New paper: Understanding mutualism with population genomics

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Comparing metrics of diversity (x axis) and geographic differentiation (y axis) for thousands of genes in the Medicago truncatula genome (gray points) reveals that some symbiosis genes (red points) are genome-wide outliers — but they are not all the same kind of outlier (crosses and triangles). Yoder (2016), Figure 1.

Comparing metrics of diversity (x axis) and geographic differentiation (y axis) for thousands of genes in the Medicago truncatula genome (gray points) reveals that some symbiosis genes (red points, crosses, and triangles) are genome-wide outliers — but they are not all the same kind of outlier. Yoder (2016), Figure 1.

My very latest scientific publication is now online at the American Journal of Botany. It’s sort of an odd paper — something of a review, or an opinion piece, discussing how population genomic data can help us understand why mutualisms stay stable [PDF] in spite of the risk of “cheating” by partners, with a “worked example” with data from the Medicago HapMap Project. Here’s some key bits from the abstract:

Different hypothesized models of mutualism stability predict different forms of coevolutionary selection, and emerging high-throughput sequencing methods allow examination of the selective histories of mutualism genes and, thereby, the form of selection acting on those genes. … As an example of the possibilities offered by genomic data, I analyze genes with roles in the symbiosis of Medicago truncatula and nitrogen-fixing rhizobial bacteria, the first classic mutualism in which extensive genomic resources have been developed for both partners. Medicago truncatula symbiosis genes, as a group, differ from the rest of the genome, but they vary in the form of selection indicated by their diversity and differentiation — some show signs of selection expected from roles in sanctioning noncooperative symbionts, while others show evidence of balancing selection expected from coevolution with symbiont signaling factors.

The paper is my contribution to a Special Section on “The Ecology, Genetics, and Coevolution of Intimate Mutualisms”, which I co-edited with Jim Leebens-Mack. You can view the whole Special Section here, and download my paper here [PDF].

My review of Lab Girl for the LA Review of Books

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How should I illustrate a review of Lab Girl? Let's go with a cool plant. This is bunchberry, Cornus canadensis (Flickr: jbyoder)

How should I illustrate a review of Lab Girl? Let’s go with a cool plant. This is bunchberry, Cornus canadensis. (Flickr: jbyoder)

You have surely, by now, heard all about Hope Jahren’s terrific scientific memoir Lab Girl, including as one of my “bookshelf” recommendations for Chronicle Vitae. My full-length review of Lab Girl is now online at the LA Review of Books, and it is, as you might expect, very positive — Jahren writes beautifully about the process of scientific discovery and the daily miracles of the natural world. As a postdoc still scrabbling for purchase on the lower rungs of the tenure track, though, Lab Girl managed to simultaneously tweak my anxieties and give me hope:

The world is heating up, and it often seems that the intellectual luxuries afforded to scientists of the past — Darwin’s leisurely publication schedule, Haldane’s dalliances with radical politics — are gone. Lab Girl’s rendition of the daily institutional frustrations of research marks it as a different kind of scientific memoir — but also as a product of twenty-first century science. If you navigate among scientists’ blogs or scroll through their Twitter feeds, you’ll quickly find the same fears and vexations and injustices Jahren describes, intertwined with accounts of the work that excites scientists’ passions. … Jahren does not makes science look like an easy career choice, but it isn’t her job to do so — and if Lab Girl chronicles the real and substantial barriers to becoming a successful scientist, it also makes that life compelling: she shows the fruit that can still grow from the rocky soil of a research career.

I do hope you’ll read the whole review, and pick up a copy of Lab Girl if you somehow haven’t already.

A new Queer in STEM starts soon!

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There’s big news today at the Queer in STEM project site: we’re about to launch a new iteration of our online survey. Queer in STEM 2.0 is happening thanks to Joey Nelson, a PhD candidate in geosciences at Stanford, who approached us last fall about developing a new study to build on what we’ve learned from the first Queer in STEM survey. He had some great ideas for new questions to tackle:

Do LGBTQ-identified people remain in the closet in STEM workplaces mainly because they feel a lack of support, or because STEM workplace cultures discourage discussion of personal lives outside the lab? How do LGBTQ-identified colleagues, mentors, and role models affect their careers? Does being “out” in the workplace affect their research productivity?

Queer in STEM 2.0 aims to answer these questions with a new online survey designed for more specific hypothesis testing. We hope to hear again from participants in the original Queer in STEM survey, and to achieve an even bigger sample from LGBTQ-identified STEM professionals across the U.S. and Canada. Finally, in our biggest innovation from the original study, we will also ask STEM professionals who don’t identify as LGBTQ to answer many of the same questions we will ask LGBTQ-identified participants, to provide a powerful new tool for understanding the survey results: a control sample.

Joey’s taken the lead in developing a new, more focused questionnaire that adjusts the questions it presents based on initial responses — so, hopefully, it’ll be a smaller time commitment for participants. We’ve also had help and input from Daniel Cruz-Ramirez de Arellano, a chemist at the University of South Florida who’s already worked with Allison to analyze one-on-one interviews from the first study. We’re also grateful to have the continued support of NOGLSTP, and now oSTEM, too.

As an aside: We’d originally planned to announce the new study on Monday, but we held off for a bit in the wake of the horrific mass killing at the Pulse nightclub in Orlando. It’s hard to think that a project like Queer in STEM matters much, in the face of that kind of hatred. I do believe, though, that working to understand individual queer experiences — the nitty gritty details of our lives and careers — is part of the much bigger project of making society kinder to all people. The Pulse massacre is only the latest act of anti-queer violence to add to the fears that LGBTQ-identified folks carry with us every day — including in our laboratories and classrooms. I know I speak for all my collaborators when I say that we hope Queer in STEM can help to make those spaces feel safer.

We’ll officially open the new survey for responses on Monday, 20 June — look for notice here, on the study site, or on social media.

Chapter on coevolution in the Encyclopedia of Evolutionary Biology

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Grant (1949).

My visualization of key data from Verne Grant’s 1949 paper showing that floral traits are more likely to be important in the taxonomic descriptions of plant species when those species are pollinated by animals — which suggests that those plant-pollinator interactions play a role in the formation of new species.

I got word this morning that the Encyclopedia of Evolutionary Biology, a huge compendium of current knowledge on evolution, systematics, and ecology, is now online. That’s exciting in and of itself, but it’s particularly so because it means you can finally see my contribution, the introduction to the topic of coevolution. Here’s the opening paragraph, of which I’m rather fond:

No organism is an island. Every living thing contends with predators, parasites, and competitors, and most also receive benefits from mutualists (Table 1). These interactions with other species exert natural selection—and predators, parasites, competitors, and mutualists may also experience selection in return. The mutual evolutionary change that results from this reciprocal selection is ‘coevolution’ (Janzen 1980; Thompson 2005).

The rest of the Encyclopedia includes contributions from a tremendous array of other authors, and I’m grateful to subject editor Andrew Forbes for the invitation to contribute. You can browse the whole thing on the publisher’s website, and download a manuscript-format PDF of the final text of my chapter here.

Chronicle Vitae: Mentorship in pop culture

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(NBC)

(NBC)

I’ve got a new piece up on Vitae looking at some inspirational (and not-so-) examples of mentoring in popular culture. Leslie Knope (duh) and Miranda Priestly (yikes) make appearances, plus I have officially managed to shoehorn Star Trek into the careers blog of The Chronicle of Higher Education:

When DS9 and the Federation are threatened by deteriorating relations with the Klingon Empire, [Benjamin] Sisko recruits the Klingon Starfleet officer Worf (Michael Dorn) to the station’s crew for his unique combination of security and tactical expertise and cross-cultural competency.

Go read the whole thing, and tweet your own picks and pans with the hashtag #PopCultureMentors.

STEM employers in North Carolina: Time to put your money where your mouths are

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Morehead Planetarium on the campus of UNC Chapel Hill (Flickr: William Yeung)

Morehead Planetarium on the campus of UNC Chapel Hill (Flickr: William Yeung)

North Carolina’s got a shiny new law legalizing antigay discrimination and legislating where trans folk can pee. (More specifically, it forbids the state’s cities and municipalities from passing nondiscrimination laws that protect sexual orientation and gender identity, which some have done.) It’s probably in violation of current Federal regulations and the Constitution, but it could be years before that’s sorted out in court.

H2 was written, passed in a special legislative session, and signed into law in about 10 hours — so quickly that some Democrats walked out of the state Senate in protest of the procedural chicanery. There was effectively no time to mount any public campaign against the law before it became law. Which is a pity, because a similar law under consideration in Georgia is now literally up against Mary Poppins and Captain America: the Walt Disney Company and its subsidiary Marvel Entertainment are threatening to pull operations from the state if the bill passes.

I’m not aware that North Carolina has much of an economic stake in making superhero science fiction, but I do happen to know that the state is deeply invested in actual science. The Research Triangle is a development region created in a public-private partnership to foster science, engineering, technology, and mathematics (STEM) businesses with close ties to Duke University, the University of North Carolina, and North Carolina State University. It was named one of the “Top 10 Biopharma Clusters” last year. So this seems like it might be a problem for the academic side of all that partnership:

As interpreted by the Department of Education, Title IX of the Education Amendments of 1972 forbids discrimination against trans students in any school that receives federal funding. These schools are prohibited from excluding trans students from the bathroom consistent with their gender identity. The new North Carolina law, dubbed H2, rebukes this federal mandate by forbidding public schools from allowing trans students to use the correct bathroom. That jeopardizes the more than $4.5 billion in federal education funding that North Carolina expected to receive in 2016.

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In which I can kinda fake Sorkin dialogue?

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images-2

(Previously, on Twitter)

OPEN ON Toby Ziegler and Josh Lyman, walking down a hallway in the West Wing.

Toby: Nominee’s out. Merrick—
Josh: Merrick?
Toby: Garland.
Josh: Merrick Garland?
Toby: Merrick Garland.
Josh: What, did Hermione Granger turn us down?
Toby: Is she on the D.C. Circuit, or the 5th?
Josh: Aw, you know what I mean. He just sounds really—
Toby: White?
Josh: I was going to say WASPy, but sure.
Toby: You work for a Josiah Bartlett.
Josh: …
Toby: Anyway, he’s a good judge. Great experience. Prosecuted Tim McVeigh.
Josh: I just thought we were going to be more, uh, creative.
Toby: It’s a bad time for creative.
Josh: Is it ever a good one?
Toby: The Judiciary Committee isn’t going to end the freezeout for creative
Josh: You think the Judiciary Committee is going to end the freezeout for Merrick Garland?
Toby: Well, they’ll look dumb if they don’t
Josh: They look dumb anyway!
Toby: Gotta heighten the contradictions. Freezing out a boring, obviously qualified nominee—
Josh: You think they’ll crack?
Toby: If they do, we get Justice Merrick Garland. If they don’t, we try again after the election.
Josh: AFTER THE ELECTION?
Toby: It’s nuts, I agree.
Josh: It’s NUTS.
Toby: The Republicans are nuts.
Josh: You’d think people who talked so much about the Constitution would—
Toby: Follow it?
Josh: Yeah.
Toby: Are you new here?
Josh: So if they freeze out Merrick Garland, AND we win the election, we can get creative?
Toby: More creative, yeah. Not much, though — because we still might not get the Senate back.
Josh: Jeez. Maybe nominating Hermione Granger would be more realistic.
Toby: [shrugs]

FIN

Coming soon: Crowd-funding a Joshua tree genome

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Joshua trees at Tikaboo Valley, Nevada (Flickr: jby)

Joshua trees at Tikaboo Valley, Nevada (Flickr: jby)

I’m very excited to announce a new project, with a new model for doing science: The Joshua Tree Genome Project, in which I’m working with a bunch of smart, accomplished folks to sequence the genome of my favourite spiky desert plant. A sequenced Joshua tree genome will provide the framework to understand how coevolution with highly specialized pollinators has shaped the history of Joshua trees, and to use the landscape genomics skills I’ve developed with the Medicago HapMap Project and AdapTree to understand how the trees cope with extreme desert climates — and how to ensure they have a future in a climate-changed world.

Perhaps most excitingly (terrifyingly?) we’re going to raise some of the funds to do the genome sequencing by crowdfunding, using the Experiment.com platform. So please keep an eye on the project site, follow our Twitter feed, and Like our Facebook page to make sure you don’t miss your chance to help understand Joshua trees’ evolutionary past and ensure their future.

Chronicle Vitae: On advice

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Truth in advertising. (Flickr: Alexander)

Truth in advertising. (Flickr: Alexander)

I’m back in Vitae this week, ruminating on the usefulness of personal advice — or rather, its frequent lack of usefulness.

The challenge with receiving and applying advice is to distinguish real, general principles from what may simply amount to another person’s recollection of a series of events that ended well. … Certainly in academia, as in any career, there are habits and choices that improve the odds of survival from graduate school to tenure. But simply making it to a particular stage doesn’t actually mean that you had all the right habits or made all the right choices — or even know which habits and choices will work for most other people.

In keeping with my established approach to these columns, I actually do circle back around to a way in which you can learn from other folks’ personal experiences, but you’ll need to read the whole thing to find out how.

How to do chili

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Not pretty, but it warms you right up. (jay)

Not pretty, but it’ll warm you right up. (jby)

We’re well into the time of year when, in Minneapolis, the air outdoors will freeze your nose hairs on the first breath, and snow has lost its charm. Here in Vancouver, the only substantial snow is on the mountains across the water, but there’s ice on the trails in Stanley Park, and the trees are lacy with frozen fog. In either city, it’s the time of year for soup: elaborately spiced pho, classic chicken-noodle, and chili.

I don’t so much have a recipe for chili as I have some rules of thumb. My preferred ratios of ingredients, and some of my spicing, are informed by the recipe in Mark Bittman’s magisterial How to Cook Everything, but really that one confirmed a lot of what I’d already arrived at through trial and error. This probably won’t win you a state-fair cook-off, but it’ll make a big pot of hot, hearty, fragrantly spiced chili of the sort that goes perfectly with some cornbread or over rice on a cold winter night.

Here’s what you do:

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