The genomic basis of adaptation in plants
Introduction
“Plants stand still and wait to be counted.” JL Harper [1]
Due to their sessile nature, plants represent an excellent system to study adaptation. The ease of sampling (and resampling) populations, the ability to systematically sample across environmental gradients, and the possibility to conduct transplant experiments provide outstanding opportunities to study temporally and spatially varying selection. In addition to adaptation to the natural environment, many plant species co-evolved with humans, either as commensals or because humans actively selected for traits that they valued. Comparing and contrasting the genomic consequences of selection from natural and human-driven forces can provide insights into adaptive processes and the constraints on these processes. Here, we review and discuss recent developments from genome-scale studies that illuminate the basis of adaptive evolution in plant species. Due to space limitations, we provide only a brief overview of models and methods and focus on studies that use population genomic approaches to interrogate the genome using dense genome-wide datasets. We refer to previous reviews for readers interested in learning more about models and methods used to detect adaptive evolution [2, 3].
Section snippets
Approaches for detecting adaptive evolution
Broadly speaking there are two approaches to detecting adaptive evolution. One works from the phenotype down and the other from the genotype up [4]. With the top down approach an adaptive phenotype is identified and then forward genetics approaches are taken to elucidate the underlying genetic factors. In the bottom up approach specific patterns of polymorphism in the genome are used to identify genomic regions that are likely to be experiencing positive selection. The advantage of the bottom
Adaptation in the wild
Natural populations are exposed to a variety of selection pressures, including climate, soil components and human-associated factors. Depending on the selection pressure and the extent of a species’ range, these factors may underlie species-wide adaptation or adaptation on a more local level.
The possibilities of obtaining genomic data across diverse species are increasing rapidly as sequencing technologies improve and costs fall. Below we highlight several such exciting studies. However, there
Adaptation during domestication
Crop species were subject to strong selective forces during the breeding process, making them prime targets for studies of adaptation. However, the genome-wide effects of domestication bottlenecks followed by massive population expansions are a major challenge for identifying adaptive loci because they mimic the patterns that result from strong selective sweeps. Explicit modeling of demographic histories provides one method to differentiate sweep signatures from patterns of reduced variation
Conclusions and future directions
Studies over the past few years have shown that there are diverse paths to adaptation both in the sources of adaptive variants (i.e., novel, pre-existing and introgressed variants) and in the scale of adaptation. These findings illustrate how important it is to study adaptive phenomena in diverse populations and species. Emerging model systems [86•], many of which have the benefit of years of ecological and/or genetic study are poised to yield exciting new results.
In addition to more thorough
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
This work was supported by the Max Planck Gesellschaft and ERC Grant CVI_ADAPT to AMH.
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