GLOBAL ANALYSIS OF GENES INVOLVED IN FRESHWATER ADAPTATION IN THREESPINE STICKLEBACKS (<i>GASTEROSTEUS ACULEATUS</i>)

DeFaveri, Jacquelin; Shikano, Takahito; Shimada, Yukinori; Gotō, Akira; Merilä, Juha

doi:10.1111/j.1558-5646.2011.01247.x

Cited by 103 publications

(158 citation statements)

References 46 publications

(93 reference statements)

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“…Overall, our genomic coverage is roughly one SNP every 600 kb (450 Mb/760 evenly spaced SNPs) with some areas of higher coverage owing to the candidate SNPs on the array (n ¼ 280). So, while our coverage is substantially higher than many previous scans of sticklebacks [38,39], ours is almost certainly not an exhaustive catalogue of the genomic loci under divergent selection. Overall, we identified 21 stringently defined outlier regions; eight of these were from the evenly distributed SNP group (i.e.…”

Section: Discussion (A)mentioning

confidence: 93%

Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions

et al. 2011

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Understanding the genetics of adaptation is a central focus in evolutionary biology. Here, we use a population genomics approach to examine striking parallel morphological divergences of parapatric stream -lake ecotypes of threespine stickleback fish in three watersheds on the Haida Gwaii archipelago, western Canada. Genome-wide variation at greater than 1000 single nucleotide polymorphism loci indicate separate origin of giant lake and small-bodied stream fish within each watershed (mean F ST between watersheds ¼ 0.244 and within ¼ 0.114). Genome scans within watersheds identified a total of 21 genomic regions that are highly differentiated between ecotypes and are probably subject to directional selection. Most outliers were watershed-specific, but genomic regions undergoing parallel genetic changes in multiple watersheds were also identified. Interestingly, several of the stream -lake outlier regions match those previously identified in marine -freshwater and benthic -limnetic genome scans, indicating reuse of the same genetic loci in different adaptive scenarios. We also identified multiple new outlier loci, which may contribute to unique aspects of differentiation in stream-lake environments. Overall, our data emphasize the important role of ecological boundaries in driving both local and broadly occurring parallel genetic changes during adaptation.

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Section: Discussion (A)mentioning

confidence: 93%

Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions

et al. 2011

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“…For instance, in pairwise comparisons of independent colonisations of freshwater environments, parallel genetic shifts in allele frequencies across population pairs give suggestive evidence for genetic parallelism, whereas non-parallel shifts are harder to interpret (DeFaveri et al, 2011). Likewise, the predominance of examples where major loci are underlying parallel genetic changes might be reflective of a bias caused by the ease at which genetic transformations in these loci can be detected.…”

Section: Convergent Genetic Basis Of Parallel Phenotypic Evolution Inmentioning

confidence: 99%

Lakes and ponds as model systems to study parallel evolution

Merilä

2013

J Limnol

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“…However, only one of the trans-eQTL hotspots n (continued) found in this study (Chr12a) overlapped with genomic regions repeatedly found to be associated with marine/freshwater divergence by Hohenlohe et al (2010), Jones et al (2012), or Terekhanova et al (2014. Nevertheless, several studies indicate that adaptation to novel aquatic environments may also involve parts of the genome outside these large target regions (DeFaveri et al 2011;Leinonen et al 2012;Ellis et al 2015;Erickson et al 2016;Ferchaud and Hansen 2016). The QTL underlying physiological adaptations to different aquatic environments in sticklebacks have not been well characterized.…”

Section: Discussionmentioning

confidence: 74%

“…Despite expectations that trans-regulatory regions might be under purifying selection due to their potentially pleiotropic effect, and that the effect of transeQTL on expression will be weaker than that of cis-eQTL, we found many cases where gene expression was influenced by regulatory variation in trans but not in cis. This suggests that a frequently-used approach of detecting local selection by examining patterns of differentiation at markers linked to genes that are adaptive candidates (e.g., DeFaveri et al 2011) may fail to identify such selection as it is acting to change gene expression via trans-regulatory regions. We did not observe any difference in additive vs. dominance variance underlying genes found to be regulated in cis vs. those regulated in trans.…”

Section: Discussionmentioning

confidence: 99%

Regulatory architecture of gene expression variation in the threespine stickleback, Gasterosteus aculeatus

Pritchard

Viitaniemi

McCairns

et al. 2016

Preprint

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Much adaptive evolutionary change is underlain by mutational variation in regions of the genome that regulate gene expression rather than in the coding regions of the genes themselves. An understanding of the role of gene expression variation in facilitating local adaptation will be aided by an understanding of underlying regulatory networks. Here, we characterize the genetic architecture of gene expression variation in the threespine stickleback (Gasterosteus aculeatus), an important model in the study of adaptive evolution. We collected transcriptomic and genomic data from 60 half-sib families using an expression microarray and genotyping-by-sequencing, and located expression quantitative trait loci (eQTL) underlying the variation in gene expression in liver tissue using an interval mapping approach. We identified eQTL for several thousand expression traits. Expression was influenced by polymorphism in both cis-and trans-regulatory regions. TranseQTL clustered into hotspots. We did not identify master transcriptional regulators in hotspot locations: rather, the presence of hotspots may be driven by complex interactions between multiple transcription factors. One observed hotspot colocated with a QTL recently found to underlie salinity tolerance in the threespine stickleback. However, most other observed hotspots did not colocate with regions of the genome known to be involved in adaptive divergence between marine and freshwater habitats.

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GLOBAL ANALYSIS OF GENES INVOLVED IN FRESHWATER ADAPTATION IN THREESPINE STICKLEBACKS (GASTEROSTEUS ACULEATUS)

Cited by 103 publications

References 46 publications

Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions

Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions

Lakes and ponds as model systems to study parallel evolution

Regulatory architecture of gene expression variation in the threespine stickleback, Gasterosteus aculeatus

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