Happy Chinese New Year

I am back from Panama. Living and working in California. This month I have to do a a lot of bioinformatics. Several datasets are waiting to be analyzed. I am now actively using R Markdown and Jupyter notebooks to make my work more transparent and reproducible. Stephanie organized a workshop for the Carlson, Power, Ruhi and Grantham group at UC Berkeley on data management plans. I found myself in all categories: the planning stage of a project, fieldwork, wet lab, data analysis, statistics, bioinformatics, preparing a paper, and post-publication. This is postdoctoral life. And it is beautiful.

Last week I read this blog several times. It gives me goosebumps because it describes my life in very beautiful words. It touches me right in the middle. What is a postdoc?

This blog post is by Jeremy Yoder, now professor Jeremy Yoder. He is a member in the committee of The Molecular Ecologist. They offered me to write blog posts for their website. I am extremely happy to fulfill this job. The journal Molecular Ecology is one of my favorites and I find it important to make its publications accessible to everybody. Writing for this website is one step in the right direction. I am planning to explain exciting Molecular Ecology articles to the general public and discuss trends in this field of research. Additionally, I am also looking forward to contributing articles about the challenges and strategies of researchers (mostly postdocs) who are trying to juggle work and family. I envision this website as a platform to assist academia in becoming a more inclusive environment. I know that the other bloggers are on the same page and I am extremely thankful that they offered me to become a part of their writing team.

I have been half sick as of yesterday and today. However, as a parent you cannot just lie in bed and wait until you recover. Sorry world for spreading my bugs. Yesterday afternoon, we went to Stinson beach to remember at what a beautiful place we are allowed to life. Today we joined the Chinese New Year party at the UC village. Such parties make this place unique. It feels so special to walk 300m to a community center and meet fellow researcher families from all over the world on a boring Sunday to celebrate the year of the dog. We met people who spoke Mandarin, Bangla, Japanese and English. We used too much glitter, ate good free food and took silly photos. I am enjoying every second of being affiliated with the best public university in this country.


Humboldt County

I have this personal feeling about Humboldt County. I seem to love it. I don’t know if I could live there. I don’t like the meth heads. However, I always love to visit. I also met the nicest people there. Tommy Williams made it possible that I could go sample fish close to Arcata. An opportunity I had already given up on. He wrote to me on Friday. And on Sunday we were already in Arcata.

I sampled young of the year from Prairie Creek the first day. Prairie Creek is super pretty. On the way there we saw lots of elk hanging out in the water. We had beautiful fall weather and sampled in the middle of a redwood forest. I joined John’s crew, including Chris and Reed. The day was phantastic! These guys are super nice and showed me how to use a seine – a kind of net to catch juveniles. At Prairie Creek there are almost only Coho salmon (Oncorhynchus kisutch) research projects. Yet, I am only interested in O. mykiss. Here comes the special challenge: at this life stage you cannot discern O. mykiss from cutthroat trout (Oncorhynchus clarki), which are also very common in this creek. Three very similar species in one little creek. I just doubled my sample size and I will use genetic markers later to find out who ist what. I was a one-woman-show and processed all my fish alone. I got a bit tired but then I met Jesse and Jolyon, two other fish researchers in the same creek. Jolyon offered me some smoked Chinook salmon that he had caught and smoked the day before. It was delicious and gave me a lot of energy to finish this field day!


Is this an O. mykiss or an O. clarki???

Looks like an O. mykiss…

little Coho YOY

Big cutthroat trout!

I spent the evening with my family. We had good food and beer. Arcata is a little jewel.

The second day I spent with Colin and Eric at Freshwater Creek. They are stars in seining. They caught whatever they wanted with their net. Two AmeriCorps had their first day in the field. AmeriCorps are volunteers who work for about a year in conservation projects at many different locations all across the state of California. Colin taught them a lot about monitoring Coho salmon and estimating their survival during the winter season. I tagged along and learned a lot.


While I was working, Donny enjoyed the area with the kids and met his old College friend Mike and his family. We heard about wildfires further down south and during the second day the sky got grey and full of smoke. The wind brought the smoke up to us. Our phones did not work anymore because some fibre cables were burnt. Luckily, we found each other again. We met at Freshwater Creek and Linnea helped me finish processing the fish.

The same night I drove the whole family back down to Albany. It was dark but we could see the wildfires between Willits and Ukiah! Right next to the highway. Huge fires. I have never seen something like that before.

I had a short night because I had to get up early the next morning to sample fish in Marin County at Walker Creek with Greg and his crew. He also had a helper from the AmeriCorps! For this sampling day Laura joined me to help. She is a great helper and very pleasant to hang out with! On the way home we went to taste some French cheese at a farm close to Point Reyes. The sky was orange and full of ashes. The particles in the air made the sun redder than usual. Totally surreal.


Sticklebacks! Very stickly!

Roach on its head

The last couple of days I had several meetings to organize lab work, work on the frog project, and teach researchers about health care. I hurried from meeting to meeting. Everything seemed pretty surreal in the constant smoke and strange sunlight. Even breathing was getting harder and harder. The Bay Area is a smoke hole!


Tristan Nuñez Finishing Talk

Animal movement in a changing world

Today, my dear neighbor and guinea pig sitter Tristan gave a talk at our Wildlife and Conservation Seminar at ESPM. I took notes and I am posting them here.

A finishing talk: That is how we mark the end in the graduate program at ESPM. Let’s honor Tristan!!!

Animals: move biomass and seeds around, alter nutrient cycles, pollinate. With warming they have to move away to find their niches (e.g., colder places).

How do animals ‘cross roads’ of climate change and of alterations in landscape. —> Human alterations of the environment. ???

I. Animal movements shape environments:

Example: Hippos graze at night on land. During the day they hang out in the water to stay cool and poop (Pennisi 2015 in Science). They connect land and water ecosystems. Webcam at mpalalive.org. They tagged hippos and studied where they are grazing, resting and moving around in space. GPS. Grazing, Resting, Transit. Taking that map, they modeled biomass transfer. Hippos remove biomass during grazing but add it again during pooping. Use GPS technology to measure how poop is moved around. Could be applied to cows and grazing in California landscapes. Places of resting and pooping are hotspots of biomass decomposition (i.e., nitrogen rich).

II. With changing environment animals move to more suitable habitats:

International agencies (banks and private) encourage Africa to do more land use and use irrigation system to produce food (crops). Species distribution models often ignore hydrology. Tristan addressed the following questions: Would the inclusion of hydrology improve distribution models? Does it change how we model species distributions? What are the effects of the conversion from rain-fed system to irrigated system?

Models including hydrology performed better than atmospheric models. What is an atmospheric model? I don’t know. Key finding: If you include hydrology into the model there are much fewer suitable areas! If you model how Africa is going to look like in 2070, including hydrology in the model, you almost don’t see any change in suitability of habitats for hippos. However, if you now also account for irrigation change due to an increase in agriculture, there is an 68% loss of suitable habitats. Take home messages: Including hydrology improves distribution models, projections differ between atmospheric and hydrological model, and land use will affect suitable habitat for animals. Don’t ignore hydrology when modeling species distributions even if you are working on terrestrial animals.

III. How do climate niches move through time:

40% of mammals are unable to keep pace with climate change. Temperature has been increasing during the last 100 years, however, there is a lot of variation in the rate of increase. For the last part of his dissertation, Tristan compared different biomes and how they move through time.

Here he showed a R simulation that shows how deserts moved through time in the western USA. Now animals need to be able to follow their niches. I think Tristan is not yet finished with this chapter.


How do animals shape the environment. Link movement metrics and human footprint. Help land managers by predicting which climate changes and landscape alterations are coming in the near future. Be able to react to it!

If you want to read more about hippos and their ecoystems check this out!

Blog post functional visualization Kamchatka

We are reaching out to hear from others what tools they are using to assign and visualize gene functions in environmental samples of microbial communities.


Our dataset is simple. We did a metagenomic analysis of two pools (samples/sites). First, we co-assembled the whole metagenome for each pool. Then, we used anvi’o to bin individual bacterial and archaeal genomes within the pools. These genomes (bins) were then fed into RAST. This online software gives you a table of known genes for each bin. At the moment we have an array of tables with known microbial genes for each pool that we would like to visualize/summarize in an aesthetically pleasing way. We tried to use summary statistics in MG-RAST, but the upload failed eight times in a row (including several attempts of uploading individual bins as fasta files, co-assembled metagenomes as fasta files, and sequence reads before assembly as fastq files). The upload failures were identified as cashing problems or internal errors.


We went back to using anvi’o using NCBI COG assignments, following their infant gut pangenome tutorial (http://merenlab.org/tutorials/infant-gut/) which in the end gives you a similar output to RAST in tabular format.


What software are people using out there to compare, assign and visualize gene functions across samples and across bins? Can these tabular outputs be used as inputs for any software producing visually pleasing figures?


ASF #147

I just came back from the American Fisheries Society conference in Tampa, Florida. This is one of the biggest conferences in fishery sciences- if not the biggest. At times we had 20 concurrent sessions on topics like fish migration, hatchery management practices, outreach, how to deal with lion fish invasions, imperiled aquatic species, and Darwinian selection. I presented my ongoing study on non-genetic paternal effects in salmonids at the Imperiled Aquatic Species and Genomics Symposium that was organized by Andrew Whiteley. The whole second day I spent at the Redefine Darwinian Fisheries Symposium (check out tweet here!).

@fishteph’s current group was represented by Stephanie Carlson, Sébastien Nusslé, Laura Härkönen, Suzanne Kelson, Jordan Wingenroth and I. We stayed at the Mariott Hotel right on the venue. We enjoyed ourselves a lot. Due to the close proximity we could engage in discussions and presentations with quick breaks at our rooms. Tampa was very hot and humid. Sometimes we just needed a quick dress change or two minutes of quiet time alone. Luckily, the hotel also had a spectacular pool.

I tried to get most out of the conference and went to social mixers, poster sessions, selected talks, networking events and the early morning spawning run. Gayle Zydlewski gave me, Louise Chavarie (@louisechavarie) and Lauren Laing (@LaurenVELaing) some good advice for our next career steps.

I want to highlight the great research of a few very nice researchers I met at this conference. Sarah Fitzpatrick is studying genetic rescue in guppies (her website). With a very intense field experiment and a lot of sequencing she could show that hybrids resulting from an experimental mix of two small and distinct populations in Trinidad (that differ mostly in predation rates) had a much higher fitness even after 10 generations of mixing. This mix of populations is called ‘genetic rescue’ and could be applied to many small and endangered species. Mark Christie is applying *omics approaches to answer very interesting questions in salmon evolutionary history. He proved that one generation in a hatchery caused very strong selection on gene expression. Traits are selected that help the fish to cope better with the hatchery environment. He also studies steelheads that had been transferred from the Pacific to the Great Lakes in Michigan. They are still trying to migrate but now they move between the river and the lake. He compared steelhead genomes of the founder population, of samples at the time when individuals were brought to Lake Michigan, and of the current population in Lake Michigan. It appears that there is selection on genes for smoltification and ion transporters. These genes usually help the fish to adapt from freshwater to saltwater when they undergo their migrations. He could also show that Omy5 seems not to be under selection. Omy5 is the chromosome region that correlates with staying or leaving in O. mykiss (his website). Anna Kupalainen said if age at maturity is inherited by a single locus (original publication by Craig Primmer here) then populations are more likely to destabilize and go extinct – compared to a multilocus inheritance. Anna is a mathematician and modeler. She presented some phantastic approaches to infer fishery-induced selection (Anna’s google scholar profile). It is clear now that fishing is a very strong selective force acting on wild fish populations. Many fish species and populations are not only becoming smaller due to fishing out the bigger individuals, they also change in their behavior because behavioral traits are often correlated with being bigger and growing faster. This was nicely shown by Laura Härkönen. Sébastien Nusslé presented a new model how you can include environmental variables when estimating the strength of fishery-induced selection (Sébastien’s new position!). Lauren Laing is working on maternal and paternal epigenetic effects in sticklebacks and zebrafish. She uses full-factorial in vitro fertilization to raise offspring. Right after fertilization she induces non-genetic factors on them to see if this results in an epigenetic response. She showed during her talk that copper contamination can greatly affect embryonic gene expression and maybe also gene methylation (Lauren’s google scholar profile)

The conference ended with an evening at the Tampa Aquarium and then a long night saying goodbye to Séb in the lobby. I tried my red snapper, my key lime pie and I saw alligators, ‘gator gars and non-native pythons. Now we are flying back to Oakland. Tired. One eye crying for Séb and one laughing to see our families again.

A few fotos:

Big fish

Us staring at the sun

Wildlife Seminar at UC Berkeley 3.3.17

Heute im Wildlife Seminar war Chris Wilmers zu Gast. Chris hat vor allem über Mountain Lions und die Rolle von Grossraubtieren in einer von Menschen dominierten Welt geredet. Mountain Lions sind sehr häufig in den Bergen um Santa Cruz. Ab und zu trifft man welche in L.A. oder hier in Berkeley. Puma concolor wird auch Puma, Panther, Cougar, Berglöwe oder Silberlöwe genannt.


Vor einigen Wochen an der Jagdmesse in Chur habe ich viel über die Verbreitung von Hirschen im Engadin bis nach Österreich gelernt. Hirsche wurden mit Halsbändern versehen, die in regelmässigen Intervallen GPS Daten aufnehmen. Die Halsbänder senden die Daten weiter (and Wildhüter oder Biologen) sobald sie Zugriff auf ein Mobilnetzwerk haben! So konnte aufgezeigt werden, wo sich die Hirsche im Sommer und im Winter aufhalten, wo sie durchwandern und ob sich dieses Verhalten zwischen Männchen und Weibchen unterscheidet. Curdin Florineth hat dazu an meinem Geburtstag einen sehr guten Vortrag gehalten.


Ganz ähnliche Studien betreibt Chris Wilmers an der Universität UC Santa Cruz. Er untersucht Grossraubtiere und verpasst ihnen Halsbänder für die Telemetrie um ganz ähnliche Frage wie mit den Hirschen zu beantworten. Im Unterschied zu herkömmlichen Halsbändern sammeln seine nicht nur GPS Daten sondern auch noch Informationen zum Energieverbrauch. Sie messen mit ‘Accelerometers’ wieviel Energie ein Raubtier alle 5 Minuten verbraucht. Pumas wandern meistens relativ langsam herum. Ansonsten schlafen sie viel. Ein Tier zu erledigen kostet sie meistens nur 5 Sekunden an Hochleistung.


Chris interessiert sich vor allem dafür, wie das Zusammenleben mit dem Menschen funktioniert. Er hat herausgefunden, dass Pumas Menschen meiden. In Gegenden, die stärker bewohnt sind reissen die Pumas auch mehr Haustiere. Nicht nur das, sie töten auch mehr Beute als in ungestörten Gebieten. Er deutet das darauf zurück, dass sie in urbanen Gegenden mehr gestört werden, öfters Beute liegen lassen müssen, und mehr Energie verbrauchen. Indirekt sorgen Pumas dafür, dass es nicht zuviele streunende Katzen und Hunde in Siedlungen gibt.


In Kalifornien wird ein Puma gleich erschossen, wenn er eine Ziege reisst. Dank den Telemetriedaten von Chris wurden jedoch auch ein paar ungestörte Gebiete festgelegt, wo Berglöwen jetzt speziell geschützt werden. Ähnlich wie unsere Wildruhezonen für Hirsche. Denn als Top Prädatoren übernehmen die Silberlöwen eine wichtige Rolle im Ökosystem. In abgelegenen Gebieten schauen sie, dass Schalentiere nicht zuviel Schaden durch Verbiss anrichten und dass genügend Pflanzen übrig sind um CO2 zu verwerten.



Kurz und klar – was ich vorhabe in Kalifornien in 2017

Die Lebensgemeinschaft der Forelle und ihrer Bakterien


Bilden Fische eine Lebensgemeinschaft mit den Bakterien die sie besiedeln? Alle mehrzelligen Lebewesen sind von Bakterien besiedelt, die wichtige Funktionen für ihren Träger übernehmen können. Besonders Darmbakterien spielen hier eine bedeutende Rolle. Untersuchungen solcher Bakterien führten in den letzten Jahren zu erstaunlichen Erkenntnissen. So haben verschiedene Forschungsgruppen aufgezeigt, dass diese winzig kleinen Mitbewohner nicht nur unsere Verdauung beeinflussen, sondern auch die Resistenz gegen Krankheiten und sogar den Gemütszustand. Ferner sind Bakteriengemeinschaften extrem vielfältig und unterscheiden sich vom einen Träger zum anderen stark. Folglich wissen wir wenig darüber, welche Faktoren die Vielfalt von Bakterien bestimmen und ob Bakterien an Nachkommen weitergegeben werden.


Für meine Arbeit habe ich die Regenbogenforelle in ihrem natürlichen Verbreitungsgebiet in Nordamerika ausgewählt. Denn diese Fische eignen sich besonders weil sie eine von zwei unterschiedlichen Lebensweisen auswählen: Entweder sie bleiben ihr Leben lang im Süsswasser oder sie wandern als Jungfische ins Meer, um erst für die Paarung wieder zu ihrem Ursprungsfluss zurück zu kehren. Dies führt zu physiologischen, morphologischen und verhaltenstypischen Unterschieden, welche ein spannendes System darstellen, um die Bedeutung von Bakterien für ihren Träger zu studieren. Überdies sind mit Regenbogenforellen gezielte Experimente im Labor möglich. Dort kann die Interaktion zwischen dem Träger und seinen Bakterien manipuliert werden und störende Umweltfaktoren sind ausgeschlossen. In diesem Projekt werde ich aufzeigen, wie Bakterien an Nachkommen weitergegeben werden und denen dabei helfen, sich an verschiedene Lebensbedingungen anzupassen.

Im Glenner

Die letzte Woche war bestimmt von Jetlag und Vorbereitungen für mein erstes SNF Projekt. Zum Glück hat mir Mami geholfen. So konnte ich alles reibungslos erledigen während sie meine Wäsche wusch und auf Jacoby schaute.


Gestern ging es dann auf Laichfischfang. Es war streng und sehr schön. Der Glenner floss wild zwischen den Valser Steinen und das Herbstwetter sorgte für eine wundervolle Stimmung. Die Forellen liessen nicht auf sich warten. Auch im Ferrera Bach fanden wir später viele.


Ich möchte mich hiermit bei all den Fischern und den Wildhütern Arnold Caminada, Moritz Schmid, Gieri Derungs, Gion Bundi, Pirmina Caminada, Patric Ragettli, Thomas Durschei und Martin Cavegn für ihre grosse Hilfe bedanken. Und natürlich Roland, der wichtigste von allen! Wir werden noch viele gemeinsame Stunden verbringen…


Bei meinen Recherchen habe ich noch diese Webseite über Pirmina gefunden:


Es war mir eine grosse Freude, Pirmina gestern kennenzulernen!


forelle4 forelle2 forelle1 img_6521 img_6518 img_6513 img_6488

First Fieldwork in California

L.A. is huge. There is no Swiss comparison. Zürich or Geneva are little villages compared to it. San Francisco and the whole Bay area are also bigger than Switzerland and overpopulated. When you drive during the night it seems like the whole world is artificially illuminated. Thousands of cars, houses and signs are flashing. It is hard to believe that 150 years ago none of these people were here. This was a wild place with whales, sharks, condors, mountain lions and even golden bears. If you want to get a glimpse of the past you should go to the Angelo Coast Range Reserve. This is a reserve that is run by the University of California, Berkeley.


We drove up the coast the night before fieldwork and slept at Fort Bragg. We had dinner with the locals. A bar full of sailors, butchers and carpenters – us in the middle with the kids. And all these rough men turned soft and playful. Challenging Linnea in dominos and watching Donny feed Jacoby. Anyways, early in the morning we drove into the reserve and I helped Suzanne collect some data for her doctoral thesis. Donny stayed at the station during the day and I followed Suzanne into the woods. Climbing up the creeks against the flow and catching rainbow trout until it got dark. The mountain lions saw us but we never saw them. Suzanne caught her fish with electro shocks. While she administers current underwater we were trying to catch all the stunned critters with hand nets. We caught lots of salamanders (Dicamptodon spp.), frogs (Foothill yellow-legged frog / Rana boylei), crabs, and even a lamprey (Lampetra tridentate). And lots of rainbow trout, maybe some steelheads. Suzanne collected scales, tissue, wrote down sizes, weights, and stuck little PIT tags into the fish. She reminded me of myself working on my PhD. She is great and it seems she has it all under control. I am looking forward to collaborate with her next summer. We want to collect lots of juveniles and sample their gut microbes and at the same time we decided we should also have a look at the gut contents.

Linnean’s name for the rainbow trout is O. mykiss. In the South Fork Eel river watershed, where I went to visit Suzanne, O. mykiss individuals exhibit two different life-forms. Some individuals stay for their whole life in the river pools. These are the ‘actual rainbow trout’. Their counterparts swim down the river as juveniles and live for part of their lives in the Pacific Ocean. They come back as much bigger fish to spawn. These individuals are called ‘steelheads’. I want to find out if the gut microbes of juvenile rainbow trout and steelheads (before they leave) from the same river pools differ. My hypothesis is that their symbiont bacteria are different. I think that bacteria help the steelheads during the process of smolting – when they prepare to swim away.

Suzanne made me familiar with the typical fieldwork that is required to sample wild O. mykiss. We were crawling up and down the creeks with all the material. I really enjoyed the reserve and its wilderness. Most of the sampling techniques (sampling tissues and scales, measuring the fish) I already knew well. I was impressed how easy it seems to tag the fish with PIT tags and then how to scan them and recognize individuals. My task before next summer is to learn how to get stomach content samples from wild fish without hurting them. I am also thinking about getting ‘stool’ samples simultaneously.

Lucky, as I am, I joined the Eisen group right after the annual STAMPS course.


Holly and Guillaume took that course this summer and devoted the last three lab meetings on summarizing the most important bits from the course and sharing it with the rest of the group. I got all the course slides about the latest advancements and conclusions how to analyze microbial genomic data. It feels like I made the right choice of groups for my project. With Suzanne and the other people at ESPM I was deeply impressed about their expertise in ecology. In Jonathan’s group I met a bunch of people who are totally specialized on the analysis of microbial communities from different angles. Needless to say again that the Lake Arrowhead conference just blew me away. Hence, both aspects of my project, the host system and its symbionts are nicely covered.


into the wild


yellow legged frog


our van and home


giant salamander


giant rainbow trout…


giant lamprey

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