The genomic basis of adaptive evolution in threespine sticklebacks

Jones, Felicity C.; Grabherr, Manfred; Chan, Yingguang Frank; Russell, Pamela; Mauceli, Evan; Johnson, Jeremy; Swofford, Ross; Pirun, Mono; Zody, Michael C.; White, Simon; Birney, Ewan; Searle, Stephen M. J.; Schmutz, Jeremy; Grimwood, Jane; Dickson, Mark; Myers, R; Miller, Craig T.; Summers, Brian R.; Knecht, Anne K.; Brady, Shannon D.; Zhang, Haili; Pollen, Alex A.; Howes, Timothy; Amemiya, Chris T.; Lander, Eric S.; Palma, Federica Di; Lindblad‐Toh, Kerstin; Kingsley, David M.

doi:10.1038/nature10944

Cited by 1,665 publications

(2,206 citation statements)

References 48 publications

Supporting

109

Mentioning

2,036

Contrasting

Unclassified

Order By: Relevance

“…2013) and genetic divergence between species can increase within inverted regions through reduction of gene flow (Navarro and Barton 2003b; Jones et al. 2012; McGaugh and Noor 2012; Lohse et al. 2015).…”

Section: Introductionmentioning

confidence: 99%

No evidence for maintenance of a sympatricHeliconiusspecies barrier by chromosomal inversions

et al. 2017

View full text Add to dashboard Cite

Mechanisms that suppress recombination are known to help maintain species barriers by preventing the breakup of coadapted gene combinations. The sympatric butterfly species Heliconius melpomene and Heliconius cydno are separated by many strong barriers, but the species still hybridize infrequently in the wild, and around 40% of the genome is influenced by introgression. We tested the hypothesis that genetic barriers between the species are maintained by inversions or other mechanisms that reduce between‐species recombination rate. We constructed fine‐scale recombination maps for Panamanian populations of both species and their hybrids to directly measure recombination rate within and between species, and generated long sequence reads to detect inversions. We find no evidence for a systematic reduction in recombination rates in F1 hybrids, and also no evidence for inversions longer than 50 kb that might be involved in generating or maintaining species barriers. This suggests that mechanisms leading to global or local reduction in recombination do not play a significant role in the maintenance of species barriers between H. melpomene and H. cydno.

show abstract

Section: Introductionmentioning

confidence: 99%

No evidence for maintenance of a sympatricHeliconiusspecies barrier by chromosomal inversions

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Evidence of convergent evolution (Arendt & Reznick, 2008), or the repeated evolution of similar phenotypes from similar genetic mechanisms is increasing (Stern, 2013; Jones et al., 2012; Yeaman et al., 2016), but it is currently limited to a few taxa. Eastern white pine ( Pinus strobus , Figure 1) and western white pine ( P. monticola ) diverged <12 million years ago (Gernandt et al., 2008) and are well suited for studying local adaptation as both species are distributed latitudinally and longitudinally across a wide variety of climates in North America.…”

Section: Introductionmentioning

confidence: 99%

The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines

Nadeau

Meirmans

Aitken

et al. 2016

Ecology and Evolution

120

View full text Add to dashboard Cite

Accurately detecting signatures of local adaptation using genetic‐environment associations (GEAs) requires controlling for neutral patterns of population structure to reduce the risk of false positives. However, a high degree of collinearity between climatic gradients and neutral population structure can greatly reduce power, and the performance of GEA methods in such case is rarely evaluated in empirical studies. In this study, we attempted to disentangle the effects of local adaptation and isolation by environment (IBE) from those of isolation by distance (IBD) and isolation by colonization from glacial refugia (IBC) using range‐wide samples in two white pine species. For this, SNPs from 168 genes, including 52 candidate genes for growth and phenology, were genotyped in 133 and 61 populations of Pinus strobus and P. monticola, respectively. For P. strobus and using all 153 SNPs, climate (IBE) did not significantly explained among‐population variation when controlling for IBD and IBC in redundancy analyses (RDAs). However, 26 SNPs were significantly associated with climate in single‐locus GEA analyses (Bayenv2 and LFMM), suggesting that local adaptation took place in the presence of high gene flow. For P. monticola, we found no evidence of IBE using RDAs and weaker signatures of local adaptation using GEA and F ST outlier tests, consistent with adaptation via phenotypic plasticity. In both species, the majority of the explained among‐population variation (69 to 96%) could not be partitioned between the effects of IBE, IBD, and IBC. GEA methods can account differently for this confounded variation, and this could explain the small overlap of SNPs detected between Bayenv2 and LFMM. Our study illustrates the inherent difficulty of taking into account neutral structure in natural populations and the importance of sampling designs that maximize climatic variation, while minimizing collinearity between climatic gradients and neutral structure.

show abstract

“…At present, the feasibility of whole genome resequencing for ecological genomics depends somewhat on genome size and complexity, as well as budget. In ecological genomics of fishes more generally, stickleback fishes (genome size 675 Mb) are now often whole genome resequenced (Jones et al, 2012;Terekhanova et al, 2014) as are some cichlids (genome size *1 Gb) either with few individuals at high coverage (e.g. Brawand et al, 2014) or with individuals pooled and overall lower coverage focusing on fixed differences (e.g.…”

Section: Whole Genome Resequencingmentioning

confidence: 99%

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Elmer

2016

Hydrobiologia

View full text Add to dashboard Cite

The past few years have seen an absolute revolution in genomic technologies and their potential applications to ecology and evolutionary biology research. Such advances open up a range of opportunities for research on non-model organisms and individuals drawn from wild populations. This has resulted in exciting new research seeking to identify the genetic polymorphisms important in adaptation and speciation and how they are organised within the genome. Building on this, there is great interest in the extent to which similar evolutionary patterns are found across multiple populations, particularly whether consistent genetic mechanisms are associated with recurrent phenotypes. A powerful context for disentangling these mechanisms is to focus on highly diverse radiations, where phenotypes vary in and across environments. Therefore, the high diversity found within and among species of salmonid fishes such as charr (Salvelinus) make for an ideal 'non'-model for genomic research. This paper outlines some of the current approaches available in ecological genomics and highlights some recent advances in salmonid research. It also suggests avenues for the sort of predictions that can be derived from ecological genomics, with the aim of understanding the genetics behind the fantastic diversity of salmonid fishes.Keywords Ecological genomics Á Transcriptomics Á Speciation Á Genetic mapping Á Salmonid fishes Á Charr Recent advances in the field of molecular biology have exciting implications for research on the ecology and evolution of natural populations. Particularly, high throughput 'next-generation' sequencing (NGS) (also known as 'second-generation', or 'massively parallel' sequencing) can generate huge amounts of genomic or transcriptomic data on almost any organism. NGS is dramatically decreasing in cost and the associated tools and pipelines are within reach of even modest research groups. This is therefore becoming an invaluable tool for understanding the origins and maintenance of biodiversity. These exciting new approaches can address long-standing questions in evolutionary biology, such as: What is the genetic basis of adaptations? How do closely related species differ? Why are some lineages more diverse than others?The challenge for 'omics' of non-model organisms now shifts away from raw data generation to focusing on informative evolutionary, ecological, and environmental contexts in order to most efficiently and

show abstract

The genomic basis of adaptive evolution in threespine sticklebacks

Cited by 1,665 publications

References 48 publications

No evidence for maintenance of a sympatricHeliconiusspecies barrier by chromosomal inversions

No evidence for maintenance of a sympatricHeliconiusspecies barrier by chromosomal inversions

The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Contact Info

Product

Resources

About