Looking into the evolutionary black box: processes and mechanisms accounting for adaptive evolution in Arabidopsis thaliana (BLACKBOX)

Spanish National Plan for R+D+i (CGL2016-77720-P). PI: F.X. Picó. 2016-2019 (extended 2020).

BLACKBOX deals with the genetic mechanisms and developmental processes accounting for genetic variation in life-cycle traits under selection to better understand adaptive evolution in plants. In particular, BLACKBOX will develop an integrative approach taking geographical, ecological (e.g. historical and contemporary environmental drivers and cues), genetic (e.g. quantitative genetic variation and functional polymorphisms in genes from regulatory pathways) and developmental (e.g. timing of main life-cycle events) components into account. To this end, the project will focus on Iberian natural populations of the annual plant Arabidopsis thaliana to carry out four specific objectives incorporating the within-population level to a large-scale geographical and environmental scheme. First, BLACKBOX will evaluate the effect of historical and contemporary ecological factors on current patterns of within- and among-population genetic variation in all study populations. We will combine the analysis of temporal series of photographs available from all populations since the 1950s with intensive field sampling in situ to quantify the species’ realized niche. Second, comparisons between quantitative genetic differentiation and neutral genetic differentiation in all populations will be performed to assess the adaptive value of life-cycle traits in A. thaliana. Field experiments will provide data to evaluate within- and among-population variation in life-cycle traits whereas next generation sequencing (NGS) will provide neutral genome-wide markers to estimate neutral genetic differentiation. Third, the genetic basis of adaptive traits will be studied by detecting functional polymorphisms of candidate flowering time genes (e.g. FRI and FLC) and seed dormancy genes (e.g. DOG1) through Sanger sequencing. And forth, demographic distribution models (DDM) will be developed and applied to Iberian A. thaliana populations, based on existing demographic data and novel data generated in this project, to explore how the plant adjusts its life cycle to the heterogeneous environments that the species encounters in the Iberian Peninsula. DDM will also be used to assess the effects of global climate change (GCC) on A. thaliana populations by taking the genetic mechanisms and developmental processes underlying demographic events and lifetime fitness into account. BLACKBOX aims to make important contributions to better comprehend novel aspects of the the population biology and adaptive evolution of A. thaliana (e.g. historical effects of land use changes on standing phenotypic and genetic variation and the species’ realized niche). Furthermore, the project will disentangle the adaptive value of flowering time and seed dormancy, two traits known to be under selection, and how such adaptive value varies geographically to illustrate the complexity of adaptive evolution in plants. The project will also reveal the geographical functional variation in two key flowering genes and the most important seed dormancy gene in A. thaliana. This will provide valuable clues on the genetic basis of adaptive traits in natural populations. Finally, BLACKBOX is expected to improve predictive GCC models by taking underlying demographic processes into account, which is currently a topic of great concern among the international community.