Convergent genome evolution in natural populations

When and under which circumstances does evolution repeat itself?

 Evolution is driven by a deterministic forces like directional selection but also by chance, what brings an intriguing question about its predictability. Because evolution is a historical process, we have limited possibilities how to experimentally test for such question in its full complexity, i.e. in natural environments. 

Distinct lineages that independently evolved under similar conditions (i.e. underwent parallel adaptation) represent rare cases of such an experiment that had happened in nature. 

Thus, knowing how predictable is parallel evolution in such natural experiments should inform about how deterministic is evolution in general. That can provide insights into predictive evolution of crops, pathogens or species under climate change.

We investigate the probability of repeated adaptive evolution on genome level, by studying genomic variation of Brassicaceae species that independently adapted to the same selective pressure.

We will combine population and structural genomics with transcriptomic and reverse genetic validations to characterize the factors determining genomic hotspots of convergence and test the hypothesis of their varying importance with divergence. The project will identify general drivers of convergent genome evolution in nature and inform evolutionary predictions essential for efficient breeding and conservation.

In the first phase of the project, our current main focus is on sampling, experimental cultivation and genome sequencing of natural diversity of the target groups in order to identify candidate loci for serpentine adaptation. We are also progressing with new genome assemblies of the representatives of the following genera: Aethionema, Alyssum, Aubrieta, Bornmuellera, Cardamine, Draba, Erysimum, Isatis, Noccaea, Odontarrhena and Rorippa. Please, contact us if you are interested in collaboration or further use of these resources.

In the new ConAdapt project, funded by a five-years high-risk Junior Research Talent (JuniorStar) funding scheme, we build on our previous research in Arabidopsis but go well beyond this system. We investigate plant adaptation to even stronger selective environment, toxic serpentine soils, to uncover mechanisms driving convergent evolution. 

As we previously found that the extent of genomic convergence scales with evolutionary distance among the compared cases, we extend our divergence scale from Arabidopsis to the entire Brassiacecae family. Leveraging 13-fold independent colonization of serpentine soil by model family Brassicaceae, we aim at systematic assessment of the factors underlying genome convergence and thus evolutionary predictability. 

Recently we also studied the probability of parallel adaptive evolution on genome level in seven independent alpine lineages in Arabidopsis. 

First, by combining transplant experiments, genome resequencing and transcritptomics, we revealed set of candidate genes and functional pathways that have been repeatedly recruited for alpine adaptation.

Using this unique seven-fold replicated system, we demonstrated that the probability of gene reuse decreased with divergence between compared lineages, likely because less alleles are shared among distantly related lineages.

This means that more divergent lineages have less variation available for gene reuse and, subsequently, are less likely to evolve parallel genetic solutions to similar challenges.

In general, our results suggest that genetic basis of adaptive evolution could be better predictable in closely related lineages with shared pool of adaptive alleles while it becomes subject of change in distantly related lineages.