How Molecular Ecologists Work: Catherine Peichel on being the earliest bird and scheduling to take out the trash

Posted on 29 Nov, 2017 by Rob Denton

Welcome to “How Molecular Ecologists Work”, the interview series that asks scientists how they get stuff done.
This week’s interview is from Dr. Catherine Peichel. Katie and her lab have used genomic data from three spine stickleback to make big discoveries about the process of speciation and sex chromosome evolution (among many, many others).

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How Molecular Ecologists Work: Richard Hamelin on Moving Art and making scientific use of sliced bread

Posted on 22 Nov, 2017 by Rob Denton

Welcome to “How Molecular Ecologists Work”, the interview series that asks scientists how they get stuff done.
This week’s interview is from Dr. Richard Hamelin. Richard and his lab investigate all things tree pathogen, from how to detect them to how to encourage resistance.

Location: University of British Columbia, Vancouver, BC and Université Laval, Quebec city, QC.
Current Position: Professor
Current mobile device(s): iPhone 6
Current computer(s): MacBook Air
What kind of research do you?
I study tree pathogens to learn how they attack trees, what special adaptation makes them pathogens and I use genomics to try to untangle their epidemiology.
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How Molecular Ecologists Work returns!

Posted on 17 Nov, 2017 by Rob Denton


Are you interested in how scientists you admire get stuff done? Do you think that reading about someone else’s productivity is a reasonable–but thinly veiled–excuse to waste ten minutes of your day? Do you enjoy comparing your desk to others’?
Well, good news. How Molecular Ecologists Work, our series of interviews that explore the day-to-day work of diverse scientists in Molecular Ecology, returns next week. Here’s the schedule:
11/22 — Dr. Richard Hamelin (University of British Columbia & Université Laval, Canada)
11/29 — Dr. Catherine Peichel (University of Bern, Switzerland)
12/6 — Dr. Tatiana Giraud (Le Centre National de la Recherche Scientifique, France)
12/13 — Dr. Craig Primmer (University of Helsinki, Finland)
12/20 — Dr. Katy Heath (University of Illinois, United States)
12/27 — Dr. Chris Jiggins (University of Cambridge, United Kingdom)
1/3 — Dr. Carlos Daniel Cadena (Universidad de los Andes, Colombia)
1/10 — Dr. Kathryn Hodgins (Monash University, Australia)
1/17 — Dr. Hanna Kokko (University of Zurich, Switzerland)
1/24 — Dr. Sean Hoban (The Morton Arboretum, United States)
Can’t wait until next Wednesday? Have a look at last year’s series to hold you over.
Thanks to the readership for all of your suggestions! See you next week….

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0.80994 leagues under the sea

Posted on 16 Nov, 2017 by Kelle Freel

The science crew


After a month on the water (and a few weeks getting my land legs again), I’m happily settling back in at home. I just returned from an expedition to a site known as North Pond along the western flank of the Mid-Atlantic Ridge aboard the research vessel (R/V) Atlantis, operated by Woods Hole Oceanographic Institute (WHOI). The cruise was fantastic and I had the chance to chat with different research groups about their projects centered on understanding the ecology of microbial communities in the deep sea. Over the course of my next set of posts, I will discuss some of the cool research led by the scientists I had the chance to work with on the cruise.
The expedition focused on understanding processes and microbial communities under the seafloor. One way to study this ecosystem involves collecting water samples (crustal fluid) from under the oceanic crust at unique platforms referred to as Circulation Obviation Retrofit Kits (CORKs) that have been installed on the seafloor. The basaltic aquifers that we collected fluid from are the largest on the planet, and studying what biogeochemical processes are doing down there helps us better understand cycles globally.
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En garde! Assortative mating in hybrid swordtails

Posted on 9 Nov, 2017 by Reid Brennan

Understanding reproductive isolation is a pretty darn important part of understanding evolution. For new species to form, gene flow needs to be limited in some way. Under allopatry, limiting gene flow is straight forward; individuals never encounter each other so there is no opportunity to interbreed. However, when individuals can access each other this process becomes more complicated. Premating isolation is one mechanism that can limit gene flow between populations or incipient species. For example, when there is selection against hybrids, premating isolation should evolve through reinforcement.
However, premating isolation is not necessarily consistent across space and time within a species. A study led by Molly Schumer focuses on the dynamics of assortative mating in recently established hybrid populations of swordtails, Xiphophorus. In short, it’s complicated and depends on many things.
Swordtails are a great evolutionary system. These are little fish that live in streams of Central America and Mexico. Two species, X. birchmanni and X. malinche, historically have not hybridized. However, around 1997, hybrids were identified (Rosenthal et al., 2003). In certain sites, only hybrids can be found, suggesting that species recognition has somehow broken down. Further studies showed that pollution in the form of sewage and agricultural runoff disrupt chemical signaling, thus inhibiting assortative mating (Fisher et al., 2006). As a result, we know when hybridization started between species, which provides a powerful system to understand the effects of admixture on reproductive isolation.
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It's decorative gourd genetics season, muppet-huggers

Posted on 8 Nov, 2017 by Jeremy Yoder

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

Posted on 3 Nov, 2017 by Jeremy Yoder

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

Posted on 22 Oct, 2017 by Jeremy Yoder
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.

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Population genomics finds veritas in the demographic history of vino

Posted on 17 Oct, 2017 by Jeremy Yoder

“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

Posted on 29 Sep, 2017 by Jeremy Yoder

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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