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Research Output 2003 2019

2019

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

Frantz, L. A. F., Haile, J., Lin, A. T., Scheu, A., Geörg, C., Benecke, N., Alexander, M., Linderholm, A., Mullin, V. E., Daly, K. G., Battista, V. M., Price, M., Gron, K. J., Alexandri, P., Arbogast, R. M., Arbuckle, B., Bǎlǎşescu, A., Barnett, R., Bartosiewicz, L., Baryshnikov, G. & 80 othersBonsall, C., Borić, D., Boroneanţ, A., Bulatović, J., Çakirlar, C., Carretero, J. M., Chapman, J., Church, M., Crooijmans, R., De Cupere, B., Detry, C., Dimitrijevic, V., Dumitraşcu, V., Du Plessis, L., Edwards, C. J., Erek, C. M., Erim-Özdoǧan, A., Ervynck, A., Fulgione, D., Gligor, M., Götherström, A., Gourichon, L., Groenen, M. A. M., Helmer, D., Hongo, H., Horwitz, L. K., Irving-Pease, E. K., Lebrasseur, O., Lesur, J., Malone, C., Manaseryan, N., Marciniak, A., Martlew, H., Mashkour, M., Matthews, R., Matuzeviciute, G. M., Maziar, S., Meijaard, E., McGovern, T., Megens, H. J., Miller, R., Mohaseb, A. F., Orschiedt, J., Orton, D., Papathanasiou, A., Pearson, M. P., Pinhasi, R., Radmanović, D., Ricaut, F. X., Richards, M., Sabin, R., Sarti, L., Schier, W., Sheikhi, S., Stephan, E., Stewart, J. R., Stoddart, S., Tagliacozzo, A., Tasić, N., Trantalidou, K., Tresset, A., Valdiosera, C., Van Den Hurk, Y., Van Poucke, S., Vigne, J. D., Yanevich, A., Zeeb-Lanz, A., Triantafyllidis, A., Gilbert, M. T. P., Schibler, J., Rowley-Conwy, P., Zeder, M., Peters, J., Cucchi, T., Bradley, D. G., Dobney, K., Burger, J., Evin, A., Girdland-Flink, L. & Larson, G., 27 Aug 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 35, p. 17231-17238 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Sus scrofa
Swine
Middle East
Mitochondrial DNA
Gene Flow
4 Citations (Scopus)

Deleterious alleles in the context of domestication, inbreeding, and selection

Bosse, M., Megens, H-J., Derks, M. F. L., de Cara, Á. M. R. & Groenen, M. A. M., 2019, In : Evolutionary Applications. 12, 1, p. 6-17

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Inbreeding
domestication
inbreeding
allele
domestic species

Genomic analysis on pygmy hog reveals extensive interbreeding during wild boar expansion

Liu, L., Bosse, M., Megens, H-J., Frantz, L. A. F., Lee, Y. L., Irving-Pease, E. K., Narayan, G., Groenen, M. A. M. & Madsen, O., 1 Dec 2019, In : Nature Communications. 10, 1992.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sus scrofa
genome
admixtures
Genes
expansion
1 Citation (Scopus)

Loss of function mutations in essential genes cause embryonic lethality in pigs

Derks, M. F. L., Gjuvsland, A. B., Bosse, M., Lopes, M. S., van Son, M., Harlizius, B., Tan, B. F., Hamland, H., Grindflek, E., Groenen, M. A. M. & Megens, H. J., 1 Mar 2019, In : Plos Genetics. 15, 3, p. e1008055

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Lethal Genes
Essential Genes
lethal genes
pig
mutation
Open Access
placenta
vertebrate
genome
vertebrates
gene
Open Access
domestication
genetic drift
population bottleneck
population size
genome
2018
Open Access
2 Citations (Scopus)
Open Access
Dwarfism
Chickens
Proteins
Nonsense Codon
Chromosomes, Human, Pair 1

A survey of deleterious variation in highly managed pig populations

Derks, M. F. L., Megens, H. J. W. C., Bosse, M., Lopes, M. S., Harlizius, B. & Groenen, M., 24 Feb 2018, Proceedings of the 11th World Congress on Genetics Applied to Livestock Production. 7 p. 11.522

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademic

Open Access
swine
genome
mutation
lethal genes
inbreeding depression
5 Citations (Scopus)

A survey of functional genomic variation in domesticated chickens

Derks, M. F. L., Megens, H. J., Bosse, M., Visscher, J., Peeters, K., Bink, M. C. A. M., Vereijken, A., Gross, C., De Ridder, D., Reinders, M. J. T. & Groenen, M. A. M., 16 Apr 2018, In : Genetics Selection Evolution. 50, 1, 17.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Chickens
genomics
purebreds
egg
chickens
2 Citations (Scopus)

Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome

Derks, M. F. L., Lopes, M. S., Bosse, M., Madsen, O., Dibbits, B., Harlizius, B., Groenen, M. A. M. & Megens, H. J., 19 Sep 2018, In : Plos Genetics. 14, 9, 20 p., e1007661.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Lethal Genes
lethal genes
allele
Swine
genome

Diversiteit en krielonderzoek: bij de traditionele Nederlandse hoenderrassen

Bortoluzzi, C., Megens, H. J. W. C., Crooijmans, R. P. M. A., de Boer, H., Taks, A., Kroon, P. & Hoving, A. H., Jun 2018, In : Kleindier magazine. 132, 6, p. 11-13

Research output: Contribution to journalArticleProfessional

Diversiteit en krielonderzoek bij de traditionele Nederlandse hoenderrassen

Bortoluzzi, C., Megens, H. J. W. C., Crooijmans, R. P. M. A., de Boer, H., Taks, A., Kroon, P. & Hoving, A. H., 2018, In : Zeldzaam huisdier. 43, 3, p. 20-21

Research output: Contribution to journalArticleProfessional

4 Citations (Scopus)

Early and late feathering in Turkey and chicken: Same gene but different mutations

Derks, M. F. L., Herrero-Medrano, J. M., Crooijmans, R. P. M. A., Vereijken, A., Long, J. A., Megens, H. J. & Groenen, M. A. M., 22 Mar 2018, In : Genetics Selection Evolution. 50, 1, 7.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Prolactin Receptors
Turkey
Chickens
mutation
Turkey (country)
1 Citation (Scopus)

Hotspots of recent hybridization between pigs and wild boars in Europe

Iacolina, L., Pertoldi, C., Amills, M., Kusza, S., Megens, H. J., Bâlteanu, V. A., Bakan, J., Cubric-Curic, V., Oja, R., Saarma, U., Scandura, M., Šprem, N. & Stronen, A. V., 1 Dec 2018, In : Scientific Reports. 8, 1, 17372.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sus scrofa
Swine
Agriculture
Bosnia and Herzegovina
Serbia

Impact of merging different commercial lines on genetic diversity of the Dutch Landrace pigs

Hulsegge, B., Calus, M. P. L., Hoving-Bolink, A. H., Lopes, M. S., Megens, H. J. W. C. & Oldenbroek, J. K., 27 Aug 2018, Book of Abstracts of the 69th Annual Meeting of the European Federation of Animal Science. Wageningen: Wageningen Academic Publishers, p. 554-554 (Book of abstracts; no. 24).

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

4 Citations (Scopus)
Inbreeding
Breeding
Chickens
Demography
Gene Flow
Open Access
selection response
marker-assisted selection
livestock
genome
alleles
6 Citations (Scopus)
Open Access
Livestock
selection response
livestock
marker-assisted selection
Multifactorial Inheritance
Open Access
homozygosity
demography
poultry
genome
2017

A genomic perspective about wild boar demography and evolution

Amills, M., Megens, H. J. W. C., Manunza, A., Ramos-Onsins, S. E. & Groenen, M., 2017, Ecology, Conservation and Management of Wild Pigs and Peccaries. Melletti, M. & Meijaard, E. (eds.). Cambridge University Press, p. 376-387

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

wild boars
demography
genomics
Suidae
Sus
6 Citations (Scopus)

A history of hybrids? Genomic patterns of introgression in the True Geese

Ottenburghs, J., Megens, H. J., Kraus, R. H. S., van Hooft, P., van Wieren, S. E., Crooijmans, R. P. M. A., Ydenberg, R. C., Groenen, M. A. M. & Prins, H. H. T., 2017, In : BMC Evolutionary Biology. 17, 1, 201.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
introgression
geese
genomics
hybridization
history

A survey of deleterious variants in highly managed commercial layer lines

Derks, M. F. L., Megens, H. J. W. C., Bosse, M., Gross, C., Reijnders, M., de Ridder, D. & Groenen, M., 2017.

Research output: Contribution to conferencePosterAcademic

Open Access
10 Citations (Scopus)

A systematic survey to identify lethal recessive variation in highly managed pig populations

Derks, M. F. L., Megens, H. J., Bosse, M., Lopes, M. S., Harlizius, B. & Groenen, M. A. M., 9 Nov 2017, In : BMC Genomics. 18, 1, 858.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Swine
Haplotypes
Population
Mummies
Genome Size
8 Citations (Scopus)

Distribution and functionality of copy number variation across European cattle populations

Upadhyay, M., Da Silva, V. H., Megens, H. J., Visker, M. H. P. W., Ajmone-Marsan, P., Bâlteanu, V. A., Dunner, S., Garcia, J. F., Ginja, C., Kantanen, J., Groenen, M. A. M. & Crooijmans, R. P. M. A., 2017, In : Frontiers in Genetics. 8, 12 p., 108.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Population
Odorant Receptors
Overlapping Genes
Balkan Peninsula
Genes
3 Citations (Scopus)

Fine-mapping of BTA17 using imputed sequences for associations with de novo synthesized fatty acids in bovine milk

Duchemin, S. I., Bovenhuis, H., Megens, H. J., Van Arendonk, J. A. M. & Visker, M. H. P. W., Nov 2017, In : Journal of Dairy Science. 100, 11, p. 9125-9135

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
single nucleotide polymorphism
Single Nucleotide Polymorphism
Milk
Fatty Acids
fatty acids
26 Citations (Scopus)

Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Upadhyay, M. R., Chen, W., Lenstra, J. A., Goderie, C. R. J., MacHugh, D. E., Park, S. D. E., Magee, D. A., Matassino, D., Ciani, F., Megens, H. J., van Arendonk, J. A. M. & Groenen, M. A. M., 2017, In : Heredity. 118, p. 169-176

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Gene Flow
Population
Ancient History
Human Migration
Demography
19 Citations (Scopus)

Genome-wide SNP data unveils the globalization of domesticated pigs

Yang, B., Cui, L., Pérez-Enciso, M., Traspov, A., Crooijmans, R. P. M. A., Zinovieva, N., Schook, L. B., 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, M. A. M. & 2 othersHuang, L. & Megens, H. J., 2017, In : Genetics, Selection, Evolution. 49, 15 p., 71.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Internationality
globalization
pig
single nucleotide polymorphism
Single Nucleotide Polymorphism

Survey of deleterious variants in highly managed commercial layer lines

Derks, M. F. L., Megens, H. J. W. C., Bosse, M., Gross, C., Reijnders, M., de Ridder, D. & Groenen, M., Apr 2017.

Research output: Contribution to conferencePosterAcademic

The impact of genome editing on the introduction of monogenic traits in livestock

Bastiaansen, J. W. M., Bovenhuis, H., Groenen, M., Megens, H. J. W. C. & Mulder, H. A., 2017, Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science. Wageningen: Wageningen Academic Publishers, p. 428-428 (Book of abstracts; no. 23).

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

livestock
genome
marker-assisted selection
selection response
alleles
2016
20 Citations (Scopus)

Accuracy of genomic prediction using imputed whole-genome sequence data in white layers

Heidaritabar, M., Calus, M. P. L., Megens, H. J., Vereijken, A., Groenen, M. A. M. & Bastiaansen, J. W. M., 2016, In : Journal of Animal Breeding and Genetics. p. 167-179 3.

Research output: Contribution to journalArticleAcademicpeer-review

Single Nucleotide Polymorphism
Genome
genomics
genome
prediction
10 Citations (Scopus)

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Ottenburghs, J., Megens, H. J., Kraus, R. H. S., Madsen, O., van Hooft, P., van Wieren, S. E., Crooijmans, R. P. M. A., Ydenberg, R. C., Groenen, M. A. M. & Prins, H. H. T., 2016, In : Molecular Phylogenetics and Evolution. 101, p. 303-313

Research output: Contribution to journalArticleAcademicpeer-review

Geese
geese
History
phylogenetics
history

Crossing species boundaries: the hybrid histories of the true geese

Ottenburghs, J., 2016, Wageningen: Wageningen University. 268 p.

Research output: Thesisinternal PhD, WUAcademic

Open Access
geese
hybridization
history
birds
introgression

Detection of deleterious genomic variation in domesticated animals

Derks, M. F. L., Megens, H. J. W. C., Bosse, M., Gross, C., Reijnders, M., de Ridder, D. & Groenen, M., 19 Apr 2016.

Research output: Contribution to conferencePosterAcademic

Open Access
2 Citations (Scopus)

Distinguishing migration events of different timing for wild boar in the Balkans

Alexandri, P., Megens, H. J. W. C., Crooijmans, R. P. M. A., Groenen, M., Goedbloed, D. J., Herrero Medrano, J. M., Rund, L. A., Schook, L. B., Chatzinikos, E., Triantaphyllidis, C. & Triantafyllidis, A., 1 Oct 2016, In : Journal of Biogeography. 44, 2, p. 259-270

Research output: Contribution to journalArticleAcademicpeer-review

Balkans
wild boars
refugium
refuge habitats
single nucleotide polymorphism
2 Citations (Scopus)

Evidence for adaptation of porcine Toll-like receptors

Darfour-Oduro, K. A., Megens, H. J., Roca, A., Groenen, M. A. M. & Schook, L. B., 2016, In : Immunogenetics. 68, 3, p. 179-189

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sus scrofa
Toll-Like Receptors
Swine
Population
Toll-Like Receptor 8
3 Citations (Scopus)

Evolutionary patterns of Toll-like receptor signaling pathway genes in the Suidae

Darfour-Oduro, K. A., Megens, H. J., Roca, A. L., Groenen, M. A. M. & Schook, L. B., 2016, In : BMC Evolutionary Biology. 16, 1, 11 p., 602.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Suidae
gene
protein
Sus
genes
57 Citations (Scopus)

Evolutionary signals of selection on cognition from the great tit genome and methylome

Laine, V. N., Gossmann, T. I., Schachtschneider, K. M., Garroway, C. J., Madsen, O., Verhoeven, K. J. F., De Jager, V., Megens, H. J., Warren, W. C., Minx, P., Crooijmans, R. P. M. A., Corcoran, P., Adriaensen, F., Belda, E., Bushuev, A., Cichon, M., Charmantier, A., Dingemanse, N., Doligez, B., Eeva, T. & 26 othersErikstad, K. E., Fedorov, S., Hau, M., Hille, S., Hinde, C., Kempenaers, B., Kerimov, A., Krist, M., Mand, R., Matthysen, E., Nager, R., Norte, C., Orell, M., Richner, H., Slagsvold, T., Tilgar, V., Tinbergen, J., Torok, J., Tschirren, B., Yuta, T., Sheldon, B. C., Slate, J., Zeng, K., Van Oers, K., Visser, M. E. & Groenen, M. A. M., 2016, In : Nature Communications. 7, 10474.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
cognition
genome
Cognition
learning
methylation

Extra genetische variatie door krielvarianten van kippenrassen

Klein Swormink, B., Hoving, A. H., Bortoluzzi, C., Megens, H. J. W. C., Crooijmans, R. P. M. A. & Hiemstra, S. J., 1 Jun 2016, In : Boerenvee. p. 4-4

Research output: Contribution to journalArticleProfessional

18 Citations (Scopus)

Genomic diversity and differentiation of a managed island wild boar population

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., 1 Jan 2016, In : Heredity. 116, 1, p. 60-67

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sus scrofa
Islands
Population
Cluster Analysis
Genetic Drift

Predicting deleterious genomic variants for conservation purposes

Bosse, M., Megens, H. J. W. C. & Groenen, M., 2016.

Research output: Contribution to conferenceOtherAcademic

Predicting Impact of Variation in Livestock

Gross, C., Reinders, M., de Ridder, D., Derks, M. F. L., Bosse, M., Megens, H. J. W. C. & Groenen, M., 19 Apr 2016.

Research output: Contribution to conferencePosterAcademic

Predicting the impact of genetic variation in livestock

Gross, C., Reinders, M., de Ridder, D., Derks, M. F. L., Bosse, M., Megens, H. J. W. C. & Groenen, M., 3 Sep 2016.

Research output: Contribution to conferencePosterAcademic

6 Citations (Scopus)

The Use of Genomics in Conservation Management of the Endangered Visayan Warty Pig (Sus cebifrons)

Nuijten, R. J. M., Bosse, M., Crooijmans, R. P. M. A., Madsen, O., Schaftenaar, W., Ryder, O. A., Groenen, M. A. M. & Megens, H. J., 2016, In : International journal of genomcs. 2016, 5613862.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Endangered Species
Genomics
Conservation
Swine
Islands
2015

Accuracy of genomic prediction using whole genome sequence data in White egg layer chickens

Heidaritabar, M., Calus, M. P. L., Megens, H. J. W. C., Groenen, M. A. M., Vereijken, A. & Bastiaansen, J. W. M., 2015, Book of Abstracts 66th Annual Meeting of the EAAP. Wageningen Academic Publishers, Vol. 21. p. 246

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

egg albumen
chickens
genomics
genome
prediction
11 Citations (Scopus)

Adaptive evolution of Toll-like receptors (TLRs) in the family Suidae

Darfour-Oduro, K. A., Megens, H. J. W. C., Roca, A. L., Groenen, M. A. M. & Schook, L. B., 2015, In : PLoS ONE. 10, 4, e0124069.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Suidae
Toll-Like Receptors
Sus
Swine
Genes
11 Citations (Scopus)

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in european commercial pigs

Bosse, M., Soares Lopes, M., Madsen, O., Megens, H. J., Crooijmans, R. P. M. A., Frantz, L. A. F., Harlizius, B., Bastiaansen, J. W. M. & Groenen, M. A. M., 2015, In : Proceedings of the Royal Society. B: Biological Sciences. 282, 1821, 9 p., 20152019.

Research output: Contribution to journalArticleAcademicpeer-review

artificial selection
pig
Haplotypes
haplotypes
Swine
27 Citations (Scopus)

Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors

Paudel, Y., Madsen, O., Megens, H. J. W. C., Frantz, L. A. F., Bosse, M., Crooijmans, R. P. M. A. & Groenen, M. A. M., 2015, In : BMC Genomics. 16, 14 p., 330.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Odorant Receptors
Swine
Gene Flow
Mya
Overlapping Genes