The story behind the Special Feature: Genomics of natural history collections

We are really excited to get a sneak peak into the story behind a new Special Feature in Molecular Ecology Resources focusing on the use of genomic techniques to better understand natural history collections. In this Special Feature, the authors led by Assistant Professor Lua Lopez, compiled a broad range of studies using a variety of methods to illustrate the enormous potential of museum samples to answer question fundamental to molecular ecology. See below for a video interview with Lua and the article. Check out the great set of articles in the special feature here.

  1. What led you to put together a special issue on this topic?
Lua Lopez. Assistant Professor at California State University

My first contact with ancient genomics was during my postdoc at PSU at the Lasky Lab. As soon as I started looking for literature to help me get the project started I realized that, except in the field of human ancient genomics, information was scattered and it was not easy to find methodological papers for wet-lab or bioinformatics of this type of data. We were lacking a strong foundation of studies using a combination of ancient, historical and modern samples stored in museums. Because of all this I wanted to put together an issue compiling a critical mass of studies using Natural History Collections (NCH) to advance the field of evolutionary biology. Although I had been thinking for a while about this, I only adventured to put this together when two new postdocs also working with NHC samples joined the lab, Dr. Kathryn Turner and Dr. Emilly Bellis. The three of us, together with our postdocsupervisor Jesse Lasky, decided it was time to get this running and I am very excited with the result.

2. Of the papers in the special feature, can you identify any broad trends?

All papers provide a significant advance in important methodological steps (from DNA extraction to data analysis) facilitating the use of NHC sample in evolutionary studies. The data used to test the methods in these papers provide a glimpse of the new research avenues that NHC samples can open.

3. What did you find the most surprising about the papers in this feature?

It was incredible to see how many fields can benefit from using NHC samples. This issue does not only cover methodological aspects but it shows how NHC samples can help answer long-standing questions in the fields of metagenomics, epigenetics, conservation genomics, evolutionary ecology and phylogenetics.

4. What do you recommend to researchers trying to collect genomic data from natural history collections?

Contact as many NHCs as you can. There are still many collections that are not digitized and being aware of what is available that can have a large impact in your experimental design. If this is your first time working with NHC samples, team up, genetic studies with NCH samples can be a big challenge (high risk, high reward). Having someone with experience to guide you is going to be one of the best things you can do to ensure the success of your research.

5. What do you think are crucial next research steps to effectively utilizing natural history collections?

I strongly believe that the next steps include digitizing NHC collections and archiving DNA data. Many  NHC samples are not yet digitized and researchers looking a particular species can only obtain a partial picture of what’s available for their studies. The accuracy we have to answer particular questions is, in most cases, determined by the samples we have access to (i.e. number of samples, geographical and temporal distribution).  In addition, any genetic data obtained from NHC samples should be publicly available. By having access to larger data sets we can not only increase the accuracy of our results but we can also better predict future scenarios.

6. What (if any) method advances are needed?

In the past 10-20 years, we have improved enormously in our wet lab protocols and bioinfomatics but the intrinsic nature of DNA from NHC samples means that we still have a long way to go. Ideally, we want standardize protocols for large taxonomic groups and identify what kind of factors have a larger impact in DNA damage. This also applies for pipelines for data analysis, in general the more standardized protocols are the best, it will hep us comparing results among studies and trying to identify broad evolutionary patters.

7. What would your message be for students about to start their first research projects on this topic?

Understand what kind of samples you have in your hands. It’s not only about how old they are, it’s also about how where they preserve after sampling and during storage, where are they coming from, how much material you have, etc. Many factors are going to influence the success of obtaining DNA of enough quality for downstream analysis. And the same goes for the data analysis, make sure you are considering the particular nature of the genetic data that you are analyzing. NHC samples are precious and destructive sampling cannot be done lightly. So, always do a test run and ask all the questions that you have.

Victoria Sork awarded the 2020 Molecular Ecology Prize

The Molecular Ecology Prize Committee is pleased to announce that the 2020 Molecular Ecology prize has been awarded to Dr. Victoria Sork, Distinguished Professor in Ecology and Evolutionary Biology, Dean of Life Sciences, and Director of the Mildred E. Mathias Botanical Garden at University of California Los Angeles. Throughout her career, Dr. Sork has made substantial and diverse scientific contributions to the field of molecular ecology – from working to build the foundation of landscape genetics, to pioneering the use of molecular markers in tracking plant dispersal, to unraveling the genomic and epi-genomic basis of climate adaptation in non-model organisms. With well over 100 publications, she has proven herself to be a preeminent scholar in her field for decades, while serving as a role model and mentor for many early career scientists, and as a continual advocate for increasing diversity and inclusion in STEM.

Dr. Sork joins the previous winners of the Molecular Ecology Prize: Godfrey Hewitt, John Avise, Pierre Taberlet, Harry Smith, Terry Burke, Josephine Pemberton, Deborah Charlesworth, Craig Moritz, Laurent Excoffier, Johanna Schmitt, Fred Allendorf, Louis Bernatchez, Nancy Moran, Robin Waples, and Scott Edwards.

Nominations for Molecular Ecology Prize

Nominations are now open for the annual Molecular Ecology Prize.

The field of molecular ecology is young and inherently interdisciplinary. As a consequence, research in molecular ecology is not currently represented by a single scientific society, so there is no body that actively promotes the discipline or recognizes its pioneers. The editorial board of the journal Molecular Ecology therefore created the Molecular Ecology Prize in order to fill this void, and recognize significant contributions to this area of research. The prize selection committee is independent of the journal and its editorial board.

The prize will go to an outstanding scientist who has made significant contributions to molecular ecology.  These contributions would mostly be scientific, but the door is open for other kinds of contributions that were crucial to the development of the field.  The previous winners are: Godfrey Hewitt, John Avise, Pierre Taberlet, Harry Smith, Terry Burke, Josephine Pemberton, Deborah Charlesworth, Craig Moritz, Laurent Excoffier, Johanna Schmitt, Fred Allendorf, Louis Bernatchez, Nancy Moran, Robin Waples, and Scott Edwards.

Please send your nomination with a short supporting statement (no more than 250 words; longer submissions will not be accepted) and the candidate’s CV directly to Andrea Sweigart (sweigart@uga.edu) by Thursday, April 2, 2020.  Organized campaigns to submit multiple nominations for the same person are not necessary and can be counterproductive.  Also, note that nominations from previous years do not roll over.

With thanks on behalf of the Molecular Ecology Prize Selection Committee

Nominations for the Harry Smith Prize in Molecular Ecology

The editorial board of the journal Molecular Ecology is seeking nominations for the Harry Smith Prize, which recognizes the best paper published in Molecular Ecology in the previous year by graduate students or early career scholars with no more than five years of postdoctoral or fellowship experience. The prize comes with a cash award of US$1000 and an announcement in the journal and in the Molecular Ecologist.  The winner will also be asked to join a junior editorial board for the journal to offer advice on changing research needs and potentially serve as a guest editor. The winner of this annual prize is selected by the junior editorial board.

The prize is named after Professor Harry Smith FRS, who founded the journal and served as both its Chief and Managing Editor during the journal’s critical early years. He continued as the journal’s Managing Editor until 2008, and he went out of his way to encourage early career scholars. In addition to his editorial work, Harry was one of the world’s foremost researchers in photomorphogenesis, where he determined how plants respond to shading, leading to concepts such as “neighbour detection” and “shade avoidance,” which are fundamental to understanding plant responses to crowding and competition. More broadly his research provided an early example of how molecular data could inform ecology, and in 2008 he was awarded the Molecular Ecology Prize that recognized both his scientific and editorial contributions to the field.

Please send a PDF of the paper you are nominating, with a short supporting statement (no more than 250 words; longer submissions will not be accepted) directly to Dr. Janna Willoughby (jrw0107@auburn.edu) by 31 May 2020. Self-nominations are accepted.

Interview with the chief editor: Molecular Ecology Resources (MER)

In this special new-years post we interview the Chief Editor of MER Shawn Narum. Shawn, based at the Columbia River Inter-Tribal Fish Commission and the University of Idaho, has been chief editor for over 5 years. In this interview we get his perspective on the journal and the field in general as well as his advice for early career researchers.

See this link for a past interview with Shawn all the way back in 2014 with the Molecular Ecologist and this link for his 2020 editorial.

Image result for shawn narum

What are some of the main changes you have witnessed in the field of molecular ecology since you became Chief Editor of MER?

The advancement of molecular and statistical methods have driven the field of molecular ecology to new heights. Questions that were previously out of reach can now be addressed for most non-model species with careful study design.

What methods and resources do you think the field needs in the future?

Advances in sequencing methods have lead to fascinating discoveries of candidate genes associated with local adaptation and phenotypic variation many species, but development of candidate markers for intensive testing and validation is lacking. For example, bioinformatic resources are needed that efficiently and accurately develop primers/baits for specific subsets of markers that can be genotyped cost effectively in many individuals (e.g., Meek & Larson, 2019).

What are some of your favourite scientific discoveries from the past two decades?

Genomic islands of divergence are real! These islands often occur as inversions with low recombination that drive life history variation in organisms ranging from plants (Hoffmann & Rieseberg, 2008), birds (Lamichhaney et al., 2016), and fish (Jones et al., 2012)

As a fish geek, I also very much enjoyed the discovery that there is a warm blooded fish! It has long been known that some species like tuna and swordfish exhibit partial endothermy in brain tissue, but discovery of whole body endothermy in Opah living in cold, deep seas makes me smile (Wegner et al., 2015).

What advice would you give students wanting to develop a career in science?

Establish close collaborations with colleagues that you trust and nurture those relationships for the long-term.

What advice would you give to your younger-self about science and life?

Seize opportunities to work with others in a team environment, but it is OK to turn down some opportunities when there is already too much on your plate. “Too much” is when you can’t keep up with expectations that you have for yourself or projects substantially interfere with spending time with the people you love

What is your writing style like? Do you have some favourite writers that inspired you earlier on during your career?

My writing tends to be structured following a mental or written outline for clearly defined study questions. I have always been inspired by papers coming from Louis Bernatchez and have been grateful to have co-authored a few recent articles with him.

What are some of the aspects of your job as a scientist that you enjoy the most?

Two of the most rewarding aspects of my work are being involved with the development of young scientists and making new genomic discoveries that contribute towards conservation and recovery of naturally occurring species.

Outside of sequencing, what is your favourite methodological advance in the last five years?

Statistical advances that improve signal to noise in order to reduce false positives are critical to our field. One such approach called “Local score” was developed by Fariello et al (2017) to account for linked SNPs from high density genome scans to yield strong candidates (after Bonferroni correction). This is a powerful approach to detect adaptive genetic variation.

References

Meek, M. H., & Larson, W. A. (2019). The future is now: amplicon sequencing and sequence capture usher in the conservation genomics era. Molecular ecology resources. 19, 795–803.
https://doi.org/10.1111/1755-0998.12998

Hoffmann, A. A., & Rieseberg, L. H. (2008). Revisiting the impact of inversions in evolution: from population genetic markers to drivers of adaptive shifts and speciation?. Annual review of ecology, evolution, and systematics, 39, 21-42.
https://doi.org/10.1146/annurev.ecolsys.39.110707.173532

Lamichhaney, S., Fan, G., Widemo, F., Gunnarsson, U., Thalmann, D. S., Hoeppner, M. P., … & Chen, W. (2016). Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nature Genetics, 48(1), 84.
https://doi.org/10.1038/ng.3430

Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., … & Birney, E. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484(7392), 55.
https://doi.org/10.1038/nature10944

Wegner, N. C., Snodgrass, O. E., Dewar, H., & Hyde, J. R. (2015). Whole-body endothermy in a mesopelagic fish, the opah, Lampris guttatus. Science, 348(6236), 786-789.
https://doi.org/10.1126/science.aaa8902

Fariello, M. I., Boitard, S., Mercier, S., Robelin, D., Faraut, T., Arnould, C., … & Gourichon, D. (2017). Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: the local score approach. Molecular ecology, 26(14), 3700-3714.
https://doi.org/10.1111/mec.14141