Climate Change Genomics Calls for Standardized Data Reporting

Waldvogel, Ann‐Marie; Schreiber, Dennis; Pfenninger, Markus; Feldmeyer, Barbara

doi:10.3389/fevo.2020.00242

Cited by 28 publications

(22 citation statements)

References 52 publications

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“…However, most of the reliably annotated genes with or close to SNP loci significantly associated with drought phenotypes had putative homologs in other plant species previously shown to be involved in drought or different environmental stress response (for citations, see Supplementary file 1C, D ). For the remaining, not annotated genes, it remained unclear whether they had really never been associated with drought before, or whether we were just unable to make this link due to the lack of (ecological) annotation and standardised reporting ( Waldvogel et al, 2021 ). The involvement of in total 67 genes, together with the relatively flat effect size distribution, suggested that drought resistance in F. sylvatica is a moderately polygenic trait, which should respond well to artificial breeding attempts and natural selection.…”

Section: Discussionmentioning

confidence: 99%

Genomic basis for drought resistance in European beech forests threatened by climate change

Pfenninger

Reuss

Kiebler

et al. 2021

eLife

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In the course of global climate change, central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) differently: even in the same stand, drought damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated SNPs throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. A SNP-assay with 70 loci allowed predicting drought phenotype in 98.6% of a validation sample of 92 trees. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding.

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Section: Discussionmentioning

confidence: 99%

Genomic basis for drought resistance in European beech forests threatened by climate change

Pfenninger

Reuss

Kiebler

et al. 2021

eLife

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“…Such differences prevail over time if selective local pressures and other evolutionary drivers overcome the homogenizing effect of gene flow (Sanford and Kelly, 2011;Blanquart et al, 2013;Whitlock, 2015). Understanding the genetic basis of adaptive phenotypes helps, eventually, to predict how populations will respond to climate change (Waldvogel et al, 2020) or human-driven habitat translocations; a common aquaculture practice, helpful as a mitigation strategy to increase genetic diversity and reduce extinction risk of inbred and small populations (Šegvić-Bubić et al, 2020). Nevertheless, translocations could increase the risk of loss of locally adapted alleles through the hybridization of divergent populations (Ottenburghs, 2021).…”

Section: Introductionmentioning

confidence: 99%

Adaptive Differences in Gene Expression in Farm-Impacted Seedbeds of the Native Blue Mussel Mytilus chilensis

et al. 2021

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The study of adaptive population differences is relevant for evolutionary biology, as it evidences the power of selective local forces relative to gene flow in maintaining adaptive phenotypes and their underlying genetic determinants. However, human-mediated hybridization through habitat translocations, a common and recurrent aquaculture practice where hybrids could eventually replace local genotypes, risk populations’ ability to cope with perturbations. The endemic marine mussel Mytilus chilensis supports a booming farming industry in the inner sea of Chiloé Island, southern Chile, which entirely relies on artificially collected seeds from natural beds that are translocated to ecologically different fattening centers. A matter of concern is how farm-impacted seedbeds will potentially cope with environmental shifts and anthropogenic perturbations. This study provides the first de novo transcriptome of M. chilensis; assembled from tissue samples of mantles and gills of individuals collected in ecologically different farm-impacted seedbeds, Cochamó (41°S) and Yaldad (43°S). Both locations and tissue samples differentially expressed transcripts (DETs) in candidate adaptive genes controlling multiple fitness traits, involved with metabolism, genetic and environmental information processing, and cellular processes. From 189,743 consensus contigs assembled: 1,716 (Bonferroni pvalue ≤ 0.05) were DETs detected in different tissues of samples from different locations, 210 of them (fold change ≥ | 100|) in the same tissue of samples from a different location, and 665 (fold change ≥ | 4|) regardless of the tissue in samples from a different location. Site-specific DETs in Cochamó (169) and Yaldad (150) in candidate genes controlling tolerance to temperature and salinity shifts, and biomineralization exhibit a high number of nucleotide genetic variants with regular occurrence (frequency > 99%). This novel M. chilensis transcriptome should help assessing and monitoring the impact of translocations in wild and farm-impacted mussel beds in Chiloé Island. At the same time, it would help designing effective managing practices for conservation, and translocation traceability.

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“…GF differs from Genotype-Environment Association (GEA) analyses (Rellstab et al 2015;Hoban et al 2016), which emphasizes the identification of environmentally-associated alleles, typically using linear univariate approaches (Waldvogel et al 2020b). In contrast, GF fits an ensemble of regression trees using Random Forest (Breiman 2001) and then constructs cumulative importance turnover functions (see Table 1 for definitions) from these models by determining how well partitions distributed at numerous "split values" along each gradient explain changes in allele frequencies on either side of a split.…”

Section: Introductionmentioning

confidence: 99%

Seeing the Forest for the trees: Assessing genetic offset predictions with Gradient Forest

Láruson

Fitzpatrick

Keller

et al. 2021

Preprint

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Gradient Forest (GF) is increasingly being used to forecast climate change impacts, but remains mostly untested for this purpose. We explore its robustness to assumption violations, and relationship to measures of fitness, using SLiM simulations with explicit genome architecture and a spatial metapopulation. We evaluate measures of GF offset in: (1) a neutral model with no environmental adaptation; (2) a monogenic "population genetic" model with a single environmentally adapted locus; and (3) a polygenic "quantitative genetic" model with two adaptive traits, each adapting to a different environment. Although we found GF Offset to be broadly correlated with fitness offsets under both single locus and polygenic architectures. It could also be confounded by neutral demography, genomic architecture, and the nature of the adaptive environment. GF Offset is a promising tool, but it is important to understand its limitations and underlying assumptions, especially when used in the context of forecasting maladaptation.

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Climate Change Genomics Calls for Standardized Data Reporting

Cited by 28 publications

References 52 publications

Genomic basis for drought resistance in European beech forests threatened by climate change

Genomic basis for drought resistance in European beech forests threatened by climate change

Adaptive Differences in Gene Expression in Farm-Impacted Seedbeds of the Native Blue Mussel Mytilus chilensis

Seeing the Forest for the trees: Assessing genetic offset predictions with Gradient Forest

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