The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
The genomic basis of adaptive evolution in threespine sticklebacks
Open accessAbstract
Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature. A reference genome sequence for threespine sticklebacks, and re-sequencing of 20 additional world-wide populations, reveals loci used repeatedly during vertebrate evolution; multiple chromosome inversions contribute to marine-freshwater divergence, and regulatory variants predominate over coding variants in this classic example of adaptive evolution in natural environments. Threespine sticklebacks have become a powerful model for studying the molecular basis of adaptive evolution. This paper presents a high-quality reference genome sequence, along with genomes of 20 further individuals from a global set of marine and freshwater populations. Genomic analysis reveals that reuse of globally shared standing genetic variation plays an important part in repeated evolution of distinct stickleback populations, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. The data are consistent with an important role for regulatory changes during parallel evolution of marine and freshwater sticklebacks.
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Cites
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971
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Self-citationThe evolutionary significance of cis-regulatory mutations
Wray, G. A. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2063 · Cited by 1,521
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
Self-citationChromosome inversions, local adaptation and speciation
Kirkpatrick, M., & Barton, N. (2006) · Genetics · doi:10.1534/genetics.105.047985 · Cited by 1,178
Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer
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Self-citationChromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry
Joron, M., Frezal, L., Jones, R. T., Chamberlain, N. L., Lee, S. F., Haag, C. R., Whibley, A., Becuwe, M., Baxter, S. W., Ferguson, L., et al. (2011) · Nature · doi:10.1038/nature10341 · Cited by 574
The genetic architecture of parallel armor plate reduction in threespine sticklebacks.
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Self-citationMiller, C. T., Beleza, S., Pollen, A. A., Schluter, D., Kittles, R. A., Shriver, M. D., & Kingsley, D. M. (2007) · Cell · doi:10.1016/j.cell.2007.10.055 · Cited by 388
Self-citationConstraints on utilization of the EDA-signaling pathway in threespine stickleback evolution.
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Cited by
A comparative encyclopedia of DNA elements in the mouse genome
Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., et al. (2014) · Nature · doi:10.1038/nature13992 · Cited by 1,781
The Ensembl gene annotation system
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Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions
Hoban, S., Kelley, J. L., Lotterhos, K. E., Antolin, M. F., Bradburd, G., Lowry, D. B., Poss, M. L., Reed, L. K., Storfer, A., & Whitlock, M. C. (2016) · The American Naturalist · doi:10.1086/688018 · Cited by 876
“…where there is known or strongly suspected differentiation caused by local adaptation, where gene fl ow should reduce differentiation of loci not under selection (e.g., Turner et al. 2010 for Arabidopsis lyrata ; Jones et al. 2012 for stickle-backs; Foll et al. 2014 for human altitude adaptations).”
The genetic causes of convergent evolution
Stern, D. L. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3483 · Cited by 818
Metadata
- Authors
- Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., Swofford, R., 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., Lander, E. S., Di Palma, F., Lindblad-Toh, K., & Kingsley, D. M.
- Venue
- Nature
- Published
- 2012-04
- Volume
- 484
- Issue
- 7392
- Pages
- 55-61
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2102163928
- Cited by
- 1,777
- References
- 10
- FWCI
- 83.97
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., Swofford, R., 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., . . . Kingsley, D. M. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature. https://doi.org/10.1038/nature10944
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