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Research Output 2003 2019

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Article
2019
1 Citation (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
2018
2 Citations (Scopus)
Open Access
Dwarfism
Chickens
Proteins
Nonsense Codon
Chromosomes, Human, Pair 1
3 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
2 Citations (Scopus)
Inbreeding
Breeding
Chickens
Demography
Gene Flow
6 Citations (Scopus)
Open Access
Livestock
selection response
livestock
marker-assisted selection
Multifactorial Inheritance
2017
5 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
9 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
7 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
21 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
17 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
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
1 Citation (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
2 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
55 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

17 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
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
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
76 Citations (Scopus)

Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes

Frantz, L. A. F., Schraiber, J. G., Madsen, O., Megens, H. J. W. C., Cagan, A., Bosse, M., Paudel, Y., Crooijmans, R. P. M. A., Larson, G. & Groenen, M. A. M., 2015, In : Nature Genetics. 47, 10, p. 1141-1148

Research output: Contribution to journalArticleAcademicpeer-review

Sus scrofa
Gene Flow
Genome
Reproductive Isolation
Swine

Genetic diversity of different indigenous chicken ecotypes using highly polymorphic MHC-linked and non-MHC microsatellite markers

Ngeno, K., van der Waaij, E. H., Megens, H. J. W. C., Kahi, A. K., van Arendonk, J. A. M. & Crooijmans, R. P. M. A., 2015, In : Animal Genetic Resources. 56, p. 1-7

Research output: Contribution to journalArticleAcademicpeer-review

major histocompatibility complex
ecotypes
microsatellite repeats
chickens
genetic variation
10 Citations (Scopus)

Hybrid origin of European commercial pigs examined by an in-depth haplotype analysis on chromosome 1

Bosse, M., Madsen, O., Megens, H. J. W. C., Frantz, L. A. F., Paudel, Y., Crooijmans, R. P. M. A. & Groenen, M., 2015, In : Frontiers in Genetics. 5, 442.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Chromosomes, Human, Pair 1
Haplotypes
Swine
Sus scrofa
Genome
8 Citations (Scopus)

Increased Mycoplasma hyopneumoniae Disease Prevalence in Domestic Hybrids Among Free-Living Wild Boar

Goedbloed, D. J., van Hooft, W. F., Lutz, W., Megens, H. J. W. C., van Wieren, S. E., Ydenberg, R. C. & Prins, H. H. T., 2015, In : EcoHealth. 12, 4, p. 571-579

Research output: Contribution to journalArticleAcademicpeer-review

Mycoplasma hyopneumoniae
disease prevalence
Sus scrofa
introgression
pathogen
24 Citations (Scopus)

Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025

Bruford, M. W., Ginja, C., Hoffmann, I. & Megens, H. J., 2015, In : Frontiers in Genetics. 6, OCT, 314.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Domestic Animals
Livestock
Policy Making
Metagenomics
Climate Change
7 Citations (Scopus)

Shallow genetic divergence and species delineations in the endemic Labeobarbus species flock of Lake Tana, Ethiopia

Nagelkerke, L. A. J., Leon-Kloosterziel, K. M., Megens, H. J. W. C., de Graaf, M., Diekmann, O. E. & Sibbing, F. A., 2015, In : Journal of Fish Biology. 87, 5, p. 1191-1208

Research output: Contribution to journalArticleAcademicpeer-review

species flock
endemic species
Ethiopia
flocks
indigenous species
34 Citations (Scopus)
Open Access
Operophtera brumata
Moths
sexual dimorphism
Sex Characteristics
moth
10 Citations (Scopus)

TRES: Identification of Discriminatory and Informative SNPs from Population Genomic Data

Kavakiotis, I., Triantafyllidis, A., Ntelidou, D., Alexandri, P., Megens, H. J. W. C., Crooijmans, R. P. M. A., Groenen, M. A. M., Tsoumakas, G. & Vlahavas, I., 2015, In : Journal of Heredity. 106, 5, p. 672-676

Research output: Contribution to journalArticleAcademicpeer-review

Metagenomics
Single Nucleotide Polymorphism
Software
Population Groups
Datasets
28 Citations (Scopus)

Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

Bosse, M., Megens, H. J. W. C., Madsen, O., Crooijmans, R. P. M. A., Ryder, O. A., Austerlitz, F., Groenen, M. A. M. & de Cara, M. A. R., 2015, In : Genome Research. 25, 7, p. 970-981

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sus scrofa
Inbreeding
Breeding
Swine
Demography
2014
1 Citation (Scopus)
Open Access
DNA Sequence Analysis
Genome
Population
Physiological Phenomena
Chromosomes, Human, Pair 14
49 Citations (Scopus)

Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression

Bosse, M., Megens, H. J. W. C., Frantz, L. A. F., Madsen, O., Paudel, Y., Duijvestein, N., Crooijmans, R. P. M. A. & Groenen, M., 2014, In : Nature Communications. 5, 8 p., 4392.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
swine
genes
Haplotypes
Sus scrofa
Swine
2 Citations (Scopus)

Host genetic heterozygosity and age are important determinants of porcine circovirus type 2 disease prevalence in European wild boar

Goedbloed, D. J., van Hooft, W. F., Megens, H. J. W. C., Bosch, T., Lutz, W., van Wieren, S. E., Ydenberg, R. C. & Prins, H. H. T., 2014, In : European Journal of Wildlife Research. 60, 5, p. 803-810

Research output: Contribution to journalArticleAcademicpeer-review

disease prevalence
Porcine circovirus-2
wild boars
heterozygosity
antibody
5 Citations (Scopus)
Open Access
Chromosomes, Human, Pair 6
Haplotypes
Testis
Alleles
Quantitative Trait Loci
11 Citations (Scopus)

Systematic differences in the response of genetic variation to pedigree and genome-based selection methods

Heidaritabar, M., Vereijken, A., Muir, W. M., Meuwissen, T. H. E., Cheng, H., Megens, H. J. W. C., Groenen, M. & Bastiaansen, J. W. M., 2014, In : Heredity. 113, p. 503-513

Research output: Contribution to journalArticleAcademicpeer-review

Pedigree
Genome
Gene Frequency
Chickens
Breeding
18 Citations (Scopus)
Sus
Islands
genome
divergence
Genome
31 Citations (Scopus)
Sus scrofa
pig
Haplotypes
haplotypes
Swine
22 Citations (Scopus)

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds.

Herrero-Medrano, J., Megens, H. J. W. C., Groenen, M., Bosse, M., Pérez-Enciso, M. & Crooijmans, R. P. M. A., 2014, In : BMC Genomics. 15, 12 p., 601.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sequence Analysis
Swine
Genome
Single Nucleotide Polymorphism
Population
2013
42 Citations (Scopus)

Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

Herrero-Medrano, J., Megens, H. J. W. C., Groenen, M., Ramis, G., Bosse, M. & Crooijmans, R. P. M. A., 2013, In : BMC Genetics. 14, 106.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sus scrofa
Population
Inbreeding
Swine
Population Density
32 Citations (Scopus)

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

Esteve-Codina, A., Paudel, Y., Ferretti, L., Megens, H. J. W. C. & Groenen, M., 2013, In : BMC Genomics. 14, 148.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Swine
Nucleotides
Genome
Genes
X Chromosome