Our lab was lucky to be part of the inaugural cohort of the awesome Openscapes champions program, which helped our lab embark on transitioning our workflows to more efficient and readily reproducible open science practices. Today, Nature's Career Column published a piece co-authored by Nina titled "Supercharge your research: a ten-week plan for open data science", which summarizes the key lessons that emerged over the course of the semester-long Openscapes program. Check it out here.
Screenshot from one of our Openscapes calls, including Maria, Nicolas, Arne and Nina
New paper out in Evolutionary Applications - showing the power of our low-coverage whole genome sequencing approach
The first results from our collaboration with Gemma Glucas and Adrienne Kovach at the University of New Hampshire has just come out in Evolutionary Applications. See the paper here. We used our very cost-effective low-coverage whole genome sequencing approach to scan for patterns of variation among Atlantic cod sampled from major spawning grounds in the Gulf of Maine and adjacent areas. We saw highly elevated levels of differentiation at four well-characterized large inversions in the cod genome, but our whole-genome dataset also identified multiple narrow peaks of differentiation, the most striking of which differentiate groups of cod that spawn in the same area, but at different times of year (winter vs. spring). Earlier studies based on SNP chips or other more sparse genome sampling would likely have missed these signatures, highlighting a key advantage to sacrificing genotype certainty for the higher resolution afforded by scanning the entire genome through low-coverage sequencing.
.The findings of this study clearly show that the current management structure for Atlantic cod does not account for the diversity and population structure in this species, providing important input for Nina's work as part of the NOAA Atlantic Cod Stock Structure Working Group tasked with providing updated scientific advice to managers.
We are very excited to welcome new members to our lab. Postdoc Diana Baetscher and lab technician Nick Locatelli are working with Nina and Pete McIntyre on the genetic tracing of marine fish sources for aquaculture feed. Welcome Diana and Nick!
Today, our paper on the genomic basis of fisheries-induced evolution came out in Science. We had returned to a seminal experiment in which fishing pressure had driven striking evolutionary shifts in growth rate of Atlantic silversides in only four generations. We sequenced the genomes of the fish from the experiment to examine the underlying genomic basis. Check out our surprising findings in the paper:
Therkildsen, N. O., Wilder, A. P., Conover, D. O., Munch, S. B., Baumann, H., & Palumbi, S. R. (2019). Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing. Science, 365(6452), 487–490.
Arne attended the Great Lakes Evolutionary Genomics Symposium at the University at Buffalo and gave an award winning poster presentation on his recent silverside work. Good work, Arne!
Many congratulations to PhD students Nicolas and Maria who both passed their A exams this semester!
Check out our Policies page to learn more about our lab code of conduct.
Nicolas has been awarded a grant from the Atkinson Center Sustainable Biodiversity Fund in support of his work using genomic tools to inform the conservation and management of Atlantic cod. Congratulations, Nicolas!
Maria presented new findings at the Annual Ecology and Evolutionary Biology December Symposium, and Nicolas presented at the Department of Natural Resources GSA Symposium in January.
We are very excited to welcome Dr. Arne Jacobs, our new postdoc who is joining us to investigate the genomic and regulatory mechanisms underlying local adaptation in silversides.
The Therkildsen lab hosts SNEEB – the weekly social hour for grad students, post-docs, and faculty from various departments including Ecology and Evolutionary Biology, Entomology, and Neurobiology and Behavior.
Nina and Maria from the Therkildsen lab and Hannes and Callie from the Baumann lab at UConn went on a joint road trip to sample juvenile Atlantic silversides for our NSF project about the genomic basis of local adaptation. We visited Morehead City NC, Oregon Inlet NC, and Chincoteague Island VA, sampling silversides with a beach seine. The weather was lousy and the work strenuous, but the mood elated, because we got all the fish we needed for subsequent genomic and otolith analyses!
Maria presented a poster at the RECOMB Comparative Genomics Satellite Conference (RECOMB-CG) in Sherbrooke, Quebec with travel support from the Center for Vertebrate Genomics at Cornell.
Former postdoc Dr. Anna Tigano has moved to New Hampshire for a postdoc in the MacManes lab. Congratulations Anna! We will miss you!
We're excited to welcome Chrissy Rochus, a postdoc from Leif Andersson’s lab at Uppsala University, who will be visiting us for three months. Chrissy is studying the patterns of genetic change in Baltic herring over the past century. During her visit, she will be extracting DNA and preparing libraries from historical Baltic herring scales in our ancient DNA lab.
Anna gave a talk in a symposium on ecological and genetic mechanisms underlying balanced polymorphisms and Nina's talk was in a symposium titled "Moving beyond point mutations: the role of structural genomic variation in adaptation and novelty".
Summertime in Ithaca means barbecues and bonding! Members of the lab gathered in Nina's backyard for food, drinks, and a game of Kubb – a Scandinavian lawn game with wooden blocks.
Anna and Nina presented at the Unveil Symposium on the Evolutionary Genomics of Adaptation at the Flathead BIological Station in Montana.
Nicolas and Nina presented at Cornell's Center for Vertebrate Genomics Symposium.
Nicolas presented at the Joint Meeting of Ichthyologists and Herpetologists in Rochester, New York.
Nicolas just had his first paper published, resulting from a collaboration with Jeremy Searle's Lab here at Cornell. Analyzing almost 200 full mitochondrial genome sequences that had resulted as a side-product from our low-coverage whole genome sequence of Atlantic silversides sampled across their distribution range, Nicolas illustrated how much more resolution longer sequences provide for phylogeography. He showed that the level of regional structuring is much stronger than previously reported for this species and he reconstructed the demographic history of the species, showing that there had been multiple waves of postglacial recolonization of northern locations. The article was highlighted by an editorial comment in the journal Marine Biology. Congratulation Nicolas!
Check out the paper here.
Nina recently visited the University of New Hampshire, first attending a great Sea Grant Symposium that synthesized current knowledge about the population structure of Atlantic cod in New England waters, integrating views from scientists with on-the-water observations from fishermen. Following this, Nina participated in the first two-day meeting of the NOAA/NESFC-sponsored working group tasked with evaluation whether current management units are consistent with the current best available information about cod stock structure.
Hannes and Maria traveled to Boston’s Harvard University to meet with Valentina di Santo from the Lauder Lab at the Museum for Comparative Zoology. Thanks to our collaborators there, we were able to use a 2D-digital X-ray machine to produce x-ray images of the silversides in our QTL mapping study. These images will allow us to count the vertebrae, which increases in wild populations from south to north.