Paper out!

Today, Cassie’s and my article on metagenome-assembled genomes in two hot springs of Kamchatka, Russia was published in Scientific Reports. Cassie and I only analyzed the data. 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.

We are all working really hard and sometimes don’t even find the time to celebrate or to be proud. I had a hard time today to enjoy. Now it is sinking in slowly. I am incredibly proud of Cassie. Working on this project with Cassie cheered me up, it motivated me to do things right, and it gave me a strong feeling of peace.

We learned a lot and we tried to do it right. In every aspect. Guillaume showed us many tricks. And Jonathan believed in us.

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.

At some point, when we are all a bit less busy, Jonathan might write a blog post about the background and history of our article…

The article itself can be found here:


I did not think I could work so much like I did lately. I did not think I could be involved in so many things. It feels like a landslide. Like free fall. I am dancing free-style.

My two little anchors are small but strong. Keeping me grounded.

Why are monarch butterflies declining in the West?

Elizabeth Crone, Tufts University

Live blogging from UC Berkeley Wildlife Seminar, January 25th 2019. (Still my favorite University. Still my favorite seminar.)

Monarch butterflies had the lowest population sizes ever in 2018! Shocking news on Thursday January 17, 2019 in the San Francisco Chronicle. What is going on??? Here is the link:

Elizabeth Crone from Tufts University came to UC Berkeley today and gave a talk at the Wildlife Seminar about the three following points:

  1. How much has the whole population declined?
  2. Why are they declining?
  3. What can we do about it?

There is a global insect Armageddon. Art Shapiro at UC Davis says: ‘No. We don’t know why.’

Western Monarch butterfly populations are much smaller and less studied than the ones at the East Coast. They spend several generations at California coasts and move then inland towards Rocky Mountains. Monarch butterflies are just awesome because their migrations include several generations. While the grandparents might have been born at the coast, their grandgrandchildren decide to fly somewhere else. The same cycle repeats many generations later.

Elizabeth’s talk was about the population in the West only!

In Central California there are volunteers, CITIZEN SCIENTISTS, who count butterflies every year around Thanksgiving. In 1997, there was a very high count, then only smaller numbers. Had numbers before 1997 been consistently higher? There were no citizen scientist projects back then. Elizabeth had to collate data from different research groups. She found quite a lot but nothing was standardized. Everybody had used different approaches. Hence, Elizabeth had to apply some statistical models to account for all this variation. She did MARSS modeling and analyzed a very long time series. This model assumes that monarchs function as a single large population in the west, with a single growth rate. For each site she estimated a rate of proportionality compared to the total population. MARSS also allows to include an observation error. –> Estimate of historic abundance. 1980s millions of butterflies, 2000 only thousands. Something happened in the 90s. Population decline is ~7% per year.

In 2018 counts dropped again. We have never had anything close to this low. Yet, it might just be ordinary fluctuations in the environment. If we loose a few hundred butterflies in a population of several millions, the population will persist. However, if we loose a few hundreds in a population of a few thousands, this population might eventually go extinct due to the extinction vortex. So Elizabeth applied for emergency funding from the NSF. Is anybody looking for an awesome postdoc position???

Picture taken from

What caused decrease: Climate (temperature, precipitation)? Everybody always thinks first it is climate change. Pesticides. Habitat loss. Overwintering habitats along the coast have become smaller due to housing development and dryland farming. How do we know which factors really drove the population decline? Don’t do linear modeling with so many correlated variables. Instead: PLSR: Partial Least Square Regression. This analysis can handle a large set of variables. Retains uncertainty about which variable is correlated with outcome. Similar to PCA. Relative importance of different variables for 1st and 2nd components (axes). What did the model spit out? Summary: Land development, glyphosate, and nicotinoids all correlated negatively with butterfly numbers. With regard to the drop in 2018, it could be attributed to the cold and wet months of February and March. They had been bad for butterfly recruitment.

Not just climate change – land use matters. And use of pesticides by everybody, farmers and hobby gardeners. This is a large landscape scale problem. Not just butterflies. Many other insects are suffering from the same problem.

During the questioning session in the end: Some monarchs don’t migrate. They sit on perennial milk weed their whole life. These populations are common in Southern California and Mexico. In Central and Northern California, populations are migratory. Don’t buy perennial milkweed in the store and plant them in the garden. They might invite butterflies to become stationary and then infected by parasites. Indeed, stationary populations have higher parasite loads! Buy endemic milkweed to support Western butterflies and plant them early in the season. Thanks.

And a little side note: Elizabeth is an awesome presenter. She must be a really great teacher. Thanks for entertaining us.

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.