Department Fish Ecology and Evolution


A de novo chromosome-level genome assembly of Coregonus sp. "Balchen": one representative of the Swiss Alpine Whitefish radiation

May 13, 2020

To understand how specific organisms evolve, adapt to new environments, and form new species it is important to be able to compare the DNA sequences of different individuals and organisms. The best way of doing this is to have species-specific genetic resources, such as a genome assembly, for the species of interest which allow us to find genetic similarities and differences between individuals. Reference genome assemblies, the complete genetic code from one organism, are the most useful resource for doing such comparisons. However, producing genome assemblies is challenging due to the size and complexity of many genomes.
Scientists have studied populations of Lake Whitefish in both Europe and North America to try to understand how they have evolved to fill many different niches in a very short period of time. To facilitate the genetic investigation of how whitefish have evolved in the last 10-15 thousand years we have produced the first whitefish genome assembly, that of a Swiss, Alpine whitefish. Our genome assembly is of high quality and represents the complete and ordered DNA sequence of each whitefish chromosome as well as the genome annotation which tells us the location and identify of genes in the whitefish genome. The genome assembly will assist future studies which aim to understand how whitefish with different physical and behavioural characteristics differ at the genetic level and how they evolved.

Original publication



Rishi De-KayneTel. +41 58 765 2269Send Mail

Seeing the rainbow: mechanisms underlying spectral sensitivity in teleost fishes

30 April 2020

In this review, the amazing variety of anatomical and molecular mechanisms of the visual system of fish is presented and their function for their visual requirements. Read more



Dr. Sara StiebTel. +41 58 765 2286Send Mail

ABCD conferences for an integrative and sustainable science

24 April 2020

ABCD: All continents, balanced gender, low carbon transport and diverse backgrounds. These criteria should shape the scientific conferences of the future. Read more



Temporally consistent species differences in parasite infection but no evidence for rapid parasite-mediated speciation in Lake Victoria cichlid fish

17 April 2020

Parasites may have strong eco-evolutionary interactions with their hosts. Consequently, they may contribute to host diversification. The radiation of cichlid fish in Lake Victoria provides a good model to study the role of parasites in the early stages of speciation. We investigated patterns of macroparasite infection in a community of 17 sympatric cichlids from a recent radiation and 2 older species from 2 nonradiating lineages, to explore the opportunity for parasite-mediated speciation. Host species had different parasite infection profiles, which were only partially explained by ecological factors (diet, water depth). This may indicate that differences in infection are not simply the result of differences in exposure, but that hosts evolved species-specific resistance, consistent with parasite-mediated divergent selection. Infection was similar between sampling years, indicating that the direction of parasite-mediated selection is stable through time. We morphologically identified 6 Cichlidogyrus species, a gill parasite that is considered a good candidate for driving parasite-mediated speciation, because it is host species-specific and has radiated elsewhere in Africa. Species composition of Cichlidogyrus infection was similar among the most closely related host species (members of the Lake Victoria radiation), but two more distantly related species (belonging to nonradiating sister lineages) showed distinct infection profiles. This is inconsistent with a role for Cichlidogyrus in the early stages of divergence. To conclude, we find significant interspecific variation in parasite infection profiles, which is temporally consistent. We found no evidence that Cichlidogyrus-mediated selection contributes to the early stages of speciation. Instead, our findings indicate that species differences in infection accumulate after speciation. Original publication



Tiziana GobbinTel. +41 58 765 2266Send Mail

Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids

9 April 2020

One hallmark of the East African cichlid radiations is the rapid evolution of reproductive isolation that is robust to full sympatry of many closely related species. Theory predicts that species persistence and speciation in sympatry with gene flow are facilitated if loci of large effect or physical linkage (or pleiotropy) underlie traits involved in reproductive isolation. Here, we investigate the genetic architecture of a key trait involved in behavioural isolation, male nuptial coloration, by crossing two sister species pairs of Lake Victoria cichlids of the genus Pundamilia and mapping nuptial coloration in the F2 hybrids. One is a young sympatric species pair, representative of an axis of colour motif differentiation, red-dorsum versus blue, that is highly recurrent in closely related sympatric species. The other is a species pair representative of colour motifs, red-chest versus blue, that are common in allopatric but uncommon in sympatric closely related species. We find significant quantitative trait loci (QTLs) with moderate to large effects (some overlapping) for red and yellow in the sympatric red-dorsum × blue cross, whereas we find no significant QTLs in the non-sympatric red-chest × blue cross. These findings are consistent with theory predicting that large effect loci or linkage/pleiotropy underlying mating trait differentiation could facilitate speciation and species persistence with gene flow in sympatry. Read more



Anna FellerTel. +41 58 765 3157Send Mail

News from 2019

Size-dependent tradeoffs in seasonal freshwater environments facilitate differential salmonid migration

December 21, 2019

Seasonal spatio-temporal variation in habitat quality and abiotic conditions leads to animals migrating between different environments around the world. Whereas mean population timing of migration is often fairly well understood, explanations for variation in migratory timing within populations are often lacking. Condition-dependent tradeoffs may be an understudied mechanism that can explain this differential migration. While fixed condition-specific thresholds have been identified in earlier work on ontogenetic niche shifts, they are rare in differential migration, suggesting that thresholds in such systems can shift based on temporally variable environmental conditions.

Original publication


Philip DermondTel. +41 58 765 2258Send Mail

Hybrids increase fish biodiversity in lakes of East Africa

December 5,  2019

The lakes of East Africa are home to a surprising number of different cichlid species. This level of biodiversity has developed partly due to hybrids that managed to take over new ecological niches in their habitats, according to recent research carried out by scientists at the Swiss Federal Institute of Aquatic Science and Technology, Eawag, and the University of Bern. Read more


Dr. Oliver SelzTel. +41 58 765 2146Send Mail

Opportunity makes species

November 13, 2019

There may be hundreds of species of char living in Greenland’s lakes and rivers, according to a team from the Swiss Federal Institute of Aquatic Science and Technology (Eawag) and the University of Bern, that has discovered the largest known diversity of char species in the catchment area of the Eqaluit River. Read more

Original publication



Dr. Jakob BrodersenTel. +41 58 765 2204Send Mail

A detailed investigation of the visual system and visual ecology of the Barrier Reef anemonefish, Amphiprion akindynos

November 22, 2019

Vision plays a major role in the life of most teleosts, and is assumingly well adapted to each species ecology and behaviour. Using a multidisciplinary approach, we scrutinised several aspects of the visual system and ecology of the Great Barrier Reef anemonefish, Amphiprion akindynos, including its orange with white patterning, retinal anatomy and molecular biology, its symbiosis with anemones and sequential hermaphroditism.

 Original publication


Dr. Sara StiebTel. +41 58 765 2286Send Mail

Important species interactions can destabilize aquatic ecosystems in response to nutrient inputs

October 16, 2019

In aquatic ecosystems, both mussels and macrophytes increase water clarity and generally help to prevent excessive algal growth. However, according to a study carried out at Eawag’s experimental pond facility, these stabilizing effects can be disrupted when the co‑occurrence of species gives rise to complex interactions. Read more


Original publication


Dr. Blake MatthewsTel. +41 58 765 2120Send Mail

Genetic development is influenced by the host-parasite relationship – but not only that!

October 2, 2019

Rapid changes in the genome of two closely interlinked species cannot be explained only by processes such as evolutionary pressure. Equally important is the role played by ecological processes, for example the dynamics of population size. This has been shown for the first time experimentally by an international team of researchers under the direction of Eawag and the University of Konstanz with an alga and a virus. The study will be published today in the magazine Science Advances. Read more

Original publication


Cas RetelTel. +41 58 765 2261Send Mail

Adaptation to a new habitat can lead to the rapid evolution of new species.

September 18, 2019

However, the genetic mechanisms allowing this are poorly known. A new publication in Nature Communications by David Marques, Kay Lucek, Vitor Sousa, Laurent Excoffier and Ole Seehausen shows now that threespine stickleback inhabiting Lake Constance have arisen from hybridization between two stickleback species from West and East Europe. The exchange of genetic material has facilitated rapid evolution of lake and stream ecotypes within the East European species, with ecotypes now breeding side by side without collapsing back into a single population. Lake Constance stickleback, alongside Lake Victoria cichlids, thus demonstrate that hybridization can be an important genetic mechanism facilitating the rapid evolution of new species.

blog digest of the paper


Interview with Dr. Sara Stieb

July 28, 2019

An insight into her molecular neurobiologist's work and about means of visual communication between fish.

link to the article Luzerner Zeitung (in German)


Dr. Sara StiebTel. +41 58 765 2286Send Mail