Supergene evolution in a classic plant system – genomic studies of distyly in Linum
Supergenes are tighly linked clusters of genes which control complex adaptive phenotypic polymorphisms, and that are inherited as a unit. Supergenes are important for a wide range of balanced polymorphisms in natural populations. An emerging insight from studies of supergenes in disparate systems is that they exhibit great similarities from an evolutionary genetic perspective. However, many fundamental questions remain regarding the tempo and mode of supergene evolution.
In this project, we will investigate evolutionary processes at one of the first discovered supergenes, the distyly S-locus. The S-locus governs distyly, a balanced floral polymorphism that ensures outcrossing and efficient pollen transfer between compatible plants. We will conduct our studies in Linum, where the dynamic nature of distyly presents an outstanding opportunity to study the evolutionary processes associated with supergene maintenance and loss. Specifically, we will make full use of the latest advances in genome sequencing to establish a genomic framework for the study of distyly in Linum. We will then use this framework to comprehensively test hypotheses on the evolution and breakdown of the distyly supergene, specifically investigating evolutionary genetic similarities to incipient sex chromosomes. This project is funded by a European Research Council Starting Grant.
The role of structural variation for the origin and evolution of a classic supergene
In this project, we will investigate the role of structural variation at the Linum distyly S-locus supergene. To do so, we will use high-quality genomic data and a comparative genomic approach. Our main aim is to investigate the role of inversions, insertions and other types of structural genomic changes at the S-locus. We are specifically interested in whether structural changes at the S-locus represent a cause vs. a consequence of suppressed recombination, and whether introgression has contributed to the origin and evolution of the S-locus in Linum. To address these questions, we will first combine de novo genome assembly of long-read data with genetic analyses to identify S-linked regions. We will then build on this knowledge to investigate structural variation, test for an effect of recombination suppression on the efficacy of selection, and test for introgression at the S-locus, in a comparative genomic framework. The results from this project are important for an improved understanding of the processes that govern supergene evolution and the origins of coadapted gene complexes. This project is funded by a project grant from the Swedish Research Council.
Evolutionary consequences of plant mating system shifts
The transition from outcrossing to predominant self-fertilization (selfing) is one of the most common mating system shifts in flowering plants. This transition can be favored if the immediate benefits of selfing outweigh the costs of inbreeding depression.
In the long term, however, selfing is thought to constitute a ‘dead end’, and self-compatible lineages experience elevated extinction rates. Selfing is predicted to lead to a reduced potential for adaptation as well as accumulation of deleterious mutations, but the relative importance of these processes for the long-term demise of selfing lineages remains unclear. Moreover, relatively few empirical studies have investigated the effect of partial selfing on adaptation and accumulation of deleterious mutations. Obtaining a better understanding of these questions is vital for our understanding of plant mating system diversity.
In this project, we undertake population genomic analyses of several parallel shifts to selfing in the Brassicaceae, in order to test for an effect of mating system on the efficacy of positive and purifying selection.
To investigate the impact of varying outcrossing rates and postglacial recolonisation, we are currently conducting large-scale population genomic analyses in the alpine plant Arabis alpina.
Effects of linked selection on plant genomic variation
Understanding the forces that shape patterns of genetic variation across the genome and how this translates into phenotypic variation is of great general and applied interest. Recent genomic studies have shown that the interaction between selection and recombination, or linked selection, can have a profound impact on levels of genetic and heritable phenotypic variation. However, so far, we know little about the general impact of linked selection on heritable phenotypic variation in plants, and the factors causing variation in the type of linked selection among species remain unclear. The main aim of this project is to quantify the relative impact of population size and mating system on the type and strength of linked selection. To achieve this, we will use a combination of population genomics analyses of whole genome resequencing data from multiple species and population genetic modeling. The results are key for a general understanding of the forces that shape genetic variation in plants. This project is funded through a SciLifeLab National Biodiversity project grant.