It’s decorative gourd genetics season, muppet-huggers

A field of domestic pumpkins, Cucurbita pepo var pepo. (Flickr: liz west)

It’s the first week of November, and we’re at Peak Pumpkin. Jack o’lanterns are passé, but Thanksgiving (in the U.S.) and traditional winter-solstice-adjacent holidays will keep pumpkin pie and its infamous espresso-based brethren in style for almost two more months.

The cucurbit family, which encompasses cucumbers, melons, and squashes, is kind of a taxonomic mess with relation to common English names. For instance, watermelon is in genus Citrullus, while most other melons are in genus Cucumis with cucumbers. (This makes sense if you’ve ever scooped out a muskmelon’s cucumber-like central mass of seeds and pulp, or if you consider that both honeydew and cucumber are pretty terrific in a gin cocktail.) The pumpkin you usually get in a can for pie filling is a variety of Cucurbita moschata, which has also been bred into hard winter squashes and something called the “Long Island cheese pumpkin.”; the pumpkin the size of a Chesterfield that took a blue ribbon at your state fair is almost certainly the aptly named C. maxima, a species that includes Hubbard squash and several other domesticates. Meanwhile the species from which domestic jack o’lantern pumpkins are derived, C. pepo, is also the source of gourds, zucchini, and summer squashes — “pepo” is the botanic name for the general structure of cucurbit fruits, a specialized form of berry.

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Friday Action Item: Tell Congress to vote down the GOP tax bill

Columbia University commencement, 1913. (Flickr: Library of Congress)

On Fridays while the current administration is in office we’re posting small, concrete things you can do to help make things better. Got a suggestion for an Action Item? E-mail us!

Here’s a last-minute Action Item prompted by an alarming Twitter thread about a report in the Chronicle of Higher Education that highlights a previously unmentioned aspect of the bill Congressional Republicans have produced to radically alter the tax code: Under the proposed law, graduate students’ tuition waivers would treated as taxable income.

As things stand now, one of the few financial benefits of graduate school in the sciences is that most programs provide tuition support and stipends, so that a Master’s or PhD doesn’t come at the cost of additional tuition debt. With the tuition support treated as an untaxed benefit, grad students only pay tax on stipends they earn as teaching or research assistants. That’s typically $20-$30,000 a year, sometimes lower, and often without annual cost-of-living increases. [Edit to add another important point from Dr. Chanda on Twitter: in the humanities, the stipends are usually lower, and often nonexistent, so tax-exempt tuition waivers have an even bigger relative impact.] Counting the dollar value of graduate tuition as taxable income would increase students’ tax bills — could even push a lot of them into a new tax bracket — even though the income they can actually spend on living expenses stays the same. Add the fact that the proposed bill eliminates the tax deduction for interest on student loans on top of its incredibly regressive baseline effect, and the change in the treatment of tuition support would make graduate school that much less affordable for anyone who isn’t independently wealthy, or doesn’t have family support.

Graduate students already make a financial sacrifice to choose study over a private-sector career. The proposed new tax code could cripple universities’ ability to recruit and train the best and brightest from all backgrounds.

You know the drill: Call your Senators and Representative ASAP, and tell them you expect them to oppose this bill. Edited to add: And while you’re at it, if you’re an academic, make sure your University’s President and Provost know what’s up.

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Star Trek Discovery made a debunked genome sequence into a plot point — but that’s not nearly the worst biology goof in the franchise

Michael Burnham (Sonequa Martin-Green), studying the giant space tardigrade. (CBS)

Anyone who’s been anywhere near my Twitter feed in the last month knows I’m pretty darned happy with Star Trek: Discovery, the latest iteration of the five-decade-old science fiction franchise. Discovery manages to build something new with the key elements of Trek and provide “fan service” by calling up beloved old characters and plot points. In addition to putting tribbles back onscreen, it’s also providing another kind of fan service that has long been a Star Trek specialty — wrapping contemporary scientific discoveries into its science-fictional future. Often in the process, the real-world science gets a bit, um, stretched. But Discovery‘s take on cutting-edge science has what is, I think, a new distinction for Star Trek: it references a specific result in genomics research that didn’t survive a year after its initial publication.

I’ll explain below the jump, and rank Discovery‘s geno-flummox against Trek’s track record on genetics and evolution. I’ll have to get into spoilers for the first five episodes of Star Trek: Discovery, so consider yourself warned. Continue reading

Posted in bioinformatics, genomics, horizontal gene transfer | Tagged , | 2 Comments

Population genomics finds veritas in the demographic history of vino

“Jefferson” (left) and “Eaton” varieties of Vitis vinifera ssp. vinifera, from The Grapes of New York (Flickr: Biodiversity Heritage Library, left and right)

One of the more, hah, fruitful applications of genomic data has been in crop and livestock improvement. Biologists know that domesticating plants and animals for human use has involved powerful artificial selection — usually inadvertent at first, then intensive and deliberate. Compared to their wild ancestors, domesticated populations usually have more cultivation-friendly phenology and mating systems, produce more of the whatever feature it is that humans use, and even show behavioral changes. Genome sequencing lets us find the actual changes in the genetic code that underly those selected changes.

A nice new example of this work is online as a preprint at bioRxiv, which reports analysis of population genomic samples of cultivated and wild grapes. The paper’s coauthors, led by Yongfeng Zhou, are particularly interested in the fact that domestic grapes are perennials, propagated by cloning from cuttings. Clonal propagation is far and away the easiest route to domestication, especially of a perennial plant, because it skips over multi-year or multi-decade generation times, and it lets cultivators and breeders rapidly access useful traits in individual lines of the plant. But it also means that the cultivated population can rapidly lose genetic diversity — this is the reason bananas are particularly vulnerable to disease — and ongoing clonal propagation may allow a buildup of deleterious mutations. Comparing population samples from both cultivated and wild grapes lets Zhou et al. examine that “cost of domestication”.

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Friday Action Item: Help Puerto Rico, and Puerto Rican science

The landmark tower of the University of Puerto Rico, in 2011. (Flickr: davsot)

On Fridays while the current administration is in office we’re posting small, concrete things you can do to help make things better. Got a suggestion for an Action Item? E-mail us!

If you’ve so much at glanced at the news this week, you’re surely aware of the ongoing disaster in Puerto Rico. In the aftermath of Hurricane Maria, the entire island is without electrical power, and relief is hampered by basic transportation issues on top of outright negligence at the federal level, as the White House dawdled over a request for relief funds, lifting a shipping restriction it waived after Hurricane Irma hit Houston or even something as basic as sending a Navy hospital ship to assist. It’s easy to feel like we’re helpless to watch this disaster proceed — but there are ways to help, right now.

The News Hour has compiled a good rundown of organizations that can use your donations to help folks on the ground in the immediate future, especially United for Puerto Rico and the Hispanic Foundation. For the longer term, you can contribute to the recovery of Puerto Rico’s science community, specifically, by offering help — workspace or equipment or teaching — through Ciencia Puerto Rico. It’s going to be a long time before life is back to normal on the island, and they’ll need all the help they can get.

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The state of debates at the 2018 Society for Systematic Biologists meeting

This is a guest post from Ohio State PhD Candidate Megan Smith

On June 1-4, 2018, the Society for Systematic Biologists will host its third annual stand-alone meeting. The meeting will be held in Columbus, OH and will include workshops, lightning talks, and debates. The planning committee is hard at work on the schedule, and we’re interested in your input!

The aim of the debates is to discuss ideas and issues that are central to the field of systematic biology. In past meetings, debaters have presented a short introduction to the topic before engaging the audience and other discussants in the topic. If all goes well, audience members will talk as much as the debaters and moderators, and the discussion will push itself forward with little need for the pre-determined questions developed by the moderator. We hope that the debates will be engaging for graduate students, postdocs, and faculty alike, and a big part of designing discussions that will engage all levels of professionals is getting input from as many of you as possible about the topics that interest you.

These topics can be wide-ranging and could focus on both theoretical and empirical issues. For example, you might think about problems that you run into when using next-generation sequence data (or other data) to answer questions that interest you. Are you at a loss when you try to decide on a method to answer a particular question? In what ways are the methods falling short of the data, or vice-versa?

Last year’s four debates covered a wide-array of topics, varying in their focus on theoretical and practical issues. Scott Edwards and Gavin Naylor kicked off the debates by delving into the theory behind gene tree variation, and Mark Holder and Rachel Schwartz wrapped things up with a more applied question: how do I deal with my missing data? In between, Emily Jane McTavish and Matt Hahn argued about when we should use gene trees and when we should use species trees, and Frank Burbrink and Robb Brumfield discussed the ever-present question: what are we actually delimiting when we use ‘species delimitation’ methods?

This year, we hope to come up with just as wide an array of questions, and we hope that you’ll help us organize debates that will make you want to stand up, grab the mic, and get involved (which is highly encouraged)!

If you have ideas, please email them to one of the meeting organizers listed here or comment below. We can’t wait for another productive meeting!


Megan Smith (

Bryan Carstens (

Laura Kubatko (

Marymegan Daly (

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We have the technology. Is sequencing getting better, smaller, faster?

Okay, I know some version of the phrase “recent developments in rapid and affordable sequencing have made blah blah blah possible…” is something you’ve probably read 10,000 times. However, third-generation sequencing platforms have turned out to be pretty darn astounding. The leaders in this area include Pacific Biosciences (aka PacBio) as well as Oxford Nanopore Technologies (think MinION). Multiple studies have recently been making the most of the portable technology provided by Oxford Nanopore, and have used the MinION to analyze reptiles in the Ecuadorian Chocó rainforest, Arabidopsis species in the Croesor Valley in Wales, and microbes from the McMurdo Dry Valleys in Antarctica.

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Posted in bioinformatics, evolution, fieldwork, genomics, methods, next generation sequencing | Tagged , , , | Leave a comment