Summer session accountability

Posted on 1 Sep, 2023 by Jeremy Yoder
A song sparrow with a snack, on Santa Cruz Island this May (Flickr, jby)

Summer, as an astronomical season, doesn’t end for a few weeks yet, but academic summer is well and truly over. Today is already the end of the first week of classes on my campus, and both the courses I’m teaching this semester have had their first two meetings. It’s past time, really, to check in with my summer session resolutions, and see how well I did with the hopeful list of things I’d do with my time while I didn’t have four lectures and two lab sessions a week to prepare and deliver.

This won’t, I hope, read as anything like bragging — though I am proud of what I got done since May — but accountability for what I wanted to do with the time I had. It’ll be less than I might manage with a fully staffed lab, since it was just me and a postdoc working through various projects this season, but multiple of the boxes I can check mark the fulfillment of efforts that started well before this summer.

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The glaciers of the last ice age left their mark on the genetic diversity of species across the globe

Posted on 28 Aug, 2023 by Jeremy Yoder
The Harding Icefield in Kenai Fjords National Park, Alaska. (Flickr, CMy23)

For the last two and a half million years or so — up until a certain species of upright-walking ape descendants really started making their presence known — the greatest force shaping Earth’s biological diversity may well have been ice. I’m talking, of course, about the global glacial cycles of the Pleistocene, a geological period during which the planet’s climate cycled between warmer periods and cooler ages in which the polar ice sheets advanced towards the equator.

These cycles left their mark on the world we see today, especially in the distributions of species that survived through the most recent cycle of glacial advance and retreat. Species that lived in temperate latitudes would have migrated (if they could) equator-ward as the ice caps expanded, and back towards the poles as they melted again. That migration remixed ecological communities and individual species everywhere the glaciers touched. It would have left a straightforward signature in the genetic diversity of any species that experienced it — and as an impressive analysis published earlier this summer in Evolution Letters shows, that signature is a global latitudinal gradient of genetic diversity.

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What internet are you reading these days?

Posted on 9 Aug, 2023 by Jeremy Yoder
A vintage teletype console from Canada’s museum of the Cold War. (Flickr, Diefenbunker Museum)

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

After my post earlier this week about how I’m organizing my online reading, it’s occurred to me that it might be useful to go into further depth about what I’m reading. Specifically, what’s in the “Science Blogs” folder I have set up on Reeder. These are as close as I can come, currently, to the experience of the peak Science Blogosphere.

That’s what we called the network of science-oriented websites updated serially with posts and articles by grad students, senior scientists, educators, journalists, and interested amateurs that really hit its stride (in my memory) in the late 2000s and early 2010s, before much of what we did with those serially-updated websites got sucked into Twitter. Some of the people in that network are still posting, at the same URLs, even — more have undergone as many career transitions as I have.

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How are you reading the Internet these days?

Posted on 7 Aug, 2023 by Jeremy Yoder
A vintage computer terminal, the Televideo pT100 (Flickr, Patrick Finnegan)

In the wake of Twitter’s ongoing uh reinvention, and my departure from the site, it’s really become apparent how much I was leaning on Science Twitter as a front page of the Internet — the place I went to find out what news items, and what new scientific results, were worth my attention. Nine months after deleting my account, I think I’ve got much of that function restored, and in some respects the new normal is better than what Twitter had become by the time I bailed on it.

In a daily scholarly Internet practice, I want to see new scientific publications relevant to my interests, and I want to see what my colleagues are saying about them. I also want to see relevant news stories and events, and what people are saying about them. “Saying”, here, is broadly defined — anything from short-form reactions like Twitter posts to the in-depth reflections and critiques you get from blogs. Twitter used to be a place that covered all this stuff, with people posting links and reactions to new science, as well as links to longer-form discussions. There isn’t, unfortunately, a single platform that covers all these bases, but I’m getting close with a patchwork of social and social-adjacent apps:

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The key to a productive ecosystem may be plant neighbors’ chemistry

Posted on 25 Jul, 2023 by Jeremy Yoder
A milkweed bug (Oncopeltus fasciatus) on butterfly weed (Asclepias tuberosa), one of the plant species in the experiment. Butterfly weed is part of a plant family that produce cardiac glycosides as a toxic defense, but some insect herbivores have adapted to overcome that defense. (Flickr: Martin LaBar)

One of the grand patterns across the diversity of flowering plants is that major groups of species are deeply united by shared chemistry, especially “secondary” biochemical products that don’t directly contribute to processes like photosynthesis, growth, and reproduction. Secondary compounds often have defensive function, and they’ve long been recognized as the key to the evolutionary history of plant-herbivore interactions. According to a nifty new study, biochemistry’s deep linkage to plants’ evolution may also make it the most useful index of a plant community’s functional diversity.

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Evolution 2023: Highlights of evolution and ecological genetics at Albuquerque

Posted on 30 Jun, 2023 by Jeremy Yoder
Fendler’s globemallow (Sphaeralcea fendlerii) along the riverfront bike trail. (jby)

Evolution is back, folks. That is, the 2023 joint annual meeting of the American Society of Naturalists, Society of Systematic Biologists, and Society for the Study of Evolution, held last week in Albuquerque, New Mexico, felt just about like its pre-pandemic self. The meeting was cancelled in 2020, then ran a fully virtual program in 2021, and went hybrid in 2022, running two days of virtual talks and a comparatively in-person event in Cleveland, Ohio. But Evolution 2023 felt like an expansion of its old form, filling five days of contributed talks and plenaries at the Albuquerque convention center, as well as a two-day virtual conference that included the SSE and SSB student award symposia and online versions of many of the meeting’s networking events.

Someday it would be nice to write a conference recap without also writing an introductory paragraph about COVID-19, but we’re not there yet. Masking was pretty sparse in the convention center, and organizers alerted us to some positive tests among attendees towards the end of the in-person meeting … and two days after I got home (by way of an unmasked layover in Phoenix) I woke up congested and achey and pegged the meter on an antibody test. I’m on the mend thanks to Paxlovid, which works as advertised — but my experience is as good a caution as any, as you depart for summer conferences and travel.

It also delayed my write up of the conference, but this has been my first post-recovery priority, because I saw a lot of good molecular ecology work, and some exciting methods and utilities, on display at Albuquerque. Without further ado, some highlights from my notes:

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The Molecular Ecologist is a Bookshop.org affiliate

Posted on 7 Jun, 2023 by Jeremy Yoder

The Molecular Ecologist is a scholarly blog, and we’ve had books and book reviews as one of our focuses for as long as I’ve been managing things here. For almost as long, we’ve been set up as an Amazon affiliate, to receive commissions from purchases that our readers make as a result of those reviews — but Amazon is (and has been for some time) not a book-lover’s choice for book purchasing. Amazon’s business model undermines local independent bookstores, and the company squeezes authors and publishers with its market power, endangering the people who write, edit, and produce new books.

That’s why I’m very happy to announce that TME has finally officially established “affiliate” status with Bookshop.org, the online bookstore that supports local brick-and-mortar independent bookstores. Bookshop works with independent stores to fulfill purchases, and returns the profits from those purchases to the stores. Our application was accepted yesterday, and I’ve spent this morning poring through our archive to update links — now, when you click a link to a book title on this site, you’ll often be taken directly to the book’s page on Bookshop, and a portion of your purchase will go to support this blog, as well as independent booksellers who work with the site. I’ve also cleaned up and refreshed formatting on some of those old review posts, and added a standardized disclaimer to clearly specify that we receive a commission from purchases made via affiliate links in a given post. (This is a practice we instituted a while ago for the old Amazon links, but it hadn’t been applied consistently.)

We’ve got an affiliate page on Bookshop, where we can offer curated lists of titles. Right now, that’s simply a list of books we’ve reviewed, but it may be there’s some other forms of curation we can do in that venue. Check it out, and happy reading!

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Write for The Molecular Ecologist

Posted on 5 Jun, 2023 by Jeremy Yoder
Bluebook pages with notes by entomologist H.G. Dyar (Flickr, Biodiversity Heritage Library)

Have you ever considered science blogging? This might sound like a question from 2011 — have you ever considered taking a smartphone into the field, or posting your conference talk on YouTube, or wearing a fedora in a non-cosplay setting — but I’m really quite serious.

The current reality is that, after years spent using a handful of centralized platforms, social media is splintering and getting noisier. If you want to build a public online profile for your scientific work, you really need more than a Twitter profile and a validated entry on Google Scholar. Blogging can build an in-depth profile of more than just dashed-off thoughts, on an independent website that’s fully connected and searchable on the open Internet.

Blogging can also be a form of scholarly writing that sits between the short informal thoughts you might exchange on Twitter or Mastodon and the deep work you put into a peer-reviewed article — a space to flesh out your notes about an exciting paper you just read, to sketch some connections you see between a handful of different concepts, to work out a new idea while it’s still forming, or to outline the steps of a method or procedure for future reference. Maybe other folks will benefit from even that preliminary work, and maybe their response will help you polish it for publication in a more formal venue; but the blogging itself is useful practice even if it doesn’t go viral or yield a new publication.

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2023 Harry Smith Prize awarded to Antonino Malacrinò, for harnessing open data to study how microbiome communities settle on their hosts

Posted on 17 May, 2023 by Jeremy Yoder
Termites, like Reticulitermes flavipes, are famously dependent on specific gut microbiota; many other insects are less reliant on microbial symbionts (Flickr: Dann Thombs)

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 Antonino Malacrinò, now an Assistant Professor at the University of Reggio Calabria, Italy. Malacrinò contributed the invited synthesis “Host species identity shapes the diversity and structure of insect microbiota,” published in the February 2022 issue of Molecular Ecology. Malacrinò assembled publicly available sequence data from more than 4,000 samples of insect-associated microbes to test whether insects’ microbial symbionts are shaped by shared evolutionary history — or assembled on a much faster, species-specific time scale.

The award committee, Kaichi Huang and Arne Jacobs, note in their decision letter that the work both demonstrates the value of open data, and identifies continuing issues in its accessibility for new, synthetic analyses:

Antonino’s article suggests that host species identity has a wider impact on the structure and diversity of microbial communities than the other factors such as diet, sex, life stage, sample origin and treatment. Notably, Antonino found that a wide portion of published studies actually does not include essential information to compare their data within a wider meta-analysis, or to even replicate their work, thus highlighting the importance of the commitment to open data policies. As a consequence, this paper not only provides novel scientific findings in insect microbiota, but also shows that open data is an extremely powerful tool that enables new discoveries.

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

The award committee also recognized an “outstanding paper” as runner-up: Alexander J. Blumenfeld’s study of social adaptation to urbanized environments by the widespread ant Tapinoma sessile.

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Summer session resolutions

Posted on 15 May, 2023 by Jeremy Yoder
I said I’d use the treadmill more often, I didn’t say how. (Flickr: normanack)

Like all good academics, I bristle at the not-infrequent suggestion, from innocent but insufficiently browbeaten friends and family, that I “take summer off”. In point of fact I am simply not paid for the months between the spring and fall semesters when I’m not teaching, which is the case for many university faculty in the U.S. But then also, free from the constraints of teaching, the summer months are the one long window each year when I can concentrate on everything else I need to do to advance an academic research career: writing up and publishing results, applying for new grant funding, advancing projects to the point that other members of the lab can pick them up when the fall semester starts and I disappear under a new wave of student emails and grading.

Forget New Year’s resolutions. For those of us on the academic schedule, the time to make ambitious and possibly Quixotic plans is now, when the summer months stretch ahead in their full, pure possibility. Of course the list of summer plans has to shrink once it’s subject to actual time constraints. But it’s nice to inventory what could be done, to name the possibilities and maybe learn from the ones that never materialize.

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