2021 Harry Smith Prize awarded to Yann Dorant, for considering CNVs in the lobster

Female (top) and male American lobsters, drawn by F.H. Herrick (Flickr: Biodiversity Heritage Library)

The Harry Smith Prize, which recognizes the best paper published in Molecular Ecology by an early career scholar within a given year, has been awarded to Yann Dorant at the Université Laval in Québec. Dorant led the 2020 paper “Copy number variants outperform SNPs to reveal genotype-environment association in a marine species,” an examination of local adaptation to climate in the American lobster, Homarus americanus. As the award committee, Alison Nazreno and Katrina West, noted in their decision letter,

Although CNVs are a major component of genotypic and phenotypic variation in genomes, their adaptive role has been largely neglected in wild populations. In this context, Dorant’s approach presents a new, cost-effective approach for reduced- representation sequencing data sets, which enables the joint analysis of sequence and structural variation. The work by Dorant and colleagues highlights the extent to which CNVs are overlooked in population genomics studies, thus underscoring the missed opportunities to reveal subtle population genetic structures and identify loci associated with local adaptation.

Dorant’s winning article is available online at the Molecular Ecology website. The award committee also recognized two graduate students at the University of British Columbia, Kaichi Huang and Tom R. Booker as second and third runners’ up, respectively. Huang and her coauthors demonstrated the role of chromosomal inversions in the adaptive divergence of a sunflower ecotype, and Booker et al. used simulations and empirical data to show that low-recombination genome regions may have unusually long-tailed distributions of FST, complicating interpretation of genome scans for locally adapted loci.

Posted in community, Molecular Ecology, the journal | Tagged | Leave a comment

#NewPI in the time of Covid – A recap

Whew. The spring semester has wound down for most of us or will in the next couple of weeks, and summer research (and recovery!) time has begun. I’m now 9 months into being a #newPI at the University of Cincinnati and given the wild ride that being a #newPI generally is, plus the clusterf*ck that was 2020-2021, it felt like time for reflection and checking in with my Pre-NewPI Summer To Do List. The first thing I want to note for postdocs who are about to transition to a faculty position or are planning to transition in the future: On our CVs, these positions have discrete start and end dates but in reality, they overlap for months. When I mentioned this to other #newPIs, they all commiserated with this issue. In the last 2-3 months of my postdoc, I was spending 5-10 hours a week on preparing to start my position – everything from planning my move to getting my institutional email set up to attending faculty meetings or orientation events, participating in discussions of who is teaching what, discussing possible lab renovations or purchases, making plans for transitioning data/grants/samples/etc. And since most positions start the same month that teaching begins, if you teach that first semester, I suggest you start working on that class material earlier than your start date. Then I moved and the situation was reversed – unless you’re extremely lucky (I was not), you’ll still be working on postdoc papers at least your first semester if not for the next couple of years. I assumed the postdoc work would bleed into the faculty work but did not realize how much the faculty work would bleed into the last few months of my postdoc.

Continue reading
Posted in career, teaching | Leave a comment

The 2021 Molecular Ecology Prize goes to Fuwen Wei, for pioneering panda genomics

A sleepy panda (Flickr: Rob Schlieffert)

The Molecular Ecology Prize Committee has announced the 2021 recipient of the award, which recognizes an outstanding scientist who has made significant contributions to the still-young field of molecular ecology:

The Molecular Ecology Prize Committee is pleased to announce that the 2021 Molecular Ecology prize has been awarded to Dr. Fuwen Wei, Professor of Animal Ecology and Conservation Biology in the Institute of Zoology, Chinese Academy of Sciences. Dr. Wei is a pioneer in conservation genomics and metagenomics of endangered animals, focusing mainly on giant and red pandas. He has applied genetic and genomic techniques to assess the past, present and future of giant panda populations, infer their evolutionary and demographic processes, and reveal their adaptive mechanisms for feeding on their specialized bamboo diet. He also has proposed and elaborated targeted strategies for the long-term survival of pandas, which were featured in Science as “Hope for Wild Pandas”. With 5 books and over 270 peer-reviewed journal articles, he is a global leader in molecular ecology and conservation genomics.  He has also trained numerous students and postdocs, and fostered international cooperation among zoologists and conservation biologists. His impressive accomplishments have earned him numerous awards and recognition, for instance, the Lifetime Achievement Award for Giant Panda Research and Conservation and the Outstanding Science and Technology Achievement Prize of Chinese Academy of Sciences.

Dr. Wei 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, Scott Edwards, and Victoria Sork.

Posted in community, Molecular Ecology Prize, Molecular Ecology, the journal | Tagged | Leave a comment

Genomic windows into ancient climate change

An infructescence of domestic rice, Oryza sativa. (Flickr: Matt Lavin)

The following is a guest post by Ornob Alam, a graduate student in Michael Purugganan’s lab at New York University. Ornob’s PhD projects examine the demographic and evolutionary history of domesticated Asian rice in the context of past climate change and human migrations; he is on Twitter as @genomeinquirer.

While modern, anthropogenic climate change threatens to be unprecedented in rapidity and scale, humans have always lived at the whim of an unpredictable planet. For decades, paleoclimatologists have been using tree ringsice coreslakebed sediments, and other natural records to reconstruct ancient climates, revealing a dynamic tapestry of global weather patterns through time. This has allowed archaeologists, paleontologists, and others concerned with understanding the past to place historical events within their climatic context, notably implicating climate change as having helped to drive the Neolithic shift from hunter-gatherer to agricultural societiesthe rise and fall of civilizations, and megafaunal extinctions.

Recently, this alliance between archaeology and paleoclimatology has welcomed genomics into the fold, with the emergence of studies that incorporate all three. As any single kind of historical record is incomplete at best and misleading at worst, such interdisciplinary collaboration strengthens our ability to make inferences about the past. Whole genome sequencing, ancient DNA extraction technologies, and population genetics methods allow us to not only study the demographic history of humans using modern and ancient human DNA, but also many aspects of their behavior and culture by exploring their biotic environments. Two studies published in 2020 used non-human genomes to show long-lasting effects of ancient climate change on human societies in different parts of eastern Asia.

Continue reading
Posted in climate change, domestication, mini-review | Tagged , , | Leave a comment

Fieldwork in the pandemic springtime

Western Joshua trees, Yucca brevifolia var. brevifolia, within sight of the snow-dusted eastern Sierras in Kern County, California. (Photo by jby)

The first thing I did after getting my first dose of the Moderna vaccine against SARS-CoV-2 was to drive from the City of Los Angeles mass vaccination clinic at Pierce College to my home campus, California State University Northridge, to print out a sheaf of field collecting permits.

I’d planned fieldwork well before anyone had any firm idea when the vaccine roll-out would reach college faculty and staff, and it was sheer silly luck that I landed the appointment at Pierce the day before I drove into the desert. That was more than a month and thousands of miles of road travel ago; since then I’ve had my second dose and seen very nearly every kind of habitat where Joshua trees grow.

Continue reading
Posted in evolution, fieldwork | Tagged , | Leave a comment

How do you use genome-wide diversity in conservation?

Measuring how genome-wide diversity matters to threatened species has been a constant endeavor of conservation genetics, and still is in the era of genomics. The main idea still goes back to the small population paradigm that demonises low genetic diversity as it can lead to genetic drift and inbreeding, and hence lower population size in the following generations and imminent extinction. As I discuss in my previous post, this is not always the case.

Continue reading
Posted in conservation, demography, evolution, genomics, mammals, population genetics, Uncategorized | Tagged , , , , , , | Leave a comment

What should conservation genomics researchers do about The Gap?

People may forget what you exactly said on your paper, but they won’t forget how your paper makes them feel. I don’t know whose adage that is I was modifying exactly, that perfectly sums my experience with a paper by Shafer et al (2015) about the conservation genomics gap. Coming from the conservation biology world with no knowledge on genomics whatsoever, that paper really makes me think about my PhD that was supposed to be on “conservation genomics” right after I enrolled. As discussed also in this blog five years ago, it is a criticism about how genomic information is still far from being regularly applied to real conservation problems. 

Coming from a somewhat practical world, it disturbs me: Can I still be regarded as a full-fledged conservation biologist if I focus my work on the genomics side of things knowing that I am not doing practical works? What to do about The Gap? Should we even do anything about it at the moment, considering that genomics is still full of uncertainties?

Continue reading
Posted in Uncategorized | Tagged , , , , , | Leave a comment

The Molecular Ecologist Podcast: Darwin Day, a glow-in-the-dark phylogeny, and pandemic PopGroup

A new episode of The Molecular Ecologist Podcast is now out on Anchor.fm. In this episode, Stacy Krueger-Hadfield, Kelle Freel, and Rishi De-Kayne chat with Jeremy Yoder about a pandemic-focused Darwin Day symposium, the phylogenetic conservation of a bioluminescence symbiosis, and the online iteration of a venerable population genetics conference.

Continue reading
Posted in career, community, conferences, TME Podcast | Tagged , , , | Leave a comment

Nominations open for the 2021 Molecular Ecology Prize

From the Molecular Ecology Prize Committee:

We are soliciting nominations 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.

Continue reading
Posted in community, Molecular Ecology Prize, Molecular Ecology, the journal | Leave a comment

In the pipeline – Part 1: ‘Plan, plan, and plan some more’

So you’ve decided it’s time to finally get around to starting that sequencing project. But before you aimlessly leap into it and generate terabytes of sequencing data, just STOP. 

It’s far too tempting to rush into sequencing projects for a number of reasons. Maybe you need to get it done quickly to spend some left-over grant money or use up some reagents. Isn’t everyone doing genomics these days? How hard can it be? But trust me on this one – before breaking out the Qiagen columns (if you’re loaded), lung melting organic solvents (if you’re not), or partaking in the world’s most annoying game of -80 hide-and-seek with your new least favourite sample, take a step back. 

This article will be the first in a series that will take you from planning your genomics project all the way through to analysing your sequence data and plotting some nice figures. One thing to bear in mind for this series is that as you might have already found out if you have spent any time on Biostars or stackoverflow, there are hundreds of ways to do even the most basic of genomics projects. What I hope to cover in this series is by no means the ‘best’ ways of doing things (not that this even exists), but rather one way of doing things, with the aim of pointing you in the right direction to finding something that works for your project.  

Continue reading
Posted in bioinformatics, evolution, genomics, howto, methods, population genetics, Uncategorized | Tagged , , , , , , | Leave a comment