The genomic basis of adaptive evolution in threespine sticklebacks

By F. Jones, Manfred G. Grabherr, Y. F. Chan, Pamela Russell, E. Mauceli, Jeremy Johnson, Ross Swofford, Mono Pirun, M. Zody, S. White and 18 more. Nature, 2012

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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.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/7c8569edd0ac0ad6bbb57e14a80b4bbb6723f3a0

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Citations in the corpus

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions (2016, neutral): “…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).”
Speciation in Freshwater Fishes (2014, background): “In addition, increasingly well-resolved genomic approaches in ecological speciation research have uncovered surprising signatures of ancient origins of alleles and perhaps larger haplotype blocks that are divergent between very young stickleback species pairs ( Jones et al. 2012), suggesting a large”
Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations (2017, background): “The stickleback fish was an early target of whole genome assembly due to interest in understanding recurrent marine–freshwater evolution by the lineage (Jones et al. 2012).”
Contemporary evolution, allelic recycling, and adaptive radiation of the threespine stickleback (2013, background): “The same set of genomic regions in multiple, isolated freshwater populations have been selected after independent colonization of fresh water by oceanic stickleback (Hohenlohe et al., 2010; DeFaveri et al., 2011; Shimada et al., 2011; Jones et al., 2012a, 2012b; Deagle et al., 2013).”
Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow (2014, result): “Finally, it should be noted that none of our results preclude the existence of true islands of divergence in other systems that have yet to be examined using absolute divergence (e.g. sticklebacks; Hohenlohe et al. 2010; Jones et al. 2012).”