I am an evolutionary biologist fascinated by the diversity of organisms and the processes shaping this diversity.
Currently, I am a Postdoctoral researcher at the University of Bern (Switzerland).
We live in a world with stunningly diverse organisms. How do ecological and evolutionary processes interact to generate and maintain this diversity, and which processes act as constraints? How repeated is evolutionary change, and how long does it take? I study these questions at the level of both the genotype and phenotype. I particularly enjoy thinking about important conceptual problems and tackling them empirically by using whatever approach is needed to get closer towards a satisfying answer. Recently, I have often combined genomics with field experiments, but I am also using various other approaches from evolutionary ecology, population genetics and molecular biology, well as theoretical simulations.
My main empirical study organism is the threespine stickleback. Stickleback have adapted rapidly and repeatedly to distinct freshwater habitats allover the Northern hemisphere since the last ice age. There are also excellent genomic resources available for this organism, and stickleback are well-suited for (field) experiments. Together, this makes this fish an excellent system to investigate how fast and predictably organisms diversify, and which factors favor, maintain or constrain evolutionary change. Besides stickleback, I have also used cichlids, icefish, lampreys, sculpins, and Daphnia crustaceans for my research.
My ongoing research includes the following topics:
Recombination: Genetic recombination is a fundamental biological and evolutionary mechanism. I have a longstanding interest in understanding how and why the rate of recombination varies across a genome, and how this variation affects adaptation and diversification. Due to their impact on recombination and linkage, I’m also interested in chromosomal inversions. To better understand the genetic consequences and evolutionary importance of recombination rate variation, I use a combination of simulations, genetics, population genomics and meta-analyses.
Habitat selection: Organisms can become fitted to an environment in various ways. One such way is through natural selection, where an organism changes over generations to become fitted to its surroundings. Another and often neglected way is habitat selection (habitat choice), where the match between an organism and its surroundings is generated by individuals choosing the environment that is best suited for them. I use mark-release-recapture field experiments, fitness assays, genomics, genetics, and morphological analyses to test the importance of habitat selection in generating and maintaining population divergence.
Genomics of adaptation: How repeatable and rapid does the genome adapt in response to similar selection pressures? And, what is the genomic footprint of parallel and divergent adaptation? To tackle these questions, I mainly use population genomics, phenotypic investigations and controlled experiments (in mostly lake-stream population pairs of threespine stickleback), as well as theoretical simulations.
Species interactions: How do species interactions contribute to diversification? In an ongoing line of research, I test whether a simple biotic change – the presence vs. absence of a species – can result in rapid change and reproductive isolation in another species. I study a system where we find each of two ecologically-similar fish species in allopatry and sympatry with respect to one another. I analyze phenotypic and genomic data to describe population divergence in these species and complement these comparative results with field and controlled pond experiments.
Predictability of evolution: The topic of the predictability of evolution has a long history in evolutionary biology. Besides being of empirical interest, the “predictability problem” is also of fundamental conceptual and philosophical relevance: what is the value and function of predictions in evolutionary biology (and science in general), and how do we go about making predictions? And, what are the factors that constrain predictability? I much enjoy thinking and writing about these and related questions.
In doing all this work, I would like to acknowledge the many great mentors and colleagues I am fortunate to work with, as well as my friends who believe in me as a scientist. For more information on my past or ongoing work – or anything else really – please do not hesitate to contact me!
SNIPPETS OF MY RESEARCH (non-chronological)
Inversions & adaptation. Here, we found that old chromosomal inversions differentiate parapatric lake and stream stickleback in a Central European watershed. Because lake-stream differentiation at inversions occurs repeatedly, these inversions are likely to be important for adaptive divergence. We show experimentally that recombination between the two inversion variants is absent. Yet, genomic differentiation between individuals carrying different inversion variants suggests that rare recombination (double crossover or gene conversion) has happened between the inversion variants in the center of the inversions (Roesti et al. 2015).
Recombination strongly influences genome-wide population divergence. Chromosome-scale patterns of genomic differentiation are similar across many organisms, with higher recombination at chromosome tips and low recombination in chromosome centers. This recombination variation, together with polygenic selection and gene flow, strongly shapes genomic patterns of divergence. Besides describing this empirical pattern, we use simulations to quantify different genetic mechanisms leading to elevated population divergence in regions of low recombination, including genetic hitchhiking and gene flow barriers. We then test the predictions from these models by comparing allopatric and parapatric populations of stickleback residing in different, or similar, environments (Berner & Roesti 2017).
Species divergence driven by resource competition and shared predation. By comparing co-occurring (sympatric) and allopatric populations of both threespine stickleback and prickly sculpin fish, we find trait shifts in opposite direction between the species when sympatric. These shifts are seen in typical trophic traits and diet, as well as in traits providing protection against large predators. Our study suggests that ecological character displacement driven by resource competition has increased vulnerability of stickleback but decreased vulnerability of sculpin to a shared predator (trout). Our study highlights the importance of the indirect interaction between prey species via shared predators for driving species divergence (Roesti et al. 2022).
Genomic architecture of adaptation with gene flow. In this perspective, I summarize why and how adaptive loci should become clustered within a genome when local adaptation occurs with maladaptive gene flow. In particular, I focus on the importance of genome regions with low recombination to generate clusters of adaptive loci. I argue that we still have a poor understanding of where in a genome the adaptive loci are, and although genome regions of low recombination appear to be promising hotspots for adaptive loci to cluster, observed patterns of ‘clustered loci’ may often be explained differently or may be a consequence of a recombination-bias in our genomic methods. I use hundreds of previously published QTLs to demonstrate this bias in threespine stickleback, and then suggest future avenues for how to get around these problems with comparative genomics (Roesti 2018).
Chromosomal inversions as a constraint to new adaptation. In this perspective, we reason and use simulations to illustrate that chromosomal inversions can limit adaptation to new habitats because inversions limit the reshuffling of existing genetic variation into newly favorable combinations (Roesti et al. 2022).
The largest test of the Biotic Interactions Hypothesis. It is generally assumed that interactions between species, such as predation, increase from the poles towards the equator and may explain why more species evolved, and are being maintained, in the tropics. We tested this so-called ‘Biotic interactions hypothesis’ in the open ocean by using catch-per-effort data from 55 years of pelagic longline fishing. Surprisingly, we found that (1) predation by large open-water fish is strongest at temperate latitudes, and (2) predation is negatively correlated with species richness. These patterns are contrary to the biotic interactions hypothesis (Roesti et al. 2020).
A function trade-off between foraging and brood care – and not sexual selection – explains sexual dimorphism in cichlids. Cichlid fish species in the East African Lake Tankanyika differ in how they care for their eggs and juvenile offspring: either only one sex or both sexes use mouthbrooding for parental care, or parental care involves no mouthbrooding at all. We predicted that due to a likely functional involvement of gill rakers in mouthbrooding besides in foraging, only uni-parental mouthbrooding species should be sexually dimorphic in gill raker morphology. Indeed, this is what we found! This study provides a largely unrecognized explanation for sexual dimorphism in nature because neither sexual selection nor initial niche divergence between the sexes can explain this sexual dimorphism (Ronco*, Roesti*, Salzburger* 2019).
A simple biotic change leads to strong genome-wide adaptation in stickleback. In many postglacial lakes in Western Canada, threespine stickleback and prickly sculpin co-occur and interact (food competition and opportunistic predation). In some lakes, however, there are only stickleback, but no sculpin. We find evidence for strong, parallel selection in the genome of stickleback as a consequence of sculpin presence/absence. The extent of phenotypic and genomic adaptive divergence are positively associated (Miller, Roesti, Schluter 2019). More work on this species interaction is forthcoming.
Left: Parallel adaptation from shared genetic variation, such as from pre-existing or introgressed variation, produces a distinct genetic signature within a genome. We predict this signature using simulation models, and then confirm the prediction by genome-wide and targeted sequencing of natural stickleback populations (Roesti et al. 2014).
Right: Chromosome-wide variation in recombination rate shapes differentiation and diversity within the stickleback genome. Recombination rate is consistently elevated towards the tips of chromosomes, and reduced in the center of chromosomes – a pattern that appears to be unrelated to the position of the centromeres, but instead, is related to functional constraints during meiosis. We further find that recombination rate variation influences nucleotide composition within a genome (Roesti et al. 2013).
Genomic signatures of a morphological adaptation. Lake-stream divergence of stickleback in lateral plating and the associated molecular signatures (Roesti et al. 2015).
Phenotypic divergence vs. genomic divergence across several lake-stream stickleback populations. We investigated stickleback from lakes and adjacent streams, and characterized phenotpyic and genome-wide signatures of habitat-specific selection. We detect the constraint of gene flow to genome-wide differentiation between diversifying populations, and find that the degree of phenotypic and genome-wide differentiation correlate positively. This study provided one of the first genome-wide demonstrations of how recombination rate variation shapes genomic differentiation during diversification (Roesti et al. 2012).
Some field work pictures.
Left: Phenotypic plasticity or genetic differentiation? In this study, we found evidence for strong genome-wide differentiation between distinct lamprey ecotypes that were previously thought to be the product of phenotypic plasticity (Mateus et al. 2013).
Right: Phylogenomics of an adaptive radiation. Patagonotothen icefish species reveals incomplete species boundaries in this adaptive radiation (Ceballos et al. 2019).
What is limiting our ability to predict evolution? Limits and implications of the predictability of evolution (Roesti 2021; a dispatch on Kirch et al. 2021).