K. Tang, K. R. Thornton, M. Stoneking, A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol. 5, e171 (2007).
This study develops an approach to detect selective sweeps that is also used in this paper,
C. Mariac et al., Genetic basis of pearl millet adaptation along an environmental gradient investigated by a combination of genome scan and association mapping. Mol. Ecol. 20, 80 (2011).
This interesting paper similarly aims to understand the genetic basis of adaptation but look at the crop pearl millet. The authors were able to detect genetic changes associated with changes in the climate.
J. Stapley et al., Adaptation genomics: The next generation. Trends Ecol. Evol. 25, 705 (2010).
This review discusses how the advance in genomic technologies has helped stimulate research on the genetic basis of adaptation.
Arabidopsis thaliana
The use of Arabidopsis thaliana has been vital for plant science research.
Learn more about the importance of this plant in this podcast by Professor Kathy Willis on BBC Radio 4.
rapid environmental change
Many locations in the world are facing rapid environmental change.
Read more about environmental change in Greenland in the Independent
alleles associated with high fitness within sites tend to be local alleles linked to particular climatic factors, providing evidence of local adaptation in A. thaliana at the scale of the European continent
The main conclusions from this papers are: alleles associated with plant fitness have undergone local adaptation, they were correlated with climatic factors suggesting they are an adaptation to the local climate, they may be rare or common, they may be in different genetic locations and can code for multiple different molecular functions. Therefore, this paper has revealed multiple aspects about the genetic basis of local adaptation in the model plant Arabidopsis.
We used maximum entropy models [MaxEnt (17)] to infer the contributions of 11 bioclimatic variables to the distribution of each SNP allele (table S3) (16) and tested whether fitness-associated alleles occupy specific climate spaces relative to genomic controls
The authors hypothesized that high fitness alleles would be associated with climate as they were the basis of local adaptation. A maximum entropy model is a way of modelling species geographic distributions with presence-only data. This means that the researcher only needs to input where the species are known to be and not where they are known not to be as this data is rarely available. This model was used to identify whether 11 climatic factors affected the distribution of the alleles.
the alleles associated with high fitness exhibited greater climate specificity
Some of the alleles that were associated with high fitness were also associated with specific climates, as hypothesized by the authors. This suggests that these alleles are locally adapted due to unique climatic pressures.
three most interesting candidate genes
The analysis was able to identify three genes that are very likely to be the basis of local adaptation in some Arabidopsis populations. The three genes are LAC2, CHR8 and SAG21.
To identify potential candidate genes for local adaptation, we searched for fitness-associated SNPs in the top 0.05% (with minor allele frequency >8% to exclude rare deleterious mutations) that also appeared in the top 0.5% of allele climate differentiation and in the top 5% of global iEH
The final analysis conducted in this paper is an attempt to identify the genes that have been vital for local adaptation in Arabidopsis populations. To do this the authors identified alleles that were present in the top 0.05% of alleles strongly correlated with plant fitness, strongly correlated with climatic factors and underwent strong selection.
no molecular function was significantly over- or underrepresented in all sets of candidate genes
There was not one molecular function that was very common in all the locally adapted populations. Therefore, the authors conclude that a large variety of molecular functions are involved in local adaptations.
whether the candidate genes present in 10,000–base pair (10-kbp) windows surrounding the associated SNPs were enriched for a particular subset of the Gene Ontology (GO slim) annotations
The authors wanted to understand what the gene functions were for the alleles that were identified as involved in local adaptation. To do this they compared the genes they identified with a large database of gene functions call the GO slim annotations
Overall, among the 797 top SNPs, only 12 SNPs were associated with fitness in more than one environment; loci with major genetic effects were largely independent across sites
It was rare to find the same allele associated with plant fitness in multiple populations. Alleles with large effects on fitness were mostly different in each population. Therefore, local adaptation acts on different genetic locations in different populations.
determining whether local selection in different environments more commonly acted upon alternate alleles of the same loci, or if entirely different loci were found among different environments.
The authors were interested to find out whether local adaptation in different populations often occurred at the same genetic site or occurred in many different sites.
no recent selective sweeps have occurred at these loci
The authors found no evidence of selective sweeps in the alleles involved in local adaptation. This suggests that the genetic basis of local adaptation is in alleles that are already present in a population rather than on new alleles that rapidly spread through the population.
We also tested whether fitness-associated SNPs were involved in recent selective sweeps by computing the integrated extended haplotype homozygosity (iEH) around each SNP
A selective sweep occurs when a new beneficial allele rapidly spreads through a population due to selection.
The authors were interested to know if local adaptation is based on selective sweeps or alleles that are already present in a population.
To do this the authors assessed the extended haplotype homozygosity around each allele involved in local adaptation. This method evaluates whether the alleles surrounding the allele of interest have been largely preserved. If they have then this suggests the allele of interest underwent a selective sweep which lead to the conservation of the surrounding alleles.
alleles improving survival were high-frequency alleles
In contrast to fecundity, alleles associated with increased survival were more common than control alleles. Therefore, for survival the genetic basis of local adaptation is the removal of locally deleterious genes. This result shows that the genetic basis for local adaptation can be different for different traits.
Alleles associated with increased silique number were significantly rarer than genomic controls
The authors found that alleles associated with increased numbers of siliques, and hence increased fecundity, were rarer than the control alleles. This suggests that for fecundity local adaptation’s genetic basis is the increase in a few beneficial genes.
We therefore tested whether the global frequency of the alleles associated with high fitness was different relative to genomic controls
The authors wanted to understand whether the genetic basis of local adaptation was a few beneficial genes that become common in a population or whether it was based on the removal of locally deleterious genes. They did this by comparing the frequency of the alleles involved in local adaptation to genomic controls that were not involved in local adaptation.
more often alleles associated with low fitness exhibited greater climate specialization
This result was not predicted by the authors. Alleles that were deemed to be associated with low fitness in the common garden experiments may be less severe in certain climates and therefore have only been retained in populations within these climates.
limited by sample size in Finland (16) as well as by the sparse sample of local ecotypes available for our sites in Finland and Spain
In Finland fewer plants could be planted in the common garden experiments and fewer Arabidopsis populations naturally occur nearby. Smaller sample sizes reduce the likelihood of identifying statistically significant results. The authors suggest that the results may have been significant if they had been able to increase the sample sizes in Finland.
we found no evidence that the alleles conferring high fitness in Finland were locally abundant.
Alleles linked to high survival and high fecundity in populations in Finland were not found to have geographic centroids significantly closer to Finland. Therefore, the authors cannot conclude that these alleles were the basis for local adaptation.
associated with higher survival in England and Spain and silique number in Germany, England, and Spain were significantly closer to the planting sites in Germany, England, and Spain, respectively, relative to genomic controls
The authors found that alleles that were linked to high survival in England and Spain, identified from the genome-wide association study, had a geographic centroid closer to these locations. The same result was found for silique number, a measure for fecundity, in Germany, England and Spain. Genomic controls on the other hand were not centered closer to these sites. This shows that these high survival and high fecundity alleles were the genetic basis for local adaptation.
geographic centroids of the alleles
In this study the geographic centroid of an allele is the average location calculated from every location where the allele is present. Such that if an allele is most abundant in Portugal than its geographic centroid will be in Portugal.
Adaptation to local environments has been observed experimentally in many organisms (1) and may critically limit a given species’ capacity to evolve in the face of rapid environmental change (2–4).
Local adaptation increases species survival in the local environment but can reduce survival in foreign environments. Unfortunately, if the climate in the local environment rapidly changes then local adaptations may no longer be beneficial.
The threat of rapidly changing environments to species has been reviewed in these papers. Jump and Penuelas discuss that as climates rapidly change migration may no longer be a solution for species survival. Therefore, the ability of species to adapt to the changes is even more important.
The worrying consequences of rapidly changing environments have stimulated research such as this paper to better understand adaptation.
We tested whether alleles associated with high fitness in a given site were more locally abundant than genomic controls, as expected if they contributed to the local adaptation of that population
In order for the researchers to investigate the genetic basis of local adaptation they first need to prove that the populations are locally adapted.
Therefore, the first hypothesis they test is that alleles that increase plants fitness in a certain location are more likely to be abundant in that location than anywhere else. Whereas genomic controls, alleles not necessary for increased fitness, will be not be abundant in one area compared to another.
fecundity
A measurement of the reproductive rate of an organism. In this research it is measured as the number of siliques.
R2 in GWAS models ranging on average from 9% for the SNP set associated with survival in England to 24% for the SNP set associated with survival in Finland
The R2 value indicates how much of the variation in a trait can be explained by the genetic markers identified. If R2 is not 100% than other locations in the genome or environmental factors are influencing the trait being analysed.
In this case the SNPs associated with survival in Finland were much more important in influencing plant survival than the SNPs associated with survival in England.
For each fitness trait in each of the four field sites, we defined a set of associated SNPs corresponding to the 0.05% of the SNPs that explained the most variance (around 100 per GWAS; figs. S2 and S3)
0.05% of all SNPs were selected as being important for explaining differences in survival and reproduction between populations. The genes that contained these SNPs are hypothesized to be important for local adaptation. These SNPs are used in the study as genetic markers to identify genetic differences in local adaptation in the populations studied.
genome-wide association study (GWAS) for survival and silique number using 213,248 single-nucleotide polymorphisms (SNPs)
The authors used a genome wide association study to identify links between plant survival (and reproduction) and single nucleotide polymorphisms (SNPs).
SNPs are mutations in DNA where one base- A, T, C or G -has been changed.
If a SNP is identified as linked to survival or reproduction then the gene that contained the SNP can be identified. Therefore, genes associated with reproduction and survival can be identified.
ecotypes
A term for plants derived from a geographically distinct population.
latitude
A geographic coordinate that specifies the north-south position of a location.
continental
A location far from the coast, such as the site in Germany.
Mediterranean
In southern Europe, Mediterranean environments are characterized by rainy winters and hot summers.
Nordic
Northern Europe where the climate is generally much colder and sees more snow than southern Europe.
we grew a geographically diverse set of ecotypes (inbred lines derived from natural populations) across their native range, in replicated common garden experiments in four European field sites
In order to show that Arabidopsis populations are locally adapted the authors used common garden experiments. In this experimental set up the effect of environment is tested by moving species from their native environment into one common environment.
It is hypothesized that if populations are locally adapted then the population that normally grows in an environment similar to the common one will have a higher survival rate. For instance, plants that naturally grow in a Mediterranean environment will be more likely to survive in Spain than plants that normally grow in the much colder climate of Finland.
the molecular basis of local adaptation remains largely unexplored (5, 6)
Ehrenreich and Purugganan reviewed research on the molecular basis of plant adaptation in 2006 and concluded that not enough is known. For instance it is not well understood how many genes are responsible per adaptation. Neither is it understood whether certain types of mutations are more likely to be responsible for adaptation.
recent observations of candidate loci associated with climate (10).
Eckert et al., used a genome wide data set of small variations in Pinus taeda (loblolly pine) to identify changes in the genome that were correlated with variations in the climate. By doing this they identified a set of genes that may have been necessary in local adaptation of the loblolly pine.
candidate loci showing high levels of environmental differentiation (9,
Local adaptation has been clear in Arabidopsis plants growing in salty soil by the coast. Alleles of the sodium transporter, HKT1, that enhance salt tolerance have been found to be much more common in populations living by the coast.
transcription factor
A protein that can bind to DNA to alter the expression of genes.
genetic architecture
The set of genes that create characteristics in the organism. In this case the genes that are involved in local adaptation.
polymorphisms
When two or more variations of a gene are present in a population.
viability
A measurement of how many seeds are able to develop into adult plants that are capable of reproduction
heritable variation
Heritability is a measurement of how much variation in a trait is caused by genetic factors, rather than environmental factors. Heritable variation occurs in a population when the influence of genetic factors on a trait differs between individuals.
silique
The fruit of the Arabidopsis plant where the seed is stored
selection
Environmental pressures result in individuals with certain characteristics reproducing more than others. This results in these individuals genes becoming more common in the population. This is the process of evolution.
molecular functions
The actions of cellular components such as DNA and proteins.
climate spaces
An area of the environment that is suitable for a particular population to survive.
alleles
A variation of a gene. Most multi-cellular organisms, including Arabidopsis, have duplicated chromosomes meaning that every gene is present twice in the genome and hence may have two variations of a gene.
fitness
This evolutionary term describes how successful an organism is at reproducing and passing its genes through the next generations. Factors such as lifespan and percentage of offspring that survive contribute to this.
genome-wide association study
This method searches for small variations in the genomes of a large population and investigates whether these variations are associated with certain characteristics. This helps researchers identify which genes might control traits in an organism. The method is used in a large variety of research including human and plant science.
candidate loci
Locations in the genome that contain genes with functions of interest, in this case this is genes that been involved in local adaptation.
Arabidopsis thaliana
Commonly called thale cress, this plant is a small flower that is a weed in the wild but is a very popular model organism used in plant science research.
genetic basis
The genes that become locally adapted.
Local adaptation
Local adaptation occurs when a population that is spatially separate from others of its species faces selective pressures unique to its environment. Therefore, the population evolves to be best suited to its local environment.