Adaptation Genomics: the next generation (original) (raw)
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Proceedings of the Royal Society B: Biological Sciences, 2012
The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.
Advances in Experimental Medicine and Biology, 2013
A key question in evolutionary biology is the reproducibility of adaptation. This question can now be quantitatively analyzed using experimental evolution coupled to whole genome sequencing (WGS). With complete sequence data, one can assess convergence among replicate populations. In turn, convergence reflects the action of natural selection and also the breadth of the field of possible adaptive solutions. That is, it provides insight into how many genetic solutions or adaptive paths may lead to adaptation in a given environment. Convergence is both a property of an adaptive landscape and, reciprocally, a tool to study that landscape. In this chapter we present the links between convergence and the properties of adaptive landscapes with respect to two types of microbial experimental evolution. The first tries to reconstruct a full adaptive landscape using a handful of carefully identified mutations (the reductionist approach), while the second uses WGS of replicate experiments to infer properties of the adaptive landscape. Reductionist approaches have highlighted the importance of epistasis in shaping the adaptive landscape, but have also uncovered a wide diversity of landscape architectures. The WGS approach has uncovered a very high diversity of beneficial mutations that affect a limited set of genes or functions and also suggests
Genomics of Adaptation and Speciation
Genes
The availability of genome data provides a unique window into speciation mechanisms with virtually infinite amounts of information, providing a pathway for a better understanding of major evolutionary questions [...]
Responsible RAD: Striving for best practices in population genomic studies of adaptation
Molecular ecology resources, 2017
We thank McKinney et al. (2017) and Catchen et al. (2017) for their recent commentaries on Lowry et al (2017), "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing scans of adaptation." Both articles argued that we overstated the limitations of RADseq for studies of local adaptation and McKinney et al. (2017) argued that "RADseq provides unprecedented insights" into mechanisms of evolutionary adaptations. While we agree with some of the comments made by the authors of the two papers, we still believe caution should be employed in RADseq studies that aim to detect loci that contribute to adaptation. In this rebuttal, we evaluate the key points made in these papers, attempt to identify a middle ground, and make suggestions for responsibly conducting future studies to understand the genomic mechanisms of adaptation. This article is protected by copyright. All rights reserved.
Abiotic environmental adaptation in vertebrates is characterized by functional genomic constraint
2019
Understanding the genomic basis of adaptation to different abiotic environments is important for understanding organismal responses to current short-term environmental fluctuations. Using functional and comparative genomics approaches, we here investigated whether genomic adaptation to a set of environmental parameters is contingent across vertebrate genomes or, alternatively, contains an element of evolutionary constraint that would be evident through recurrent involvement of specific subsets of genes and functions in adaptation to similar environments. We first identified 200 genes with signatures of selection from transcriptomes of 24 species of lacertid lizards with known adaptations in preferred temperature, correlated with thermal environment experienced by these lizards in their range. In order to discern genes adapting to climate from other selective factors, we then performed a meta-analysis of 1100 genes with signatures of selection obtained from-omics studies in vertebrat...
Triangulating the genetic basis of adaptation to multifarious selection
Molecular Ecology, 2012
Understanding how natural populations adapt to their local environments is a major research theme for ecological genomics. This endeavour begins by sleuthing for shared genetic similarities among unrelated natural populations sharing adaptive traits to documented selective pressures. When the selective pressures have low dimensionality, and the genetic response is localized to a few genes of major effect, this detective work is relatively straightforward. However, in the real world, populations face a complex mixture of selective pressures and many adaptive responses are the result of changes in quantitative traits that have a polygenic genetic basis. This complex relationship between environment and adaptation presents a significant challenge. How can we begin to identify drivers of adaptation in natural settings? In this issue of Molecular Ecology, Orsini et al. (2012) take advantage of the biological attributes of the freshwater microcrustacean Daphnia to disentangle multidimensional selection's signature on the genome of populations that have repeatedly evolved adaptive responses to isolated selective pressures including predation, parasitism and anthropogenic changes in land use. Orsini et al.
Heredity, 2014
Evolve and resequence (E&R) is a new approach to investigate the genomic responses to selection during experimental evolution. By using whole genome sequencing of pools of individuals (Pool-Seq), this method can identify selected variants in controlled and replicable experimental settings. Reviewing the current state of the field, we show that E&R can be powerful enough to identify causative genes and possibly even single-nucleotide polymorphisms. We also discuss how the experimental design and the complexity of the trait could result in a large number of false positive candidates. We suggest experimental and analytical strategies to maximize the power of E&R to uncover the genotype-phenotype link and serve as an important research tool for a broad range of evolutionary questions.Heredity advance online publication, 1 October 2014; doi:10.1038/hdy.2014.86.
Current Opinion in Plant Biology, 2008
Recent advances in molecular biology have opened new perspectives for the study of plant adaptation, especially at the intraspecific level. Nowadays, scientists employing-omic results in multiple scientific fields can be optimistic of their chances of revealing mechanisms involved in adaptive population divergence. However, the investment required by integrative studies greatly reduces the number of experiments that can be performed. In this context, a comprehensive choice of accessions under study is crucial. We maintain this choice could be appreciably enlightened by population genetics because it helps putting adaptive population divergence in a spatial and historical context. As an example, we highlight the usefulness of knowledge about population genetic structure in the integrative study of metal tolerance in Arabidopsis halleri.