Progress in molecular technology is opening unprecedented opportunities for unraveling the mechanisms of evolutionary diversification. One promising avenue is to enrich organismal systems for which detailed background information about ecology and adaptive diversification is available with insights from developmental genetics. Another attractive opportunity is to transfer the power of genomic approaches established in well-developed research models to organisms offering fascinating ecological backgrounds, yet remaining unexplored at the molecular level. In this proposal, I describe two subprojects taking up these challenges. The first subproject focuses on my long-term research model, threespine stickleback fish. Populations of this species exhibit striking evolutionary reduction in skeletal traits in response to acidic waters on the island of North Uist, Scotland. Applying methodology from developmental genetics (fine-mapping using genome-wide association; developmental series and histological analyses; gene expression analysis based on RNA sequencing and in situ hybridization; genome editing), my objective is to elucidate how genetic variation modifies developmental pathways to produce the phenotypic diversity seen in nature. The second subproject will uncover the genomic underpinnings of rapid range expansion across Europe in a butterfly. This contemporary biological invasion will be examined at the whole-genome level by building a high-quality reference genome, dissecting the colonization history based on dozens of samples across the ancestral and new range, and finally by performing genome scans to search for genome regions and associated candidate genes promoting the rapid colonization of new territory. I anticipate that the proposed work will make strong contributions to understanding the developmental basis of vertebrate morphological evolution, and ecological and evolutionary responses of organisms to global change.

Investigations of the molecular basis of adaptive diversification among populations from ecologically distinct habitats have started to provide a fresh perspective on evolutionary mechanisms and to inform long-standing theoretical questions in genetics. Nevertheless, research combining ecologically interesting organismal systems, strong experimental designs, and powerful genomic resources are still scarce. In this proposal, I describe two such studies using threespine stickleback fish, each representing a separate PhD. The first subproject will involve the release of genetically heterogeneous stickleback obtained by crossing lake and stream populations from Switzerland into replicate natural stream habitats, followed by genome-wide marker-based tracking of allele frequency shifts driven by natural selection over multiple generations. This innovative study design will thus characterize evolution in action at the genomic level. The second project will focus on stickleback populations that have recently adapted to multiple basic and acidic lakes on the island of North Uist, Scotland. Combining genome-wide marker data and targeted sequencing in ten total populations, the study will scan for genes important to evolution driven by different water chemistries. These projects will address major unresolved issues in current adaptation genetics and will pave the way for functional investigations using evo-devo approaches.

Die Anpassung von Organismen an unterschiedliche Lebensräume, und die damit einhergehende Entstehung von Biodiversität, fasziniert Biologen seit Darwin. Über die molekulargenetischen Grundlagen dieses Prozesses ist allerdings noch sehr wenig bekannt, da bis vor kurzem die technischen Möglichkeiten zur Erforschung des Erbguts in natürlichen Populationen stark eingeschränkt waren. In diesem Projekt untersuchen wir Populationen des Dreistachligen Stichlings (einer Fischart), die sich einerseits an sehr saure, andererseits an basische Gewässer auf der Insel North Uist (Äussere Hebrieden, Schottland) angepasst haben. Mittels neu entwickelter Methodik werden wir das Erbgut der Fische nach Genen absuchen, die in den beiden Lebensraumtypen unterschiedliche Varianten aufweisen und somit für die Anpassung des Stichlings verantwortlich sind. Die Studie wird einen wichtigen Beitrag leisten zum Verständnis der Grundmechanismen biologischer Diversifizierung.

In the past decade, much of the research in the field of evolutionary genetics has been focused on identifying connections between genotype and phenotype. The next frontier in evolutionary biology is to connect specific genotypes and phenotypes to the survival of organisms in the wild. An ideal experimental approach would track survival (or fitness), all possible phenotypes and genotypes on a genome-wide scale, but this has not yet been done in any system. Threespine stickleback (Gasterosteus aculeatus) fish provide a remarkable opportunity to connect genotype, phenotype, and fitness. Here, we propose an ambitious and novel study using the lake-stream stickleback pairs, which have evolved repeatedly and independently in different watersheds, providing a striking example of parallel evolution. We will examine natural selection in action in an archetypal lake-stream pair, the Misty Lake system by following phenotypes and genotypes in fish that have survived in a stream environment using a large collection of marked (starting) and recaptured (surviving) fish. Next, we will measure phenotypes on all of the starting and surviving fish, and also genotype these fish at markers distributed across the genome using RAD-tag genotyping. With these genotype data, we will: (1) identify the genetic loci that show changes in allele frequency between starting and surviving fish; and (2) determine whether the loci that appear to be targets of selection are also associated with phenotypic differences between the starting and surviving populations. Our data will further allow us to address a major question in evolutionary biology: does ecological divergence result from multifarious selection across a number of traits or from strong selection on one or a few traits? Identifying the distribution of loci that are under selection across the genome and associating these loci with the phenotypes under selection will provide important and novel insights into this question, and into the connections between genotype, phenotype and fitness.

Facilitated by recent technological advances, research linking DNA sequence data to phenotypic and ecological information is beginning to offer exciting new molecular insights into the mechanisms underlying evolutionary diversification. Nevertheless, this line of research is incomplete because phenotypic evolution might often be driven by direct interactions between genetic systems and environmental conditions experienced by an organism (phenotypic plasticity). A complete understanding of adaptive diversification thus benefits greatly from empirical approaches simultaneously addressing genetic and plastic components within the same organismal system and in a strong ecological framework. Such integrative research is rare but forms the subject of the proposed study, building on a powerful natural model system - threespine stickleback fish. The project will investigate the relative role of genetic differentiation and phenotypic plasticity in rapid life history divergence between lake and stream stickleback populations residing within the Lake Constance basin (Switzerland, Germany, Austria). This work will combine laboratory and field transplant experiments with QTL mapping and replicated high-resolution genome scans for signatures of selection. By providing a highly complete dissection of evolutionary divergence in an emerging model system for ecological genetics, the study will inform fundamental issues in understanding the mechanisms driving biological diversification.

A complete understanding of the evolutionary process has long been impeded by limited knowledge about the genetic and developmental basis of functionally relevant phenotypic variation. This situation has changed with the advent of genomic and developmental tools, making possible integrative research linking molecular variation to fitness-relevant phenotypic variation in some model organisms. The aim of the present proposal is to carry out such an integrative study in Swiss populations of threespine stickleback fish. I will focus on populations that have repeatedly and independently evolved highly divergent foraging morphologies (gill raker apparatus) in response to contrasting foraging conditions between limnetic and benthic habitats (parallel evolution). These populations will be subject to powerful molecular genetic experiments, including QTL mapping, candidate and comparative gene expression analysis, and selective sweep analysis. These molecular experiments will uncover the genetic architecture of phenotypic variation, identify key genes and developmental pathways in morphogenesis, and determine the role natural selection in driving molecular shifts. The proposed study will shed light on mechanisms underlying parallel evolution, and thereby contribute to our understanding of adaptation and biological diversification.

Organisms occurring in ecologically distinct environments often show predictable differences in traits that influence performance in the respective environments. However, a few exceptions aside, we generally do not know how and which genes and developmental pathways are involved in the formation of ecologically relevant phenotypic diversity. This situation is changing with the advent of genomic and developmental research tools, making possible integrative investigation that links variation at the molecular level to fitness-relevant phenotypic variation. The aim of my project is to carry out such an integrative study in Swiss populations of threespine stickleback fish (Gasterosteus aculeatus). I focus on populations that have evolved differences in foraging traits (gill raker apparatus, body shape) in response to contrasting foraging conditions between limnetic (zooplankton-dominated) and benthic (macroinvertebrate-dominated) habitats. These populations will be subject to several complementary molecular genetic experiments, including quantitative trait locus (QTL) mapping, candidate and comparative gene expression analysis, and selective sweep analysis. These molecular experiments will uncover the genetic architecture of phenotypic variation among natural populations, identify key genes and developmental pathways in morphogenesis, and inform on the role natural selection in driving genetic shifts. My project will therefore shed light on the molecular mechanisms underlying evolution, and thereby contribute to our understanding of adaptation and biological diversification.

The understanding of adaptive evolution has long been impeded by limited knowledge about the genetic and developmental basis of functionally relevant phenotypic variation. This situation has changed with the advent of genomic and developmental tools, making possible integrative research linking molecular variation to fitness-relevant phenotypic variation in some model organisms, including threespine stickleback fish. The aim of the present proposal is to carry out such an integrative study in Swiss populations of stickleback. I will focus on populations that have repeatedly and independently evolved highly divergent foraging morphologies (gill raker apparatus and body shape) in response to contrasting foraging conditions between limnetic and benthic habitats (parallel evolution). These populations will be subject to extensive morphometric analysis, and their natural selective environments will be quantified. This work will be complemented by powerful molecular genetic and developmental experiments, including candidate gene and comparative gene expression analysis, and QTL mapping. These molecular experiments will uncover the genetic architecture of ecologically relevant phenotypic traits, and identify key genes and developmental pathways in their morphogenesis. The synthesis of morphological, ecological, and molecular information will in turn shed light on the mechanisms interacting during parallel evolution. My work will thereby contribute to resolving fundamental issues in evolutionary genetics and understanding biological diversification.