Significant Synteny and Colocalization of Ecologically Relevant Quantitative Trait Loci Within and Across Species of Salmonid Fishes

Jacobs, Arne; Womack, Robyn; Chen, Mel; Gharbi, Karim; Elmer, Kathryn R.

doi:10.1534/genetics.117.300093

Cited by 17 publications

(31 citation statements)

References 86 publications

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“…To further test for the potential influence of background selection on genetic differentiation, we tested if the density of functional regions (gene density) is increased within genomic outlier windows compared to the genomic background, as (ii) gene dense regions have a higher probability of experiencing background or positive selection, (ii) gene density is potentially positively correlated with recombination rate [ 14 ] and (iii) gene density has been shown to be positively correlated with density of quantitative trait loci in salmonids [ 96 ]. However, the mean gene density within genomic outlier windows did not significantly differ compared to the genomic background ( Figure 4 D; Wilcoxon test, p = 0.8385), suggesting that background selection is not higher in genomic outlier windows compared the genomic background and does not explain increased differentiation in those regions.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, we found that five genomic outlier windows overlapped with QTL for body shape, body weight, condition factor and timing of sexual maturation, which were derived from Atlantic salmon [ 96 ], suggesting that these genomic regions are potentially involved in the divergence of those phenotypic traits.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, to indirectly infer potential functional genomic regions, we used a publicly available database of QTL for six salmonid species and their location on the Atlantic salmon genome [ 96 ] to identify QTL, derived from Atlantic salmon studies, that overlap with genomic outlier windows and loci under selection. We used Atlantic salmon derived QTL, as no QTL information are available for brown trout.…”

Section: Methodsmentioning

confidence: 99%

“…Genomic outlier windows are highlighted with red bars. QTL derived from Atlantic salmon [ 96 ] that overlap with genomic outlier windows are highlighted by stars. BS: body shape, BW: body weight, SM: Timing of sexual maturation, CF: Condition factor.…”

Section: Figurementioning

confidence: 99%

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The Genetic Architecture Underlying the Evolution of a Rare Piscivorous Life History Form in Brown Trout after Secondary Contact and Strong Introgression

Jacobs

Hughes

Robinson

et al. 2018

Genes

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Identifying the genetic basis underlying phenotypic divergence and reproductive isolation is a longstanding problem in evolutionary biology. Genetic signals of adaptation and reproductive isolation are often confounded by a wide range of factors, such as variation in demographic history or genomic features. Brown trout (Salmo trutta) in the Loch Maree catchment, Scotland, exhibit reproductively isolated divergent life history morphs, including a rare piscivorous (ferox) life history form displaying larger body size, greater longevity and delayed maturation compared to sympatric benthivorous brown trout. Using a dataset of 16,066 SNPs, we analyzed the evolutionary history and genetic architecture underlying this divergence. We found that ferox trout and benthivorous brown trout most likely evolved after recent secondary contact of two distinct glacial lineages, and identified 33 genomic outlier windows across the genome, of which several have most likely formed through selection. We further identified twelve candidate genes and biological pathways related to growth, development and immune response potentially underpinning the observed phenotypic differences. The identification of clear genomic signals divergent between life history phenotypes and potentially linked to reproductive isolation, through size assortative mating, as well as the identification of the underlying demographic history, highlights the power of genomic studies of young species pairs for understanding the factors shaping genetic differentiation.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

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The Genetic Architecture Underlying the Evolution of a Rare Piscivorous Life History Form in Brown Trout after Secondary Contact and Strong Introgression

Jacobs

Hughes

Robinson

et al. 2018

Genes

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“…This indicates that ecologically-relevant QTL do not only occur non-randomly within the stickleback genome with respect to their physical position [ 91 ], but also with respect to the frequency of crossovers occurring between them (see also [ 99 ]). Similar evidence comes from QTL of traits distinguishing hybridizing sister species of European campion flowers [ 100 ], ecotypes of Australian groundsel flowers [ 101 ], divergent life history types of a North American trout species [ 102 ], and salmonid fish in general [ 103 ]. Next, I used genome-wide crossover rate data available for threespine stickleback [ 23 ] to associate each QTL with a crossover estimate from its respective genome region.…”

Section: Does Qtl Mapping Allow Testing For Adaptive mentioning

confidence: 96%

Varied Genomic Responses to Maladaptive Gene Flow and Their Evidence

Roesti

2018

Genes

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Adaptation to a local environment often occurs in the face of maladaptive gene flow. In this perspective, I discuss several ideas on how a genome may respond to maladaptive gene flow during adaptation. On the one hand, selection can build clusters of locally adaptive alleles at fortuitously co-localized loci within a genome, thereby facilitating local adaptation with gene flow (‘allele-only clustering’). On the other hand, the selective pressure to link adaptive alleles may drive co-localization of the actual loci relevant for local adaptation within a genome through structural genome changes or an evolving intra-genomic crossover rate (‘locus clustering’). While the expected outcome is, in both cases, a higher frequency of locally adaptive alleles in some genome regions than others, the molecular units evolving in response to gene flow differ (i.e., alleles versus loci). I argue that, although making this distinction is important, we commonly lack the critical empirical evidence to do so. This is mainly because many current approaches are biased towards detecting local adaptation in genome regions with low crossover rates. The importance of low-crossover genome regions for adaptation with gene flow, such as in co-localizing relevant loci within a genome, thus remains unclear. Future empirical investigations should address these questions by making use of comparative genomics, where multiple de novo genome assemblies from species evolved under different degrees of genetic exchange are compared. This research promises to advance our understanding of how a genome adapts to maladaptive gene flow, thereby promoting adaptive divergence and reproductive isolation.

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Genomic signatures and correlates of widespread population declines in salmon

et al. 2019

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Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon ( Salmo salar ) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size ( N e ) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, N e has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability.

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Significant Synteny and Colocalization of Ecologically Relevant Quantitative Trait Loci Within and Across Species of Salmonid Fishes

Cited by 17 publications

References 86 publications

The Genetic Architecture Underlying the Evolution of a Rare Piscivorous Life History Form in Brown Trout after Secondary Contact and Strong Introgression

The Genetic Architecture Underlying the Evolution of a Rare Piscivorous Life History Form in Brown Trout after Secondary Contact and Strong Introgression

Varied Genomic Responses to Maladaptive Gene Flow and Their Evidence

Genomic signatures and correlates of widespread population declines in salmon

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