The topic that has always fascinated me is how organisms adapt to climate. I am particularly interested in experimental ecology and population genomics. On one hand, ecology looks for general patterns of phenotypic evolution. On the other hand, genetics provides insights on the molecular basis of ecologically relevant traits and sets the statistical framework to study the interplay of evolutionary forces: migration, drift, mutation, and selection. It is in the intersection of ecology x genetics x bioinformatics, where cool stuff happens!
The annual, cosmopolitan, and self-fertilizing plant Arabidopsis thaliana, from which 1001 genomes have been recently produced (1001 Genomes Consortium, 2016 CELL), is a formidable model system to understand how environmental selective forces shape species diversity. And it is my favorite model system. Below are short descriptions of my ongoing projects.
Evolution of a newly colonizing plant lineage
Exposito-Alonso & Becker et al.(2016) The rate and effect of de novo mutations in a colonizing lineage of Arabidopsis thaliana. bioRxiv, doi:10.1101/050203
Scenarios of low complex evolutionary history can help to characterize and understand the essential processes of evolution. We have been able to sequence multiple individuals from a single North American Arabidopsis thaliana lineage, including historical DNA from herbarium speciments collected as far back as 1864. Leveraging this lineage, which likely was originated from a single colonization event from Eurasia, we tracked the speed at which diversity is generated by de novo mutations and learned about the equilibriums with population size and natural selection. We discovered that the dynamics were dominated by multiple bottleneck events with sudden exponential growths. Although phenotype mapping is challenging due to high LD, we gathered evidences that some functional new mutations probably had an adaptive advantage.
Climate adaptation from standing variation
This project takes most of my time currently and involves high-throughput phenotype experiments in the greenhouse and in the field to study climatic adaptation. I use world wide distributed accessions sequenced in the 1001 genomes project and measure several fitness traits using image processing tools (see above). Combining it with whole-genome sequences, I aim to identify genetic variation associated with high performance under harsh climatic conditions such as drought. Also, based on genome patterns and population genetics models, I reconstruct population sizes, admixture of ancestral populations, and geographic spread of genetic diversity, and connect those with climatic adaptation events in the past.
Adaptation to simulated drought and forecast under climate change
Exposito-Alonso et al. (2017) Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana. bioRxiv, doi:10.1101/118067
Because earth is currently experiencing a dramatic climate change, it is of critical interest to predict how species will respond to it. However, most predictive studies ignore that species comprise genetically diverse individuals. Thus, the chance of a species to withstand climate change will likely depend on how many subpopulations are already adapted to extreme environments. Because a major consequence of global warming will be an increase in extreme drought events, we first identified genetic variants in Arabidopsis thaliana that predict survival of such an event. Subsequently, we determined how these variants are distributed across the native range of the species. Genetic variants conferring higher drought survival showed signatures of polygenic adaptation, and were more frequently found in Mediterranean and Scandinavian regions. Using geo-environmental models, we predicted that Central European populations might lag behind in adaptation by the end of the 21 st century. Further analyses showed that a population decline could nevertheless be compensated by natural selection acting efficiently over standing variation or by migration of adapted individuals from populations at the margins of the species’ distribution. These findings highlight the importance of within-species genetic heterogeneity in facilitating an evolutionary response to a changing climate.
Natural selection under manipulated rainfall at Mediterranean and European field stations
More about the results from the semi-field experiments under reduced rainfall coming soon..
Genomics of rapid Evolution in Novel Environments GrENE-net
On fall 2017 we are carrying out evolution experiments in natural conditions in over 30 locations for several generations (see below). This project will provide insights on the actual natural selection coefficients genome-wide under an array of natural environments. For more information visit the web grene-net.org