Fröhlichi Wianacht – liaba Götti

Liaba Götti Mathias,

mier wünschend Diar ganz schöni Wianachtsferia. Mis Gschenk für Di isch en Video vum Schnorchle in Panamá. Ich möchti mit Dier go schnorchla und im Dschungel go Fröschli suacha. Und wenn i grösser bin möchti mit Dier go flüga. Aber jetzt find i das scary.


Der Buddha isch no z’kli und wartet uf üs.

Und das isch üses Gschenk für Di. Mier teilend eini vu üserna beschta Erinneriga mit Dier.


#istmobiome workshop in Panamá

I am writing a personal blog post about my most recent Panama trip. A more scientific summary will follow soon through RCN’s website about evolution in changing seas.

I flew to Bocas del Toro on November 27th to finalize our workshop preparations with the two co-organizers Matthieu Leray and Jarrod Scott at STRI (Smithsonian Tropical Research Institute). We took care of the last logistical preparations and rehearsed our presentations. Ben Yuen from the Petersen lab in Vienna also arrived early and helped us with the workshop preparations. He also joined me on my hunt for lucinid clams.

Jarrod @metacrobe, myself @M_helvetiae, and Matt @Matt_Leray

Ben and I digging for clams at the STRI dock in Bocas del Toro

Maggie Sogin @MaggieSogin is giving us mental support. And it helped!

Ben and I searched all over the Bocas del Toro archipelago for Codakia, Ctena and Clathrolucina species. These are clams that live in seagrass. They have bacterial symbionts  in their gills that are able to oxidize sulfide. The clam filters water that is rich in sulfur through its gills. The endosymbiont bacteria are able to use these compounds to fix carbon. This carbon is then used as nutrients for its host – the clam. Seagrass beds are very rich in sulfides and lucinid clams have evolved a three-way symbiosis with seagrass and their bacterial endosymbionts. Because of the lack of oxygen in coastal marine sediments, dense seagrass meadows produce sulfide-rich sediments by trapping organic matter that is later decomposed by sulfate-reducing bacteria. The lucinid-symbiont holobiont removes toxic sulfide from the sediment, and the seagrass roots provide oxygen to the bivalve-symbiont system. 

Thalassia seagrass habitat

Lucinid clams checking out what’s going on?!

Funded by the Gordon and Betty Moore foundation, I am studying how this symbiosis evolved after the rise of the isthmus of Panama. I am also looking at patch effects and comparing local populations on both sides of the isthmus. My project is based on population genetic and coalescent theory. I am collaborating with ecologists in Vienna – the Petersen lab, and at Stony Brook University – the Peterson lab!

Ben and I found a valuable set of clams before, during and after the workshop!

Snorkeling and digging…

Two Ctena imbricatula individuals!

And more digging. We need bigger sample sizes…

A very happy digger!

We are being stalked by Jonathan’s underwater drone!

Trident, one of the top ten drones on the market:

The workshop itself took place from December 3rd until the 8th. Matt, Jarrod and I prepared the whole program which mostly consisted of questions that the participants would answer in groups, followed by plenary discussions. We also sprinkled in a few lightning talks to learn more about each other’s research. And we organized two excursions. One was a snorkeling trip to familiarize everybody with the different marine habitats and ecosystems at Bocas del Toro. The other one was of palaeontological nature where we went to an island with plenty of fossils. We brought a few hammers and collection bags. Everybody would spread out and collect fossils. Most of these fossils are more than 3.5 Million years old. This is older than the isthmus, hence these fossils lived in the big ocean that was later split into Pacific Ocean and Caribbean Sea. This excursion was led by Aaron O’Dea. It was my personal highlight. I got very emotional. Happy. Standing there and embracing one of the most awesome natural Darwinian experiments by nature.

Lots of fun in class…

… and in the field!!! Wall of fossils on the right and the isthmus straight ahead.

The raise of the isthmus of Panama is not only the playground of our research, it also affected the evolution of us humans. I learned at the Biomuseo in Panama City that the closure of the isthmus gave birth to the Gulf Stream. The Gulf Stream affected the climate all over the planet. It was after the final closure that humans migrated out of Africa. There is evidence that the Gulf Stream made Northern Africa drier and savannahs developed where previously had been forests. This coincides with humans walking more upright. I never thought about the relationship of this small strip of land and human migration out of Africa. Sure, it makes sense that this land bridge would allow species to cross from North America to South America and would ultimately affect biodiversity on land. But would it also affect global climate and indirectly facilitate human evolution?

All our #istmobiome workshop participants. A diverse sample of contemporary Homo sapiens.

What we are studying right now is how the rise of the isthmus affected marine life and symbioses in particular. We are working on many different marine host systems including urchins, porcelain crabs, snapping shrimp, reef fish and lucinid clams. If you want to read more about the workshop and what we discussed, check out our istmobiome website:

Now we are writing a white paper about what we discussed at the workshop. Stay tuned!

I would like to shout out a big thank you to all participants, the Moore foundation for giving us money and sending Jon Kaye – a very congenial person; and the Smithsonian Tropical Research Institute (STRI) for financing and facilitating this workshop. Last but not least, I want to thank Ben for keeping me sane.

Full of good spirits

And Jonathan for mentoring me. Jonathan is such a good person that there are no English words for him. Hence, I tried to introduce him in Swiss German… Check out our live tweets from the workshop under the hashtag #istmobiome!


After the workshop and collecting more clams, my family came and spent a few days with me in the jungle of isla Bastimento. I love Panama. And I am trying to share this with my closest ones.

Precious cargo




Department of destruction

Five weeks ago, we landed in Zürich. Back home in Switzerland. Since then I went through many emotions and memories. Constantly inhaling everything around me. Privilege. Mostly privilege. Swiss people don’t know how privileged they are. I have been breathing cristal clean air and drinking the most pure and tasty water since months. I have talked to researchers being funded by millions of Swiss taxpayer dollars (Franken, actually). I have looked at sparsely populated paradise valleys. I have touched the most happy and friendly cows in the world.

Lots of fieldwork on brown trout in Graubünden with Roland Tomaschett, graduate student Victor Ammann and many invaluable helpers from my family

Giachen explores his home

Trip to Vienna with my mom to meet Jillian Petersen

Ennio growing up

Family time with Mayra and Miguel

Gelateria di Berna Nostalgia

Ennio creating mosaics with the kids at Lake Geneva during my collaboration with the Engel lab at UNIL

Quality family time at my brother Emanuel’s farm

Linnea playing in front of EAWAG, The Swiss Federal Institute of Aquatic Science and Technology where I met professors Jakob Brodersen and Ole Seehausen

Now I am back in California. We were looking forward to returning to heaven. Instead, we realized that the apocalypse is here. Right now.

Today: Smoke in the city

Fires in July: The County Fire west towards Lake Berryessa has burned over 22,000 acres without containment on Sunday, July 1, 2018 in Napa County.

Donny and I made a list. I accomplished 40 important tasks in Switzerland. I worked without a break. Now I am looking out of the window and wonder about life. Davis is covered in smoke. Inside. Outside. Everywhere. Climate change is here. Right now. We are all in it. Privileged people and less privileged people as well. Everybody. It is absolutely surreal for me to see people walking through the smoke with face masks. In the most beautiful state in the world. It is burning down.

UC Davis closed two days ago. Jonathan Eisen, my sponsor and mentor at UC Davis fought for it. The health risks are simply too big. Public schools were open until today. Mostly because so many parents work and can’t afford to keep their kids at home. However, the air quality became so bad today that all schools are closed now. We are not sure if we will stay in Davis over the weekend.

It seems like we are all working for the department of destruction. By the way, did you know that there is a Department of Destruction? We learned about it after we forgot our passports in the airplane from Paris to Zürich. We had been flying from San Francisco to Paris. The kids were super nice, but Jacoby decided not to sleep. So, we stayed up with him. Doing things. After immigration and transfer in Paris, we fell asleep on the plane to Switzerland. All four of us. Like a coma. We actually fell asleep before the plane departed from Paris. Somebody had to wake us up in Zürich. When we rushed out of the plane, we forgot the passports on the plane. When I called later and asked at Air France, the cleaning personnel, the airport police; we were told that our passport were found. Somebody brought them to the airport police. The Swiss one was destroyed immediately according to Swiss law. The Americans were sent to the embassy and were going to be destroyed within 21 days. At the Department of Destruction. This is us.

Poster of our research at #LAMG2018

Two weeks ago, we presented at poster about our current fish research at the Lake Arrowhead Microbial Genomics Meeting #LAMG2018.


In most species with an external breeding system and no parental care it is generally assumed that males only provide genes to the next generation. Recent studies however demonstrated that offspring can also inherit non-genetic traits, such as epigenetic effects or bacteria. Here we characterized symbiont bacterial communities in milt of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) and tested whether bacteria are transferred from the father vertically to the next generation. We used a full-factorial breeding design and in vitro fertilizations in order to separate genetic and environmental effects on offspring performance. For the fertilizations we either washed milt with antimicrobial compounds or we left it untreated. We found a high diversity of bacteria in the milt of different sires and we monitored bacterial communities on developing embryos until one day after hatching. Offspring that originated from washed milt hatched later and were smaller than their natural fullsiblings. This difference in size persisted until ten days after hatching (the end of our experiment). Our results are discussed in the light of anthropogenic influences (i.e., micropollutants in freshwater systems) and the coevolution of hosts and their microbiomes.

Family dinners

We started this new tradition of having dinner together. This was just not our thing. However, it is wonderful if it is just Donny, Linnea, Jacoby and I.

The rules are: Everybody has to say something about their day. Everybody has to listen to the others talk. In the end everybody has to ask a question about the world.

Linnea hit off the first couple of nights by asking:

  • Are all stars suns?
  • How many days since you were five years old?
  • How old is God?
  • Would you have enough time to count to one hundred trillions before you die if you spoke it out loud?
  • Why are you sometimes angry at me and sometimes you feel sorry for the same thing?

PIT tagging

Während meinen Untersuchungen im Winter 2016 und 2017 in Zusammenarbeit mit Claus Wedekind von der Uni Lausanne, dem Kanton Graubünden (Marcel Michel, Amt für Jagd und Fischerei AJF) und Roland Tomaschett, dem Fischereiaufseher in Trun haben wir bereits einiges über die Bachforellen in Vals gelernt.

Etwa 40% der Weibchen laichen während der Laichzeit nicht. Sie sehen normal und gesund aus. Genetisch stellen sie keine Untergruppe dar. Es gibt keine Anzeichen von Inzucht. Ihr genetisches Geschlecht stimmt mit dem Phänotypen überein. Sie haben kein Y-Chromosom und besitzen normale Ovarien. Wir wissen immer noch nicht warum sie nicht laichen. Diesen Winter möchten wir sie markieren um herauszufinden, ob sie ein Jahr später laichen werden. Vielleicht laichen sie nur jedes zweite Jahr um Ressourcen zu sparen.

Im Rahmen des jährlichen Laichfischfangs in Trun (geplant für den 17. Oktober 2018) schlagen wir vor, eine Stichprobe von laichreifen Rognern, sowie auch eine Stichprobe von unreifen Laichtieren nach Trun in die Fischzucht zu bringen (analog zu den Versuchen in 2017).  In der Fischzucht in Trun werden diese Fische dann nach Laichreife sortiert und sachgemäss betäubt. Die betäubten Fische werden vermessen und mit einem Transponder markiert. Gemessen werden Fischlänge, Gewicht und Fettanteil (ich werde mein persönliches Messgerät mitbringen, das wir erfolgreich für Regenbogenforellen in Kalifornien eingesetzt haben).  Als Transponder werden PIT tags (Passive Integrative Transponders) vorgeschlagen da sie (i) inaktiv sind (senden keine Radiowellen aus und brauchen keine Batterien), (ii) einen individuellen Barcode enthalten und so jedes einzelne Tier wiedererkannt werden kann, (iii) wasserdicht, steril und für das Tier störungsfrei sind.  Die Fische werden nach dem Experiment wieder am natürlichen Laichplatz ausgesetzt.

Beim Laichfischfang ein Jahr später können die Fische individuell wiedererkannt werden und es wird bestimmt werden, welche Fische nun laichen oder nicht. Weiter können dank den individuellen Transpondern auch wertvolle demographische Daten über Laichreife, Fruchtbarkeit und Überlebensraten gesammelt werden. Falls das Aussetzen von Laichen keine natürliche Überlebensstrategie darstellt sondern ein Problem müssen wir herausfinden, was mit den Valser Forellen nicht stimmt. Vielleicht hat es Mikroverunreinigungen im Wasser? Der Steinbruch oder Verhütungshormone könnten da eine Rolle spielen.

Als Vorbereitung für dieses Markierungsprojekt habe ich vor zwei Wochen einen Kurs im Markieren von Fischen in der Warm Springs Hatchery in Geyserville, Kalifornien besucht. Mein Lehrer war Ben White, der lokale Fischereiaufseher.

Linnea durfte seine Fische füttern!

Normalerweise werden die Transponder einfach in die Bauchhöhle eingeführt. Da unsere Fische in Vals aber kurz vor dem Laichen stehen ist das keine gute Idee. Die Wahrscheinlichkeit ist gross, dass die Transponder während dem Laichen verloren gehen. Sie können mit den Eiern abgelaicht werden. Deshalb musste ich lernen, wie ich die Fische im Rücken in den dorsalen Muskel markieren kann ohne sie dabei zu verletzen.

Zuerst habe ich mit ein paar toten Silberlachsen (Oncorhynchus kisutch) geübt. Die sind am gleichen Morgen gestorben und ich durfte sie zum Üben brauchen.

Das hat gleich gut geklappt. Als Test habe ich dann meinen Tag wieder gesucht…

Am Nachmittag haben wir zehn junge Regenbogenforellen markiert (2 Jahre alt). Diese Fische hat Ben nach der Markierung eine Woche lang überwacht. Alle haben die Prozedur überlebt und schon nach zwei Tagen war keine Wunde mehr erkennbar.

Da Geyserville nicht gerade auf dem Weg liegt haben wir gleich das Wochenende in der Gegend verbracht und im Zelt an ein paar spektakulären Orten übernachtet.

Hier schlagen wir das Nachtlager auf!

Geyserville heisst nicht umsonst Geyserville. Hier gibt es viele heisse Quellen und Geysire. Wir haben einen verässlichen Geyser besucht. Er hat mich sehr beeindruckt. Und auch motiviert. Während den letzten zwei Wochen habe ich drum mit Cassie unser Paper über Mikroorganismen in heissen Quellen auf der Kamchatka Halbinsel in Russland fertig geschrieben.

Old faithful in Geyserville

Embracing advocacy in science

Freshwater systems are endangered. Habitat degradation, chemical pollution, altered hydrology, species invasions, overexploitation and climate change are threatening these habitats, here and now. The American Fisheries Society is trying to raise awareness about the importance of freshwater ecosystems. These systems can be considered biodiversity hotspots and they provide ecosystem services. However, it is really hard to lobby for them because the human use of freshwater for agriculture, energy and other economic developments (T)trumps conservation concerns in the society. We are responsible – I feel responsible, for making the public aware of their freshwater systems. We need to go out and communicate with the people.

Two weeks ago, I was invited by Suzanne Kelson, a PhD student in Stephanie’s lab to go talk to high school students from Moraga, a small town in the neighborhood of Berkeley. We went out to a little creek and discussed this freshwater habitat in the field with students. We measured stream flow, invertebrate biodiversity, hydrology and explained how a watershed is built up. I talked about fish migration, reproduction and the interaction with bacteria in salmonids, mostly steelheads. Each little station that was led by Suzanne, Hana Moidu, Jordan Wingenroth, and Brian Kastl gave the students insight into a different study area of freshwater biology. Together we provided each puzzle piece to give the students a greater picture. I felt like they walked away with more awareness for their surrounding environment. They were surprised to see so much in their little neighborhood creek. I am convinced they will experience their party/stroll/car- or bike ride at the river differently next time.

Back at home I read an essay in the Fisheries Magazine April 2018 by Marcy Cockrell, Kate Dubickas, Megan Hepner, and Matthew McCarthy (Fisheries, Vol 43, No. 4). They are reaching out to scientists and encourage them to advocate for policy issues. The believe that all citizens have a responsibility to engage in the political process, especially scientists. Advocating for science-related issues should not be a conflict of interest but a necessary step towards a more holistic scientific method and a more informed society.

They list the following nine guidelines how scientists could advocate:

  1. Gain experience working with a variety of activities and organizations.
  2. Join a professional society that already plays a role in advocacy, for example AAAS (the American Association for the Advancement of Science).
  3. Become involved with local or national chapters of conservation-minded NGOs, trade organizations, or general membership groups.
  4. Be proactive in communicating science.
  5. Engage in dialogue with decision makers.
  6. Gauge interest among colleagues.
  7. Build and use your network.
  8. Apply to formal opportunities for communication training and professional development.
  9. Vote!

Thank you Suzanne for inviting me to your outreach activity. I think we took care of points 4, 6 and 7. I also would like to thank Stephanie for being a great role model how to actively pursue all numbers 1-9, advocating for freshwater sciences and building a great community of freshwater scientists (for example Mary Power, Ted Grantham and Albert Ruhi), a new hotspot at UC Berkeley!

Brian Kastl explains to the students how to calculate water flows in the creek.

Internship and Master thesis project of David Zeugin

This post is written by David Zeugin, University of Lausanne

My project with Laetitia was about the decline of a European grayling (Thymallus thymallus) population in Lake Thun, Switzerland. We looked at the effects of inbreeding on offspring survival. To manage this population, juveniles are bred each year in a hatchery from a stock of captive fish and released into the wild. However, breeding fish in a hatchery leads inevitably to inbreeding. We investigated the effects of this inbreeding by comparing reproduction success of wild fish and captive ones simultaneously in a climate chamber at the university. During the course of their development, we measured embryo survival, time until hatching and sizes of larvae. Additionally, we tried to develop a gynogenesis protocol.

Getting the fish (grayling) in Kandersteg, BE.

Gynogenesis allows the creation of artificial diploid homozygote offspring from the haploid genetic material in the eggs of the mother. Eggs are fertilized with inactivated sperm and then exposed to heat shock or radiation to trigger cell division. Eggs and sperm from wild fish and hatchery stock were used for this protocol. The effects of inbreeding at different levels; i.e., crossing wild individuals vs. crossing hatchery stock fish vs. crossing a female with itself was measured by stressing the resulting embryos with three fish pathogens, Pseudomonas fluorescens, Aeromonas salmonicida and Aeromonas sobria.

Inactivating the sperm.

Inside the UV box.

We had a very low success rate of gynogenesis. The number of viable diploid offspring for each female was so low that we could not statistically compare their performance to the other grayling embryos and larvae. The number of viable embryos was relatively high but they all died before hatching. However, grayling embryos coming from parents that had been produced and raised in hatcheries reacted with a higher mortality and earlier hatching compared to the offspring of wild fish when presented to both A. salmoncida and A. sobria

fertilized eggs

Most of the gynogens are dying.

Head and eyes become visible.

The supervision of Laetitia in this project helped me to take initiatives, to be rigorous in my experimental design and conduct, and to develop my communication skills. I directly profited from her large knowledge on the subject and appreciated that Laetitia was supervising my work and at the same time giving me the opportunity to develop my own hypothesis on the project.

I am now a Ph.D. candidate in the Ionta lab and work on neuroscience. I am studying the neural basis of visuo-motor control and how they interact in the human brain.

In the climate chamber

lots of data

freshly hatched