Capturing the rapidly evolving study of adaptation

Fruciano, Carmelo; Franchini, Paolo; Jones, Julia C.

doi:10.1111/jeb.13871

Cited by 9 publications

(5 citation statements)

References 110 publications

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“…A major goal of evolutionary biology is to identify the relative importance of adaptive evolution through genomic signatures of natural selection (Fruciano et al, 2021). The widespread focus on genome scanning techniques (De Villemereuil et al, 2014), which rely primarily on SNPs, is based on their abundance in the genome (González et al, 2009; Hoban et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say)

2023

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Structural variation has been associated with genetic diversity and adaptation. Despite these observations, it is not clear what their relative importance is for evolution, especially in rapidly adapting species. Here, we examine the significance of structural polymorphisms in pesticide resistance evolution of the agricultural super-pest, the Colorado potato beetle, Leptinotarsa decemlineata. By employing a parent offspring trio sequencing procedure, we develop highly contiguous reference genomes to characterize structural variation. These updated assemblies represent >100-fold improvement of contiguity and include derived pest and ancestral nonpest individuals. We identify >200,000 structural variations, which appear to be nonrandomly distributed across the genome as they co-occur with transposable elements and genes. Structural variations intersect with exons in a large proportion of gene annotations (~20%) that are associated with insecticide resistance (including cytochrome P450s), development, and transcription. To understand the role structural variations play in adaptation, we measure their allele frequencies among an additional 57 individuals using whole genome resequencing data, which represents pest and nonpest populations of North America. Incorporating multiple independent tests to detect the signature of natural selection using SNP data, we identify 14 genes that are probably under positive selection, include structural variations, and SNPs of elevated frequency within the pest lineages. Among these, three are associated with insecticide resistance based on previous research. One of these genes, CYP4g15, is coinduced during insecticide exposure with glycosyltransferase-13, which is a duplicated gene enclosed within a structural variant adjacent to the CYP4g15 genic region. These results demonstrate the significance of structural variations as a genomic feature to describe species history, genetic diversity, and adaptation.

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Section: Discussionmentioning

confidence: 99%

The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say)

2023

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“…The CPLs detected in this study were found located in both gene body and upstream–downstream regions close to genes. The distribution of SNPs in distinct genomic regions is important in evolutionary studies and is now often reported in the literature ( e.g ., Fruciano et al ., 2021; She & Jarosz, 2018). Within pigmentation studies, the literature initially emphasized both the relative roles of coding (Protas & Patel, 2008; Uy et al ., 2016) and upstream‐downstream regulatory variation (Larter et al ., 2018; Toomey et al ., 2018)—more rarely their interactions (Vickrey et al ., 2018)—during colour pattern establishment and evolution.…”

Section: Discussionmentioning

confidence: 99%

Redundancy analysis, genome‐wide association studies and the pigmentation of brown trout (Salmo trutta L.)

Valette

Leitwein

Lascaux³

et al. 2022

Journal of Fish Biology

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The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single-and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single-and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium-and ionbinding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.

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“…It denotes the strategic actions and instruments used to anticipate disaster risk; reduce existing exposure, hazard, or vulnerability, as well as improve resilience; considering that environmental stability, hazard threat, and socioeconomic vulnerability together determine the way that disasters are formed, establish the spatial extent of disaster impact, and generate the scale of losses (Shi et al 2020); d) Adaptation actions must respond to the problems identified in the corresponding diagnoses: The prioritization of adaptation actions has to be related to the problems identified in the climate agenda and to the analysis of current and future vulnerability, these measures must consider the participation of social actors. Consequently, it is suggested to meet the following characteristics: 1) Feasible; (2) Budgeted; (3) Synergistic; (4) Co-benefits; (5) Aligned; (6) Evaluable; (7) Equity; (8) Credibility; (9) No Regret; and (10) Reversibility. Monitoring and Evaluation (M&E) of climate change adaptation measures is also a very important step.…”

Section: Is Adaptation Enough To Face Climate Change?mentioning

confidence: 99%

A Current Look at Adaptation to Climate Change: A Brief Review

Russo,

Figueroa

2023

IJLSAR

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Climate change is already an evident reality and an issue discussed globally. Natural and water resources are declining in most basins, sea levels are rising; and even if it is possible to reduce the emissions of greenhouse gases (GHG) that cause climate change, and thus avoid its most serious consequences, the negative trends will continue in the coming decades due to the inertia of the climate system (UN 2022). Today, no country is free from the bio-physical impacts of climate change; additional costs are also generated, with both the most vulnerable people and ecosystems being most affected. Adaptation is a top priority for developing countries, including more resilient agricultural practices and migration to safer places. The mitigation actions that the Member States of the United Nations have committed to undertake are not enough to achieve the reduction in greenhouse gases necessary for climate stabilization. So, to achieve climate adaptation the climate costs and the management of sustainable and resilient development require an enormous number of new resources.

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Capturing the rapidly evolving study of adaptation

Cited by 9 publications

References 110 publications

The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say)

The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say)

Redundancy analysis, genome‐wide association studies and the pigmentation of brown trout (Salmo trutta L.)

A Current Look at Adaptation to Climate Change: A Brief Review

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