Publications

Journal Article (19)

1.
Journal Article
Venu, V.; Harjunmaa, E.; Dreau, A.; Brady, S.; Absher, D.; Kingsley, D.; Jones, F.: Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish. Nature Ecology & Evolution Epub ahead (2024)
2.
Journal Article
Dean, L.; Whiting, J.; Jones, F.; Maccoll, A.: Reproductive isolation in a three-way contact zone. Molecular Ecology 33 (5), e17275 (2024)
3.
Journal Article
Laine, J.; Mak, S.; Martins, N.; Chen, X.; Gilbert, M.; Jones, F.; Winther Pedersen, M.; Romundset, A.; Foote, A.: Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation. Current Biology 34 (5), pp. 1142 - 1147 (2024)
4.
Journal Article
Čapek, D.; Safroshkin, M.; Morales-Navarrete, H.; Toulany, N.; Arutyunov, G.; Kurzbach, A.; Bihler, J.; Hagauer, J.; Kick, S.; Jones, F. et al.; Jordan, B.; Müller, P.: EmbryoNet: using deep learning to link embryonic phenotypes to signaling pathways. Nature Methods 20 (6), pp. 815 - 823 (2023)
5.
Journal Article
Marques, D.; Jones, F.; Di Palma, F.; Kingsley, D.; Reimchen, T.: Genomic changes underlying repeated niche shifts in an adaptive radiation. Evolution: international journal of organic evolution 76 (6), pp. 1301 - 1319 (2022)
6.
Journal Article
Roberts Kingman, G.; Vyas, D.; Jones, F.; Brady, S.; Chen, H.; Reid, K.; Milhaven, M.; Bertino , T.; Aguirre, W.; Heins, D. et al.; von Hippel, F.; Kirch, M.; Absher, D.; Myers, R.; Di Palma, F.; Bell, M.; Kingsley, D.; Veeramah, K.: Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. Science Advances 7 (25), eabg5285 (2021)
7.
Journal Article
Kirch, M.; Romundset, A.; Gilbert, M.; Jones, F.; Foote, A.: Ancient and modern stickleback genomes reveal the demographic constraints on adaptation. Current Biology 31 (9), pp. 2027 - 2036 (2021)
8.
Journal Article
Verta, J.-P.; Jones, F.: mRNA Extraction from Gill Tissue for RNA-sequencing. Bio-protocol 10 (5), e3539 (2020)
9.
Journal Article
Dréau, A.; Venu, V.; Avdievich, E.; Gaspar, L.; Jones, F.: Genome-wide recombination map construction from single individuals using linked-read sequencing. Nature Communications 10 (1), 4309 (2019)
10.
Journal Article
Verta, J.-P.; Jones, F.: Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks. eLife 8, e43785 (2019)
11.
Journal Article
Marques, D.; Jones, F.; Di Palma, F.; Kingsley, D.; Reimchen, T.: Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation. Nature Ecology & Evolution 2 (7), pp. 1128 - 1138 (2018)
12.
Journal Article
Lv, S.; Wu, W.; Wang, M.; Meyer, R.; Ndjiondjop, M.-N.; Tan, L.; Zhou, H.; Zhang, J.; Fu, Y.; Cai, H. et al.; Sun, C.; Wing, R.; Zhu, Z.: Genetic control of seed shattering during African rice domestication. Nature Plants 4 (6), pp. 331 - 337 (2018)
13.
Journal Article
Stein, J.; Yu, Y.; Copetti, D.; Zwickl, D.; Zhang, L.; Zhang, C.; Chougule, K.; Gao, D.; Iwata, A.; Goicoechea, J. et al.; Wei, S.; Wang, J.; Liao, Y.; Wang, M.; Jacquemin, J.; Becker, C.; Kudrna, D.; Zhang, J.; Londono, C.; Song, X.; Lee, S.; Sanchez, P.; Zuccolo, A.; Ammiraju, J.; Talag, J.; Danowitz, A.; Rivera, L.; Gschwend, A.; Noutsos, C.; Wu, C.; Kao, S.; Zeng, J.; Wei, F.; Zhao, Q.; Feng, Q.; El Baidouri, M.; Carpentier, M.; Lasserre, E.; Cooke, R.; Rosa Farias, D.; da Maia, L.; Dos Santos, R.; Nyberg, K.; McNally, K.; Mauleon, R.; Alexandrov, N.; Schmutz, J.; Flowers, D.; Fan, C.; Weigel, D.; Jena, K.; Wicker, T.; Chen, M.; Han, B.; Henry, R.; Hsing, Y.; Kurata, N.; de Oliveira, A.; Panaud, O.; Jackson, S.; Machado, C.; Sanderson, M.; Long, M.; Ware, D.; Wing, R.: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics 50 (2), pp. 285 - 296 (2018)
14.
Journal Article
Stein, J.; Yu, Y.; Copetti, D.; Zwickl, D.; Zhang, L.; Zhang, C.; Chougule, K.; Gao, D.; Iwata, A.; Goicoechea, J. et al.; Wei, S.; Wang, J.; Liao, Y.; Wang, M.; Jacquemin, J.; Becker, C.; Kudrna, D.; Zhang, J.; Londono, C.; Song, X.; Lee, S.; Sanchez, P.; Zuccolo, A.; Ammiraju, J.; Talag, J.; Danowitz, A.; Rivera, L.; Gschwend, A.; Noutsos, C.; Wu, C.; Kao, S.; Zeng, J.; Wei, F.; Zhao, Q.; Feng, Q.; El Baidouri, M.; Carpentier, M.; Lasserre, E.; Cooke, R.; Rosa Farias, D.; da Maia, L.; Dos Santos, R.; Nyberg, K.; McNally, K.; Mauleon, R.; Alexandrov, N.; Schmutz, J.; Flowers, D.; Fan, C.; Weigel, D.; Jena, K.; Wicker, T.; Chen, M.; Han, B.; Henry, R.; Hsing, Y.; Kurata, N.; de Oliveira, A.; Panaud, O.; Jackson, S.; Machado, C.; Sanderson, M.; Long, M.; Ware, D.; Wing, R.: Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics 50 (11), p. 1618 (2018)
15.
Journal Article
Marques, D.; Taylor, J.; Jones, F.; Di Palma, F.; Kingsley, D.; Reimchen, T.: Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments. PLoS Biology 15 (4), e2001627 (2017)
16.
Journal Article
Prunier, J.; Verta, J.-P.; MacKay, J.: Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function. New Phytologist 209 (1), pp. 44 - 62 (2016)
17.
Journal Article
Arif, S.; Kittelmann, S.; McGregor, A.: From shavenbaby to the naked valley: trichome formation as a model for evolutionary developmental biology. Evolution and Development 17 (1), pp. 120 - 126 (2015)
18.
Journal Article
Seehausen, O.; Butlin, R.; Keller, I.; Wagner, C.; Boughman, J.; Hohenlohe, P.; Peichel, C.; Saetre, G.-P.; Bank, C.; Brännström, A. et al.; Brelsford, A.; Clarkson, C.; Eroukhmanoff, F.; Feder, J.; Fischer, M.; Foote, A.; Franchini, P.; Jiggins, C.; Jones, F.; Lindholm, A.; Lucek, K.; Maan, M.; Marques, D.; Martin, S.; Matthews, B.; Meier, J.; Möst, M.; Nachman, M.; Nonaka, E.; Rennison, D.; Schwarzer, J.; Watson, E.; Westram, A.; Widmer, A.: Genomics and the origin of species. Nature Reviews Genetics 15 (3), pp. 176 - 192 (2014)
19.
Journal Article
Faria, R.; Renaut, S.; Galindo, J.; Pinho, C.; Melo-Ferreira, J.; Melo, M.; Jones, F.; Salzburger, W.; Schluter, D.; Butlin, R.: Advances in Ecological Speciation: an integrative approach. Molecular Ecology 23 (3), pp. 513 - 521 (2014)

Meeting Abstract (13)

20.
Meeting Abstract
Laine, J.; Mak, S.; Martins, N.; Chen, X.; Gilbert, T.; Jones, F.; Winther Pedersen, M.; Romundset, A.; Foote, A.: Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation. In Population Genetics Group 57 (PopGroup57), 48, p. 48. Population Genetics Group 57 (PopGroup57), St. Andrews, Scotland, January 08, 2024 - January 10, 2024. (2024)
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