF, Hall SJ, Hanotte O, Hassan FU, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra JA, Ajmone-Marsan P, Masembe C, Megens HJ, Miele M, Neuditschko M, Nicolazzi EL, Pompanon F, Roosen J, Sevane N, Smetko A, Štambuk A, Streeter I, Stucki S, Supakorn C, Telo Da Gama L, Tixier-Boichard M, Wegmann D, and Zhan X
- Abstract
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that "…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity." However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.
- Published
- 2015
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45. Mitochondrial CR-1 variation in Sardinian hares and its relationships with other Old World hares (Genus Lepus).
- Author
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Scandura M, Iacolina L, Ben Slimen H, Suchentrunk F, and Apollonio M
- Subjects
- Animals, Base Sequence, Geography, Haplotypes, Italy, Molecular Sequence Data, DNA, Mitochondrial genetics, Genetic Variation genetics, Hares genetics, Phylogeny, Regulatory Sequences, Nucleic Acid genetics
- Abstract
Among the European fauna, the Sardinian hare (Lepus sp.) is peculiar in that it differs from all other hares inhabiting the continent. Here, we report on the variation of a 461 bp sequence of hypervariable domain 1 of the mitochondrial control region, examined in 42 hares collected throughout Sardinia and compared to the corresponding sequences of different Lepus taxa. Seventeen novel haplotypes were found in the Sardinian population, resulting in a haplotype diversity of 0.840 and a nucleotide diversity of 0.012. As a result of Bayesian and principal coordinates analyses, Sardinian hares were grouped with North African hares, constituting a monophyletic clade that diverges from all other Old World hares, including Cape hares from South Africa and East Asia. Hence, our data agree that populations inhabiting North Africa and Sardinia form a distinct taxon, which could possibly be included in the L. capensis superspecies. Moreover, two corresponding lineages can be found in Sardinia and Tunisia, providing evidence of a common origin of the two populations and thus supporting the hypothesis that North African hares were introduced into the island in historical times. Our data show that the two lineages differ in their geographic distribution throughout the island and that the wild Sardinian population also shows the signature of a postintroduction demographic expansion.
- Published
- 2007
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