Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
Open accessAbstract
Rabbits softly swept to domestication: When people domesticate animals, they select for tameness and tolerance of humans. What else do they look for? To identify the selective pressures that led to rabbit domestication, Carneiro et al. sequenced a domestic rabbit genome and compared it to that of its wild brethren (see the Perspective by Lohmueller). Domestication did not involve a single gene changing, but rather many gene alleles changing in frequency between tame and domestic rabbits, known as a soft selective sweep. Many of these alleles have changes that may affect brain development, supporting the idea that tameness involves changes at multiple loci. Science , this issue p. 1074 ; see also p. 1000
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Recent genomic studies have found evidence of selection at a few handfuls of genes that have molecular functions associated with the neural crest, but that in itself is not good evidence that neural crest cell proliferation and migration are underlying the domestication syndrome.
“Recent genomic studies (Carneiro et al. 2014; Pendleton et al. 2018; Wang et al. 2018) have found evidence of selection at a few handfuls of genes that have molecular functions associated with the neural crest, but that in itself is not good evidence that neural crest cell proliferation and migration are underlying the domestication syndrome.”
From The neural crest cell hypothesis: no unified explanation for domestication (2021) · cites this paper as Carneiro et al. 2014
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Experimental — accuracy not yet measuredThese results are in line with claims in other studies on domestication, where categories like 'neurological process' frequently stand out strongly in gene ontology category enrichment analyses.
“These results are in line with claims in other studies on domestication [49, 123–125], where categories like ‘neurological process’ frequently stand out strongly in gene ontology category enrichment analyses.”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [125]
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- Authors
- Carneiro, M., Rubin, C.-J., Di Palma, F., Albert, F. W., Alföldi, J., Barrio, A. M., Pielberg, G., Rafati, N., Sayyab, S., Turner-Maier, J., Younis, S., Afonso, S., Aken, B., Alves, J. M., Barrell, D., Bolet, G., Boucher, S., Burbano, H. A., Campos, R., Chang, J. L., Duranthon, V., Fontanesi, L., Garreau, H., Heiman, D., Johnson, J., Mage, R. G., Peng, Z., Queney, G., Rogel-Gaillard, C., Ruffier, M., Searle, S., Villafuerte, R., Xiong, A., Young, S., Forsberg-Nilsson, K., Good, J. M., Lander, E. S., Ferrand, N., Lindblad-Toh, K., & Andersson, L.
- Affiliations
- Universidade do Porto (PT)
- Uppsala University (SE)
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA.
- Max Planck Institute for Evolutionary Anthropology (DE)
- Broad Institute (US)
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Swedish University of Agricultural Sciences (SE)
- Ain Shams University (EG)
- European Bioinformatics Institute (GB)
- Institut National de la Recherche Agronomique (INRA), UMR1388 Génétique, Physiologie et Systèmes d’Elevage, F-31326 Castanet-Tolosan, France.
- Labovet Conseil, BP539, 85505 Les Herbiers Cedex, France.
- INRA, UMR1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
- University of Bologna (IT)
- Génétique Physiologie et Systèmes d'Elevage (FR)
- National Institutes of Health (US)
- Lawrence Berkeley National Laboratory (US)
- ANTAGENE, Animal Genomics Laboratory, Lyon, France.
- Génétique Animale et Biologie Intégrative (FR)
- Wellcome Sanger Institute (GB)
- Consejo Superior de Investigaciones Científicas (ES)
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
- ORCID
- Carneiro, Miguel
- Rubin, Carl-Johan
- Albert, Frank W.
- Alföldi, Jessica
- Pielberg, Gerli
- Rafati, Nima
- Sayyab, Shumaila
- Turner-Maier, Jason
- Younis, Shady
- Afonso, Sandra
- Aken, Bronwen
- Alves, Joel M.
- Barrell, Daniel
- Burbano, Hernán A.
- Campos, Rita
- Fontanesi, Luca
- Garreau, Hervé
- Heiman, David
- Johnson, Jeremy
- Peng, Ze
- Queney, Guillaume
- Rogel-Gaillard, Claire
- Ruffier, Magali
- Villafuerte, Rafael
- Xiong, Anqi
- Young, Sarah
- Good, Jeffrey M.
- Lander, Eric S.
- Ferrand, Nuno
- Andersson, Leif
- Venue
- Science
- Published
- 2014-08-29
- Volume
- 345
- Issue
- 6200
- Pages
- 1074-1079
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC5421586
- OpenAlex
- W2132261072
- Cited by
- 404
- References
- 63
- Citations by year
- 2026: 16 · 2025: 21 · 2024: 22 · 2023: 22 · 2022: 36 · 2021: 53 · 2020: 44 · 2019: 41 · 2018: 47 · 2017: 38 · 2016: 37 · 2015: 23 · 2014: 4
- FWCI
- 22.33
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion)
- HAL (submittedVersion, other-oa)
- Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Funders
- National Science Foundation (WT098051, 0754461)
- Wellcome Trust (095908, WT095908, WT 098051)
- European Molecular Biology Laboratory
- Broad Institute
- Ministério da Ciência, Tecnologia e Ensino Superior
- Science for Life Laboratory
- National Institutes of Health (HG003067)
- Biotechnology and Biological Sciences Research Council (BBS/E/T/000PR5885, BBS/E/T/000PR6193)
- Fundação para a Ciência e a Tecnologia (COMPETE, SFRH/BPD/64365/2009, PTDC/BIA-EVF/115069/2009, 2007/2013, /2009)
- European Regional Development Fund (COMPETE, 2007 – 2013)
- National Human Genome Research Institute (U54HG003067, HG003067)
- National Institute of Allergy and Infectious Diseases
- Office of International Science and Engineering
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Human-Animal Interaction Studies
- Keywords
- selective sweeps, single nucleotide polymorphisms, brain development genes, allele frequency change, reference genome
- MeSH terms
- Animals, Animals, Domestic, Animals, Wild, Base Sequence, Behavior, Animal, Breeding, Gene Frequency, Molecular Sequence Data, Phenotype, Rabbits, Selection, Genetic, Genome, Sequence Analysis, DNA, Evolution, Molecular, Polymorphism, Single Nucleotide, Genetic Loci
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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