Publications

Full List

_{Lab members italicized.}

Patents

• 2020 Kučka, M., Dréau, A., Chan, Y.F., Haplotagging — Single tube combinatorial barcoding of nucleic acid molecules. European Patent Office, PCT/EP2020/053948, filed 14.Feb.2020 and 24.Apr.2020 Pending

Research articles

• 2021 Montejo-Kovacevich, G., J. I. Meier, C. N. Bacquet, I. A. Warren, Y. F. Chan, M. Kučka,  C. Salazar, N. Rueda, S. H. Montgomery, W. O. McMillan, K. M. Kozak, N. J. Nadeau, S. Martin, C. D. Jiggins. Repeated genetic adaptation to high altitude in two tropical butterflies. In review at Nat. Comm., also bioRxiv, doi: 10.1101/2021.11.30.470630
• 2021 Martin Cerezo, M.L., R. Rohan, B. De Haro Reyes, M. Kučka, Y.F. Chan, J. Bryk. Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol. Mol. Ecol. Res., in revision, also bioRxiv, doi: 10.1101/2021.09.21.461194
• 2021 Song, J.H.T., R. L. Grant, V. C. Behrens, M. Kučka, G. A. R. Kingman, V. Soltys, Y.F. Chan, D. M. Kingsley. Genetic studies of human-chimpanzee divergence using stem cell fusions. PNAS, 118(51) e2117557118, doi: 10.1073/pnas.2117557118
• 2021 Meier, J.I.*, Salazar, P.A.*, Kučka, M.*, Davies, R.W., Dréau, A., Aldás, I., Box-Power, O., Nadeau, N., Bridle, J.R., Rolian, C.P., Barton, N.H., McMillan, W.O., Jiggins, C.D.^†, Chan, Y.F.^† Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. (* co-first authors; † co-last authors). PNAS, 118 (25) e2015005118, doi: 10.1073/pnas.2015005118
• 2021 Davies, R.W, Kučka, M., Su, D., Shi, S., Flanagan, M., Cunniff, C.M., Chan, Y.F.*, Myers, S.*, Rapid genotype imputation from sequence with reference panels. (* co-last authors). Nature Genetics. doi: 10.1038/s41588-021-00877-0
• 2021 Montejo-Kovacevich, G., P. A. Salazar, S. H. Smith, K. Gavilanes, C. N. Bacquet, Y. F. Chan, C. D., Jiggins, J. I. Meier, N. J. Nadeau, Genomics of altitude-associated wing shape in two tropical butterflies. Accepted at Molecular Ecology, bioRxiv, doi: 10.1101/2020.12.05.412882
• 2021 Wilches, R., Beluch, W.H., McConnell, E., Tautz, D., Chan, Y.F. Independent evolution towards large body size in the distinctive Faroe Island mice. G3, doi: 10.1093/g3journal/jkaa051; bioRxiv, doi: 10.1101/747097 
• 2020 Hillis, D., Yadgary, L., Weinstock, G.M., Pardo-Manuel de Villena, F., Pomp, D., Chan, Y.F., Xu, S. Fowler, A., Garland Jr., T. Genetic basis of aerobically supported voluntary exercise: results from a selection experiment with house mice. Genetics 216(3): 781-804., doi: 10.1534/genetics.120.303668
• 2020 Martin Cerezo, M.L., Kučka, M., Zub., K., Chan, Y.F., Bryk, J. Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in Poland using ddRAD-seq. BMC Genomics. 21, 241. doi: 10.1186/s12864-020-6603-3 PDF
• 2020 Byers, K.J.R.P., Darragh, K., Musgrove, J., Abondano Almeida, D., Garza, S.F., Kučka, M., Chan, Y.F., Rastas, P., Merrill, R.M., McMillan, O.W., Schulz, S., Jiggins, C.D. A major genetic locus controls a biologically active pheromone component in Heliconius melpomene. Evolution 74-2: 349–364, doi: 10.1111/evo.13922
• 2019 Daugherty, R.R., Hare, E.E., Chan, Y.F., Jones, F.C., Kingman, G.A., Howes. T., Zhang H., Pollen A.A., Brady S.D., Xie, K.T., Lowe, C., Grimwood, J., Schmutz, J., Myers R.M., Schluter D., Heins D., Reyes M.L., Baker J.A., Reimchen T.E., Bell, M.A., Kingsley D.M., Rapid and repeated evolution of myosin copy number in threespine sticklebacks. Submitted to Current Biology.
• 2019 Lustyk, D., Kinský, S., Ullrich, K., Yancoskie, M.N., Kašíková, L., Gergelits, V., Sedláček, R., Chan, Y.F., Odenthal-Hesse, L., Forejt, J., Jansa, P. Fine mapping and positional cloning of the Hstx1/2 locus modulating the Prdm9-dependent hybrid male sterility in mice. Genetics. doi: 10.1534/genetics.119.302554. 
• 2019 Dréau, A., Venu, V., Gaspar, L., Jones, F.C. Genome-wide recombination map construction from single individuals using linked-read sequencing. Nature Communications 10: 4309. 
• 2019 Zhou, S., Fu, X., Pei, P., Kučka, M., Liu, J., Tang, L., Zhan, T., He, S., Lu, Z., Chan, Y.F., Rödelsperger, C., Liu, D., Streit, A. Identification of a non-sexual population of Strongyloides stercoralis with hybrid 18S rDNA haplotypes in Guangxi, Southern China. PLoS Neglected Tropical Disease. 13(5): e0007396. 
• 2019 Castro, J.P.L.*, Yancoskie, M.N.*, Marchini, M., Belohlavy S., Hiramatsu, L., Kučka, M., Beluch, W.H., Naumann R., Barton, N.H., Rolian, C.^†, Chan, Y.F^†. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife, (8):e42014. doi: 10.7554/eLife.42014. * co-first authors; † co-last authors; PDF Supplementary Fig.
• 2018 Thompson, A.C., Capellini, T.D., Guenther, C.A., Chan, Y.F., Infante, C.R., Menke, D.B., Kingsley, D.M. A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates. eLife, (7):e38555.
• 2018 Lazzarano, S., Kučka, M., Castro, J.P.L., Naumann, R., Medina, P., Fletcher, M.N-C., Wombacher, R., Gribnau, J., Hochepied, T., Van Montagu M., Libert C., Chan, Y.F. Genetic mapping of species differences via “in vitro crosses” in mouse embryonic stem cells. PNAS 115 (14) 3680-3685; Online Early. doi: 10.1073/pnas.1717474115. PDF
• 2017 Bay, R.A., Arnegard, M.E., Conte, G.L., Best, J., Bedford, N.L., McCann, S.R., Dubin, M.E., Chan, Y.F., Jones, F.C., Kingsley, D.M., Schluter, D., Peichel, C.L., Genetic coupling of female mate choice with polygenic ecological divergence facilitates stickleback speciation. Current Biology, 27(21):3344-3349.
• 2015 Conte, G.L., Arnegard, M.E., Best, J., Chan Y.F., Jones, F.C., Kingsley, D.M., Schluter, D., Peichel, C.L. The extent of parallel genetic evolution underlying parallel phenotypic evolution in threespine stickleback species pairs. Genetics. 201: 1189-1200.
• 2014 Arnegard, M.E., McGee, M.D., Matthews, B.W., Marchinko, K.B., Conte, G.L., Kabir, S., Bedford, N., Bergek, S., Jones, F.C., Chan, Y.F., Kingsley, D.M., Peichel, C.L., Schluter, D. Genetics of ecological divergence during speciation. Nature (Article) 511: 307-311.
• 2012 Wark, A.R., Mills, M.G., Dang, L-H., Chan, Y.F., Jones, F.C., Brady, S.D., Absher, D.M., Grimwood, J., Schmutz, J., Myers, R.M., Kingsley, D.M., Peichel, C.L. Genetic architecture of variation in the lateral line sensory system of threespine sticklebacks. G3: Genes, Genomes, Genetics. 2 (9): 1047-1056.
• 2012 Jones, F.C.*, Grabherr M.G.*, Chan, Y.F.*, Russell, P.*, Mauceli, E., Johnson, J., Pirun, M., Zody, M. C., White, S., Birney, E., Searle, S., Schmutz, J., Grimwood, J., Dickson, M.C., Myers, R.M., Miller, C.T., Summers, B.R., Knecht, A.K., Brady, S.D., Zhang, H., Pollen, A.A., Howes, T., Amemiya, C., Broad Institute Genome Sequencing Platform and Whole Genome Assembly Team, Lander, E.S., Di Palma, F., Lindblad-Toh, K., Kingsley, D.M. The genomic basis of adaptive evolution in threespine sticklebacks. Nature (Article). 484 (7392): 55-61. (* co-first authorship) PDF 

   

  • Featured in Nature

   

• 2012 Chan, Y.F., Jones, F.C., McConnell, E., Bryk, J., Bünger, L., Tautz, D. 2012. Parallel selection mapping using artificially selected mice reveals bodyweight control loci. Current Biology. 22 (9): 794-800. PDF

   

  • Featured in Nature Review Genetics, Current Biology

   

• 2011 Jones, F.C., Chan, Y.F., Schmutz, J., Grimwood, J. Brady, S.D., Southwick, A.M., Absher, D.M., Myers, R.M., Reimchen, T.E., Deagle, B.E., Schluter, D., Kingsley, D.M. A genome-wide genotyping array reveals patterns of global and repeated species pair divergence in sticklebacks. Current Biology. 22 (1): 83-90.
• 2011 Deagle, B., Jones, F.C., Chan, Y.F., Absher, D.M., Kingsley, D.M., Reimchen, T.E. Population genomics of parallel phenotypic evolution in stream–lake stickleback. Proceedings of the Royal Society B. 279 (1732): 1277-1286.
• 2011 Greenwood, A.K., Jones, F.C., Chan, Y.F., Brady, S.D., Absher, D.M., Grimwood, J., Schmutz, J., Myers, R.M., Kingsley, D.M., Peichel, C.L. The genetic basis of cryptic pigment patterns in juvenile threespine sticklebacks. Heredity. 107: 155-166.
• 2010 Chan, Y.F., Marks, M.E., Jones, F.C., Villarreal G. Jr., Shapiro, M.D., Brady, S.D., Southwick, A.M., Absher, D.M., Grimwood, J., Schmutz, J., Myers, R.M., Petrov, D., Jónsson, B., Schluter, D., Bell, M.A., Kingsley D.MAdaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science (Article) 327 (5963): 302-305. PDF 

   

  • Featured in Science, Nature
  • Section highlight in Developmental Biology, 9^th Ed (p. 686) by S. Gilbert
  • Featured in NPR Science Friday & New York Times Science

   

• 2009 Kitano, J., Ross, J. A., Mori, S., Kume, M., Jones, F. C., Chan, Y.F., Absher^, D.M., Grimwood, J., Schmutz, J., Myers R.M., Kingsley, D.M., Peichel, C.L. A role for neo-sex chromosomes in stickleback speciation. Nature (Article) 461 (7267): 1079-1083.

Book chapters

• 2017 Ullate-Agote A., Chan Y.F., Tzika, A.C. A step-by-step guide to assemble a reptilian genome. Chapter in Methods in Molecular Biology - Avian and Reptilian Developmental Biology. Guojun Sheng (ed.). Springer, New York.

Commentary or Book reviews

• 2015 Chan, Y.F. Evolution: two (very long) legs to stand on. (News and Commentary). Curr Biol. 2015 Nov 2;25(21):R1037-40.
• 2012 Chan, Y.F. A personal primer for modern biology. (Book review). Trends in Ecology and Evolution. DOI: 10.1016/j.tree.2012.07.012.
• 2012 Chan, Y.F. Parallel evolution: hearing echoes. (News & Commentary) Heredity 108: 471-472.