Returning to Asilomar

A white-crowned sparrow on the Asilomar dunes (jby)

Asilomar Conference Grounds is a beautiful, peculiar place. Built in the early decades of the 20th Century as a “leadership camp” for the Young Women’s Christian Association, it’s a collection of warmly beautiful Arts and Crafts buildings nestled among Monterey pines in the dunes between the town of Pacific Grove and the Pacific Ocean. When the YWCA ran into financial trouble in the Great Depression, the State of California bought the property to establish a state park, and today operates it — via an Aramark concession — as a hotel and conference center. For years, now, it’s been the chosen venue for the American Society of Naturalists‘ biennial meeting, three days of research talks and poster sessions and symposia held in an elegant timbered chapel with beams carved with triumphal passages from the Psalms.

ASN’s Asilomar meeting was the last in-person conference I attended before SARS CoV-2 taught us all how to give our talks over video-stream; there was a fully online edition of the meeting in 2021, off the established cycle but making up for the cancelation of the summer Evolution meetings. At that time it was a relief to get back to any sort of interaction with the broader community, and although this wasn’t actually my first in-person conference since 2020 — I’ve now been to a couple of small meetings, and Botany 2022 this past summer — walking the paths of Asilomar and watching talks in the chapel and rolling my eyes at the inadequate supply of coffee in the dining hall’s breakfast service felt like coming home.

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Four science books for 2022

(Flickr, Akshay Hallur)

The Molecular Ecologist receives a small commission for purchases made on via links from this post.

Books occupy a curious place in my reading life. I read a lot as an academic biologist, from research papers to grant proposals to student assignments, but I struggle to carve out time for longer reading commitments that don’t have a work-related purpose. Most years since before I began a faculty position, I set myself a goal of 20 books read for extracurricular enjoyment, and I have never quite hit that mark. This year isn’t over yet, though! And, in fact, between holiday breaks and long-distance travel, I have managed to cover a pretty good range of fiction and non-fiction in 2022. Here’s four science books I read this year that are, I think, well worth your time — and maybe helpful if you’re still filling in the cracks of a holiday gift-giving list.

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Falling through the gap

George C. Scott as General Buck Turgidson, famously opposed to gaps.

There is a hole. Right at the top of our science. In the introductions to our peer-reviewed papers, where we should explain the need for the new research results we are about to present, there is more and more often … an absence. An emptiness. A lacuna, even. Or, more conventionally: a gap.

I refer to a distressing trend — or at least, a thing I am noticing more and more in the papers I edit and review and read — in how my fellow researchers describe what we do. In introductions and abstracts from the pages of Science and Nature to graduate theses, authors explain that their motivation for doing scientific research is to fill “knowledge gaps.”

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Recent reading: 18 Sept 2022

Polymorphic Linanthus parryae (CalPhotos, Jean Paweck)

Los Angeles doesn’t really get full-on summer heat until September, after months of building warmth and time elapsed since that last gasp of winter rains and spring fog. This year we (and most of the rest of the western U.S.) were hit with a record-breaking heatwave, which locally meant daily high temperatures above 100°F (38°C) from August 31 to September 8 — and then on the 9th, we were rescued by an incoming tropical storm. Through it all I hiked across campus from the faculty parking lot every morning, various short-sleeved dress shirts stuck to my back with sweat, and then tweeted excitedly when relief stirred the surface of my apartment building’s swimming pool.

And here’s some of what I read, in my thoroughly air-conditioned campus office:

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Recent reading: 2 Sept 2022

A grand old coast live oak for a new semester (jby)

It’s the end of the first week of classes on my campus, after a spring and summer of more or less successful, mostly in-person conferences (more on that later, I think). I’ve got two big lecture sections of Evolutionary Biology students who are actually in the room with me (still mostly masked, per common sense and campus policy) and the adjustment to non-videoconferenced class has been really delightfully easy. Breakout discussions don’t take an extra five minutes of everyone negotiating an online interface; I can actually hear when someone (it’s usually just one) catches and reacts to one of my passing jokes. There’s energy.

It was also, mostly, a pretty productive and enjoyable summer. There were the conferences; and I got to see some of a state and a biome I’d never visited before. I saw a graduate student through her thesis defense, shepherded one big paper to final acceptance and advanced some others, finalized the hiring of the lab’s first postdoc, and got word I’d earned tenure, a year early. I think I’m going to be spending a lot of the coming semester figuring out what my research program looks like now that it’s as “established” as it can be, and that’s exciting in a way I haven’t felt since I started as faculty.

And here’s some of what I’ve been reading, as I’m thinking about this new phase:

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Revealing the natural history of yeast

The following is a guest post by Matthew Vandermeulen, PhD, at the University at Buffalo. Matthew studies the regulation of responses to environmental variation; he is on Twitter as @mvandermeulen.

Saccharomyces cerevisiae, baker’s and brewer’s yeastmay be one organism that could contend with dogs for the title of man’s best friend.  Saccharomyces cerevisiae has been associated with human culture for thousands of years for use in baking and making alcoholic beverages. In modern times, yeast has become a model to study cell and molecular biology: it was the first eukaryote to have a fully sequenced genome, and it has been reprogrammed to produce pharmaceuticals.  The economic and cultural value of S. cerevisiae has led to debates on what type of evolutionary processes have shaped this organism’s natural history — but to this day we don’t know where, exactly, yeast was first “domesticated” for human uses. 

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2022 Molecular Ecology Prize goes to Kerstin Johannesson, for building big science to study a tiny marine snail

Multi-angle views of a shell of Littorina saxitilis (Wikimedia: H Zell)

The Molecular Ecology Prize Committee has announced the 2022 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 2022 Molecular Ecology prize has been awarded to Dr. Kerstin Johannesson, Professor of Marine Ecology, University of Gothenburg, Sweden. Trained as a marine ecologist, her research over the past 40 years has focussed on understanding how marine organisms become adapted to their environment. Towards this goal, she performed pioneering molecular ecology work that fully integrated ecological and molecular approaches to study the sea snail, Littorina saxatilis, which she developed into a model species. Her work has inspired numerous researchers across Europe to also use Littorina as an ideal model to study the ‘tug of war’ between evolutionary forces that have driven ecotypic divergence across different habitats of littoral zones. She has authored 150 peer-reviewed articles, which have been cited nearly 9,000 times with an h-index of 56. She has trained 35 Ph.D. students and postdocs from Europe and abroad. Her impressive accomplishments have earned her 10 major awards, the most prestigious being The Swedish Börssällskapet Research Award and election to the Royal Swedish Academy of Sciences. She also has received awards (e.g., the Swedish “Kunskapspriset”) in recognition of her outreach activities and the impact of her science on society.  In brief, Dr. Johannesson has been a pioneer and is still an influential leader in the field of marine molecular ecology in Europe and beyond.

Dr. Johannesson 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, Victoria Sork, and Fuwen Wei.

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2022 Harry Smith Prize awarded to Arne Jacobs, for revealing the role of alternative splicing in parallel evolution

Arctic char, illustrated in Unsere Süßwasserfische: eine Übersicht über die heimische Fischfauna nach vorwiegend biologischen und fischereiwirtschaftlichen Gesichtspunkten, by Emil Walter (Flickr: Biodiversity Heritage Library)

This year’s Harry Smith Prize, which recognizes the best paper published in the field of molecular ecology by an early career scholar, has been awarded to Arne Jacobs at the University of Glasgow. Jacobs led the 2021 paper “Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish,” published as the cover article of the October 11, 2021 issue of Molecular Ecology. Jacobs and his mentor Kathryn Elmer demonstrated, in part, that populations of Arctic char have evolved different alternative splicing of key genes involved in replicated divergence into benthic and pelagic ecotypes. As the award committee, Alison Nazreno and Kaichi Huang, noted in their decision letter,

Alternative splicing plays an important but largely neglected role in phenotypic change and adaptation. In this context, Arne’s article provides meaningful insights and analytical approach into diverse mechanisms underlying adaptive divergence. By strikingly linking distinct types of analyses and lines of evidence, the work leading by Arne highlights the role of alternative splicing in adaptive evolution, contrasting the more commonly studied gene expression. Notably, Arne’s approach showed that mechanisms such as splicing and expression underlie the divergence of different phenotypic axes. As a consequence, this paper will contribute to a shift of molecular ecology studies toward a more holistic view of transcriptome, looking deeply into the mechanisms for evolutionary change and regulation of biological processes through complimentary ways.

Dorant’s winning article is available Open Access at the Molecular Ecology website.

The award committee also recognized two “outstanding nominees” as second and third runners-up: Angel G. Rivera-Colón and Jana Wold, respectively. Rivera-Colón led another “From the Cover” article in Molecular Ecology, presenting a software package to simulate RADseq data for protocol optimization; and Wold led a synthetic review of the potential value in considering structural genomic variants in conservation genomics.

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Nominations open for the 2022 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.

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Recent reading: 29 April 2022

Joshua trees in profuse flower in the San Bernardinos (jby)

How is this month already almost over? Four weeks ago I was just starting to realize that an unexpected, astonishingly good flowering season for Joshua trees meant I needed to shoehorn in some fieldwork, eyeing the data analysis I needed to do for not one but two in-person conferences coming up in the first weeks of May, and hitting the hard phase of a training sequence for a marathon. Now I’m a week out from that first conference and still grasping for free days to drive into the desert, and the marathon has been … delayed a week? (This is not a thing that happens so late in the game! And yet.) Also I’ve had multiple workweeks with more days spent on campus than not, to the point that the morning commute feels dangerously routine.

Whether or not we’re ready for it there’s a whole backlog of things that weren’t properly possible for the last two years that are suddenly crashing back into place.

I have managed to do some reading, though! Here’s the highlights:

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