Genomic diversity and evolution of the head crest in the rock pigeon
Open accessAbstract
The geographic origins of breeds and the genetic basis of variation within the widely distributed and phenotypically diverse domestic rock pigeon (Columba livia) remain largely unknown. We generated a rock pigeon reference genome and additional genome sequences representing domestic and feral populations. We found evidence for the origins of major breed groups in the Middle East and contributions from a racing breed to North American feral populations. We identified the gene EphB2 as a strong candidate for the derived head crest phenotype shared by numerous breeds, an important trait in mate selection in many avian species. We also found evidence that this trait evolved just once and spread throughout the species, and that the crest originates early in development by the localized molecular reversal of feather bud polarity.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The HGFv1 assembly is compatible with current poultry reference genomes.
“The HGFv1 assembly is compatible with current poultry reference genomes (Dalloul et al. 2010; Shapiro et al. 2013; Lu et al. 2015; ZhOu et al. 2018; Morris et al. 2020).”
From Genomic Analyses Unveil Helmeted Guinea Fowl (<i>Numida meleagris</i>) Domestication in West Africa (2021) · cites this paper as Shapiro et al. 2013
The paper’s Abstract describes sequencing a rock-pigeon reference genome, and its References list turkey and chicken genome studies. Searches for HGFv1 and for assembly comparisons found no passage assessing whether the HGFv1 assembly is compatible with poultry reference genomes. (LLM, conf=0.75)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617 · see citing works
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr121 · Cited by 39,795 · see citing works
KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077 · see citing works
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089 · see citing works
KEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232 · see citing works
MODELTEST: testing the model of DNA substitution.
Posada, D., & Crandall, K. A. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.817 · Cited by 19,820 · see citing works
ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
Weir, B. S., & Cockerham, C. C. (1984) · Evolution · doi:10.1111/j.1558-5646.1984.tb05657.x · Cited by 18,909 · see citing works
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556 · see citing works
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108 · see citing works
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879 · see citing works
APE: Analyses of Phylogenetics and Evolution in R language
Paradis, E., Claude, J., & Strimmer, K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg412 · Cited by 12,037 · see citing works
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,477 · see citing works
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
Lowe, T. M., & Eddy, S. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.5.955 · Cited by 11,120 · see citing works
Estimating F-Statistics for the Analysis of Population Structure
Weir, B. S., & Cockerham, C. C. (1984) · Evolution · doi:10.2307/2408641 · Cited by 11,023 · see citing works
TCS: a computer program to estimate gene genealogies
Clement, M., Posada, D., & Crandall, K. A. (2000) · Molecular Ecology · doi:10.1046/j.1365-294x.2000.01020.x · Cited by 9,924 · see citing works
Fast model-based estimation of ancestry in unrelated individuals
Alexander, D. H., Novembre, J., & Lange, K. (2009) · Genome Research · doi:10.1101/gr.094052.109 · Cited by 9,898 · see citing works
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374 · see citing works
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480 · see citing works
UniProt: the Universal Protein knowledgebase
Apweiler, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh131 · Cited by 7,535 · see citing works
The rapid generation of mutation data matrices from protein sequences
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 6,916 · see citing works
Darwin, C. R., Murray, J. J., Sons, W. C. A., & Evans., B. &. (1859) · doi:10.5962/bhl.title.82303 · Cited by 5,610 · see citing works
distruct : a program for the graphical display of population structure
Rosenberg, N. A. (2003) · Molecular Ecology Notes · doi:10.1046/j.1471-8286.2003.00566.x · Cited by 4,959 · see citing works
Prediction of complete gene structures in human genomic DNA
Burge, C., & Karlin, S. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0951 · Cited by 4,211 · see citing works
SOAP2: an improved ultrafast tool for short read alignment
Li, R., Yu, C., Li, Y., Lam, T., Yiu, S., Kristiansen, K., & Wang, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp336 · Cited by 3,763 · see citing works
Self-citationBrowning, S. R., & Browning, B. L. (2007) · The American Journal of Human Genetics · doi:10.1086/521987 · Cited by 3,138 · see citing works
GeneWise and GenomewisePreprint
Birney, E., Clamp, M. E., & Durbin, R. M. (2004) · Genome Research · doi:10.1101/gr.1865504 · Cited by 2,799 · see citing works
International Chicken Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03154 · Cited by 2,750 · see citing works
Generating samples under a Wright–Fisher neutral model of genetic variation
Hudson, R. R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.2.337 · Cited by 2,397 · see citing works
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906 · see citing works
CAFE: a computational tool for the study of gene family evolution
De Bie, T., Cristianini, N., Demuth, J. P., & Hahn, M. W. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl097 · Cited by 1,790 · see citing works
The variation of animals and plants under domestication /
Darwin, C. R. (1905) · J. Murray eBooks · doi:10.5962/bhl.title.84435 · Cited by 1,719 · see citing works
Gene prediction with a hidden Markov model and a new intron submodel
Stanke, M., & Waack, S. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg1080 · Cited by 1,643 · see citing works
Griffiths‐Jones, S. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg006 · Cited by 1,574 · see citing works
Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles.
Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villarreal, G., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Schluter, D., & Kingsley, D. M. (2005) · Science · doi:10.1126/science.1107239 · Cited by 1,448 · see citing works
Infernal 1.0: inference of RNA alignments
Nawrocki, E. P., Kolbe, D. L., & Eddy, S. R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp157 · Cited by 1,428 · see citing works
Database indexing for production MegaBLAST searches
Morgulis, A. O., Coulouris, G., Raytselis, Y., Madden, T., Agarwala, R., & Schäffer, A. A. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn322 · Cited by 1,352 · see citing works
The sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180 · see citing works
Self-citationApweiler, R. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.37 · Cited by 1,079 · see citing works
A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig
Laere, A.-S. V., Nguyen, M. Q., Braunschweig, M., Nezer, C., Collette, C., Moreau, L., Archibald, A. L., Haley, C., Buys, N., Tally, M., et al. (2003) · Nature · doi:10.1038/nature02064 · Cited by 949 · see citing works
Estimating Maximum Likelihood Phylogenies with PhyML
Guindon, S., Delsuc, F., Dufayard, J.-F., & Gascuel, O. (2009) · Methods in molecular biology · doi:10.1007/978-1-59745-251-9_6 · Cited by 822 · see citing works
Warren, W. C., Clayton, D. F., Ellegren, H., Arnold, A. P., Hillier, L. W., Künstner, A., Searle, S. M. J., White, S. J., Vilella, A. J., Fairley, S., et al. (2010) · Nature · doi:10.1038/nature08819 · Cited by 813 · see citing works
Why are female birds ornamented?
Amundsen, T., & Amundsen, T. (2000) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(99)01800-5 · Cited by 712 · see citing works
A Single IGF1 Allele Is a Major Determinant of Small Size in Dogs
Sutter, N. B., Bustamante, C. D., Chase, K., GRAY, M. M., Zhao, K., Zhu, L., Padhukasahasram, B., Karlins, E., Davis, S. R., Jones, P. G., et al. (2007) · Science · doi:10.1126/science.1137045 · Cited by 673 · see citing works
The genomic landscape of species divergence in Ficedula flycatchers
Ellegren, H., Smeds, L., Burri, R., Olason, P. I., Backström, N., Kawakami, T., Künstner, A., Mäkinen, H., Nadachowska‐Brzyska, K., Qvarnström, A., et al. (2012) · Nature · doi:10.1038/nature11584 · Cited by 640 · see citing works
From wild animals to domestic pets, an evolutionary view of domestication
Driscoll, C. A., Macdonald, D. W., & O'Brien, S. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0901586106 · Cited by 639 · see citing works
TreeFam: a curated database of phylogenetic trees of animal gene families
Li, H. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj118 · Cited by 523 · see citing works
Dalloul, R. A., Long, J. A., Zimin, A. V., Aslam, L., Beal, K., Ann Blomberg, L., Bouffard, P., Burt, D. W., Crasta, O., Crooijmans, R. P. M. A., et al. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000475 · Cited by 416 · see citing works
Creating a honey bee consensus gene set
Elsik, C. G., Mackey, A. J., Reese, J., Milshina, N. V., Roos, D. S., & Weinstock, G. M. (2007) · Genome biology · doi:10.1186/gb-2007-8-1-r13 · Cited by 327 · see citing works
Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders
Pacheco, M. A., Battistuzzi, F. U., Lentino, M., Aguilar, R. F., Kumar, S., & Escalante, A. A. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr014 · Cited by 244 · see citing works
A probabilistic disease-gene finder for personal genomes.Preprint
Yandell, M., Huff, C., Hu, H., Singleton, M., Moore, B., Xing, J.-C., Jorde, L., & Reese, M. G. (2011) · Genome Research · doi:10.1101/gr.123158.111 · Cited by 210 · see citing works
Self-citationStripes and belly-spots—A review of pigment cell morphogenesis in vertebrates
Kelsh, R. N., Harris, M. L., Colanesi, S., & Erickson, C. A. (2009) · Seminars in Cell & Developmental Biology · doi:10.1016/j.semcdb.2008.10.001 · Cited by 202 · see citing works
Molecular evolution of genes in avian genomes
Nam, K., Mugal, C. F., Nabholz, B., Schielzeth, H., Wolf, J. B. W., Backström, N., Künstner, A., Balakrishnan, C. N., Heger, A., Ponting, C. P., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-6-r68 · Cited by 182 · see citing works
The Characterization of Twenty Sequenced Human Genomes
Pelak, K., Shianna, K., Ge, D., Maia, J., Zhu, M., Smith, J. P., Cirulli, E., Fellay, J., Dickson, S., Gumbs, C., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001111 · Cited by 168 · see citing works
Divergence, Convergence, and the Ancestry of Feral Populations in the Domestic Rock Pigeon
Stringham, S. A., Mulroy, E. E., Xing, J., Record, D., Guernsey, M. W., Aldenhoven, J., Osborne, E. J., & Shapiro, M. D. (2012) · Current Biology · doi:10.1016/j.cub.2011.12.045 · Cited by 108 · see citing works
Self-citationCryptic Patterning of Avian Skin Confers a Developmental Facility for Loss of Neck Feathering
Mou, C., Frédérique Pitel, A., Gourichon, D., Vignoles, F., Tzika, A. C., Tato, P., Yu, L., Burt, D. W., Bed’Hom, B., Tixier‐Boichard, M., et al. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001028 · Cited by 103 · see citing works
Balakrishnan, C. N., & Edwards, S. V. (2008) · Genetics · doi:10.1534/genetics.108.094250 · Cited by 97 · see citing works
Linkage Disequilibrium Between Loci With Unknown Phase
Rogers, A. R., & Huff, C. D. (2009) · Genetics · doi:10.1534/genetics.108.093153 · Cited by 89 · see citing works
Self-citationA MOLECULAR PHYLOGENY OF THE DOVE GENERA STREPTOPELIA AND COLUMBA
Johnson, K. P., de Kort, S. R., Dinwoodey, K., Mateman, A. C., ten Cate, C., Lessells, C. M., & Clayton, D. H. (2001) · The Auk · doi:10.1642/0004-8038(2001)118[0874:ampotd]2.0.co;2 · Cited by 81 · see citing works
Domesticated Birds as a Model for the Genetics of Speciation by Sexual Selection
Price, T. D. (2002) · Genetica · doi:10.1023/a:1021248913179 · Cited by 70 · see citing works
Elder, M. E., Skoda‐Smith, S., Kadlecek, T. A., Wang, F., Wu, J., & Weiss, A. (2001) · The Journal of Immunology · doi:10.4049/jimmunol.166.1.656 · Cited by 63 · see citing works
The Crest Phenotype in Chicken Is Associated with Ectopic Expression of HOXC8 in Cranial Skin
Wang, Y., Gao, Y., Imsland, F., Gu, X., Feng, C., Liu, R., Song, C., Tixier‐Boichard, M., Gourichon, D., Li, Q., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034012 · Cited by 63 · see citing works
Extent of linkage disequilibrium in chicken
Aerts, J. A., Megens, H., Veenendaal, T., Ovcharenko, I., Crooijmans, R. P. M. A., Gordon, L. A., Stubbs, L. J., & Groenen, M. A. M. (2007) · Cytogenetic and Genome Research · doi:10.1159/000103196 · Cited by 55 · see citing works
Abler, L. L., Mehta, V., Keil, K. P., Joshi, P. S., Flucus, C.-L., Hardin, H. A., Schmitz, C. T., & Vezina, C. M. (2011) · Journal of Visualized Experiments · doi:10.3791/2912 · Cited by 53 · see citing works
A Molecular Phylogeny of the Dove Genera Streptopelia and Columba
Johnson, K. P., de Kort, S. R., Dinwoodey, K., Mateman, A. C., ten Cate, C., Lessells, C. M., Clayton, D. H., & Sheldon, F. H. (2001) · The Auk · doi:10.1093/auk/118.4.874 · Cited by 38 · see citing works
McKinnell, I. W., Makarenkova, H. P., de Curtis, I., Turmaine, M., & Patel, K. (2004) · Developmental Biology · doi:10.1016/j.ydbio.2004.02.007 · Cited by 16 · see citing works
DARWIN'S PIGEONS AND THE EVOLUTION OF THE COLUMBIFORMS: RECAPITULATION OF ANCIENT GENES
Baptista, L. F., Martínez‐Gómez, J. E., & Horblit, H. M. (2009) · Biodiversity Heritage Library (Smithsonian Institution) · Cited by 15 · see citing works
NOTES ON TWO CROSSES BETWEEN DIFFERENT RACES OF PIGEONS
Morgan, T. H. (1911) · Biological Bulletin · doi:10.2307/1536043 · Cited by 9 · see citing works
Pigeons: their structure, varieties, habits, and management
Tegetmeier, W. B., Weir, H., & (Printer), L. B. (1868) · doi:10.5962/bhl.title.61355 · Cited by 7 · see citing works
Abler, L. L., Mehta, V., Keil, K. P., et al. (2011) · Journal of Visualized Experiments · doi:10.3791/2912-v · Cited by 6 · see citing works
Levi, M. (1986) · The British Journal of Criminology · doi:10.1093/oxfordjournals.bjc.a047602 · Cited by 1 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science · doi:10.1126/science.1253451 · Cited by 1,901 · see citing works
Self-citationComparative genomics reveals insights into avian genome evolution and adaptation
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., Storz, J. F., Antunes, A., Greenwold, M. J., Meredith, R. W., et al. (2014) · Science · doi:10.1126/science.1251385 · Cited by 1,055 · see citing works
Self-citationGenome sequencing and population genomics in non-model organisms
Ellegren, H. (2013) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2013.09.008 · Cited by 760 · see citing works
Ai, H., Fang, X., Yang, B. J., Huang, Z., Chen, H., Mao, L., Zhang, F., Zhang, L., Cui, L., He, W., et al. (2015) · Nature Genetics · doi:10.1038/ng.3199 · Cited by 374 · see citing works
An intercross population study reveals genes associated with body size and plumage color in ducks
Zhou, Z., Li, M., Cheng, H., Fan, W., Yuan, Z., Gao, Q., Xu, Y., Guo, Z., Zhang, Y., Hu, J., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04868-4 · Cited by 333 · see citing works
The Genome 10K Project: A Way Forward
Koepfli, K.-P., Paten, B., Scientists, T. G. 1. C. O., & O’Brien, S. J. (2015) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-090414-014900 · Cited by 311 · see citing works
Teeling, E. C., Vernes, S. C., Dávalos, L. M., Ray, D. A., Gilbert, M. T. P., & Myers, E. W. (2017) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-022516-022811 · Cited by 233 · see citing works
Self-citationKawakami, T., Smeds, L., Backström, N., Husby, A., Qvarnström, A., Mugal, C. F., Olason, P. I., & Ellegren, H. (2014) · Molecular Ecology · doi:10.1111/mec.12810 · Cited by 221 · see citing works
Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms
Beichman, A. C., Huerta‐Sánchez, E., & Lohmueller, K. E. (2018) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110617-062431 · Cited by 207 · see citing works
Drastic population fluctuations explain the rapid extinction of the passenger pigeon
Hung, C.-M., Shaner, P.-J. L., Zink, R. M., Liu, W.-C., Chu, T.-C., Huang, W.-S., & Li, S.-H. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1401526111 · Cited by 186 · see citing works
Evolution of bird genomes—a transposon's‐eye view
Kapusta, A., & Suh, A. (2016) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13295 · Cited by 171 · see citing works
Comparative genomic data of the Avian Phylogenomics Project
Zhang, G., Li, B., Li, C., Gilbert, M. T. P., Jarvis, E. D., & Wang, J. (2014) · GigaScience · doi:10.1186/2047-217x-3-26 · Cited by 141 · see citing works
Self-citationWham: Identifying Structural Variants of Biological Consequence
Kronenberg, Z. N., Osborne, E. J., Cone, K. R., Kennedy, B., Domyan, E. T., Shapiro, M. D., Elde, N. C., & Yandell, M. D. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004572 · Cited by 135 · see citing works
Self-citationNatural selection shaped the rise and fall of passenger pigeon genomic diversity
Murray, G. G. R., Soares, A. E. R., Novak, B. J., Schaefer, N. K., Cahill, J. A., Baker, A. J., Demboski, J. R., Doll, A. C., da Fonseca, R. R., Fulton, T. L., et al. (2017) · Science · doi:10.1126/science.aao0960 · Cited by 135 · see citing works
Self-citationWhole-genome resequencing reveals signatures of selection and timing of duck domestication
Zhang, Z., Jia, Y., Almeida, P., Mank, J. E., van Tuinen, M., Wang, Q., Jiang, Z., Chen, Y., Zhan, K., Hou, S., et al. (2018) · GigaScience · doi:10.1093/gigascience/giy027 · Cited by 135 · see citing works
Field, D. J., Gauthier, J. A., King, B. L., Pisani, D., Lyson, T. R., & Peterson, K. J. (2014) · Evolution & Development · doi:10.1111/ede.12081 · Cited by 131 · see citing works
Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars
Cooke, T. F., Fischer, C. R., Wu, P., Jiang, T., Xie, K. T., Kuo, J., Doctorov, E., Zehnder, A. M., Khosla, C., Chuong, C., et al. (2017) · Cell · doi:10.1016/j.cell.2017.08.016 · Cited by 126 · see citing works
The Evolutionary Genomics of Birds
Ellegren, H. (2013) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110411-160327 · Cited by 121 · see citing works
Vaudry, H., Leprince, J., Chatenet, D., Fournier, A., Lambert, D. G., Mével, J. L., Ohlstein, E. H., Schwertani, A. G., Tostivint, H., & Vaudry, D. (2014) · Pharmacological Reviews · doi:10.1124/pr.114.009480 · Cited by 104 · see citing works
Testing the Hamilton-Zuk Hypothesis: Past, Present, and Future
Balenger, S. L., & Zuk, M. (2014) · Integrative and Comparative Biology · doi:10.1093/icb/icu059 · Cited by 100 · see citing works
Damas, J., O’Connor, R. E., Farré, M., Lenis, V. P. E., Martell, H. J., Mandawala, A. A., Fowler, K. E., Joseph, S., Swain, M., Griffin, D. K., et al. (2016) · Genome Research · doi:10.1101/gr.213660.116 · Cited by 98 · see citing works
Hu, H., Roach, J. C., Coon, H. H., Guthery, S. L., Voelkerding, K. V., Margraf, R. L., Durtschi, J., Tavtigian, S. V., Shankaracharya, N. A., Wu, W., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2895 · Cited by 94 · see citing works
Self-citationIndependent domestication events in the blue‐cheese fungus Penicillium roqueforti
Dumas, É., Feurtey, A., de la Vega, R. C. R., Prieur, S. L., Snirc, A., Coton, M., Thierry, A., Coton, E., Piver, M. L., Roueyre, D., et al. (2020) · Molecular Ecology · doi:10.1111/mec.15359 · Cited by 94 · see citing works
Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting
Kretschmer, R., Ferguson-Smith, M., & de Oliveira, E. H. C. (2018) · Genes · doi:10.3390/genes9040181 · Cited by 93 · see citing works
Møller, H. D., Ramos‐Madrigal, J., Prada-Luengo, I., Gilbert, M. T. P., & Regenberg, B. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz281 · Cited by 93 · see citing works
Self-citationGenomic approaches to understanding population divergence and speciation in birds
Toews, D. P. L., Campagna, L., Taylor, S. A., Balakrishnan, C. N., Baldassarre, D. T., Deane‐Coe, P. E., Harvey, M. G., Hooper, D. M., Irwin, D. E., Judy, C. D., et al. (2015) · The Auk · doi:10.1642/auk-15-51.1 · Cited by 92 · see citing works
Third Report on Chicken Genes and Chromosomes 2015
Schmid, M., Smith, J., Burt, D. W., Aken, B. L., Antin, P. B., Archibald, A. L., Ashwell, C. M., Blackshear, P. J., Boschiero, C., Brown, C. T., et al. (2015) · Cytogenetic and Genome Research · doi:10.1159/000430927 · Cited by 91 · see citing works
Domyan, E. T., Kronenberg, Z. N., Infante, C. R., Vickrey, A. I., Stringham, S. A., Bruders, R., Guernsey, M. W., Park, S., Payne, J. A., Beckstead, R. B., et al. (2016) · eLife · doi:10.7554/elife.12115 · Cited by 83 · see citing works
Self-citationEpistatic and Combinatorial Effects of Pigmentary Gene Mutations in the Domestic Pigeon
Domyan, E. T., Guernsey, M. W., Kronenberg, Z. N., Krishnan, S., Boissy, R. E., Vickrey, A. I., Rodgers, C., Cassidy, P. B., Leachman, S. A., Fondon, J. W., et al. (2014) · Current Biology · doi:10.1016/j.cub.2014.01.020 · Cited by 82 · see citing works
Self-citationFriedman‐Einat, M., Cogburn, L. A., Yosefi, S., Hen, G., Shinder, D., Shirak, A., & Seroussi, E. (2014) · Endocrinology · doi:10.1210/en.2014-1273 · Cited by 76 · see citing works
Vickrey, A. I., Bruders, R., Kronenberg, Z. N., Mackey, E. J., Bohlender, R. J., Maclary, E. T., Maynez, R., Osborne, E. J., Johnson, K. P., Huff, C. D., et al. (2018) · eLife · doi:10.7554/elife.34803 · Cited by 76 · see citing works
Self-citationGenetic and Molecular Basis of Feather Diversity in Birds
Ng, C. S., & Li, W. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy180 · Cited by 70 · see citing works
The Genome Sequence of a Widespread Apex Predator, the Golden Eagle (Aquila chrysaetos)
Doyle, J. M., Katzner, T. E., Bloom, P. H., Ji, Y., Wijayawardena, B. K., & DeWoody, J. A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0095599 · Cited by 70 · see citing works
Shapiro, M. D., & Domyan, E. T. (2013) · Current Biology · doi:10.1016/j.cub.2013.01.063 · Cited by 70 · see citing works
Self-citationGodinho, R., López‐Bao, J. V., Castro, D., Llaneza, L., Lopes, S., Silva, P., & Ferrand, N. (2014) · Molecular Ecology Resources · doi:10.1111/1755-0998.12313 · Cited by 69 · see citing works
Pigeonetics takes flight: Evolution, development, and genetics of intraspecific variation
Domyan, E. T., & Shapiro, M. D. (2016) · Developmental Biology · doi:10.1016/j.ydbio.2016.11.008 · Cited by 67 · see citing works
Self-citationTsai, H., Chang, M., Liu, S., Abe, G., & Ota, K. G. (2013) · Developmental Dynamics · doi:10.1002/dvdy.24022 · Cited by 66 · see citing works
Rapid molecular evolution across amniotes of the IIS/TOR network
McGaugh, S. E., Bronikowski, A. M., Kuo, C., Reding, D. M., Addis, E. A., Flagel, L., Janzen, F. J., & Schwartz, T. S. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419659112 · Cited by 62 · see citing works
Besnard, G., Bertrand, J. A. M., Delahaie, B., Bourgeois, Y., Lhuillier, É., & Thébaud, C. (2015) · Biological Journal of the Linnean Society · doi:10.1111/bij.12494 · Cited by 62 · see citing works
Goldfish: an old and new model system to study vertebrate development, evolution and human disease
Omori, Y., & Kon, T. (2018) · The Journal of Biochemistry · doi:10.1093/jb/mvy076 · Cited by 60 · see citing works
Developmental plasticity shapes social traits and selection in a facultatively eusocial bee
Kapheim, K. M., Jones, B. M., Pan, H., Li, C., Harpur, B. A., Kent, C. F., Zayed, A., Ioannidis, P., Waterhouse, R. M., Kingwell, C. J., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2000344117 · Cited by 60 · see citing works
Self-citationPowder, K. E., Cousin, H., McLinden, G. P., & Albertson, R. C. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu267 · Cited by 57 · see citing works
Goldfish morphology as a model for evolutionary developmental biology
Ota, K. G., & Abe, G. (2016) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.224 · Cited by 57 · see citing works
Kratochwil, C. F., & Meyer, A. (2014) · BioEssays · doi:10.1002/bies.201400142 · Cited by 56 · see citing works
Āboliņš-Ābols, M., Kornobis, É., Ribeca, P., Wakamatsu, K., Peterson, M. P., Ketterson, E. D., & Milá, B. (2018) · Molecular Ecology · doi:10.1111/mec.14878 · Cited by 55 · see citing works
Improved Genome Assembly and Annotation for the Rock Pigeon ( Columba livia )
Holt, C., Campbell, M. S., Keays, D. A., Edelman, N. B., Kapusta, A., Maclary, E. T., Domyan, E. T., Suh, A., Warren, W. C., Yandell, M. D., et al. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.117.300443 · Cited by 55 · see citing works
Self-citationCraniofacial diversification in the domestic pigeon and the evolution of the avian skull
Young, N. M., Linde‐Medina, M., Fondon, J. W., Hallgrímsson, B., & Marcucio, R. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0095 · Cited by 49 · see citing works
Comparative population genomics reveals genetic basis underlying body size of domestic chickens
Wang, M., Huo, Y., Li, Y., Otecko, N. O., Su, L., Xu, H., Wu, S., Peng, M., Liu, H., Zeng, L., et al. (2016) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjw044 · Cited by 46 · see citing works
Genome-Wide Analysis Identifies Candidate Genes Encoding Feather Color in Ducks
Guo, Q., Jiang, Y. Q., Wang, Z., Bi, Y., Chen, G., Bai, H., & Chang, G. (2022) · Genes · doi:10.3390/genes13071249 · Cited by 45 · see citing works
MacManes, M. D., Austin, S. H., Lang, A. S., Booth, A. M., Farrar, V. S., & Calisi, R. M. (2017) · Scientific Reports · doi:10.1038/srep45125 · Cited by 45 · see citing works
Whenham, N., Lu, T. C., Maidin, M. B. M., Wilson, P. W., Bain, M., Stevenson, M. L., Stevens, M. P., Bedford, M. R., & Dunn, I. (2015) · Biology of Reproduction · doi:10.1095/biolreprod.114.126839 · Cited by 44 · see citing works
Jones, M. E. H., Button, D. J., Barrett, P. M., & Porro, L. B. (2019) · Zoological Letters · doi:10.1186/s40851-019-0129-z · Cited by 44 · see citing works
Reversible Trait Loss: The Genetic Architecture of Female Ornaments
Kraaijeveld, K. (2014) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-120213-091550 · Cited by 44 · see citing works
Cahill, J. A., Armstrong, J. C., Deran, A., Khoury, C. J., Paten, B., Haussler, D. H., & Jarvis, E. D. (2021) · Genome Research · doi:10.1101/gr.275989.121 · Cited by 41 · see citing works
New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)
Doyle, J. M., Bell, D. A., Bloom, P. H., Emmons, G., Fesnock, A. L., Katzner, T. E., LaPré, L., Leonard, K., SanMiguel, P. J., Westerman, R., et al. (2018) · BMC Genomics · doi:10.1186/s12864-018-4615-z · Cited by 40 · see citing works
Ontologies and Politics of Biogenomic 'Race'
Winther, R. G., & Kaplan, J. M. (2013) · Theoria · doi:10.3167/th.2013.6013605 · Cited by 39 · see citing works
Bruxaux, J., Gabrielli, M., Ashari, H., Prŷs‐Jones, R., Joseph, L., Milá, B., Besnard, G., & Thébaud, C. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.11.022 · Cited by 39 · see citing works
Parallel Genetic Origin of Foot Feathering in Birds
Bortoluzzi, C., Megens, H., Bosse, M., Derks, M. F. L., Dibbits, B. W., Laport, K., Weigend, S., Groenen, M. A. M., & Crooijmans, R. P. M. A. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa092 · Cited by 39 · see citing works
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye
Sohn, J.-I., Nam, K., Hong, H., Kim, J., Lim, D., Lee, K., Do, Y. J., Cho, C. Y., Kim, N., Chai, H., et al. (2018) · GigaScience · doi:10.1093/gigascience/giy086 · Cited by 38 · see citing works
Gazda, M. A., Andrade, P., Afonso, S., Dilytė, J., Archer, J. P., Lopes, R. J., Faria, R., & Carneiro, M. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy030 · Cited by 35 · see citing works
Tracing the evolution of amniote chromosomes
Deakin, J. E., & Ezaz, T. (2014) · Chromosoma · doi:10.1007/s00412-014-0456-y · Cited by 35 · see citing works
A field ornithologist's guide to genomics: Practical considerations for ecology and conservation
Oyler‐McCance, S. J., Oh, K. P., Langin, K. M., & Aldridge, C. L. (2016) · The Auk · doi:10.1642/auk-16-49.1 · Cited by 34 · see citing works
Postembryonic staging of wild‐type goldfish, with brief reference to skeletal systems
Li, I., Chang, C., Liu, S., Abe, G., & Ota, K. G. (2015) · Developmental Dynamics · doi:10.1002/dvdy.24340 · Cited by 33 · see citing works
Unifying and generalizing the two strands of evo-devo
Parsons, K. J., & Albertson, R. C. (2013) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2013.06.009 · Cited by 32 · see citing works
Genomic and Phenotypic Analyses Reveal Mechanisms Underlying Homing Ability in Pigeon
Shao, Y., Tian, H.-Y., Zhang, J., Kharrati-Koopaee, H., Guo, X., Zhuang, X.-L., Li, M., Nanaei, H. A., Tafti, E. D., Shojaei, B., et al. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz208 · Cited by 32 · see citing works
Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies
Stiller, J., & Zhang, G. (2019) · Diversity · doi:10.3390/d11070115 · Cited by 31 · see citing works
Self-citationInherency and agency in the origin and evolution of biological functions
Newman, S. A. (2022) · Biological Journal of the Linnean Society · doi:10.1093/biolinnean/blac109 · Cited by 31 · see citing works
Tang, Q., Low, G. W., Lim, J. Y., Gwee, C. Y., & Rheindt, F. E. (2018) · Evolutionary Applications · doi:10.1111/eva.12650 · Cited by 30 · see citing works
Sex-biased transcriptomic response of the reproductive axis to stress
Calisi, R. M., Austin, S. H., Lang, A. S., & MacManes, M. D. (2018) · Hormones and Behavior · doi:10.1016/j.yhbeh.2017.11.011 · Cited by 30 · see citing works
Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies
Card, D. C., Schield, D. R., Reyes‐Velasco, J., Fujita, M. K., Andrew, A. L., Oyler‐McCance, S. J., Fike, J. A., Tomback, D. F., Ruggiero, R. P., & Castoe, T. A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0106649 · Cited by 29 · see citing works
Using VAAST to Identify Disease‐Associated Variants in Next‐Generation Sequencing Data
Kennedy, B., Kronenberg, Z. N., Hu, H., Moore, B., Flygare, S. D., Reese, M. G., Jorde, L. B., Yandell, M. D., & Huff, C. D. (2014) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg0614s81 · Cited by 29 · see citing works
Self-citationGuernsey, M. W., Ritscher, L., Miller, M., Smith, D. A., Schöneberg, T., & Shapiro, M. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074475 · Cited by 29 · see citing works
Self-citationMueller, J. C., Kuhl, H., Timmermann, B., & Kempenaers, B. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12450 · Cited by 27 · see citing works
Genomic determinants of epidermal appendage patterning and structure in domestic birds
Boer, E. F., Hollebeke, H. F. V., & Shapiro, M. D. (2017) · Developmental Biology · doi:10.1016/j.ydbio.2017.03.022 · Cited by 27 · see citing works
Self-citationA Natural Animal Model System of Craniofacial Anomalies: The Blind Mexican Cavefish
Gross, J. B., & Powers, A. K. (2018) · The Anatomical Record · doi:10.1002/ar.23998 · Cited by 26 · see citing works
Molecular Signatures of Placentation and Secretion Uncovered in Poeciliopsis Maternal Follicles
Guernsey, M. W., van Kruistum, H., Reznick, D. N., Pollux, B. J. A., & Baker, J. C. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa121 · Cited by 26 · see citing works
Ericsen, A. J., Starrett, G. J., Greene, J., Lauck, M., Raveendran, M., Deiros, D. R., Mohns, M. S., Vince, N., Cain, B. T., Pham, N. H., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0478-z · Cited by 25 · see citing works
Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles
Yun, S.-C., Jun, J., Kim, J., Kim, H.-M., Chung, O., Kang, S.-G., Park, J.-Y., Kim, H.-J., Kim, S.-H., Kim, H.-J., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1793-1 · Cited by 25 · see citing works
Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs
Huang, M., Zhang, H., Wu, Z., Wang, X. P., Li, D. S., Liu, S. J., Zheng, S., Yang, L., Liu, B. B., Li, G. X., et al. (2021) · animal · doi:10.1016/j.animal.2021.100354 · Cited by 25 · see citing works
Hernández, F., Brown, J. I., Kaminski, M. H., Harvey, M. G., & Lavretsky, P. (2021) · Animals · doi:10.3390/ani11092677 · Cited by 24 · see citing works
Słowińska, M., Liszewska, E., Nynca, J., Wiśniewska, J., Hejmej, A., Bilińska, B., Szubstarski, J., Kozłowski, K., Jankowski, J., & Ciereszko, A. (2014) · Biology of Reproduction · doi:10.1095/biolreprod.114.118836 · Cited by 24 · see citing works
Martin, C. H., Erickson, P. A., & Miller, C. T. (2016) · Molecular Ecology · doi:10.1111/mec.13935 · Cited by 24 · see citing works
Darwin’s Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds
Pacheco, G., van Grouw, H., Shapiro, M. D., Gilbert, M. T. P., & Vieira, F. G. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa027 · Cited by 23 · see citing works
Self-citationVickrey, A. I., Domyan, E. T., Horvath, M. P., & Shapiro, M. D. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv140 · Cited by 23 · see citing works
Self-citationDetecting mitochondrial signatures of selection in wild Tibetan pigs and domesticated pigs
Li, M., Jin, L. G., Ma, J., Tian, S., Li, R., & Li, X. (2014) · Mitochondrial DNA Part A · doi:10.3109/19401736.2014.913169 · Cited by 23 · see citing works
Albertson, R. C., Kawasaki, K. C., Tetrault, E. R., & Powder, K. E. (2018) · Communications Biology · doi:10.1038/s42003-018-0060-4 · Cited by 23 · see citing works
Oldeschulte, D. L., Halley, Y., Wilson, M. L., Bhattarai, E. K., Brashear, W. A., Hill, J., Metz, R. P., Johnson, C. D., Rollins, D., Peterson, M. J., et al. (2017) · G3 Genes Genomes Genetics · doi:10.1534/g3.117.043083 · Cited by 22 · see citing works
Nimmagadda, S., Buchtová, M., Fu, K., Geetha‐Loganathan, P., Hosseini-Farahabadi, S., Trachtenberg, A. J., Kuo, W. P., Veselá, I., & Richman, J. M. (2015) · Developmental Biology · doi:10.1016/j.ydbio.2015.09.007 · Cited by 22 · see citing works
Ruíz-Jarabo, I., Martos-Sitcha, J. A., Barragán-Méndez, C., Martı́nez-Rodrı́guez, G., Mancera, J. M., & Arjona, F. J. (2017) · Fish Physiology and Biochemistry · doi:10.1007/s10695-017-0457-x · Cited by 22 · see citing works
A global screen for magnetically induced neuronal activity in the pigeon brain
Nordmann, G. C., Balay, S. D., Kapuruge, T. N., Numi, M., Leeb, C., Nimpf, S., Malkemper, E. P., Landler, L., & Keays, D. A. (2025) · Science · doi:10.1126/science.aea6425 · Cited by 21 · see citing works
Deciphering principles of morphogenesis from temporal and spatial patterns on the integument
Li, A., Lai, Y., Figueroa, S., Yang, T., Widelitz, R. B., Kobielak, K., Nie, Q. H., & Chuong, C. (2015) · Developmental Dynamics · doi:10.1002/dvdy.24281 · Cited by 21 · see citing works
Liu, S., Chen, H., Ouyang, J., Huang, M., Zhang, H., Zheng, S., Xi, S., Tang, H., Gao, Y., Xiong, Y., et al. (2022) · GigaScience · doi:10.1093/gigascience/giac018 · Cited by 20 · see citing works
Adaptation to nocturnality – learning from avian genomes
Duc, D. L., & Schöneberg, T. (2016) · BioEssays · doi:10.1002/bies.201600006 · Cited by 20 · see citing works
Pujolar, J. M., Dalén, L., Hansen, M. M., & Madsen, J. J. (2017) · Molecular Ecology · doi:10.1111/mec.14374 · Cited by 20 · see citing works
Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences
Hernández‐Alonso, G., Ramos‐Madrigal, J., van Grouw, H., Ciucani, M. M., Cavill, E. L., Sinding, M. S., Gopalakrishnan, S., Pacheco, G., & Gilbert, M. T. P. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad243 · Cited by 19 · see citing works
Self-citationPigeon foot feathering reveals conserved limb identity networks
Boer, E. F., Hollebeke, H. F. V., Park, S., Infante, C. R., Menke, D. B., & Shapiro, M. D. (2019) · Developmental Biology · doi:10.1016/j.ydbio.2019.06.015 · Cited by 19 · see citing works
Self-citationMorimoto, K., Suzuki, N., Tanida, I., Kakuta, S., Furuta, Y., Uchiyama, Y., Hanada, K., Suzuki, Y., & Yamaji, T. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.013926 · Cited by 19 · see citing works
Cellular and molecular mechanisms of EPH/EPHRIN signaling in evolution and development
Bush, J. O. (2022) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2022.02.005 · Cited by 19 · see citing works
A high sensitivity ZENK monoclonal antibody to map neuronal activity in Aves
Nordmann, G. C., Malkemper, E. P., Landler, L., Ushakova, L., Nimpf, S., Heinen, R., Schüchner, S., Ogris, E., & Keays, D. A. (2020) · Scientific Reports · doi:10.1038/s41598-020-57757-6 · Cited by 19 · see citing works
Haug-Baltzell, A. K., Jarvis, E. D., McCarthy, F., & Lyons, E. H. (2015) · Frontiers in Neuroscience · doi:10.3389/fnins.2015.00361 · Cited by 18 · see citing works
- Authors
- Shapiro, M. D., Kronenberg, Z., Li, C., Domyan, E. T., Pan, H., Campbell, M., Tan, H., Huff, C. D., Hu, H., Vickrey, A. I., Nielsen, S. C. A., Stringham, S. A., Hu, H., Willerslev, E., Gilbert, M. T. P., Yandell, M., Zhang, G., & Wang, J.
- Affiliations
- University of Utah (US)
- BGI Group (China) (CN)
- The University of Texas MD Anderson Cancer Center (US)
- University of Copenhagen (DK)
- Corresponding author
- Shapiro, Michael D.
- Wang, Jun
- ORCID
- Venue
- Science
- Published
- 2013-03
- Volume
- 339
- Issue
- 6123
- Pages
- 1063-1067
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3778192
- OpenAlex
- W2062533068
- Cited by
- 265
- References
- 70
- Citations by year
- 2026: 11 · 2025: 10 · 2024: 9 · 2023: 21 · 2022: 23 · 2021: 26 · 2020: 18 · 2019: 16 · 2018: 25 · 2017: 23 · 2016: 15 · 2015: 23 · 2014: 33 · 2013: 12
- FWCI
- 18.34
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eSpace (Curtin University) (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Funders
- Agence Nationale de la Recherche
- Lundbeckfonden (R109-2012-9995, R70-2010-6286, R155-2013-16338, R38-2008-3048, R24-2008-2527)
- National Human Genome Research Institute (R01HG004694, R44HG006579, GO RC2HG005619, RC2HG005619)
- National Institute of General Medical Sciences (R01GM104390, T32GM007464)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (T32HD07491, T32HD007491)
- 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 › Genetic diversity and population structure
- Keywords
- Columba livia, domestication, breed origin, feral populations, reference genome, EphB2, mate choice, genomic diversity
- MeSH terms
- Amino Acid Sequence, Animals, Animals, Domestic, Animals, Wild, Breeding, Feathers, Head, Models, Genetic, Molecular Sequence Data, Phylogeny, Columbidae, Genetic Variation, Genome, Sequence Analysis, DNA, Evolution, Molecular, Quantitative Trait, Heritable, Polymorphism, Single Nucleotide, Receptor, EphB2
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 ›
Are you an author, or do you see a problem with this page? Request a review