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1. Exploiting phenotypic plasticity in animal breeding

Author

Kebede, F.G., Komen, H., Dessie, T., Hanotte, O., Kemp, S., Pita Barros, C., Crooijmans, R., Derks, M., Alemu, S.W., Bastiaansen, J.W.M., Kebede, F.G., Komen, H., Dessie, T., Hanotte, O., Kemp, S., Pita Barros, C., Crooijmans, R., Derks, M., Alemu, S.W., and Bastiaansen, J.W.M.

Abstract

Livestock populations can have different genetic backgrounds and may vary in their capacity to respond to environmental changes. Our findings suggest that improved chicken breeds differ in growth performance and phenotypic plasticity (yield stability) when they are introduced into new tropical environments. Dual consideration of productivity and phenotypic plasticity gives opportunities to select or recommend genotypes with optimal performance and wider adaptability for smallholder farmers raising livestock in different agroecologies.

Published
2022

2. Mapping genetic diversity in European gene banks: preliminary results on chickens for the validation of IMAGE001 array

Author

Tixier-Boichard, M., Peynot, N., Duclos, D., Weigend, S., Monteagudo, L., Martinez Martinez, A., Delgado, J.V., Gonzalez Prendes, R., Crooijmans, R., Restoux, G., Tixier-Boichard, M., Peynot, N., Duclos, D., Weigend, S., Monteagudo, L., Martinez Martinez, A., Delgado, J.V., Gonzalez Prendes, R., Crooijmans, R., and Restoux, G.

Abstract

Gene banks are a component of a national strategy for the preservation of genetic diversity. Gene bank managers need to have a global and comparable picture of the diversity in their collections in order to rationalize them. Facing a diversity of molecular tools is a difficulty. The IMAGE H2020 project aimed at developing a low cost 60k SNP array to facilitate the mapping of diversity in gene banks. The first test of this array was performed for chicken with 204 samples from 18 local breeds and nine experimental lines provided by Germany, France and Spain. The MAF across population was 0.34, showing that this tool is useful over a range of populations. The principal component analysis and the Neighbor-joining tree showed that local breeds did not cluster according to country and were generally homogenous. Comparison with on-farm populations remains to be done to assess the value of the gene bank collections.

Published
2022

3. Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs

Author

Upadhyay, M., Bortoluzzi, C., Barbato, Mario, Ajmone Marsan, Paolo, Colli, Licia, Ginja, C., Sonstegard, T. S., Bosse, M., Lenstra, J. A., Groenen, M. A. M., Crooijmans, R. P. M. A., Barbato M. (ORCID:0000-0002-7203-1549), Ajmone Marsan P. (ORCID:0000-0003-3165-4579), Colli L. (ORCID:0000-0002-7221-2905), Upadhyay, M., Bortoluzzi, C., Barbato, Mario, Ajmone Marsan, Paolo, Colli, Licia, Ginja, C., Sonstegard, T. S., Bosse, M., Lenstra, J. A., Groenen, M. A. M., Crooijmans, R. P. M. A., Barbato M. (ORCID:0000-0002-7203-1549), Ajmone Marsan P. (ORCID:0000-0003-3165-4579), and Colli L. (ORCID:0000-0002-7221-2905)

Abstract

The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might ac

Published
2019

4. The influence of facies heterogeneity on the doublet performance in low-enthalpy geothermal sedimentary reservoirs

Author

Crooijmans, R. A., Willems, C. J L, Nick, Hamid, Bruhn, D. F., Crooijmans, R. A., Willems, C. J L, Nick, Hamid, and Bruhn, D. F.

Abstract

A three-dimensional model is used to study the influence of facies heterogeneity on energy production under different operational conditions of low-enthalpy geothermal doublet systems. Process-based facies modelling is utilised for the Nieuwerkerk sedimentary formation in the West Netherlands Basin to construct realistic reservoir models honouring geological heterogeneity. A finite element based reservoir simulator is used to model the fluid flow and heat transfer over time. A series of simulations is carried out to examine the effects of reservoir heterogeneity (Net-to-Gross ratio, N/G) on the life time and the energy recovery rate for different discharge rates and the production temperature (Tmin) above which the doublet is working. With respect to the results, we propose a design model to estimate the life time and energy recovery rate of the geothermal doublet. The life time is estimated as a function of N/G, Tmin and discharge rate, while the design model for the energy recovery rate is only a function of N/G and Tmin. Both life time and recovery show a positive relation with an increasing N/G. Further our results suggest that neglecting details of process-based facies modelling may lead to significant errors in predicting the life time of low-enthalpy geothermal systems for N/G values below 70%.

Published
2016

5. RECON: Reef effect structures in the North Sea, islands or connections? : Summary report

Author

Coolen, J.W.P., Jak, R.G., van der Weide, B.E., Cuperus, J., Luttikhuizen, P., Schutter, M., Dorenbosch, M., Driessen, F., Lengkeek, W., Blomberg, M., van Moorsel, G., Faasse, M.A., Bos, O.G., Dias, I.M., Spierings, M., Glorius, S.G., Becking, L.E., Schol, T., Crooijmans, R., Boon, A.R., van Pelt, H., Kleissen, F., Gerla, D., Degraer, S., Lindeboom, H.J., Coolen, J.W.P., Jak, R.G., van der Weide, B.E., Cuperus, J., Luttikhuizen, P., Schutter, M., Dorenbosch, M., Driessen, F., Lengkeek, W., Blomberg, M., van Moorsel, G., Faasse, M.A., Bos, O.G., Dias, I.M., Spierings, M., Glorius, S.G., Becking, L.E., Schol, T., Crooijmans, R., Boon, A.R., van Pelt, H., Kleissen, F., Gerla, D., Degraer, S., and Lindeboom, H.J.

Published
2018

7. Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)

Author

Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., R. H. S., Kraus, Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., and R. H. S., Kraus

Abstract

Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the most numerous and widespread duck in the world, yet each year more than three million farmed mallard ducklings are released into the wild in the European Union alone to increase the harvestable population. This study aimed to determine the genetic effects of such large-scale releases of a native species, specifically if wild and released farmed mallards differ genetically among subpopulations in Europe, if there are signs of admixture between the two groups, if the genetic structure of the wild mallard population has changed since large-scale releases began in the 1970s, and if the current data matches global patterns across the Northern hemisphere. We used Bayesian clustering (Structure software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n = 171 and n = 209, respectively) as well as farmed (n = 211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.

Published
2017
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8. Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)

Author

Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., R. H. S., Kraus, Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., and R. H. S., Kraus

Abstract

Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the most numerous and widespread duck in the world, yet each year more than three million farmed mallard ducklings are released into the wild in the European Union alone to increase the harvestable population. This study aimed to determine the genetic effects of such large-scale releases of a native species, specifically if wild and released farmed mallards differ genetically among subpopulations in Europe, if there are signs of admixture between the two groups, if the genetic structure of the wild mallard population has changed since large-scale releases began in the 1970s, and if the current data matches global patterns across the Northern hemisphere. We used Bayesian clustering (Structure software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n = 171 and n = 209, respectively) as well as farmed (n = 211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.

Published
2017
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9. Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)

Author

Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., R. H. S., Kraus, Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., and R. H. S., Kraus

Abstract

Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the most numerous and widespread duck in the world, yet each year more than three million farmed mallard ducklings are released into the wild in the European Union alone to increase the harvestable population. This study aimed to determine the genetic effects of such large-scale releases of a native species, specifically if wild and released farmed mallards differ genetically among subpopulations in Europe, if there are signs of admixture between the two groups, if the genetic structure of the wild mallard population has changed since large-scale releases began in the 1970s, and if the current data matches global patterns across the Northern hemisphere. We used Bayesian clustering (Structure software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n = 171 and n = 209, respectively) as well as farmed (n = 211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.

Published
2017
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10. Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)

Author

Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., R. H. S., Kraus, Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., and R. H. S., Kraus

Abstract

Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the most numerous and widespread duck in the world, yet each year more than three million farmed mallard ducklings are released into the wild in the European Union alone to increase the harvestable population. This study aimed to determine the genetic effects of such large-scale releases of a native species, specifically if wild and released farmed mallards differ genetically among subpopulations in Europe, if there are signs of admixture between the two groups, if the genetic structure of the wild mallard population has changed since large-scale releases began in the 1970s, and if the current data matches global patterns across the Northern hemisphere. We used Bayesian clustering (Structure software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n = 171 and n = 209, respectively) as well as farmed (n = 211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.

Published
2017
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11. Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)

Author

Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., R. H. S., Kraus, Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., and R. H. S., Kraus

Abstract

Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the most numerous and widespread duck in the world, yet each year more than three million farmed mallard ducklings are released into the wild in the European Union alone to increase the harvestable population. This study aimed to determine the genetic effects of such large-scale releases of a native species, specifically if wild and released farmed mallards differ genetically among subpopulations in Europe, if there are signs of admixture between the two groups, if the genetic structure of the wild mallard population has changed since large-scale releases began in the 1970s, and if the current data matches global patterns across the Northern hemisphere. We used Bayesian clustering (Structure software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n = 171 and n = 209, respectively) as well as farmed (n = 211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.

Published
2017
Full Text
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12. Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)

Author

Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., R. H. S., Kraus, Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, C-G, Champagnon, J, Guillemain, M, Kreisinger, J, Prins, H T, Crooijmans, R. P. M. A., and R. H. S., Kraus

Abstract

Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the most numerous and widespread duck in the world, yet each year more than three million farmed mallard ducklings are released into the wild in the European Union alone to increase the harvestable population. This study aimed to determine the genetic effects of such large-scale releases of a native species, specifically if wild and released farmed mallards differ genetically among subpopulations in Europe, if there are signs of admixture between the two groups, if the genetic structure of the wild mallard population has changed since large-scale releases began in the 1970s, and if the current data matches global patterns across the Northern hemisphere. We used Bayesian clustering (Structure software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n = 171 and n = 209, respectively) as well as farmed (n = 211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.

Published
2017
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13. Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds

Author

Axelsson, Erik Gunnar, Albrechtsen, Anders, Van, A. P., Li, L., Megens, H. J., Vereijken, A. L. J., Crooijmans, R. P. M. A., Groenen, M. A. M., Ellegren, H., Willerslev, Eske, Nielsen, R., Axelsson, Erik Gunnar, Albrechtsen, Anders, Van, A. P., Li, L., Megens, H. J., Vereijken, A. L. J., Crooijmans, R. P. M. A., Groenen, M. A. M., Ellegren, H., Willerslev, Eske, and Nielsen, R.

Abstract

As all four meiotic products give rise to sperm in males, female meiosis result in a single egg in most eukaryotes. Any genetic element with the potential to influence chromosome segregation, so that it is preferentially included in the egg, should therefore gain a transmission advantage; a process termed female meiotic drive. We are aware of two chromosomal components, centromeres and telomeres, which share the potential to influence chromosome movement during meioses and make the following predictions based on the presence of female meiotic drive: (1) centromere-binding proteins should experience rapid evolution as a result of a conflict between driving centromeres and the rest of the genome; and (2) segregation patterns should be skewed near centromeres and telomeres. To test these predictions, we first analyze the molecular evolution of seven centromere-binding proteins in nine divergent bird species. We find strong evidence for positive selection in two genes, lending support to the genomic conflict hypothesis. Then, to directly test for the presence of segregation distortion, we also investigate the transmission of approximately 9000 single-nucleotide polymorphisms in 197 chicken families. By simulating fair Mendelian meioses, we locate chromosomal regions with statistically significant transmission ratio distortion. One region is located near the centromere on chromosome 1 and a second region is located near the telomere on the p-arm of chromosome 1. Although these observations do not provide conclusive evidence in favour of the meiotic drive/genome conflict hypothesis, they do lend support to the hypothesis that centromeres and telomeres drive during female meioses in chicken.

Published
2010

14. Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds

Author

Axelsson, Erik Gunnar, Albrechtsen, Anders, Van, A. P., Li, L., Megens, H. J., Vereijken, A. L. J., Crooijmans, R. P. M. A., Groenen, M. A. M., Ellegren, H., Willerslev, Eske, Nielsen, R., Axelsson, Erik Gunnar, Albrechtsen, Anders, Van, A. P., Li, L., Megens, H. J., Vereijken, A. L. J., Crooijmans, R. P. M. A., Groenen, M. A. M., Ellegren, H., Willerslev, Eske, and Nielsen, R.

Abstract

As all four meiotic products give rise to sperm in males, female meiosis result in a single egg in most eukaryotes. Any genetic element with the potential to influence chromosome segregation, so that it is preferentially included in the egg, should therefore gain a transmission advantage; a process termed female meiotic drive. We are aware of two chromosomal components, centromeres and telomeres, which share the potential to influence chromosome movement during meioses and make the following predictions based on the presence of female meiotic drive: (1) centromere-binding proteins should experience rapid evolution as a result of a conflict between driving centromeres and the rest of the genome; and (2) segregation patterns should be skewed near centromeres and telomeres. To test these predictions, we first analyze the molecular evolution of seven centromere-binding proteins in nine divergent bird species. We find strong evidence for positive selection in two genes, lending support to the genomic conflict hypothesis. Then, to directly test for the presence of segregation distortion, we also investigate the transmission of approximately 9000 single-nucleotide polymorphisms in 197 chicken families. By simulating fair Mendelian meioses, we locate chromosomal regions with statistically significant transmission ratio distortion. One region is located near the centromere on chromosome 1 and a second region is located near the telomere on the p-arm of chromosome 1. Although these observations do not provide conclusive evidence in favour of the meiotic drive/genome conflict hypothesis, they do lend support to the hypothesis that centromeres and telomeres drive during female meioses in chicken.

Published
2010

15. Farmed European mallards are genetically different and cause introgression in the wild population following releases

Author

Elmberg, Johan, Söderquist, Pär, Gunnarsson, Gunnar, Thulin, Carl-Gustaf, Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, H. H. T., Crooijmans, R. P. M. A., Kraus, R. H. S., Elmberg, Johan, Söderquist, Pär, Gunnarsson, Gunnar, Thulin, Carl-Gustaf, Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, H. H. T., Crooijmans, R. P. M. A., and Kraus, R. H. S.

Abstract

The practice of restocking already viable populations to increase harvest potential has since long been common in forestry, fisheries and wildlife management. The potential risks of restocking native species have long been overshadowed by the related issue of invasive alien species. However, during the last decade releases of native species with potentially non-native genome have received more attention. A suitable model to study genetic effects of large-scale releases of native species is the Mallard Anas platyrhynchos, being the most widespread duck in the world, largely migratory, and an important quarry species. More than 3 million unfledged hatchlings are released each year around Europe to increase local harvest. The aims of this study were to determine if wild and released farmed Mallards differ genetically, if there are signs of previous or ongoing introgression between wild and farmed birds, and if the genetic structure of the wild Mallard population has changed since large-scale releases started in Europe in the 1970s. Using 360 Single Nucleotide Polymorphisms (SNPs) we found that the genetic structure differed among historical wild, present-day wild, and farmed Mallards in Europe. We also found signs of introgression in the wild Mallard population, that is, individuals with a genetic background of farmed stock are part of the present free-living population. Although only a small proportion of the released Mallards appears to survive to merge with the free-living breeding population, their numbers are still so large that the genetic impact may have significance for the wild population in terms of individual survival and longterm fitness.

Published
2016

16. Freigelassenes Federwild führt zu kontinent-weiter genetischer Introgression : die sich ändernde genetische Landschaft der Stockente (Anas platyrhynchos) in Europa

Author

Kraus, R. H. S., Söderquist, Pär, Gunnarsson, Gunnar, Thulin, C.-G., Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, H. H. T., Crooijmans, R. P. M. A., Elmberg, Johan, Kraus, R. H. S., Söderquist, Pär, Gunnarsson, Gunnar, Thulin, C.-G., Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, H. H. T., Crooijmans, R. P. M. A., and Elmberg, Johan

Published
2015

17. Released game birds cause introgression in European mallard

Author

Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, Carl-Gustaf, Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, Herbert, Crooijmans, R, Kraus, Robert, Söderquist, Pär, Elmberg, Johan, Gunnarsson, Gunnar, Thulin, Carl-Gustaf, Champagnon, Jocelyn, Guillemain, Matthieu, Kreisinger, Jakub, Prins, Herbert, Crooijmans, R, and Kraus, Robert

Abstract

The practice of restocking already viable populations to improve harvest has since long been common in forestry, fisheries and wildlife management. The potential risks with restocking of native species has for a long time been overshadowed by the related issue of invasive species. However, during the last decade releases of native species with a potential non-native genome have attained more attention. A suitable model species for studying genetic effects of large-scale releases of a native species is the Mallard, Anas platyrhynchos; it is the most widespread duck in the world, it is a migrating species, and an important game bird. In several European countries it is also farmed and released to increase the harvestable population, and more than 3 million unfledged hatchlings are released each year around Europe. The aims of this study were to determine if wild and released farmed Mallards differed genetically among subpopulations in Europe, if there are signs of previous or ongoing introgression between wild and farmed Mallards, and if the genetic structure of the wild Mallard population has changed since large-scale releases started in the 1970s. We used 360 Single Nucleotide Polymorphisms (SNPs) to analyze the genetic structure of historical wild, present-day wild, and farmed Mallards. We found a clear genetic difference between wild and farmed Mallards in Europe. We also found signs of introgression of farmed genes in the wild Mallard population, however, the rate of hybridization is probably minor due to low survival of released farmed Mallards and a change of the wild population since the start of large-scale releases is therefore limited. A low level of hybridization between farmed and wild Mallard is desired as introgressed genes may be detrimental for wild Mallards, and efforts to increase survival of farmed Mallards should therefore not be encouraged.

Published
2015

18. Porcine colonization of the Americas A 60k SNP story

Author

Burgos-Paz, W., Souza, C. A., Megens, H. J., Ramayo-Caldas, Y., Melo, M., Lemús-Flores, C., Caal, E., Soto, H. W., Martínez, R., Álvarez, L. A., Aguirre, L., Iñiguez, V., Revidatti, M. A., Martínez-López, O. R., Llambi, S., Esteve-Codina, A., Rodríguez, M. C., Crooijmans, R. P. M. A., Paiva, S. R., Schook, L. B., Groenen, M. A. M., Pérez-Enciso, M., Burgos-Paz, W., Souza, C. A., Megens, H. J., Ramayo-Caldas, Y., Melo, M., Lemús-Flores, C., Caal, E., Soto, H. W., Martínez, R., Álvarez, L. A., Aguirre, L., Iñiguez, V., Revidatti, M. A., Martínez-López, O. R., Llambi, S., Esteve-Codina, A., Rodríguez, M. C., Crooijmans, R. P. M. A., Paiva, S. R., Schook, L. B., Groenen, M. A. M., and Pérez-Enciso, M.

Abstract

The pig, Sus scrofa, is a foreign species to the American continent. Although pigs originally introduced in the Americas should be related to those from the Iberian Peninsula and Canary islands, the phylogeny of current creole pigs that now populate the continent is likely to be very complex. Because of the extreme climates that America harbors, these populations also provide a unique example of a fast evolutionary phenomenon of adaptation. Here, we provide a genome wide study of these issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across 14 countries and 183 pigs from outgroup breeds that are potential founders of the American populations, including wild boar, Iberian, international and Chinese breeds. Results show that American village pigs are primarily of European ancestry, although the observed genetic landscape is that of a complex conglomerate. There was no correlation between genetic and geographical distances, neither continent wide nor when analyzing specific areas. Most populations showed a clear admixed structure where the Iberian pig was not necessarily the main component, illustrating how international breeds, but also Chinese pigs, have contributed to extant genetic composition of American village pigs. We also observe that many genes related to the cardiovascular system show an increased differentiation between altiplano and genetically related pigs living near sea level. © 2013 Macmillan Publishers Limited All rights reserved.

Published
2013

19. Analyses of pig genomes provide insight into porcine demography and evolution

Author

Groenen, M. A., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H. J., Li, S., Larkin, D. M., Kim, H., Frantz, L. A., Caccamo, M., Ahn, H., Aken, B. L., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C. W., Bendixen, C., Berman, D., Blecha, F., Blomberg, Jonas, Bolund, L., Bosse, M., Botti, S., Bujie, Z., Byström, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S. H., Chow, W., Clark, R. C., Clee, C., Crooijmans, R. P., Dawson, H. D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z. Q., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G. J., Fowler, K. E., Fredholm, M., Fritz, E., Gilbert, J. G., Giuffra, E., Gorodkin, J., Griffin, D. K., Harrow, J. L., Hayward, Alexander, Howe, K., Hu, Z. L., Humphray, S. J., Hunt, T., Hornshoj, H., Jeon, J. T., Jern, Patric, Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J. H., Kim, K. W., Kim, T. H., Larson, G., Lee, K., Lee, K. T., Leggett, R., Lewin, H. A., Li, Y., Liu, W., Loveland, J. E., Lu, Y., Lunney, J. K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M. P., Narayan, J., Nguyen, D. T., Ni, P., Oh, S. J., Onteru, S., Panitz, F., Park, E. W., Park, H. S., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J. M., Rodriguez-Zas, S., Rohrer, G. A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J. G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B. R., Sperber, Göran, Stadler, P., Sweedler, J. V., Tafer, H., Thomsen, B., Wali, R., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhao, S., Rogers, J., Churcher, C., Schook, L. B., Groenen, M. A., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H. J., Li, S., Larkin, D. M., Kim, H., Frantz, L. A., Caccamo, M., Ahn, H., Aken, B. L., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C. W., Bendixen, C., Berman, D., Blecha, F., Blomberg, Jonas, Bolund, L., Bosse, M., Botti, S., Bujie, Z., Byström, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S. H., Chow, W., Clark, R. C., Clee, C., Crooijmans, R. P., Dawson, H. D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z. Q., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G. J., Fowler, K. E., Fredholm, M., Fritz, E., Gilbert, J. G., Giuffra, E., Gorodkin, J., Griffin, D. K., Harrow, J. L., Hayward, Alexander, Howe, K., Hu, Z. L., Humphray, S. J., Hunt, T., Hornshoj, H., Jeon, J. T., Jern, Patric, Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J. H., Kim, K. W., Kim, T. H., Larson, G., Lee, K., Lee, K. T., Leggett, R., Lewin, H. A., Li, Y., Liu, W., Loveland, J. E., Lu, Y., Lunney, J. K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M. P., Narayan, J., Nguyen, D. T., Ni, P., Oh, S. J., Onteru, S., Panitz, F., Park, E. W., Park, H. S., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J. M., Rodriguez-Zas, S., Rohrer, G. A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J. G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B. R., Sperber, Göran, Stadler, P., Sweedler, J. V., Tafer, H., Thomsen, B., Wali, R., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhao, S., Rogers, J., Churcher, C., and Schook, L. B.

Abstract

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Published
2012
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20. Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks

Author

Kraus, R.H.S., Kerstens, H.H.D., Hooft, P. van, Megens, H.J., Elmberg, J., Tsvey, A., Sartakov, D., Soloviev, S.A., Crooijmans, R., Groenen, M.A.M., Ydenberg, R.C., Prins, H.H.T., Kraus, R.H.S., Kerstens, H.H.D., Hooft, P. van, Megens, H.J., Elmberg, J., Tsvey, A., Sartakov, D., Soloviev, S.A., Crooijmans, R., Groenen, M.A.M., Ydenberg, R.C., and Prins, H.H.T.

Abstract

Contains fulltext : 103891.pdf (publisher's version ) (Open Access)

Published
2012

21. Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks

Author

Kraus, R.H.S., Kerstens, H.H.D., Hooft, P. van, Megens, H.J., Elmberg, J., Tsvey, A., Sartakov, D., Soloviev, S.A., Crooijmans, R., Groenen, M.A.M., Ydenberg, R.C., Prins, H.H.T., Kraus, R.H.S., Kerstens, H.H.D., Hooft, P. van, Megens, H.J., Elmberg, J., Tsvey, A., Sartakov, D., Soloviev, S.A., Crooijmans, R., Groenen, M.A.M., Ydenberg, R.C., and Prins, H.H.T.

Abstract

Contains fulltext : 103891.pdf (publisher's version ) (Open Access)

Published
2012

22. Genetisch onderzoek bij de kip

Author

Crooijmans, R. and Crooijmans, R.

Abstract

Vakgroep Fokkerij en Genetica van Wageningen Universiteit heeft een nieuwe DNA-bank opgezet van oud-Hollandse kippenrassen.

Published
2012

23. Grote verschillen in diversiteit Chinese en Europese varkensrassen

Author

Megens, H.-J., Crooijmans, R., Megens, H.-J., and Crooijmans, R.

Abstract

De vakgroep Fokkerij en Genetica van Wageningen Universiteit heeft met behulp van genetische merkers de verwantschap van honderd rassen en commerciële lijnen in kaart gebracht. Dit is gebeurd in een groot samenwerkingsproject tussen Chinese en Europese onderzoeksinstituten. Het resultaat van dit unieke onderzoek is een genetische boom, die in dit artikel wordt uitgelegd

Published
2009

24. Gebruik DNA-technieken versterkt de biodiversiteit

Author

Crooijmans, R. and Crooijmans, R.

Abstract

Van oudsher zijn verschillen tussen rassen en soorten vastgelegd. Lange tijd is dat gebeurd door verschillen in voorkomen te beschrijven en productie-eigenschappen te meten. De beschreven verschillen vormdende fenotypische variatie. Sinds de jaren negentig wordt ook steeds meer getracht om verschillen tussen dieren op moleculair niveau te beschrijven. De wijze waarop deze moleculaire variatie een bijdrage kan leveren voor het verbeteren van de biodiversiteit, wordt in dit artikel voor de kippen beschreven

Published
2009

27. Clinical efficacy and patients’ perception of virtual reality during wound care in adults:A systematic review with meta-analysis of randomised clinical trials

Author

Mazaheri, Masood, Crooijmans, Raoul F., Vereen, Maya, Corten, Eveline M.L., Mazaheri, Masood, Crooijmans, Raoul F., Vereen, Maya, and Corten, Eveline M.L.

Abstract

This study was aimed to review Virtual Reality's (VR) impact on pain, anxiety, opioid usage, physiological and behavioural responses, and patients’ experience during wound care (WC) in adults. We searched multiple databases (Embase, Medline ALL, Web of Science Core Collection, Cochrane Central Register of Controlled Trials, CINAHL, Scopus and Google Scholar) from inception until January 27th, 2023. Included studies compared VR alone or as an adjunct to standard WC with standard WC or other distraction methods, in adults with burn or non-burn-related wounds. The risk of bias was assessed using the revised Cochrane risk-of-bias tool for randomised parallel-group and crossover trials. The review followed PRISMA guidelines for reporting. Fourteen studies were eligible for inclusion. The meta-analysis was limited to studies comprising solely of adult participants. VR reduced pain intensity compared to standard WC in all study designs. Despite not being included in the meta-analysis due to reasons such as mixed population or lack of sufficient statistical data, other studies showed significant pain reduction using VR. Additionally, VR improved patients' experience of WC. No clear effect was found on other outcomes including anxiety, opioid usage and physiological and behavioural responses. VR shows promise in reducing acute pain and enhancing patients' experience of WC. The observed variations in the effects of VR at group and individual levels indicate the need for a personalised treatment plan by selecting the right VR for the right patient given at the right time.

Published
2023

28. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geoerg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Balasescu, Adrian, Barnett, Ross, Bartosiewicz, Laszlo, Baryshnikov, Gennady, Bonsall, Clive, Boric, Dusan, Boroneant, Adina, Bulatovic, Jelena, Cakirlar, Canan, Carretero, Jose-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitrascu, Valentin, du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Ozdogan, Asli, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Gotherstrom, Anders, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophelie, Lesur, Josephine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Joerg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanovic, Darko, Ricaut, Francois-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasic, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jorg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, Larson, Greger, Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geoerg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Balasescu, Adrian, Barnett, Ross, Bartosiewicz, Laszlo, Baryshnikov, Gennady, Bonsall, Clive, Boric, Dusan, Boroneant, Adina, Bulatovic, Jelena, Cakirlar, Canan, Carretero, Jose-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitrascu, Valentin, du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Ozdogan, Asli, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Gotherstrom, Anders, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophelie, Lesur, Josephine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Joerg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanovic, Darko, Ricaut, Francois-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasic, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jorg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Published
2019

29. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geoerg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Balasescu, Adrian, Barnett, Ross, Bartosiewicz, Laszlo, Baryshnikov, Gennady, Bonsall, Clive, Boric, Dusan, Boroneant, Adina, Bulatovic, Jelena, Cakirlar, Canan, Carretero, Jose-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitrascu, Valentin, du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Ozdogan, Asli, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Gotherstrom, Anders, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophelie, Lesur, Josephine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Joerg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanovic, Darko, Ricaut, Francois-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasic, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jorg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, Larson, Greger, Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geoerg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Balasescu, Adrian, Barnett, Ross, Bartosiewicz, Laszlo, Baryshnikov, Gennady, Bonsall, Clive, Boric, Dusan, Boroneant, Adina, Bulatovic, Jelena, Cakirlar, Canan, Carretero, Jose-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitrascu, Valentin, du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Ozdogan, Asli, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Gotherstrom, Anders, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophelie, Lesur, Josephine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Joerg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanovic, Darko, Ricaut, Francois-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasic, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jorg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Published
2019

30. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geoerg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Balasescu, Adrian, Barnett, Ross, Bartosiewicz, Laszlo, Baryshnikov, Gennady, Bonsall, Clive, Boric, Dusan, Boroneant, Adina, Bulatovic, Jelena, Cakirlar, Canan, Carretero, Jose-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitrascu, Valentin, du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Ozdogan, Asli, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Gotherstrom, Anders, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophelie, Lesur, Josephine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Joerg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanovic, Darko, Ricaut, Francois-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasic, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jorg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, Larson, Greger, Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geoerg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Balasescu, Adrian, Barnett, Ross, Bartosiewicz, Laszlo, Baryshnikov, Gennady, Bonsall, Clive, Boric, Dusan, Boroneant, Adina, Bulatovic, Jelena, Cakirlar, Canan, Carretero, Jose-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitrascu, Valentin, du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Ozdogan, Asli, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Gotherstrom, Anders, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophelie, Lesur, Josephine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Joerg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanovic, Darko, Ricaut, Francois-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasic, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jorg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Published
2019

31. Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

Author

Smitz, Nathalie, Van Hooft, Pim, Heller, Rasmus, Cornélis, Daniel, Chardonnet, Philippe, Kraus, Robert, Greyling, Ben, Crooijmans, Richard, Groenen, Martien, Michaux, Johan, Smitz, Nathalie, Van Hooft, Pim, Heller, Rasmus, Cornélis, Daniel, Chardonnet, Philippe, Kraus, Robert, Greyling, Ben, Crooijmans, Richard, Groenen, Martien, and Michaux, Johan

Published
2016

32. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

Author

Huang, Yinhua, Li, Yingrui, Burt, David W., Chen, Hualan, Zhang, Yong, Qian, Wubin, Kim, Heebal, Gan, Shangquan, Zhao, Yiqiang, Li, Jianwen, Yi, Kang, Feng, Huapeng, Zhu, Pengyang, Li, Bo, Liu, Qiuyue, Fairley, Suan, Magor, Katharine E., Du, Zhenlin, Hu, Xiaoxiang, Goodman, Laurie, Tafer, Hakim, Vignal, Alain, Lee, Taeheon, Kim, Kyu-Won, Sheng, Zheya, An, Yang, Searle, Steve, Herrero, Javier, Groenen, Martien A. M., Crooijmans, Richard P. M. A., Faraut, Thomas, Cai, Qingle, Webster, Robert G., Aldridge, Jerry R., Warren, Wesley C., Bartschat, Sebastian, Kehr, Stephanie, Marz, Manja, Stadler, Peter F., Smith, Jacqueline, Kraus, Robert H. S., Zhao, Yaofeng, Ren, Liming, Fei, Jing, Morisson, Mireille, Kaiser, Pete, Griffin, Darren K., Rao, Man, Pitel, Frederique, Wang, Jun, Li, Ning, Huang, Yinhua, Li, Yingrui, Burt, David W., Chen, Hualan, Zhang, Yong, Qian, Wubin, Kim, Heebal, Gan, Shangquan, Zhao, Yiqiang, Li, Jianwen, Yi, Kang, Feng, Huapeng, Zhu, Pengyang, Li, Bo, Liu, Qiuyue, Fairley, Suan, Magor, Katharine E., Du, Zhenlin, Hu, Xiaoxiang, Goodman, Laurie, Tafer, Hakim, Vignal, Alain, Lee, Taeheon, Kim, Kyu-Won, Sheng, Zheya, An, Yang, Searle, Steve, Herrero, Javier, Groenen, Martien A. M., Crooijmans, Richard P. M. A., Faraut, Thomas, Cai, Qingle, Webster, Robert G., Aldridge, Jerry R., Warren, Wesley C., Bartschat, Sebastian, Kehr, Stephanie, Marz, Manja, Stadler, Peter F., Smith, Jacqueline, Kraus, Robert H. S., Zhao, Yaofeng, Ren, Liming, Fei, Jing, Morisson, Mireille, Kaiser, Pete, Griffin, Darren K., Rao, Man, Pitel, Frederique, Wang, Jun, and Li, Ning

Published
2013

33. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

Author

Huang, Yinhua, Li, Yingrui, Burt, David W., Chen, Hualan, Zhang, Yong, Qian, Wubin, Kim, Heebal, Gan, Shangquan, Zhao, Yiqiang, Li, Jianwen, Yi, Kang, Feng, Huapeng, Zhu, Pengyang, Li, Bo, Liu, Qiuyue, Fairley, Suan, Magor, Katharine E., Du, Zhenlin, Hu, Xiaoxiang, Goodman, Laurie, Tafer, Hakim, Vignal, Alain, Lee, Taeheon, Kim, Kyu-Won, Sheng, Zheya, An, Yang, Searle, Steve, Herrero, Javier, Groenen, Martien A. M., Crooijmans, Richard P. M. A., Faraut, Thomas, Cai, Qingle, Webster, Robert G., Aldridge, Jerry R., Warren, Wesley C., Bartschat, Sebastian, Kehr, Stephanie, Marz, Manja, Stadler, Peter F., Smith, Jacqueline, Kraus, Robert H. S., Zhao, Yaofeng, Ren, Liming, Fei, Jing, Morisson, Mireille, Kaiser, Pete, Griffin, Darren K., Rao, Man, Pitel, Frederique, Wang, Jun, Li, Ning, Huang, Yinhua, Li, Yingrui, Burt, David W., Chen, Hualan, Zhang, Yong, Qian, Wubin, Kim, Heebal, Gan, Shangquan, Zhao, Yiqiang, Li, Jianwen, Yi, Kang, Feng, Huapeng, Zhu, Pengyang, Li, Bo, Liu, Qiuyue, Fairley, Suan, Magor, Katharine E., Du, Zhenlin, Hu, Xiaoxiang, Goodman, Laurie, Tafer, Hakim, Vignal, Alain, Lee, Taeheon, Kim, Kyu-Won, Sheng, Zheya, An, Yang, Searle, Steve, Herrero, Javier, Groenen, Martien A. M., Crooijmans, Richard P. M. A., Faraut, Thomas, Cai, Qingle, Webster, Robert G., Aldridge, Jerry R., Warren, Wesley C., Bartschat, Sebastian, Kehr, Stephanie, Marz, Manja, Stadler, Peter F., Smith, Jacqueline, Kraus, Robert H. S., Zhao, Yaofeng, Ren, Liming, Fei, Jing, Morisson, Mireille, Kaiser, Pete, Griffin, Darren K., Rao, Man, Pitel, Frederique, Wang, Jun, and Li, Ning

Published
2013

34. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

Author

Huang, Yinhua, Li, Yingrui, Burt, David W., Chen, Hualan, Zhang, Yong, Qian, Wubin, Kim, Heebal, Gan, Shangquan, Zhao, Yiqiang, Li, Jianwen, Yi, Kang, Feng, Huapeng, Zhu, Pengyang, Li, Bo, Liu, Qiuyue, Fairley, Suan, Magor, Katharine E., Du, Zhenlin, Hu, Xiaoxiang, Goodman, Laurie, Tafer, Hakim, Vignal, Alain, Lee, Taeheon, Kim, Kyu-Won, Sheng, Zheya, An, Yang, Searle, Steve, Herrero, Javier, Groenen, Martien A. M., Crooijmans, Richard P. M. A., Faraut, Thomas, Cai, Qingle, Webster, Robert G., Aldridge, Jerry R., Warren, Wesley C., Bartschat, Sebastian, Kehr, Stephanie, Marz, Manja, Stadler, Peter F., Smith, Jacqueline, Kraus, Robert H. S., Zhao, Yaofeng, Ren, Liming, Fei, Jing, Morisson, Mireille, Kaiser, Pete, Griffin, Darren K., Rao, Man, Pitel, Frederique, Wang, Jun, Li, Ning, Huang, Yinhua, Li, Yingrui, Burt, David W., Chen, Hualan, Zhang, Yong, Qian, Wubin, Kim, Heebal, Gan, Shangquan, Zhao, Yiqiang, Li, Jianwen, Yi, Kang, Feng, Huapeng, Zhu, Pengyang, Li, Bo, Liu, Qiuyue, Fairley, Suan, Magor, Katharine E., Du, Zhenlin, Hu, Xiaoxiang, Goodman, Laurie, Tafer, Hakim, Vignal, Alain, Lee, Taeheon, Kim, Kyu-Won, Sheng, Zheya, An, Yang, Searle, Steve, Herrero, Javier, Groenen, Martien A. M., Crooijmans, Richard P. M. A., Faraut, Thomas, Cai, Qingle, Webster, Robert G., Aldridge, Jerry R., Warren, Wesley C., Bartschat, Sebastian, Kehr, Stephanie, Marz, Manja, Stadler, Peter F., Smith, Jacqueline, Kraus, Robert H. S., Zhao, Yaofeng, Ren, Liming, Fei, Jing, Morisson, Mireille, Kaiser, Pete, Griffin, Darren K., Rao, Man, Pitel, Frederique, Wang, Jun, and Li, Ning

Published
2013

35. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

Author

Huang, Yinhua, Li, Yingrui, Burt, David W., Chen, Hualan, Zhang, Yong, Qian, Wubin, Kim, Heebal, Gan, Shangquan, Zhao, Yiqiang, Li, Jianwen, Yi, Kang, Feng, Huapeng, Zhu, Pengyang, Li, Bo, Liu, Qiuyue, Fairley, Suan, Magor, Katharine E., Du, Zhenlin, Hu, Xiaoxiang, Goodman, Laurie, Tafer, Hakim, Vignal, Alain, Lee, Taeheon, Kim, Kyu-Won, Sheng, Zheya, An, Yang, Searle, Steve, Herrero, Javier, Groenen, Martien A. M., Crooijmans, Richard P. M. A., Faraut, Thomas, Cai, Qingle, Webster, Robert G., Aldridge, Jerry R., Warren, Wesley C., Bartschat, Sebastian, Kehr, Stephanie, Marz, Manja, Stadler, Peter F., Smith, Jacqueline, Kraus, Robert H. S., Zhao, Yaofeng, Ren, Liming, Fei, Jing, Morisson, Mireille, Kaiser, Pete, Griffin, Darren K., Rao, Man, Pitel, Frederique, Wang, Jun, Li, Ning, Huang, Yinhua, Li, Yingrui, Burt, David W., Chen, Hualan, Zhang, Yong, Qian, Wubin, Kim, Heebal, Gan, Shangquan, Zhao, Yiqiang, Li, Jianwen, Yi, Kang, Feng, Huapeng, Zhu, Pengyang, Li, Bo, Liu, Qiuyue, Fairley, Suan, Magor, Katharine E., Du, Zhenlin, Hu, Xiaoxiang, Goodman, Laurie, Tafer, Hakim, Vignal, Alain, Lee, Taeheon, Kim, Kyu-Won, Sheng, Zheya, An, Yang, Searle, Steve, Herrero, Javier, Groenen, Martien A. M., Crooijmans, Richard P. M. A., Faraut, Thomas, Cai, Qingle, Webster, Robert G., Aldridge, Jerry R., Warren, Wesley C., Bartschat, Sebastian, Kehr, Stephanie, Marz, Manja, Stadler, Peter F., Smith, Jacqueline, Kraus, Robert H. S., Zhao, Yaofeng, Ren, Liming, Fei, Jing, Morisson, Mireille, Kaiser, Pete, Griffin, Darren K., Rao, Man, Pitel, Frederique, Wang, Jun, and Li, Ning

Published
2013

36. Analyses of pig genomes provide insight into porcine demography and evolution

Author

Groenen, Martien A, Archibald, Alan L., Uenishi, Hirohide, Tuggle, Christopher K., Takeuchi, Yasuhiro, Rothschild, Max F., Rogel-Gaillard, Claire, Park, Chankyu, Milan, Dennis, Megens, Hendrik-Jan, Li, Shengting, Larkin, Denis M., Kim, Heebal, Frantz, Laurent A. F., Caccamo, Mario, Ahn, Hyeonju, Aken, Bronwen L., Anselmo, Anna, Anthon, Christian, Auvil, Loretta, Badaoui, Bouabid, Beattie, Craig W., Bendixen, Christian, Berman, Daniel, Blecha, Frank, Blomberg, Jonas, Bolund, Lars, Bosse, Mirte, Botti, Sara, Zhan, Bujie, Bystrom, Megan, Capitanu, Boris, Carvalho-Silva, Denise, Chardon, Patrick, Chen, Celine, Cheng, Ryan, Choi, Sang-Haeng, Chow, William, Clark, Richard C., Clee, Christopher, Crooijmans, Richard P. M. A., Dawson, Harry D., Dehais, Patrice, Sapio, Fioravante De, Dibbits, Bert, Drou, Nizar, Du, Zhi-Qiang, Eversole, Kellye, Fadista, João, Fairley, Susan, Faraut, Thomas, Faulkner, Geoffrey J., Fowler, Katie E., Fredholm, Merete, Fritz, Eric, Gilbert, James G. R., Giuffra, Elisabetta, Gorodkin, Jan, Griffin, Darren K., Harrow, Jennifer L., Hayward, Alexander, Howe, Kerstin, Hu, Zhi-Liang, Humphray, Sean J., Hunt, Toby, Jensen, Henrik Hornshøj, Jeon, Jin-Tae, Jern, Patric, Jones, Matthew, Jurka, Jerzy, Kanamori, Hiroyuki, Kapetanovic, Ronan, Kim, Jaebum, Kim, Jae-Hwan, Kim, Kyu-Won, Kim, Tai-Hun, Larson, Greger, Lee, Kyooyeol, Lee, Kyung-Tai, Leggett, Richard, Lewin, Harris A., Li, Yingrui, Liu, Wansheng, Loveland, Jane E., Lu, Yao, Lunney, Joan K., Ma, Jian, Madsen, Ole, Mann, Katherine, Matthews, Lucy, McLaren, Stuart, Morozumi, Takeya, Murtaugh, Michael P., Narayan, Jitendra, Nguyen, Dinh Truong, Ni, Peixiang, Oh, Song-Jung, Onteru, Suneel, Panitz, Frank, Park, Eung-Woo, Park, Hong-Seog, Pascal, Geraldine, Paudel, Yogesh, Perez-Enciso, Miguel, Ramirez-Gonzalez, Ricardo, Reecy, James M., Rodriguez-Zas, Sandra, Rohrer, Gary A., Rund, Lauretta, Sang, Yongming, Schachtschneider, Kyle, Schraiber, Joshua G., Schwartz, John, Scobie, Linda, Scott, Carol, Searle, Stephen, Servin, Bertrand, Southey, Bruce R., Sperber, Goran, Stadler, Peter, Sweedler, Jonathan V., Tafer, Hakim, Thomsen, Bo, Wali, Rashmi, Wang, Jian, Wang, Jun, White, Simon, Xu, Xun, Yerke, Martine, Zhang, Guojie, Zhang, Jianguo, Zhang, Jie, Zhao, Shuhong, Rogers, Jane, Churcher, Carol, Schook, Lawrence B., Groenen, Martien A, Archibald, Alan L., Uenishi, Hirohide, Tuggle, Christopher K., Takeuchi, Yasuhiro, Rothschild, Max F., Rogel-Gaillard, Claire, Park, Chankyu, Milan, Dennis, Megens, Hendrik-Jan, Li, Shengting, Larkin, Denis M., Kim, Heebal, Frantz, Laurent A. F., Caccamo, Mario, Ahn, Hyeonju, Aken, Bronwen L., Anselmo, Anna, Anthon, Christian, Auvil, Loretta, Badaoui, Bouabid, Beattie, Craig W., Bendixen, Christian, Berman, Daniel, Blecha, Frank, Blomberg, Jonas, Bolund, Lars, Bosse, Mirte, Botti, Sara, Zhan, Bujie, Bystrom, Megan, Capitanu, Boris, Carvalho-Silva, Denise, Chardon, Patrick, Chen, Celine, Cheng, Ryan, Choi, Sang-Haeng, Chow, William, Clark, Richard C., Clee, Christopher, Crooijmans, Richard P. M. A., Dawson, Harry D., Dehais, Patrice, Sapio, Fioravante De, Dibbits, Bert, Drou, Nizar, Du, Zhi-Qiang, Eversole, Kellye, Fadista, João, Fairley, Susan, Faraut, Thomas, Faulkner, Geoffrey J., Fowler, Katie E., Fredholm, Merete, Fritz, Eric, Gilbert, James G. R., Giuffra, Elisabetta, Gorodkin, Jan, Griffin, Darren K., Harrow, Jennifer L., Hayward, Alexander, Howe, Kerstin, Hu, Zhi-Liang, Humphray, Sean J., Hunt, Toby, Jensen, Henrik Hornshøj, Jeon, Jin-Tae, Jern, Patric, Jones, Matthew, Jurka, Jerzy, Kanamori, Hiroyuki, Kapetanovic, Ronan, Kim, Jaebum, Kim, Jae-Hwan, Kim, Kyu-Won, Kim, Tai-Hun, Larson, Greger, Lee, Kyooyeol, Lee, Kyung-Tai, Leggett, Richard, Lewin, Harris A., Li, Yingrui, Liu, Wansheng, Loveland, Jane E., Lu, Yao, Lunney, Joan K., Ma, Jian, Madsen, Ole, Mann, Katherine, Matthews, Lucy, McLaren, Stuart, Morozumi, Takeya, Murtaugh, Michael P., Narayan, Jitendra, Nguyen, Dinh Truong, Ni, Peixiang, Oh, Song-Jung, Onteru, Suneel, Panitz, Frank, Park, Eung-Woo, Park, Hong-Seog, Pascal, Geraldine, Paudel, Yogesh, Perez-Enciso, Miguel, Ramirez-Gonzalez, Ricardo, Reecy, James M., Rodriguez-Zas, Sandra, Rohrer, Gary A., Rund, Lauretta, Sang, Yongming, Schachtschneider, Kyle, Schraiber, Joshua G., Schwartz, John, Scobie, Linda, Scott, Carol, Searle, Stephen, Servin, Bertrand, Southey, Bruce R., Sperber, Goran, Stadler, Peter, Sweedler, Jonathan V., Tafer, Hakim, Thomsen, Bo, Wali, Rashmi, Wang, Jian, Wang, Jun, White, Simon, Xu, Xun, Yerke, Martine, Zhang, Guojie, Zhang, Jianguo, Zhang, Jie, Zhao, Shuhong, Rogers, Jane, Churcher, Carol, and Schook, Lawrence B.

Published
2012

37. Analyses of pig genomes provide insight into porcine demography and evolution

Author

Groenen, Martien A, Archibald, Alan L., Uenishi, Hirohide, Tuggle, Christopher K., Takeuchi, Yasuhiro, Rothschild, Max F., Rogel-Gaillard, Claire, Park, Chankyu, Milan, Dennis, Megens, Hendrik-Jan, Li, Shengting, Larkin, Denis M., Kim, Heebal, Frantz, Laurent A. F., Caccamo, Mario, Ahn, Hyeonju, Aken, Bronwen L., Anselmo, Anna, Anthon, Christian, Auvil, Loretta, Badaoui, Bouabid, Beattie, Craig W., Bendixen, Christian, Berman, Daniel, Blecha, Frank, Blomberg, Jonas, Bolund, Lars, Bosse, Mirte, Botti, Sara, Zhan, Bujie, Bystrom, Megan, Capitanu, Boris, Carvalho-Silva, Denise, Chardon, Patrick, Chen, Celine, Cheng, Ryan, Choi, Sang-Haeng, Chow, William, Clark, Richard C., Clee, Christopher, Crooijmans, Richard P. M. A., Dawson, Harry D., Dehais, Patrice, Sapio, Fioravante De, Dibbits, Bert, Drou, Nizar, Du, Zhi-Qiang, Eversole, Kellye, Fadista, João, Fairley, Susan, Faraut, Thomas, Faulkner, Geoffrey J., Fowler, Katie E., Fredholm, Merete, Fritz, Eric, Gilbert, James G. R., Giuffra, Elisabetta, Gorodkin, Jan, Griffin, Darren K., Harrow, Jennifer L., Hayward, Alexander, Howe, Kerstin, Hu, Zhi-Liang, Humphray, Sean J., Hunt, Toby, Jensen, Henrik Hornshøj, Jeon, Jin-Tae, Jern, Patric, Jones, Matthew, Jurka, Jerzy, Kanamori, Hiroyuki, Kapetanovic, Ronan, Kim, Jaebum, Kim, Jae-Hwan, Kim, Kyu-Won, Kim, Tai-Hun, Larson, Greger, Lee, Kyooyeol, Lee, Kyung-Tai, Leggett, Richard, Lewin, Harris A., Li, Yingrui, Liu, Wansheng, Loveland, Jane E., Lu, Yao, Lunney, Joan K., Ma, Jian, Madsen, Ole, Mann, Katherine, Matthews, Lucy, McLaren, Stuart, Morozumi, Takeya, Murtaugh, Michael P., Narayan, Jitendra, Nguyen, Dinh Truong, Ni, Peixiang, Oh, Song-Jung, Onteru, Suneel, Panitz, Frank, Park, Eung-Woo, Park, Hong-Seog, Pascal, Geraldine, Paudel, Yogesh, Perez-Enciso, Miguel, Ramirez-Gonzalez, Ricardo, Reecy, James M., Rodriguez-Zas, Sandra, Rohrer, Gary A., Rund, Lauretta, Sang, Yongming, Schachtschneider, Kyle, Schraiber, Joshua G., Schwartz, John, Scobie, Linda, Scott, Carol, Searle, Stephen, Servin, Bertrand, Southey, Bruce R., Sperber, Goran, Stadler, Peter, Sweedler, Jonathan V., Tafer, Hakim, Thomsen, Bo, Wali, Rashmi, Wang, Jian, Wang, Jun, White, Simon, Xu, Xun, Yerke, Martine, Zhang, Guojie, Zhang, Jianguo, Zhang, Jie, Zhao, Shuhong, Rogers, Jane, Churcher, Carol, Schook, Lawrence B., Groenen, Martien A, Archibald, Alan L., Uenishi, Hirohide, Tuggle, Christopher K., Takeuchi, Yasuhiro, Rothschild, Max F., Rogel-Gaillard, Claire, Park, Chankyu, Milan, Dennis, Megens, Hendrik-Jan, Li, Shengting, Larkin, Denis M., Kim, Heebal, Frantz, Laurent A. F., Caccamo, Mario, Ahn, Hyeonju, Aken, Bronwen L., Anselmo, Anna, Anthon, Christian, Auvil, Loretta, Badaoui, Bouabid, Beattie, Craig W., Bendixen, Christian, Berman, Daniel, Blecha, Frank, Blomberg, Jonas, Bolund, Lars, Bosse, Mirte, Botti, Sara, Zhan, Bujie, Bystrom, Megan, Capitanu, Boris, Carvalho-Silva, Denise, Chardon, Patrick, Chen, Celine, Cheng, Ryan, Choi, Sang-Haeng, Chow, William, Clark, Richard C., Clee, Christopher, Crooijmans, Richard P. M. A., Dawson, Harry D., Dehais, Patrice, Sapio, Fioravante De, Dibbits, Bert, Drou, Nizar, Du, Zhi-Qiang, Eversole, Kellye, Fadista, João, Fairley, Susan, Faraut, Thomas, Faulkner, Geoffrey J., Fowler, Katie E., Fredholm, Merete, Fritz, Eric, Gilbert, James G. R., Giuffra, Elisabetta, Gorodkin, Jan, Griffin, Darren K., Harrow, Jennifer L., Hayward, Alexander, Howe, Kerstin, Hu, Zhi-Liang, Humphray, Sean J., Hunt, Toby, Jensen, Henrik Hornshøj, Jeon, Jin-Tae, Jern, Patric, Jones, Matthew, Jurka, Jerzy, Kanamori, Hiroyuki, Kapetanovic, Ronan, Kim, Jaebum, Kim, Jae-Hwan, Kim, Kyu-Won, Kim, Tai-Hun, Larson, Greger, Lee, Kyooyeol, Lee, Kyung-Tai, Leggett, Richard, Lewin, Harris A., Li, Yingrui, Liu, Wansheng, Loveland, Jane E., Lu, Yao, Lunney, Joan K., Ma, Jian, Madsen, Ole, Mann, Katherine, Matthews, Lucy, McLaren, Stuart, Morozumi, Takeya, Murtaugh, Michael P., Narayan, Jitendra, Nguyen, Dinh Truong, Ni, Peixiang, Oh, Song-Jung, Onteru, Suneel, Panitz, Frank, Park, Eung-Woo, Park, Hong-Seog, Pascal, Geraldine, Paudel, Yogesh, Perez-Enciso, Miguel, Ramirez-Gonzalez, Ricardo, Reecy, James M., Rodriguez-Zas, Sandra, Rohrer, Gary A., Rund, Lauretta, Sang, Yongming, Schachtschneider, Kyle, Schraiber, Joshua G., Schwartz, John, Scobie, Linda, Scott, Carol, Searle, Stephen, Servin, Bertrand, Southey, Bruce R., Sperber, Goran, Stadler, Peter, Sweedler, Jonathan V., Tafer, Hakim, Thomsen, Bo, Wali, Rashmi, Wang, Jian, Wang, Jun, White, Simon, Xu, Xun, Yerke, Martine, Zhang, Guojie, Zhang, Jianguo, Zhang, Jie, Zhao, Shuhong, Rogers, Jane, Churcher, Carol, and Schook, Lawrence B.

Published
2012

40. Familial follicular cell thyroid carcinomas in a large number of Dutch German Longhaired Pointers

Author

Veterinair Pathologisch Diagnostisch Cnt, VPDC pathologie, dPB CR, VP pathologie, Yu, Yun, Krupa, Adriana, Keesler, Rebekah I, Grinwis, Guy C M, de Ruijsscher, Mariska, de Vos, Johan, Groenen, Martien A M, Crooijmans, Richard P M A, Veterinair Pathologisch Diagnostisch Cnt, VPDC pathologie, dPB CR, VP pathologie, Yu, Yun, Krupa, Adriana, Keesler, Rebekah I, Grinwis, Guy C M, de Ruijsscher, Mariska, de Vos, Johan, Groenen, Martien A M, and Crooijmans, Richard P M A

Published
2022

42. Ancient globetrotters—connectivity and putative native ranges of two cosmopolitan biofouling amphipods

Author

Beermann, Jan, Hall-Mullen, Allison K., Havermans, Charlotte, Coolen, Joop WP, Crooijmans, Richard PMA, Dibbits, Bert, Held, Christoph, Desiderato, Andrea, Beermann, Jan, Hall-Mullen, Allison K., Havermans, Charlotte, Coolen, Joop WP, Crooijmans, Richard PMA, Dibbits, Bert, Held, Christoph, and Desiderato, Andrea

Abstract

The geographic distributions of some coastal marine species have appeared as cosmopolitan ever since they were first scientifically documented. In particular, for many benthic species that are associated with anthropogenic substrata, there is much speculation as to whether or not their broad distributions can be explained by natural mechanisms of dispersal. Here, we focused on two congeneric coastal crustaceans with cosmopolitan distributions—the tube-dwelling amphipods Jassa marmorata and Jassa slatteryi. Both species are common elements of marine biofouling on nearly all kinds of artificial hard substrata in temperate to warm seas. We hypothesized that the two species’ modern occurrences across the oceans are the result of human shipping activities that started centuries ago. Mitochondrial DNA sequences of the CO1 fragment of specimens from distinct marine regions around the world were analysed, evaluating genetic structure and migration models and making inferences on putative native ranges of the two Jassa species. Populations of both species exhibited considerable genetic diversity with differing levels of geographic structure. For both species, at least two dominant haplotypes were shared among several geographic populations. Rapid demographic expansion and high migration rates between geographically distant regions support a scenario of ongoing dispersal all over the world. Our findings indicate that the likely former native range of J. marmorata is the Northwest Atlantic, whereas the likely former native range of J. slatteryi is the Northern Pacific region. As corroborated by the genetic connectivity between populations, shipping still appears to be the more successful vector of the two species’ dispersal when compared to natural mechanisms. Historical invasion events that likely started centuries ago, along with current ongoing dispersal, confirm these species’ identities as true “neocosmopolitans”.

Published
2020

43. Marine stepping‐stones: Connectivity of Mytilus edulis populations between offshore energy installations

Author

Coolen, Joop W. P., Boon, Arjen R., Crooijmans, Richard, Pelt, Hilde, Kleissen, Frank, Gerla, Daan, Beermann, Jan, Birchenough, Silvana N. R., Becking, Leontine E., Luttikhuizen, Pieternella C., Coolen, Joop W. P., Boon, Arjen R., Crooijmans, Richard, Pelt, Hilde, Kleissen, Frank, Gerla, Daan, Beermann, Jan, Birchenough, Silvana N. R., Becking, Leontine E., and Luttikhuizen, Pieternella C.

Abstract

Recent papers have suggested that epifaunal organisms use artificial structures as stepping‐stones to spread to areas that are too distant to reach in a single generation. With thousands of artificial structures present in the North Sea, we test the hypothesis that these structures are connected by water currents and act as an interconnected reef. Population genetic structure of the blue mussel, Mytilus edulis, was expected to follow a pattern predicted by a particle tracking model (PTM). Correlation between population genetic differentiation, based on microsatellite markers, and particle exchange was tested. Specimens of M. edulis were found at each location, although the PTM indicated that locations >85 km offshore were isolated from coastal subpopulations. The fixation coefficient FST correlated with the number of arrivals in the PTM. However, the number of effective migrants per generation as inferred from coalescent simulations did not show a strong correlation with the arriving particles. Isolation by distance analysis showed no increase in isolation with increasing distance and we did not find clear structure among the populations. The marine stepping‐stone effect is obviously important for the distribution of M. edulis in the North Sea and it may influence ecologically comparable species in a similar way. In the absence of artificial shallow hard substrates, M. edulis would be unlikely to survive in offshore North Sea waters.

Published
2020

44. Ancient globetrotters—connectivity and putative native ranges of two cosmopolitan biofouling amphipods

Author

Beermann, Jan, Hall-Mullen, Allison K., Havermans, Charlotte, Coolen, Joop WP, Crooijmans, Richard PMA, Dibbits, Bert, Held, Christoph, Desiderato, Andrea, Beermann, Jan, Hall-Mullen, Allison K., Havermans, Charlotte, Coolen, Joop WP, Crooijmans, Richard PMA, Dibbits, Bert, Held, Christoph, and Desiderato, Andrea

Abstract

The geographic distributions of some coastal marine species have appeared as cosmopolitan ever since they were first scientifically documented. In particular, for many benthic species that are associated with anthropogenic substrata, there is much speculation as to whether or not their broad distributions can be explained by natural mechanisms of dispersal. Here, we focused on two congeneric coastal crustaceans with cosmopolitan distributions—the tube-dwelling amphipods Jassa marmorata and Jassa slatteryi. Both species are common elements of marine biofouling on nearly all kinds of artificial hard substrata in temperate to warm seas. We hypothesized that the two species’ modern occurrences across the oceans are the result of human shipping activities that started centuries ago. Mitochondrial DNA sequences of the CO1 fragment of specimens from distinct marine regions around the world were analysed, evaluating genetic structure and migration models and making inferences on putative native ranges of the two Jassa species. Populations of both species exhibited considerable genetic diversity with differing levels of geographic structure. For both species, at least two dominant haplotypes were shared among several geographic populations. Rapid demographic expansion and high migration rates between geographically distant regions support a scenario of ongoing dispersal all over the world. Our findings indicate that the likely former native range of J. marmorata is the Northwest Atlantic, whereas the likely former native range of J. slatteryi is the Northern Pacific region. As corroborated by the genetic connectivity between populations, shipping still appears to be the more successful vector of the two species’ dispersal when compared to natural mechanisms. Historical invasion events that likely started centuries ago, along with current ongoing dispersal, confirm these species’ identities as true “neocosmopolitans”.

Published
2020

45. Marine stepping‐stones: Connectivity of Mytilus edulis populations between offshore energy installations

Author

Coolen, Joop W. P., Boon, Arjen R., Crooijmans, Richard, Pelt, Hilde, Kleissen, Frank, Gerla, Daan, Beermann, Jan, Birchenough, Silvana N. R., Becking, Leontine E., Luttikhuizen, Pieternella C., Coolen, Joop W. P., Boon, Arjen R., Crooijmans, Richard, Pelt, Hilde, Kleissen, Frank, Gerla, Daan, Beermann, Jan, Birchenough, Silvana N. R., Becking, Leontine E., and Luttikhuizen, Pieternella C.

Abstract

Recent papers have suggested that epifaunal organisms use artificial structures as stepping‐stones to spread to areas that are too distant to reach in a single generation. With thousands of artificial structures present in the North Sea, we test the hypothesis that these structures are connected by water currents and act as an interconnected reef. Population genetic structure of the blue mussel, Mytilus edulis, was expected to follow a pattern predicted by a particle tracking model (PTM). Correlation between population genetic differentiation, based on microsatellite markers, and particle exchange was tested. Specimens of M. edulis were found at each location, although the PTM indicated that locations >85 km offshore were isolated from coastal subpopulations. The fixation coefficient FST correlated with the number of arrivals in the PTM. However, the number of effective migrants per generation as inferred from coalescent simulations did not show a strong correlation with the arriving particles. Isolation by distance analysis showed no increase in isolation with increasing distance and we did not find clear structure among the populations. The marine stepping‐stone effect is obviously important for the distribution of M. edulis in the North Sea and it may influence ecologically comparable species in a similar way. In the absence of artificial shallow hard substrates, M. edulis would be unlikely to survive in offshore North Sea waters.

Published
2020

46. Low genetic connectivity in a fouling amphipod among man-made structures in the southern North Sea

Author

Luttikhuizen, Pieternella C., Beermann, Jan, Crooijmans, Richard P.M.A., Jak, Robbert G., Coolen, Joop W.P., Luttikhuizen, Pieternella C., Beermann, Jan, Crooijmans, Richard P.M.A., Jak, Robbert G., and Coolen, Joop W.P.

Abstract

Offshore environments are increasingly invaded by man-made structures that form hard-substrate habitats for many marine species. Examples include oil and gas platforms, wind turbines and shipwrecks. One of the hypothesised effects is an increased genetic connectivity among natural populations due to new populations growing on man-made structures that may act as stepping stones. However, few data are available on genetic connectivity among organisms inhabiting artificial offshore structures. Here, we present a study on the common fouling amphipod Jassa herdmani from offshore structures in the southern North Sea. Partial mitochondrial DNA sequences (cytochrome-c-oxidase 1, N = 514) were obtained from artificial structures at 17 locations in the southern North Sea, including 13 shipwrecks, 2 wind turbines and 2 platforms. Samples from these locations were significantly differentiated, meaning that strong population structure exists for this species in the area. Levels of intraspecific variation were consistent with stable population sizes. No evidence was found for isolation by distance. Using coalescent simulations, the oldest population subdivision events were estimated to date back to the time the study area was flooded following the Last Glacial Maximum. We therefore tentatively conclude that J. herdmani may have colonised man-made structures from previously existing populations on the sea floor, and that the increase in offshore installations has not led to an overall increase in genetic connectivity for this species.

Published
2019

47. Low genetic connectivity in a fouling amphipod among man-made structures in the southern North Sea

Author

Luttikhuizen, Pieternella C., Beermann, Jan, Crooijmans, Richard P.M.A., Jak, Robbert G., Coolen, Joop W.P., Luttikhuizen, Pieternella C., Beermann, Jan, Crooijmans, Richard P.M.A., Jak, Robbert G., and Coolen, Joop W.P.

Abstract

Offshore environments are increasingly invaded by man-made structures that form hard-substrate habitats for many marine species. Examples include oil and gas platforms, wind turbines and shipwrecks. One of the hypothesised effects is an increased genetic connectivity among natural populations due to new populations growing on man-made structures that may act as stepping stones. However, few data are available on genetic connectivity among organisms inhabiting artificial offshore structures. Here, we present a study on the common fouling amphipod Jassa herdmani from offshore structures in the southern North Sea. Partial mitochondrial DNA sequences (cytochrome-c-oxidase 1, N = 514) were obtained from artificial structures at 17 locations in the southern North Sea, including 13 shipwrecks, 2 wind turbines and 2 platforms. Samples from these locations were significantly differentiated, meaning that strong population structure exists for this species in the area. Levels of intraspecific variation were consistent with stable population sizes. No evidence was found for isolation by distance. Using coalescent simulations, the oldest population subdivision events were estimated to date back to the time the study area was flooded following the Last Glacial Maximum. We therefore tentatively conclude that J. herdmani may have colonised man-made structures from previously existing populations on the sea floor, and that the increase in offshore installations has not led to an overall increase in genetic connectivity for this species.

Published
2019

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