Breathtaking Baikal

RT recently produced a nice short clip about Lake Baikal and what makes it unique. In the video, correspondent Thabang Motsei travels over the ice by hovercraft, visits the Limnological Museum, and speaks to local people about the lake’s biodiversity, beauty, and place in culture and history.


Although Baikal is still frozen over (as is typical for this time of year), Siberia is experiencing abnormally high temperatures. The lake froze later than usual this winter, and this year’s April 1st was the hottest on record for several Siberian cities. The combination of high temperatures and low precipitation have caused the forest fire season to begin early.

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My job is done.

About 5 years ago Elena called me and asked, without much introduction: – Can you characterize the genetics structure of Baikal zooplankton population? – What, right now? – said I. – No, in the future, if we get funded? – I can try, said I. Lots of time elapsed. We did get funded. The plans to characterize the genetic differentiation of Baikal Epischura changed from microsats (oh so 20th century) to RADseq to, finally, pooled RNAseq, which is what we ended up doing. So. Is there or is there no genetic differentiation among samples of Epischura from different parts of Baikal? On Wednesday Larry will have his MS defense and, with his permission, I am posting some of our results here.

Fig. 1. Principle component analysis based on minor allele frequency of 2000 randomly selected SNPs. Individual points are pooled RNAseq biological replicates, 3 per sample. Blue – South Baikal (“St.1″), red – Central Baikal, yellow – North Baikal, green – Maloe More.
Fig. 1
Fig. 2. Actual (green) and expected based on random assignment of alleles to populations distribution of Fst values in 4 samples shown on Fig.1.
Fig. 2
We expect to add 2 more samples from each region plus separate top 50 and 250-100 m depth layers at Station 1. Hopefully before summer.


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Shoutout to Baikal at the 2014 Olympics

This short film kicked off coverage of the 2014 Winter Olympics on Russian TV. The film begins with an alphabet primer in which each letter corresponds to some facet of Russian history and culture, and it goes on to depict major moments in the history of Russian civilization up to the present. In the alphabet section, the Russian letter “Б” is for “Байкал” (Baikal) and the film’s protagonist is shown taking a nice, cool drink from the waters of the lake.

Baikal was also featured in the Olympic spotlight a few months ago when SCUBA divers took the Olympic torch below its surface.

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A first glance at differential gene expression in Epischura baikalensis from different parts of Baikal

This plot (called a heatmap) is essentially a table with genes as rows and populations as columns. Genes (rows) are arranged in such a way that genes with the most similar expression profile across populations are next to each other (clustered together, see the cluster dendrogram on the right; populations (columns) are arranged in such a way that two populations with the most similar expression profile are next to each other (see cluster dendrogram on top). Each cell of the table is painted by a scale of colors from red to black to green; red means that this gene is up-regulated (transcribed at a higher rate) in this population, relative to overall mean, green means that this gene is down-regulated in this population.

You can see a clear 2 clusters of genes: up-regulated in the North Basin and upregulated in Maloe More. Maloe More is also the highest fat content samples by far. We plan to sequence more samples from each region.


NB: North Baikal station 2, MM – Maloe More station 2, CB: Central Baikal station 2, SB: South Baikal station 2.

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Study Abroad: Baikal 2014

East Tennessee State University International Programs Office has approved the 2014 Study Abroad program at Lake Baikal in Siberia, Russia. Led by one of our coPIs (me) and our new chair Joe Bidwell, an accomplished aquatic biologist, this study abroad will allow participants to learn about evolution and ecology of biodiversity hotspots using Baikal biota, this wonderful Nature’s laboratory, as a brilliant example. Tentative dates July 10-10 2014.

Details here:

Like us here:

The trip is open for any students. (But only full time ETSU students eligible for ETSU financial aid).

Contact Lev Yampolsky if you are interested.

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Our outreach work in Russia featured in the ASLO bulletin!

Kirill and Ted prepare our net on board the Kozhov. Photo: K. Woo.

Kirill and Ted prepare our net on board the Kozhov. Photo: K. Woo.

The latest issue of the bulletin of the Association for the Sciences of Limnology and Oceanography featured a number of exciting international outreach projects, including our own work [pdf file] on Lake Baikal!

Our outreach project focused on facilitating communication between Russian early career scientists and the public, as well as enabling a young Russian researcher to work with a large international and multidisciplinary research team. The young Russian PhD student who worked with us, Kirill Shchapov, had the opportunity to work with our team and to speak about Lake Baikal to students, scientists and members of a local NGO.

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Dreaming about Baikal at Kellogg Biological Station

Elena and Sabine showing Steve the Baikal plankton cultures - careful, we have to keep them cold! Photo S.E. Hampton, 9 November 2013

Elena and Sabine showing Steve the Baikal plankton cultures – careful, we have to keep them cold! Photo S.E. Hampton, 9 November 2013

Last week Steve and I visited the Baikal crew at Kellogg Biological Station to exchange results and new ideas for collaborations on the Baikal project. KBS has a famous history of important work in aquatic science, and it is always a special destination for limnologists.

It was especially exciting for us to be there while there is so much activity around culturing the Baikal plankton isolates from the summer field season, and at a time when all of us have projects with new results we are puzzling over and needing lots of feedback. Paul showed us some results of the genetic characterizations of the microbial community of Baikal open waters, hot off the presses, and we speculated wildly about the many new species that the team might be discovering – wild speculation is the most fun part of new results, and the hard work of figuring out what is actually going on will soon displace the wild speculations! We discussed Danny’s nutrient-temperature phytoplankton experiments, and interesting possibilities for developing niche models for the phytoplankton based on both observational and experimental data. Continue reading

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