My research focuses on understanding the genomic basis and regulatory mechanisms underlying adaption and phenotypic divergence in natural systems. My main research questions aim to understand:

i) the evolutionary and genomic responses by which organisms adapt to different environments

ii) the genetic basis and functional genomic mechanisms of phenotypic evolution

iii) and the regulatory and functional genomic basis of adaptive divergence and ecological speciation.

I mostly address these questions by combining population genomic and gene expression analyses of natural populations, particularly along natural environmental clines or in cases of parallel evolution. More recently, I have started focusing on also studying the functional genomic mechanisms, such as divergence in gene regulatory mechanisms and alternative splicing, in natural and experimental populations.  

My research is mostly driven by exciting natural history observations and I aim to generate a better understanding of how the biodiversity around us has evolved and how species adapt to different environments, including those created by humans, e.g. cities. Although I am mainly interested in fishes and other aquatic organisms, I also venture out and collaborate with a range of researchers to study adaptive processes in birds and other vertebrates.

Below is an overview of my main research projects that address one or several of my major research topics:

Topic: Evolutionary Processes | Functional Genomics | Genetics of  Phenotypic Evolution

Understanding the genetics and the functional mechanisms of variation in intestine development in an ancient vertebrate, the lamprey.

Lampreys have evolved over 500 million years ago and are the only ancestrally-parasitic vertebrate. Yet, non-parasitic species have evolved multiple times independently as an alternative life history from closely-related parasitic species. Although parasitic and non-parasitic sister species don’t differ in their morphology or ecology during their larval stage, they show striking phenotypic differences as adults. For example, during metamorphosis from larvae to adult, the intestine of non-parasitic forms does not fully remodel, leaving non-parasitic adults unable to feed, making them the only vertebrate that doesn’t feed as adult.

European lamprey ecotypes | Examples of the three different European river lamprey ecotypes (or species) found in the Loch Lomond catchment in Scotland.

However, despite their important position at the base of the vertebrate tree, we don’t have a good understanding of the genetic and functional genomic differences underlying the evolution and development of lamprey. Thus, I am leading a research project into the genetic and functional genomic basis of life history evolution and intestine development in this species complex. As part of this project, we sequence and assemble a reference genome for the European river lamprey (Lampetra fluviatilis) and use a combination of population genomics, evo-devo and functional genomics to identify the underlying genes and mutations, as well as the evolutionary history of these life history forms.

Topic: Evolutionary Processes | Local Adaptation | Functional Genomics

The genomic and functional basis of local adaptation under pervasive gene flow in marine fish.

Using an ecological model organism, the Atlantic silverside (Menidia menidia), I am trying to understand how marine species locally adapt to distinct environmental conditions in the face of gene flow. The Atlantic silverside is a small estuarine species that is distributed along of the steepest temperature clines in the world along the North American Atlantic coast.

Silversides show strong variation in a range of adaptive phenotypes along this latitudinal cline, such as growth rate or the level of temperature-dependent sex determination. Using a combination of low-coverage whole-genome sequencing, experimental crosses, temperature treatment experiments and gene expression analysis, I am investigating the genetic basis of phenotypic divergence and genomic architecture of local adaptation.

Topic: Gene regulation | Functional Genomics

Gene regulatory mechanisms underlying rapid phenotypic divergence.

Understanding how genetic changes or environmental responses are translated into divergent phenotypes is a major question in evolutionary and developmental biology. This so called genotype-phenotype map consists of several molecular levels, including the transcription of the genotype into RNA, the post-transcriptional processing of this RNA, and the subsequent translation of this variation into proteins, which underlie many major measurable phenotypes. While we have a growing understanding of the role of transcription variation (differential gene expression) in adaptive divergence, our knowledge of the role of post-transcriptional processing in adaptation is very limited.

I am using RNA sequencing data from parallel Arctic charr ecotypes and other salmonid fishes to better understand the role of post-transcriptional processing, particularly alternative splicing, in their adaptive phenotypic divergence. The main questions I am trying to answer is i) How do patterns of gene expression and alternative splicing differ?,  ii) What is the potential phenotypic effect of differential alternative splicing? and iii) How is alternative splicing regulated?

Topic: Evolutionary processes | Local Adaptation | Population Genomics | Functional Genomics

Rapid adaptation to urban environments in great tits (Parus major).

Great tits are one of the most widely distributed passerine birds in Europe, occurring in all kinds of environments, including urban habitats, making them an ecological model system. In collaboration with a range of European researchers from Sweden to Spain, I am investigating the genomic signatures of local adaptation to urban habitats. To achieve this, we are comparing the genomes (based on SNP chips and whole-genome sequencing) of great tits from urban sites with those from close-by rural sites in multiple European cities. The first results of these productive collaborations will be published soon!



Previous research: 

Topic: Evolutionary processes | Local Adaptation | Functional Genomics | Population Genomics

Rapid and parallel phenotypic evolution in salmonid fishes

These projects were the focus of my PhD with Kathryn Elmer at the University of Glasgow.

Project 1: How predictable is evolution? – Integrative analysis of rapid and parallel evolution. 

Using instances of parallel evolution in salmonid fishes, I aim to better understand the predictability of evolution, particularly of ecological divergence. Arctic charr is one of the most diverse vertebrate species and has repeatedly evolved diverse ecotypes across lakes in the northern hemisphere, including in Scotland and Siberia. These ecotypes include benthic-feeding specialists (‘benthivorous’) occupying the littoral-profundal habitat, plankton-feeding specialists (‘planktivorous’) living in the open water, fish-feeding specialists (‘piscivorous’).

Examples of Arctic charr ecotypes | a. Benthivorous and planktivorous ecotypes from Scotland. b. Planktivorous and piscivorous ecotypes from Siberia. (not to scale)

Despite numerous studies investigating the ecological and phenotypic adaptation to different trophic niches and habitats, we still have a limited understanding about the extent of phenotypic parallelism in this species and how replicated ecotypes have evolved.

Integrating ecological, phenotypic, population genomic and gene expression data I aim to understand i) how replicated ecotypes have evolved, ii) if parallel genomic and functional changes underly parallel evolution and iii) what determines or constrains the extent of parallel phenotypic and genomic evolution. Together, this will provide us with a better understanding of the repeatability of evolution, allowing us to better predict evolutionary responses in the face of environmental change.

Using this integrated approach, we investigated the evolution of of replicated ecotype pairs within the Atlantic lineage of Arctic charr (Scottish lakes) and the Siberian lineage (Transbaikalian lakes), as well as across these two distinct evolutionary lineages. Overall, we found varying levels of phenotypic parallelism across populations that could be explained by variation in evolutionary history, environmental stochasticity and variation in molecular responses. The results can be found here.

Project 2: The functional and genomic basis of rapid ecological and phenotypic re-expansion in European whitefish (Coregonus lavaretus) from Lake Constance.

Project 3: The evolutionary history and genomic basis of a rare piscivorous brown trout (Salmo trutta) ecotype, the ferox trout.