Aquatic Ecology & Evolution

Fishes are the most diverse group of vertebrates, are key players in aquatic ecosystems, provide a diverse set of ecosystem services, and are sensitive to environmental change. We study their ecology, evolution and conservation. We work with fish diversity from traits and genes in populations to the diversity of species assemblages, their change through time and the ecosystem consequences. We are particularly interested in understanding the evolution of endemic diversity within individual ecosystems, such as the radiations of cichlid fish in African lakes and the radiation of whitefish in the lakes around the European Alps. We are a single research group led by Ole Seehausen at the University of Bern but Ole also leads the Department Fish Ecology and Evolution at the Eawag Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, where we currently host four other research groups that are all associated with the IEE too. The work of the Eawag department is motivated by the aim to contribute to the emerging synthesis between evolutionary biology and ecosystems ecology. There we also host the Swiss Fisheries Advisory Service. Researchers in the department of vertebrates at the Natural History Museum Bern, NMBE, are also affiliated with our University division.

News

David Frei defended his PhD successfully - congratulations!

Congratulations to a very successfully defended Phd! David worked over the last four years on the role of hybridization on extinction and speciation reversal in the whitefish species of Lake Constance. Among other things he showed that alleles allowing adaptions to live in the deep waters origination from an extinct species are still around in the population of other withefish species that may allow them to recolonise the deep waters of Lake Constance.

"Good science has to be open, diverse and inclusive"

Tomorrow, 11 February, is the International Day of Women and Girls in Science, an initiative supported by UNESCO encouraging women and girls to pursue a career in science and promoting diversity in research.

How giants became dwarfs

Pooja Singh recently published together with Michael Taborsky and Katie Peichel a paper on the genetic sex determinism mechanism in a Lake Tanganyika cichlid, Lamprologus callipterus, which has two types of males: giant, territorial males that collect empty snail shells in which the females of this species spawn their eggs, and tiny dwarf males - even smaller than the females - that fit into the snail shells to attempt to fertilize the eggs from inside the shell. Read more about the story on this link.

Seven new species of whitefish described in Central Switzerland

Oliver Selz and Ole Seehausen have identified ten species of whitefish in the lakes of the Reuss river system. Of these, seven have been described as distinct species for the first time – although in two cases this required inspection of specimens from historical collections, since eutrophication of lakes in the 20th century also led to the extinction of fish species in Central Switzerland. Read more about it on this link!

Paper - Introgression from extinct species facilitates adaptation to its vacated niche

David Frei published the first paper of his PhD thesis on speciation and its genomics in alpine whitefish. In Lake Constance, an endemic profundal whitefish species went extinct during a period of anthropogenic eutrophication. In the process of extinction, this species hybridized with three surviving whitefish species of Lake Constance, resulting in introgression of genetic variation that is potentially adaptive in deep-water habitats. The results are consistent with the syngameon hypothesis, proposing that hybridization between members of an adaptive radiation can promote further niche expansion and diversification. Furthermore, these findings demonstrate that introgression from extinct into extant species can be a source of evolvability enabling rapid adaptation to environmental change and may contribute to the ecological recovery of ecosystem functions after extinctions.

NatComm - A functional vulnerability framework for biodiversity conservation

Conor published a paper in Nature Communications together with a large group of international researchers on a new tool to quantify the vulnerability of species communities. This framework also incorporates uncertainty and reference conditions into a generalizable tool. Combined with future ecosystem risk assessment studies, this tool should help decision-makers identify management priorities and guide protection efforts where they are most needed.

PRSB - Climate, immigration and speciation shape terrestrial and aquatic biodiversity in the European Alps

Luiz and many colleagues from Eawag, WSL, NMBE and the IEE discuss the relative contribution of immigration, speciation and extinction to the assembly of biodiversity in island-like habitats. They detect biogeographic and genetic signatures associated with two mechanisms, namely (i) a glacial species pump where isolation in glacial refugia accelerates allopatric speciation and (ii) adaptive radiation in underused adaptive zones during ice-free periods. A high proportion of the endemic Alpine biodiversity is very young making it very vulnerable to climate change. The mechanisms and consequences of species loss will likely differ for different species groups with different evolutionary history.

NatComm - Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Rishi and many colleagues from our research group recently published one of his PhD chapters in Nature Communications. They address questions revolving around the roles of the genomic architecture and hybridization in the Alpine whitefish radiation, using a whole-genome dataset that includes multiple individuals of each of the 22 species belonging to six ecologically distinct ecomorph classes across several lake-systems. The results reveal that repeated ecological and morphological diversification along a common environmental axis is associated with both genome-wide allele frequency shifts and a specific, larger effect, locus. They further highlight the role of introgression between species from different lake-systems in facilitating the evolution and persistence of species with unique trait combinations and ecology.

photo of Pooja Singh by Christian Dinkel

Interview with Pooja Singh - The genome of 100'000 African species will be decoded

Africa is home to a large part of the world's biodiversity. Many species are native only to this continent. So far, the genome of only a tiny proportion of them has been decoded, but this is an important prerequisite for their protection. The large-scale African BioGenome Project, in which Eawag researchers are also involved, now aims to change this.

PRSB - Genetic architecture of adaptive radiation across two trophic levels

In most young fish radiations, transitions between invertivory and herbivory are unusual. Haplochromine cichlid fish of the African Great Lakes are exceptional in this regard. Lake Victoria was colonized by an insectivorous generalist and in less than 20 000 years, several clades of specialized herbivores evolved. Anna and Ole investigated components of the genetic architecture of a suite of traits that distinguish invertivores from algae scrapers by QTL mapping based on a second-generation hybrid cross. There were indeed indications of linkage/pleiotropy within trait complexes. However, QTLs for distinct traits were distributed across several unlinked genomic regions. Thus, a mixture of independently segregating variation and some pleiotropy may underpin the rapid trophic transitions.

Interview with Wyss Academy Prof. Margaret Owuor

An interview with Prof. Dr. Margaret Owuor ahead of the 2022 UN Biodiversity Conference:
Margaret Owuor, Professor for Integrative Biodiversity Conservation Science at the Wyss Academy for Nature, knows all too well that policy statements and declarations for conservation are being decided on a global level. Which is one of the reasons why the scientist wants to see such issues broken down to the local level. With this strategy she intends to empower communities in her native Kenya. Which in turn could contribute to the goal of an ecosystem-based management approach.

JEB - Multispecies colour polymorphisms associated with contrasting microhabitats in two Mediterranean wrasse radiations

Sarya, Ole and colleagues studied Mediterranean wrasses of the tribe Labrini which evolved two species radiations each harbouring several species with a brown and a green morph. The colour morphs occur in complete sympatry in mosaic habitats with rocky outcrops and Neptune grass patches. With genome-wide data for almost all Labrini species, we show that species with colour polymorphisms are distributed across the phylogeny, but show evidence of hybridization. This suggests that the colour morphs are either ancient and have been lost repeatedly, that they have evolved repeatedly or have been shared via hybridization.

PRSB - Competition among small individuals hinders adaptive radiation despite ecological opportunity

Ontogenetic diet shifts, where individuals change their resource use during development, are the rule rather than the exception in the animal world. Hanna studied the effects of competition among juveniles on the likelihood of an adaptive radiation to arise using a size-structured consumer-resource model and the adaptive dynamics approach.

Nature - Africa: sequence 100,000 species to safeguard biodiversity

A consortium led by African biodiversity and genomics researchers, that includes some researchers from our division, published a manifesto in Nature about a new project called "The African BioGenome Project (AfricaBP)". Africa had been left out of global genomics efforts so far. The AfricaBP is an effort to sequence the genomes of 105'000 endemic species (plants, animals, fungi, protists, and other eukaryotes). The project has three main goals: improve food systems, improve biodiversity conservation and improve sharing of data and benefits.

JMS Prize Winner 2022 - Catalina Chaparro

Congratulations to Catalina Chaparro-Pedraza for receiving the John Maynard-Smitz Prize of the European Society for Evolutionary Biology (ESEB) in 2022!

Anna Feller wins faculty prize for best PhD thesis 2021!

Many congratulations to Anna for winning the faculty prize for best PhD thesis in biology in 2021 at University of Bern! Her thesis is entitled "On the genetic architecture of an adaptive radiation". She studied the genetic architecture of various traits such as head morphology, colour traits and sex determination in Lake Victoria cichlids that form one of the most spectacular adaptive radiations.

NEE - Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

Nearly a hundred year old tissue samples from Lake Constance have enabled David, Rishi, Oli, Ole, and Philine to compare genetic material of an extinct whitefish species with that of extant co-occurring species. Their investigation showed that fragments of the genome of the extinct species have survived in today’s species. This could potentially facilitate the recolonization of the currently not occupied deep-water habitat.

Virus Evolution - Chlorovirus evolution is characterized by strong selection and high mutation suppl

Cas, Philine, and colleagues studied the evolutionary change of Paramecium bursaria chlorella virus 1 during experimental coevolution with its algal host across six experimental replicates and found single nucleotide polymorphisms (SNPs) at sixty-seven sites. The occurrence of genetic variants was highly repeatable and three genes showed an excess of variable sites, providing new information about potential targets of selection during Chlorella–Chlorovirus coevolution. The data indicated that the studied populations were not mutation-limited and experienced strong positive selection and with that highlighted relevant processes governing the evolution of aquatic large dsDNA viruses.

Ecology Letters - The enrichment paradox in adaptive radiations: Emergence of predators hinders diversification in resource rich environments

Traditional theory predicts that during the course of a radition, diversification rate slows down as vacant niches are being occupied. However, the influence of novel niches emerging during the process is unclear. Catalina and Ole tackled this problem from a theoretical perspective using a combination of analytical and numerical techniques based on an eco-evolutionary model of a radiating clade. They find that the effect of intraclade consumes on the radiation depends on the productivity of the system. Highly productive systems allow earlier evolution of intra-clade consumers, which in turn end up harbouring less species-rich radiations compared to less productive environments.

Projet Lac synthesis report published!

Today the synthesis report of the Projet Lac is published. It summarises the work of over 10 years in which 35 peri-alpine lakes in Switzerland and neighbouring countries were quantitively fished to the first time resulting in a great fish inventory for the alpine region.
One result is the recognition that the large and deep lakes of the region have exceptionally rich fish assemblages because they combine species-rich warm water and species-rich cold water faunas in a unique way: The combination of cold, deep and well oxygenated lakes with geographical proximity to the southern European glacial refugia for warm water fish has led to biogeographical "hybrid communities" rich in warm water species that inhibit the littoral zones and rich in locally endemic cold water species that dominate the open and deep waters (the Galapagos for cold water fish). It is this "hybrid fauna" that explains the richness. It is also the cause of the extreme vulnerability of many species to climate warming and lake pollution.

Scientific Reports - The emerging vertebrate model species for neurophysiological studies is Danionella cerebrum, new species (Teleostei: Cyprinidae)

Lukas and colleagues found that the emerging model species in neurophysiology is a new species called Danionella cerebrum. They describe it based on both morphological as well as molecular Data. All five known species of the genus Danionella are tiny, transparent fishes of only 1-1.5cm length and are textbook examples for the link between miniaturization via developmental truncation and evolutionary morphological novelty.

Paper - A subterranean adaptive radiation of amphipods in Europe

Ole collaborated with researchers from University of Ljubljana, Slovenia, to study the subterranean adaptive radiation of Niphargus spp. amphipods, counting hundreds of species. The spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago.

Paper – Genomic consequences of domestication of the Siamese fighting fish

It is only published in BioRXiv so far, however, it made it already into the media such as e.g. the New York Times. Lukas Rüber and many colleagues from Europe, the US and Singapore assembled de novo the genome of Betta splendens and other species of that complex including domesticated ornamental Betta. They found that the breeding and domestication of the betta has a surprisingly long history of at least 1000 years. In addition, they discovered that in the process of the domestication the sex determining system was radically changed.
The BioRXiv page also contains links to the media articles.

The Scientist - Hybrid animals are not nature's misfits

Science writer Ashley Yeager has written a nice piece in The Scientist about the paradigm shift in our understanding of the role that interspecific hybridization plays in the evolution of biological diversity, featuring our own work and that of others.

PRSB - The propagation of admixture-derived adaptive radiation potential

Kotaro and Ole published a theory paper in Proceedings of the Royal Society on how genetic variation generated through hybridization between distantly related lineages can promote adaptive radiations. They were particularly interested in the problem as to how such genetic variation can persist in space and time. Their computer simulations demonstrate that admixture variation can geographically spread and persist for long periods if the hybrid population becomes separated into isolated sub-lineages. Their simulations further revealed conditions where exceptional genetic variation, once generated through a rare hybridization event, can facilitate multiple adaptive radiations exploiting ecological opportunities available at distant points in time and space.

Nature - The ecological and genomic basis of explosive adaptive radiation

Analysing a phylogeny of all 1700 described cichlid fish species and whole genomes of 100 species endemic to Lake Victoria, Matt, Joana, David, Salome, Remy, Laurent and Ole, together with collaborators in Tanzania, Uganda and the US, have investigated the striking variation observed in cichlid fish speciation rates. Their analyses reveal that Lake Victoria cichlids diversify orders of magnitude faster than most other cichlids, and that exchange of ancient genetic variants between species dramatically accelerates the origin of new species – given favourable ecological conditions.

MolEcolRes - A denovo chromosome-level genome assembly of a Swiss Alpine whitefish

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 are the most useful resource for doing such comparisons. However, producing genome assemblies is challenging due to the size and complexity of many genomes. To facilitate the genetic investigation of how whitefish have evolved in the last 10-15 thousand years Rishi and colleagues have produced the first whitefish genome assembly. Their high quality and complete and ordered 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.

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

Anna Feller recently published her first paper from her PhD in Proceedings of the Royal Society on the genetic architecture of traits involved in reproductive isolation in Lake Victoria cichlid sister species. Through the phenotypic and genetic analysis of hundreds of hybrids bred in the aquarium she shows that the genetic architecture of traits determining mate choice also determines which species can coexist in sympatry and which not. If that trait is determined by only few genes with large effect then sympatry is possible, while when the trait is determined by many genes with small effect, persistence in sympatry may not be possible. This further suggests that the genetic architecture of traits involved in reproductive isolation also determines whether rapid speciation can lead to high local, sympatric species richness.

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Agenda

Aquatic Ecology Excursion block 2 - fish excursion

07 June

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