Local adaptation is a fundamental phenomenon in evolutionary biology, with relevance to formation of ecotypes, and ultimately new species, and application to restoration and species’ response to climate change. Reciprocal transplant gardens, a common garden in which ecotypes are planted among home and away habitats, are the gold standard to detect local adaptation in populations. This review focuses on reciprocal transplant gardens to detect local adaptation, especially in grassland species beginning with early seminal studies of grass ecotypes. Fast forward more than half a century, reciprocal gardens have moved into the genomic era, in which the genetic underpinnings of ecotypic variation can now be uncovered. Opportunities to combine genomic and reciprocal garden approaches offer great potential to shed light on genetic and environmental control of phenotypic variation. Our decadal study of adaptation in a dominant grass across the precipitation gradient of the US Great Plains combined genomic approaches and realistic community settings to shed light on controls over phenotype. Common gardens are not without limitations and challenges. A survey of recent studies indicated the modal study uses a tree species, three source sites and one growing site, focuses on one species growing in a monoculture, lasts 3 years, and does not use other experimental manipulations and rarely employs population genetic tools. Reciprocal transplant gardens are even more uncommon, accounting for only 39% of the studies in the literature survey with the rest occurring at a single common site. Reciprocal transplant gardens offer powerful windows into local adaptation when (a) placed across wide environmental gradients to encompass the species’ range; (b) conducted across timespans adequate for detecting responses; (c) employing selection studies among competing ecotypes in community settings and (d) combined with measurements of form and function which ultimately determine success in home and away environments.
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 conditions. 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 correction 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.
- NSF-PAR ID:
- 10443041
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- New Phytologist
- Volume:
- 237
- Issue:
- 5
- ISSN:
- 0028-646X
- Format(s):
- Medium: X Size: p. 1590-1605
- Size(s):
- ["p. 1590-1605"]
- Sponsoring Org:
- National Science Foundation
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Abstract Synthesis . Reciprocal transplant gardens have been one of the foundations in evolutionary biology for the study of adaptation for the last century, and even longer in Europe. Moving forward, reciprocal gardens of foundational non‐model species, combined with genomic analyses and incorporation of biotic factors, have the potential to further revolutionize evolutionary biology. These field experiments will help to predict and model response to climate change and inform restoration practices. -
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Abstract Understanding how the environment shapes genetic variation provides critical insight about the evolution of local adaptation in natural populations. At multiple spatial scales and multiple geographic contexts within a single species, such information could address a number of fundamental questions about the scale of local adaptation and whether or not the same loci are involved at different spatial scales or geographic contexts. We used landscape genomic approaches from three local elevational transects and rangewide sampling to (a) identify genetic variation underlying local adaptation to environmental gradients in the California endemic oak,
Quercus lobata ; (b) examine whether putatively adaptive SNPs show signatures of selection at multiple spatial scales; and (c) map putatively adaptive variation to assess the scale and pattern of local adaptation. Of over 10 k single‐nucleotide polymorphisms (SNPs) generated with genotyping‐by‐sequencing, we found signatures of natural selection by climate or local environment at over 600 SNPs (536 loci), some at multiple spatial scales across multiple analyses. Candidate SNPs identified with gene–environment tests (LFMM) at the rangewide scale also showed elevated associations with climate variables compared to the background at both rangewide and elevational transect scales with gradient forest analysis. Some loci overlap with those detected in other oak species, raising the question of whether the same loci might be involved in local climate adaptation in different congeneric species that inhabit different geographic contexts. Mapping landscape patterns of adaptive versus background genetic variation identified regions of marked local adaptation and suggests nonlinear association of candidate SNPs and environmental variables. Taken together, our results offer robust evidence for novel candidate genes for local climate adaptation at multiple spatial scales. -
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Fontainea species. Our aim was to compare spatial patterns of genetic variation between the vulnerableFontainea australis (Southern Fontainea) and critically endangeredF. oraria (Coastal Fontainea), endemic to the heterogeneous subtropical region of central, eastern Australia, where large-scale clearing has severely reduced rainforest habitat to a fraction (< 1%) of its pre-European settlement extent.Methods We used a set of 10,000 reduced-representation markers to infer genetic relationships and the drivers of spatial genetic variation across the two species. In addition, we employed a combination of univariate and multivariate genome-environment association analysis using a set of topo-climatic variables to explore potential patterns of local adaptation as a factor impacting genomic divergence.
Results Our study revealed that Coastal Fontainea have a close genetic relationship with Southern Fontainea. We showed that isolation by distance has played a key role in their genetic variation, indicating that vicariance can explain the spatial genetic distribution of the two species. Genotype-environment analyses showed a strong association with temperature and topographic features, suggesting adaptation to localised thermal environments. We used a multivariate redundancy analysis to identify a range of putatively adapted loci associated with local environmental conditions.
Conclusions Divergent selection at the local-habitat scale as a result of dispersal limitations and environmental heterogeneity (including physical barriers) are likely contributors to adaptive divergence between the two
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Using common gardens, we investigated the adaptive divergence of various constitutive and inducible defence‐related traits between the native North American and introduced European and Australian ranges, while controlling for divergence due to latitudinal trait clines, individual resource budgets, and population differentiation, using >11,000 SNPs.
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Synthesis : The rapid spread of invasive species is affected by a multitude of factors, likely including adaptation to climate and escape from natural enemies. Unravelling the mechanisms underlying invasives' success enhances understanding of eco‐evolutionary theory and is essential to inform management strategies in the face of ongoing climate change.OPEN RESEARCH BADGES This article has been awarded Open Materials, Open Data, Preregistered Research Designs Badges. All materials and data are publicly accessible via the Open Science Framework at
https://doi.org/10.6084/m9.figshare.8028875.v1 ,https://github.com/lotteanna/defence_adaptation ,https://doi.org/10.1101/435271 . -
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Abstract Disentangling the effects of neutral and adaptive processes in maintaining phenotypic variation across environmental gradients is challenging in natural populations. Song sparrows (
Melospiza melodia ) on the California Channel Islands occupy a pronounced east‐west climate gradient within a small spatial scale, providing a unique opportunity to examine the interaction of genetic isolation (reduced gene flow) and the environment (selection) in driving variation. We used reduced representation genomic libraries to infer the role of neutral processes (drift and restricted gene flow) and divergent selection in driving variation in thermoregulatory traits with an emphasis on the mechanisms that maintain bill divergence among islands. Analyses of 22,029 neutral SNPs confirm distinct population structure by island with restricted gene flow and relatively large effective population sizes, suggesting bill differences are probably not a product of genetic drift. Instead, we found strong support for local adaptation using 3294 SNPs in differentiation‐based and environmental association analyses coupled with genome‐wide association tests. Specifically, we identified several putatively adaptive and candidate loci in or near genes involved in bill development pathways (e.g.,BMP ,CaM ,Wnt ), confirming the highly complex and polygenic architecture underlying bill morphology. Furthermore, we found divergence in genes associated with other thermoregulatory traits (i.e., feather structure, plumage colour, and physiology). Collectively, these results suggest strong divergent selection across an island archipelago results in genomic changes in a suite of traits associated with climate adaptation over small spatial scales. Future research should move beyond studying univariate traits to better understand multidimensional responses to complex environmental conditions.
