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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Nominations open for the 2024 Harry Smith Prize, recognizing early career research published in Molecular Ecology

Posted on 16 Feb, 2024 by Jeremy Yoder

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 or Molecular Ecology Resources in the previous calendar year (2023) 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 Molecular Ecology and served as both 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 molecol.social@gmail.com by Friday 26 April 2024. Self-nominations are encouraged.

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Nominations open for the 2024 Molecular Ecology Prize

Posted on 5 Feb, 2024 by Jeremy Yoder

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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Don’t ask “When is it coevolution?” — ask “How is it coevolution?”

Posted on 13 Oct, 2023 by Jeremy Yoder
A rough-skinned newt, Taricha granulosa, somewhere on the Marin headlands of California. Rough-skinned newts’ geographically varying arms race with predatory garter snakes has made them a classic case study for “geographic mosaic” coevolution. (Flickr, matt “smooth tooth” knoth)

Ask me to pick a single word that describes what I study, and I’ll typically say “coevolution.” This is probably true of most evolutionary biologists who study interactions between species — plants and pollinators, hosts and symbionts, predators and prey, et cetera and so on. I can also rattle off a definition drilled into my memory by repeated exposure in graduate school, and then just repetition over a half-dozen semesters teaching evolutionary biology: Coevolution is reciprocal adaptation of interacting species. We usually understand that to mean coevolution is specific, that the interacting species are interacting one-on-one; and that the adaptation is more or less simultaneous, that one species adapts to adaptive changes in the other as those changes occur, and vice-versa. So really, coevolution is specific, simultaneous, reciprocal adaptation of interacting species.

Like a chromosome unspooling into megabases of DNA sequence, that definition unpacks into a huge research effort. Evaluating whether or not adaptation has occurred (or is occurring) requires identifying genes or genetically determined traits involved in a species interaction, then testing for evidence of natural selection on those genes or traits — either relationships between trait values and growth, survival, or reproductive success, or else population genetic patterns consistent with a history of selection. That’s a lot of work when you’re studying the adaptation of one species. Make it two, and you’re beyond what may be possible in a single doctoral dissertation, or even a collaborative grant proposal.

Lately, though, I’ve started to wonder: what if we don’t actually need to do all that work?

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A paleogenomic peek into the human history of the Americas — and all its complications

Posted on 20 Sep, 2023 by Jeremy Yoder
A “birdman” tablet unearthed at the Cahokia Mounds site in what is now Illinois, a massive earthworks that was the centerpiece of a community of tens of thousands at its peak in the 12 Century CE. (Flickr, Don Sniegowski)

The following is a guest post from Ellen Quinlan, a PhD Candidate in Biology at Wake Forest University. Ellen’s dissertation work studies the ecology and population genomics of altitudinal range limits in Andean trees. 

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

Who, when, and how the Americas were first peopled is one of the biggest mysteries in human history. If you’ve heard anything of this story, it’s likely the same one I learned in my college anthropology course and the same one that dominated the fields of archaeology and biological anthropology throughout the 20th century. Under this model, a small group of humans arrived in the Americas fairly recently (~13,000 ya), after walking across the Bering Land Strait, following animal and plant migrations as ice retreated. However, over the last two decades this narrative has been dismantled by new archaeological discoveries and, of course, modern paleogenomics, which have introduced new evidence and prompted the re-examination of old. Geneticist and anthropologist Jennifer Raff’s book Origin: A Genetic History of the Americas is a deep but accessible overview of the new insights yielded by paleogenomics to this rapidly evolving field. 

While I admittedly came to Origin for some cool paleogenomics (of which there are plenty), the book has stuck with me because it is about so much more. Through Origin, Raff eloquently tells both the history of the science as well as the history of how colonialism and misogyny have impacted scientists’ interpretations and harmed the communities involved for centuries. Further, she demonstrates how these stories are deeply intertwined and offers a clear roadmap (with examples from her own work and others) for how the fields of anthropology and human genomics can begin to repair that harm and develop more ethical approaches for the future. 

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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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