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!

seining

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.

Bluegill

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.

Outlook:

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!

PANAMA

Well, on Friday, almost two weeks ago, we decided to fly to Panama. It just made sense to join our STRI collaborators during their field trip and to take Linnea out of school while her regular teacher was still sick. When we arrived at San Francisco airport very early in the morning of Saturday, the lady at the check-in told us that we could not fly to Panama because Linnea’s passport will expire on December 1st and to fly to Panama you would need your passport to be valid for 3 full months. This is where our Panama trip ended.

We went back home to Albany and slept for an hour. Then I had the brilliant idea of calling the Swiss embassy and asking them for an emergency passport. Unfortunately, they were closed on a Saturday. Donny spent some time on google and found out that today (!) there was the yearly passport day in San Francisco where people, especially families, can get passports. So, we drove to Berkeley, made passport photos, copied birth certificates, called grandma, and rushed to San Francisco. At the passport office, we got called up immediately and ordered Linnea’s passport. However, the friendly lady told us that it would take 4-6 weeks to mail the passport to us. If we wanted if faster it would cost extra and still take 2 weeks. Then, Donny started crying. He explained the lady that this trip to Panama could change our lives. He told them about me and my research and that he wanted to see the country before moving there with the kids. The lady left, talked to her supervisor and came back. She told us that Linnea’s passport will be ready in 2h.

Seven hours later we sat on the plane to Miami, 15 hours later we arrived in Panama City.

We arrived on a Sunday. The first evening we went for a 2h walk with the stroller and both kids to check out downtown Panama City. It was interesting, safe, but not very exciting. After a trip to ‘Price Smart’, the brother of ‘Sams’ we had gotten enough snacks for the rest of the days and enough of downtown City. On Monday, I went on a field trip with Jarrod and Harilaos. Jarod picked me up from my hotel and I helped him prepare tubes and stuff in the lab on the island of Naos for our dissections later that day. The lab is very impressive. They have every kind of equipment, from gel electrophoresis to fume hood and MiSeq sequencer. Better than most of the Swiss labs I have seen.

Then Harilaos invited me for coffee at his house. An old colonial house with lots of Coatimundis begging for toast.

Coatimundi

I liked the experienced greek and his strong, Italian coffee. He drove us across the country to the Carribean site, to Galeta, where we sampled urchins. We drove through a rainforest, the autopista and in the end a beautiful mangrove forest. There were several checkpoints where they asked us for identification and collection permits. At Galeta we met Haris’ technician Axel, his postdoc Carlos, and his intern Tanner. Here is a link to Carlos‘ personal blog!

We collected four different species of urchins (Diadema sp., Eucidaris sp., Echinometra lucintra, and Echinometra viridis).

Galeta:

Underwater:

Diadema in their natural habitat:

Three different species of Sea urchins in their natural habitat:

Then, we drove back to the laboratory and dissected them to identify the microbes living on and inside them. Harilaos, Jarrod and I dissected. We split the work up so that each of us would dissect at least 3 individuals of each species and we kept track of who did what. We collected their fecal pellets first. Then, we poked them with a syringe and sucked out their coelomic fluid. Then, we collected a few spines. After cutting the poor animal open, we also took a piece of their intestines and a piece of gonad.

Diadema dissections:

Eucideris dissections:

Late at night I made it back to the hotel and passed out pretty soon. The next day I went back to Naos and had more time to talk to Harilaos. He showed me all their facilities and how to keep urchins and crabs in tanks. Later that day he introduced me to Alexandra Hiller, a collaborator who works on Porcellanidae. We talked for several hours and she told me some fascinating stories. I got lots of ideas.

That night we went to see Dumas, a Panamanian friend who was in my PhD cohort at Lausanne University. He and his wife Emilie (jurasienne) have a nice little house in Paraiso. We stayed until late and talked. Linnea fell in love with Emilie. We played with their two dogs (Chocolate and Dubois – or something similar) and hung out in their hammock.

The next morning, we got picked up early and drove to the jungle of Gamboa. Our guide Carl (the owner of the Jungle Land Panama Ecolodge) drove us on a boat along the Panama Canal. He enjoys talking. We took several side rivers and met monkeys. Capuchin monkeys, Spider monkeys, Howler monkeys, and Cotton-top tamarin monkeys. Carl goes and feeds them every day, so they recognize him and jump on the boat when he shows up. Not sure what I should think about it. The French-Canadian tourists with flip flops and beers on our boat definitely enjoyed it.

The canal is pretty impressive. They are constantly dredging and making it wider and bigger. Some of their cranes are from Germany from post-war times.

On the canal:

2000 containers of toys, cars, crap from Asia to Europe…

Then we arrived at the lodge. It is a wild and fantastic place!!!

After a rich lunch, Linnea and I went kayaking while Donny and Jacoby took a little nap. Linnea is a great companion! She told me everything she knows about the jungle. We left the kayaks and took a little hike to a waterfall. I jumped down and Linnea was a bit jealous. I promised we could come back when she is a bit older and can jump too. She was sitting in the water and waiting for me until the little minnows started nibbling on her.

We stayed overnight at the lodge. I went swimming with Jacoby and we enjoyed all the night creatures. Linnea sat on the balcony at dark and looked at the bats. There were lots of them. During the day, we saw a lot of birds. However, I do not know them all by name. I am not a passionate birder. I recognized the Brown pelican, Snail Kites, Purple Marten, some swifts, hummingbirds,

On Thursday, we traveled back to the big city of Panama. On the way, we saw a sloth. People here like to take them down from the trees so that tourists can take pictures of them. That is pretty sad. It costs them a lot of energy to climb back up the trees. Their diet is not very nutrient rich and they need to save their energy!

I don’t even want to start writing about the sad Boa constrictor that is living with Carl. She does not live a very happy life.

On my last day I saw Alexandra one more time and we talked crabs.

Panama is beautiful. There is such a rich life here. Most people I met were very nice. However, it is also very complicated. Last night I went to a bar alone. I ordered a beer and a sandwich. The bartender told me that I was absolutely crazy to walk alone into a bar without speaking Spanish and being a white lady. It confuses me that I do not know the rules here in Panama. Three people pointed out that I am white during my trip. I do not fully understand what is going on. I am motivated to learn Spanish and I think it will help. However, as blond as I am, I think I will never be taken seriously in Panama. I find this pretty racist. I am feeding a family of four with a postdoc salary. My computer was stolen two weeks ago. I have almost no money left and still I got charged ten times more than locals. A weird feeling. Tomorrow we are flying to Florida for the weekend before returning back to California.

We saw alligators in the Everglades and I found a dead Porcellanid during snorkeling at Bill Baggs State Park in Key Biscayne while Donny took care of the last Baseball moves on my phone. This is called convenience.

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?

 

Fieldwork at Scott Creek with Katie Kobayashi

I had to show you these pictures from my field trip with Katie Kobayashi at Scott Creek in Santa Cruz. Katie is studying O. mykiss life-history strategies. She compares the diet of young fish that had been born this year. They are referred to as YOYs (young of the year). To find out what they are eating she makes them throw up. This is called ‚gastric lavage‘. She gently massages their abdomen while inserting a tube and flushing their stomachs out with water. Then she tags them with PIT tags (Passive Integrated Transponder). PIT tags will allow her to track the fish and find out whether they stayed in their natal rivers or whether they left to migrate into the ocean. Katie is studying whether their diet plays a role in deciding to leave or stay.

I tagged along with Katie and sampled stomach and gut microbes. The trip was a great success. Thanks to the heavy rainfalls last winter many fish managed to spawn and produce a lot of offspring. These YOYs are the ones that we are interested in. They seem to be doing very well this summer!

Scott Creek below the dam

Goin‘ fishin‘

My best friends – the Redwoods

Working with NOAA is always great!

Collecting precious data!

Und ein Film zum Abschluss:

Link to Youtube Video

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

Fieldwork for my fellowship project

After all the preparations and concerns for state and federal permits to work with an endangered species, I finally got out into the field and collected data for my second Swiss National Science project. Everything worked out. I got a satisfyingly big sample size and I feel very relieved. I had the greatest people helping me and spent an unforgettable time in nature. Elder Creek and Fox Creek in the South Fork Eel River system, Big Creek in Big Sur and Scott Creek close to Santa Cruz. All the microbes are resting in RNA/DNA shield buffer from ZymoBiomics and I am breathing in and out on my couch.

My sister helped me at Fox Creek. It has been 25 years since I last spent time alone with her. This was a unique experience. We drove into the wild, talked, enjoyed the Angelo Coast Range Reserve, the Pacific Coast, Piaci Pizza and a lot of E-fishing.

Shortly thereafter I brought Sabina back to Berkeley to turn around myself and collect in Elder Creek. Thanks to Suzanne the impossible was rendered possible, Suzanne always finds a way. After a lot of rock hopping we could also cross Elder off of my list. Chapeau and all my respect to Suzanne’s hard working interns who helped us fish, measure and tag, and most of all, carry buckets. The Angelo is the most special place where I have experienced nature. It is remote and wild. Kristen Shekelle, an undergrad scientist in the Carlson group, underlined this by showing me a few pictures of racoons, black bears and a mountain lion! (as well as Phil Georgakakos who photobombed the motion cameras a couple of times).

Back in Berkeley we had some permit issues. My heart fell into my pants and I had to shiver for a few days before Stephanie could resolve it and I continued my sampling streak. I spent a wonderful time at the Big Creek reserve last week with Dave Rundio, Heidi Fish and Russell Neches – my devoted field workers. My SAAB was packed with field material, tent, sleeping bag and camera. My colleagues at NOAA offered to help me with my project and I got spoiled with a huge 4WD truck, chairs to sit on in the field and two personal assistants. My friend Russell (a rockstar physicist) got his feet wet and kept us entertained during the long ride from Santa Cruz to the Big Creek Reserve. Highway 1 is still closed and we had to drive through the Salinas Valley and Fort Hunter Liggett. I think I slept most of the drive. Getting my samples after weeks of preparations was a huge relief and I felt the tension to disappear. At the same time I just let myself doze off in the shaking NOAA vehicle.

The last two days I spent in the Santa Cruz area working with Katie Kobayashi and her crew. She is studying food webs and makes O. mykiss regurgitate their food; that is, gastric lavage. I tagged along and sampled symbiotic microbes. Now we have all the measurements we need, fish are photographed and tagged and I am getting ready for my last sampling sites. It finally happened.

In a week the Carlson group is taking off for Tampa, FL. I will blog next time from Florida.

 

Sierra Nevada World Music Festival 2017

in Boonville.

Well, I did not expect I would have such a good time with Donny and the kids at the world music festival. It was too hot and too loud. It was at times 41° C in the shade! But we had a great time. Donny talked to many artists, collected jingles, interviewed, and we enjoyed the songs. Linnea made friends in the family zone. We arrived late so we could say a proper good bye to the Nusslés and we left early so we would not cook in the heat. After watching the kids during all my field trips and meetings, Donny deserved this special treat. It feels good to be married to a DJ.

hanging

family picture

teaching him some dance moves

my friend the redwood

DJW with Christopher Ellis (youngest male progeny of the Godfather of Jamaican Rocksteady)

DJW with Gappy Ranks from Oakland (Jacoby Lee Williams)

Linnea with Marla Brown – daughter of legendary Dennis Brown

Linnea going wild

Lee Scratch Perry during his interview

DJW with Macka B

DJW and Gentleman (my first live Reggae act 16 years ago)