Coming to PAG 32 this January? Join the first-ever Molecular Ecology workshop

Posted on 31 Oct, 2024 by Jeremy Yoder

Posted on behalf of Loren Rieseburg and Shawn Narum, workshop organizers.

We are pleased to announce the inaugural workshop for Molecular Ecology at the Plant & Animal Genomics (PAG) conference. The field of Molecular Ecology has been revolutionized by advances in genomics and computational biology that have enabled us to test hypotheses that were previously unanswerable. Topics that may be addressed in the workshop include the following: ecological genomics, ecological interactions, molecular adaptation, environmental nucleic acids, behavioural genomics, population and conservation genomics, epigenomics, and speciation and hybridization.

Email your abstract by November 12, 2024 to Loren Rieseberg/Shawn Narum to be considered for an oral presentation (loren.rieseberg@botany.ubc.ca; shawnn@uidaho.edu)

This initial workshop will include four invited speakers plus presentations from contributed speakers. Contributed oral presentations will be selected from abstracts submitted to the workshop by November 12, 2024. This workshop aims to bring together researchers, students, and practitioners in the field to explore how recent advances in genomics and molecular biology can be integrated with theory, concepts, and approaches of organismal biology.

Join us January 14, 2025 (10:30 AM-12:40 PM) in San Diego, CA!

For questions regarding abstracts, please contact Loren Rieseberg (loren.rieseberg@botany.ubc.ca) or Shawn Narum (shawnn@uidaho.edu).

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Molecular natural history: Chickadees

Posted on 22 Aug, 2024 by Jeremy Yoder
A black-capped chickadee, Poecile atricapillus, outside Westport, Washington. (Flickr, jby)

Molecular Natural History is a series of posts highlighting what population genetic data reveals about some of my favorite organisms. There’s no rhyme or reason to what species I’ll feature for this, beyond the fact that they’ve made me stop and look closer when I see them along a trail or in my neighborhood. If you’d like to write about the molecular natural history of a favorite taxon, why not pitch a guest post?

Step into the woods almost anywhere in North America and odds are good you’ll be met by a welcoming committee of tiny birds darting among the lower branches of the trees, shouting their name at you, chick-a-dee-dee-dee. Chickadees are delightful and accessible birds: proportioned like live, flying Peeps; curious and bold enough to risk visibility when you venture into their territory; happy to put on a show in your backyard for the low low price of unlimited sunflower seeds.

In many parts of the continent, they’re also an introduction to the challenges of bird identification. Starting with my mother’s old Peterson field guide, I followed the novice birder’s classic emotional arc from excitement at being able to name the songbirds and raptors and corvids that flew through our backyard — to the realization that some of those names were much trickier to apply than others. The first of these challenges I remember cracking was the distinction between the black-capped chickadee, Poecile atricapillus, and the Carolina chickadee, P. carolinensis, whose ranges abut in south-central Pennsylvania. Their size, shape, and shading of wings and underparts seemed relatively distinguishable, as did their songs —until I learned that they hybridize.

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FAQ: Should I invent an acronym?

Posted on 13 Aug, 2024 by Jeremy Yoder
“Moveable type” (Flickr, David DeSandro)

Q. I’m writing a research article, and the text frequently mentions the biological process that is the subject of the article. I’m also worried about exceeding the length limit for the journal I have in mind to send the article. Can I create a nice compact acronym for my favorite biological process? Perhaps … FBP?

A. No!

Q. Are you sure? It would really save me a lot of space.

A. Sorry, the answer is still no!

Q. For an FAQ you sure are down on acronyms.

A. That’s right, I am. And thank you for pointing out the critical issue here: you knew what “FAQ” stands for long before you arrived here. It’s not a barrier to reader comprehension; people will simply absorb it and move on to the Qs and As.

In contrast, if you create an acronym from whole cloth for use in your paper, readers won’t be familiar with it. They’ll have to do the extra cognitive work of remembering what the acronym means. If the acronym stands for the process that’s the subject of the paper, that means you’ve made it harder for readers to remember what the paper is about. How does that help you communicate what you discovered about that process?

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What do we know about the genetics of “born this way?” — and how does it help us to know it?

Posted on 20 Jun, 2024 by Jeremy Yoder
(Flickr, karendasuyo)

Not quite five years ago, a collaboration led by researchers at the Broad Institute published what seemed like the last word in “born this way”: a genomic study of same-sex sexual behavior in a cohort of almost half a million people. That project promised to provide, finally, a window into the evolution of human sexual diversity. It demonstrated, about as clearly as we can demonstrate for any behavioral trait, that some element of sexual orientation is inborn — and that the genetic variation underlying human sexual diversity is deeply woven into the history of our species.

Five years later, in the U.S., we’re facing an ongoing wave of state legislation against basic aspects of queer life and culture, from bans on gender-affirming medical care to restrictions targeting drag performances and history lessons. Worldwide, we’ve seen renewed action against sexual and gender minorities, up to and including the imposition of the death penalty for “aggravated homosexuality.” We’ve long thought legal protections for sexual and gender diversity flowed logically from the idea that sexual orientation and gender identity are deeply inborn and immutable, in the way that most people understand genetics — so why didn’t a modern genome-wide association study in the pages of Science move the needle?

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Mini Reviews provide a new format for brief overviews of trending topics

Posted on 7 Jun, 2024 by Jeremy Yoder

Sometimes you want to introduce an idea or review a topic that doesn’t support an in-depth review of the literature. Molecular Ecology and Molecular Ecology Resources are introducing a new article format that may be what you’re looking for: Mini Reviews. In a joint editorial published online this week, editors Joanna Freeland, Ben Sibbett, and Loren Rieseberg outline plans for the new format, which will be limited to 3,000 words and two display items. They also suggest some examples of Mini Review topics that might be appropriate for each of the sister journals:

  • A new topic or research area for which there is not yet sufficient data for a full review (MEC).
  • A focused overview of a niche topic (MEC).
  • Best practices for a particular technique or analysis (MER).
  • Emerging techniques that have been adopted relatively recently (MER).
  • Older techniques with novel applications (MER).
  • A novel insight or perspective on a topic that has previously been reviewed (MEC).
  • A connection between two or more topics that have previously been addressed in isolation (MEC).
  • The development of a novel hypothesis that could frame future research (MEC).

The journals will accept unsolicited Mini Review submissions through the usual process — just select the Mini Review format when you’re setting it up in Manuscript Central — but the editors encourage pre-submission inquiries, which can be sent to molecol@wiley.com.

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2024 Harry Smith Prize awarded to Robert Masaki Hechler, for demonstrating the potential of environmental transcriptomics

Posted on 28 May, 2024 by Jeremy Yoder
Daphnia pulex (WikiMedia Commons, Paul Hebert)

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 Robert Masaki Hechler, now a PhD student working with Martin Krkosek at the Univeristy of Toronto.

With collaborators at McGill University and the University of Massachusetts Lowell, Hechler demonstrated the use of environmental RNA as an indicator of physiological responses to temperature stress in experimental microcosm communities, with Daphnia pulex as a focal species. The work appears in the paper “Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms?”, which was published on the Molecular Ecology website last October.

In selecting Hechler’s study for the 20204 prize, the award committee of Jana Wold, Angel Rivera-Colon, and Arne Jacobs wrote

An accumulating body of studies had been published describing the use of environmental DNA to investigate species composition and distribution. However, the use of eRNA has been far less studied. Robert investigated gene expression changes in Daphnia exposed to heat-stress and control conditions in a common garden set up to show that eRNA collected from tanks shows similar patterns of gene expression changes compared to RNA extracted from Daphnia tissue. Therefore, this is the first paper, to our knowledge, to show that eRNA can be used to detect the molecular responses of macroorganisms to environmental stress, opening up a wide potential for further studies.

The winning article is available Open Access at the Molecular Ecology website.

The award committee also recognized an “outstanding paper” as runner-up: Aurora García-Berro’s demonstration that migratory butterfly species maintain greater genome-wide genetic diversity.

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2024 Molecular Ecology Prize goes to Michael Whitlock, for foundational contributions to the study of population genetics in space

Posted on 15 May, 2024 by Jeremy Yoder

The Molecular Ecology Prize Committee has announced the 2024 recipient of the award, which recognizes an outstanding scientist who has made significant contributions to the still-young field of molecular ecology:

The 2024 Molecular Ecology Prize has been awarded to Professor Michael Whitlock, Department of Zoology, University of British Columbia, Vancouver. Professor Whitlock is a world authority on the role of spatial population structure in evolutionary biology and population genetics.  He derived basic population genetic results for spatially structured populations, including the effective population size, rate of evolution due to selection, probability of fixation of beneficial and deleterious alleles, mutation load, and inbreeding depression. These results added a ubiquitous, but mainly ignored aspect of real biology to population genetics, i.e., spatial population structure.  He also established the pervasive influence of non-equilibrium processes in genetic spatial structure, demonstrated important limitations of widely used models for statistical genetics inference, derived the first proper statistical treatment of QST, and identified many sources of potential bias in genomic methods for detecting loci underlying local adaptation. This work has had lasting impacts on numerous topics of interest to molecular ecologists, ranging from landscape genomics to conservation genetics to speciation. Whitlock has further to contributed to the field through exceptional service, include writing a leading text on statistical methods, serving as President of the American Society of Naturalists, and establishing a data archiving policy at the major publications in his field, including Molecular Ecology.

Dr. Whitlock 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, Fuwen Wei, Kerstin Johannessen, and Uma Ramakrishnan.

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Molecular Ecology call for papers: Genomics of Speciation

Posted on 19 Apr, 2024 by Jeremy Yoder
Helianthus anomalus, the western sunflower, which likely formed by homoploid hybrid speciation. (Loren Rieseberg)

Molecular Ecology invites papers to be considered for inclusion in a planned Special Issue on the genomics of speciation. The special issue editors are interested in new empirical studies, theory results, and analytic advances, as well as syntheses, reviews, and opinions. Candidate papers should be submitted via Manuscript Central in the usual way, with the Genomics of Speciation special issue indicated in the “Special Issue” section of the manuscript information page. Submissions are due at the end of December, 2024, and the finished special issue is planned for publication in November 2025.

For full details, read the complete solicitation below:

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Molecular natural history: Lupines

Posted on 29 Mar, 2024 by Jeremy Yoder
Lupines on the Icicle Ridge trail above Leavenworth, Washington. (Flickr, jby)

Molecular Natural History is a series of posts highlighting what genetic data has revealed about some of my favorite organisms. There’s no rhyme or reason to what species I’ll feature for this, beyond the fact that they’ve made me stop and look closer when I see them along a trail or in my neighborhood. If you’d like to write about the molecular natural history of a favorite taxon, why not pitch a guest post?

Choosing a favorite wildflower is a challenge for anyone with a little depth of botanical experience, but if I had to pick one I appreciate purely for its decorative presence on the landscape, it would probably be a lupine.

Genus Lupinus includes hundreds of species across the globe, with centers of diversity in the mountain ranges that run down the western spines of North and South America. In spring and summer, you don’t need to hike far into the Rockies or the Cascades or the Sierras before you’ll find their racemes of blue-and-white or yellow or pink flowers marking the edge of the trail. In much of Western North America, you can see multiple species in a few miles of hiking.

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Molecular natural history: The Channel Island foxes

Posted on 1 Mar, 2024 by Jeremy Yoder
A Santa Cruz Island fox, Urocyon littoralis santacruzae, on the prowl. (Flickr, jby)

Molecular Natural History is a series of posts highlighting what population genetic data has revealed about some of my favorite organisms. There’s no rhyme or reason to what species I’ll feature for this, beyond the fact that they’ve made me stop and look closer when I see them along a trail or in my neighborhood, and I need to find at least a little interesting research addressing their molecular ecology.

California’s Channel Islands, an archipelago tucked into the bight formed by concave coastline between Conception and San Diego, are home to a long list of endemic flora and fauna. Of these, the Channel Island foxes, Urocyon littoralis, are arguably the most charismatic — and unquestionably the cutest. They are sister species of the gray fox, and have very similar coloration, but they’re as little as half the size, or a third of the mass, of their mainland congener. It’s not unusual for animals to evolve dramatically smaller (or greater) body size on isolated islands, and the Channel Island foxes provide a case study of the phenomenon within an hour’s boat-ride from Los Angeles.

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