more projects

Here you can find other projects I am working on/ I have been involved into.

2018, Population dynamics of the Sierra Nevada yellow-legged frog (Rana sierrae) in Dusy Basin, Kings Canyon National Park

Rana sierrae (the Sierra Nevada yellow-legged frog) in California is critically endangered. This 18y-long demographic study shows the negative effects of introduced fish presence and drought years on frog counts. The Population eventually crashed due to Bd (chytrid fungus) in 2013.

Frog abundance in all life stages was positively correlated with lake surface area. Managing large lakes that persist during droughts and removing introduced fish in the short-term is crucial for Rana sierrae survival. Reducing greenhouse gas emissions is the goal for the long-term.

Find the paper here, it is all open access.

2017-18, Metagenome-assembled genomes from two thermal pools in the Uzon Caldera, Kamchatka, Russia

In this paper, Cassandra Ettinger and I analyzed metagenome assembled genomes of two hot springs on the Kamchatka peninsula in Russia.

The whole story is much older and involves many more people, including Elizabeth Burgess who originally collected the samples as a graduate student in Jürgen Wiegel’s lab; or Russell Neches, who went to Kamchatka himself and had played with this dataset before us; and Ray Keren who encouraged and distracted me with his fascination for arsenic biochemical pathways.

Laura Hug led the way in the beginning and Chris Brown provided the tools when we got stuck.

And A. Murat Eren was very important too. A bright star on the horizon. And the Banfield lab. We got a lot of inspiration. Obscure archaea are awesome.

2015-17, Sex differentiation and its implications for conservation in grayling

For this project we investigated the effects of synthetic estrogenic pollutants that are commonly used as birth control on the development and the demography of river-dwelling salmonids. We measured gene expression around the onset of sex differentiation in a population of European grayling (Thymallus thymallus) that suffers from sex ratio distortions. We found that the exposure to estrogens affected gene expression of a large number of genes, especially around the timing of hatching. These effects were strongly sex dependent!

Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae)

Sex differentiation in grayling (Salmonidae) goes through an all-male stage and is delayed in genetic males who instead grow faster

This work was led by two awesome Master students at the University of Lausanne, Oliver Selmoni and Diane Maitre.

2015, Maternal allocation of egg carotenoids in brown trout

As part of my Ph.D., I have investigated maternal investment into their offspring. Life-history theory predicts that iteroparous females allocate their resources differentially among different breeding seasons depending on their residual reproductive value. Typically, there is much variation in egg size, egg number, and in the compounds that females allocate to their clutch. We quantified this investment with a special focus on carotenoids to infer maternal strategies.

Maternal allocation of carotenoids increases tolerance to bacterial infection in brown trout

Consumption of carotenoids not increased by bacterial infection in brown trout embryos (Salmo trutta)

Environmental stress linked to consumption of maternally derived carotenoids in brown trout embryos (Salmo trutta)

Supervision and Mentoring

This paragraph is a niche for students I supervised or mentored. I asked them to write about their projects in guest posts. Let’s start with David Zeugin in Claus Wedekind’s lab. We studied grayling embryos and how they respond to pathogens and gynogenesis in the context of inbreeding. He explains it here.

2010-14, my PhD thesis: Diversity of bacterial symbionts on salmonid eggs: genetic and environmental effects

Because I was very interested in the immune system, mate choice and conservation genetics, I applied for a fellowship to do a PhD in the Ecology & Evolution Department at the University of Lausanne, Switzerland with Claus Wedekind (T-shirt study) and Luca Fumagalli (conservation geneticist) on the MHC and its implications in salmonid fishes. I received the fellowship. Here is my first paper/chapter of my PhD thesis on embryonic MHC gene expression in whitefish, Coregonus spp. In this project we investigated whether the MHC is already relevant for embryos when they mount their first immune response against a pathogen. We measured gene expression, and we quantified the heritability of this trait using a powerful experimental design and a quantitative genetics approach. This chapter was published in the journal Molecular Ecology. During this first project I became very interested in using salmonid embryos as a system to study host-microbiome interactions. How I got fascinated by fish embryos is described in a blog post here.

During the second winter as a PhD student, I collected naturally-spawned fish eggs of wild populations in different lakes and rivers in Switzerland. Then I applied environmental sequencing to characterize the bacteria living on them. Next, I quantified the effects of geographic distance, host species diversity, and water temperature on bacterial community composition in the wild. The results were published in the journal of Aquatic Sciences and Scientific Reports. They are explained in more detail in this blog post. This first part of my PhD included many field trips to find eggs; for example diving in Lake Thun, canoeing in the capital of Switzerland, more diving in Lake Thun with my invaluable student and friend Grégory Brazzola, training my eyes to see eggs in the wild, developing tools to collect eggs buried brown trout eggs in river beds, as well as grayling eggs. During my last trip for this project, I had the opportunity to bring my family from Houston, Texas to my home canton Graubünden, and I started my long-term collaboration with Marcel Michel, Reto Gritti and Roland Tomaschett from the department of fish and wildlife (Amt für Jagd und Fischerei, Graubünden).

What ultimately had to follow these field studies were controlled experimental set-ups to study the interaction of salmonid embryos and their associated bacterial communities in more detail.

Accordingly, we brought gametes from wild fish into our lab and fertilized them in vitro to have embryos. The eggs of many females were fertilized with sperm from many males to quantify maternal and paternal effects on embryo traits. These embryos were then used to run experiments. In the first experiment we manipulated the microbiome growing on the eggs with nutrients to study the effects of host genetics and available resources on egg-associated bacterial community composition. This study was published in the journal Molecular EcologyIn another experiment with a similar design, we measured whole genome expression responses in the embryos to infection with an opportunistic fish pathogen, Pseudomonas fluorescens. This study can be found in the journal of Fish & Shellfish Immunology 

2009-10, my Master thesis: Female mating preferences and probabilistic paternity analysis in the MHC of humpback whales, Megaptera novaeangliae

For my Master thesis I joined Per Palsbøll and Martine Bérubé at Stockholm University, Sweden to learn more about evolutionary genetics of marine mammals. My project was a genetic investigation of female mating preferences in humpback whales. We sampled mother-calf pairs in the Gulf of Maine, USA, during their feeding season; as well as males in the West Indies, Caribbean, during their breeding season. I amplified, cloned and sequenced a locus in their major histocompatibility complex (MHC) and inferred the nucleotide similarity between mothers and their calves. Then I used the alleles in the males and simulated many humbpack whale generations by mating these alleles with the mothers’ alleles and creating simulated calves. I used these simulated calves to compare the observed to the simulated similarity of mother calf pairs at the MHC. The simulations assumed no female mate choice. Deviations from these values could be interpreted as female mate choice for males with particularly similar or dissimilar alleles at this locus. Interestingly, the real calves were more similar to their mothers at the MHC than expected. These results were never published but I attached my Master thesis.

Martine trained me very thoroughly in their molecular genetic lab and Per took a lot of time to explain and discuss population genetics. Per arranged a fieldwork trip for me to help his friends and collaborators Jooke Robbins and David Mattila at the Provincetown Center for Coastal Studies in Massachusetts. Here are some photographs I took during this trip: first encounter with the whales; getting used to living on a boat (in German); becoming experienced.

My Master project is also explained in a blog post here (English) and here (German).

2007, Sweden: Saving the Endangered Fennoscandinavian Arctic Fox, Alopex lagopus

As and undergraduate student I worked as a volunteer for Prof. Anders Angerbjörn at Stockholm University, Sweden. He dedicated his life and research to studying and protecting the endangered Arctic Fox in the Swedish mountain Tundra. My contribution included a several weeks long hiking and camping trip during which we searched for wild foxes, caught them, marked them and took blood and feces samples for genetic parentage analyses. I learned a lot about wildlife biology and the logistics of large-scale field experiments.

Link to one of my first blog posts — about this project. Not much text at that time but many photos and impressions.