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Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in adaptive evolution, in particular the extent to which similar genetic mechanisms drive adaptation to common selective forces. Here, we investigated the genomics of local adaptation in two nonsister woodpeckers that are codistributed across an entire continent and exhibit remarkably convergent patterns of geographic variation. We sequenced the genomes of 140 individuals of Downy (Dryobates pubescens) and Hairy (Dryobates villosus) woodpeckers and used a suite of genomic approaches to identify loci under selection. We showed evidence that convergent genes have been targeted by selection in response to shared environmental pressures, such as temperature and precipitation. Among candidates, we found multiple genes putatively linked to key phenotypic adaptations to climate, including differences in body size (e.g., IGFPB) and plumage (e.g., MREG). These results are consistent with genetic constraints limiting the pathways of adaptation to broad climatic gradients, even after genetic backgrounds diverge.
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From common gardens to candidate genes: exploring local adaptation to climate in red spruce
-Local adaptation to climate is common in plant species and has been studied in a range of contexts, from improving crop yields to predicting population maladaptation to future condi- tions. The genomic era has brought new tools to study this process, which was historically explored through common garden experiments. - In this study, we combine genomic methods and common gardens to investigate local adaptation in red spruce and identify environmental gradients and loci involved in climate adaptation. We first use climate transfer functions to estimate the impact of climate change on seedling performance in three common gardens. We then explore the use of multivariate gene–environment association methods to identify genes underlying climate adaptation, with particular attention to the implications of conducting genome scans with and without correc- tion for neutral population structure. -This integrative approach uncovered phenotypic evidence of local adaptation to climate and identified a set of putatively adaptive genes, some of which are involved in three main adaptive pathways found in other temperate and boreal coniferous species: drought tolerance, cold hardiness, and phenology. These putatively adaptive genes segregated into two ‘modules’ associated with different environmental gradients. -This study nicely exemplifies the multivariate dimension of adaptation to climate in trees.
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- PAR ID:
- 10384033
- Date Published:
- Journal Name:
- New Phytologist
- ISSN:
- 0028-646X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Rapid environmental change poses unprecedented challenges to species persistence. To understand the extent that continued change could have, genomic offset methods have been used to forecast maladaptation of natural populations to future environmental change. However, while their use has become increasingly common, little is known regarding their predictive performance across a wide array of realistic and challenging scenarios. Here, we evaluate the performance of currently available offset methods (gradientForest, the Risk‐Of‐Non‐Adaptedness, redundancy analysis with and without structure correction and LFMM2) using an extensive set of simulated data sets that vary demography, adaptive architecture and the number and spatial patterns of adaptive environments. For each data set, we train models using eitherall,adaptiveorneutralmarker sets and evaluate performance using in silico common gardens by correlating known fitness with projected offset. Using over 4,849,600 of such evaluations, we find that (1) method performance is largely due to the degree of local adaptation across the metapopulation (LA), (2)adaptivemarker sets provide minimal performance advantages, (3) performance within the species range is variable across gardens and declines when offset models are trained using additional non‐adaptive environments and (4) despite (1) performance declines more rapidly in globally novel climates (i.e. a climate without an analogue within the species range) for metapopulations with greaterLAthan lesserLA. We discuss the implications of these results for management, assisted gene flow and assisted migration.more » « less
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Summary Genetic load can reduce fitness and hinder adaptation. While its genetic underpinnings are well established, the influence of environmental variation on genetic load is less well characterized, as is the relationship between genetic load and putatively adaptive genetic variation. This study examines the interplay among climate, species range dynamics, adaptive variation, and mutational load – a genomic measure of genetic load – inVitis arizonica, a wild grape native to the American Southwest.We estimated mutational load and identified climate‐associated adaptive genetic variants in 162 individuals across the species' range. Using a random forest model, we analyzed the relationship between mutational load, climate, and range shifts.Our findings linked mutational load to climatic variation, historical dispersion, and heterozygosity. Populations at the leading edge of range expansion harbored higher load and fewer putatively adaptive alleles associated with climate. Climate projections suggest thatV. arizonicawill expand its range by the end of the century, accompanied by a slight increase in mutational load at the population level.This study advances understanding of how environmental and geographic factors shape genetic load and adaptation, highlighting the need to integrate deleterious variation into broader models of species response to climate change.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1111/nph.18465
