Dreau A, Venu V, Gaspar L, Jones FC (2018) Genome-wide recombination map construction from single individuals using linked-read sequencing. Nature Communications. 10:4309-4320. PDF
Verta J-P, Jones FC (2018) Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks. eLife 8:e43785. PDF
Marques DA, Jones FC, Di Palma F, Kingsley D & Reimchen TE (2018) Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation. Nature Ecology & Evolution 2:1128–1138.
Lowe CB, Sanchez-Luege N, Howes TR, Brady SD, Daugherty RR, Jones FC, Bell MA, Kingsley DM. (2018) Detecting differential copy number variation between groups of samples. Genome Research, 28(2):256-265.
Marques DA, Taylor JS, Jones FC, Di Palma F, Kingsley D & Reimchen TE (2017) Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments. PLoS Biology 15(4): e2001627.
Bay RA, Arnegard ME, Conte GL, Best J, Bedford NL, McCann SR, Dubin ME, Chan YF, Jones FC, Kingsley DM, Schluter D, Peichel CL. Genetic Coupling of Female Mate Choice with Polygenic Ecological Divergence Facilitates Stickleback Speciation. (2017) Current Biology 27:3344-3349.
Indjeian VB, Kingman GA, Jones FC, Guenther CA, Grimwood J, Schmutz J, Kingsley DM (2016) Evolving new skeletal traits by regulatory changes in bone morphogenetic proteins. Cell 164, 45-56. PDF
Conte GL, Arnegard ME, Best J, Chan YF, Jones FC, Kingsley DM, Schluter D, Peichel, K. (2015) Extent of QTL Reuse During Repeated Phenotypic Divergence of Sympatric Threespine Stickleback. Genetics 201, 1189–1200.
O'Brown NM, Summers BR, Jones FC, Brady SD, Kingsley DM (2015) A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA. eLife 10.7554/eLife.05290
Arnegard ME, McGee MD, Matthews B, Marchinko KB, Conte GL, Kabir S, Bedford N, Bergek S, Chan YF, Jones FC, Kingsley DM, Peichel CL and Schluter D. (2014) Genetics of ecological divergence during speciation. Nature, 511: 307-311.
Seehausen et al (2014) Genomics and the origin of species. Nature Reviews Genetics, 15: 176–192.
Faria R., Renaut S., Galindo J., Pinho C., Melo-Ferreira J., Melo M., Jones F., Salzburger W., Schluter D., Butlin R. (2014) Advances in Ecological Speciation: an integrative approach. Molecular Ecology, 23, 513–521.
Deagle B, Jones FC, Absher D, Kingsley D, Reimchen T. (2013) Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide SNP genotyping. Molecular Ecology 22(7):1917-1932.
AR Wark, MG Mills, LH Dang, YF Chan, FC Jones, SD Brady, DM Absher, J Grimwood, J Schmutz, RM Myers, DM Kingsley, CL Peichel (2012) Genetic architecture of variation in the lateral line sensory system of threespine sticklebacks. Genes, Genomes, Genetics 2(9):1047-56.
Jones FC*, Grabherr MG*, Chan YF*, Russell P*, Mauceli E, Zody MC, Pirun M, Johnson J, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady, SD, Zhang H, Pollen AA, Howes T, Amemiya C, Broad Whole Genome Sequencing Platform and Whole Genome Assembly Team, Lander ES, DiPalma F, Lindblad-Toh K, and Kingsley DM. (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484:55-61. PDF
Chan YF, Jones FC, McConnell E, Bryk J, Bünger L, Tautz D. (2012) Parallel selection mapping using artificially selected mice reveals bodyweight control genes. Current Biology 22:794-800.
Jones FC, Chan YF, Schmutz J., Brady SD, Southwick A, Myers RM, Schluter D, & Kingsley DM. (2012) A genome-wide genotyping array reveals patterns of global and species-pair divergence in threespine stickleback. Current Biology 22, 83-90.
Deagle B, Jones FC, Chan YF, Absher DM, Kingsley DM & Reimchen TE. (2012) Population genomics of parallel phenotypic evolution in stream–lake stickleback. Proceedings of the Royal Society of London, Series B. 279:1277-1286.
Greenwood AK, Jones FC, Chan YF, Brady SD, Absher DM, Grimwood J, Schmutz J, Myers RM, Kingsley DM & Peichel, CL. (2011) The genetic basis of divergent pigment patterns in juvenile threespine sticklebacks. Heredity 107, 155-166.
Chan YF, Marks ME, Jones FC, Villarreal G Jr, Shapiro MD, Brady SD, Southwick AM, Absher, DM, Grimwood J, Schmutz J, Myers RM, Petrov D, Jonsson B, Schluter D, Bell MA & Kingsley DM. (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 327 (5963): 302-305. PDF
Kitano J, Ross JA, Mori S, Kume M, Jones FC, Chan YF, Absher DM, Grimwood J, Schmutz J, Myers RM, Kingsley DM & Peichel CL. (2009) A role for a neo-sex chromosome in stickleback speciation. Nature 461, 1079-1083.
Jones FC, Brown C, & Braithwaite VA. (2008) Lack of assortative mating between incipient species of sticklebacks from a hybrid zone. Behaviour 145, 463-484.
Brown C, Jones FC, & Braithwaite VA. (2007) Correlation between boldness and bodymass in natural populations of the poeciliid, Brachyraphis episcopi. Journal of Fish Biology 71, 1590-1601.
Harding J, Brown C, Jones FC & Taylor R. (2007) Distribution & habitats of mosquito larvae in the kingdom of Tonga. Australian Journal of Entomology 46, 332-338.
Jones FC, Brown C, Pemberton JM & Braithwaite VA. (2006) Reproductive isolation in a threespine stickleback hybrid zone. Journal of Evolutionary Biology 19 (5), 1531-1544.
Brown C, Jones FC & Braithwaite VA. (2005) In situ examination of boldness-shyness traits in the tropical poeciliid, Brachyraphis episcopi. Animal Behaviour 70, 1003-1009.
Gaggiotti OE, Jones F, Lee WM, Amos W, Harwood J & Nichols RA. (2002) Patterns of colonization in a metapopulation of grey seals. Nature 416, 424-427.