How Molecular Ecologists Work: it’s back and we need your help

Molecular Ecologist contributors are hard at work behind the scenes filling out a busy fall of new posts. Part of the renewed push includes a new season of “How Molecular Ecologists Work”, a chance to sit down at the desks of our colleagues and see their approaches on productivity. Along the way, we picked up on a few dozen helpful tips, saw offices that varied from coffee shops to beautiful views, and learned that no one actually believes they are all that productive.

The response to last year’s interviews were fantastic, and it was clear that the readers of this blog have an intense curiosity for the details that make up our daily work, whether it be in the lab, out in the field, or at a computer terminal. However, it was clear that How Molecular Ecologists Work was biased towards the United States. This might not be surprising since most of us contributors are based at US universities (spatial autocorrelation?), but we can do better profiling molecular ecologists from across the world.

This is where you come in. Take a look at series 1 of How Molecular Ecologists Work, then ask yourself: Do I admire an international scientist and want to know more about how they work? If you do, contact me (robert.d.denton@gmail.com)!

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The largest mammalian genome is not polyploid

Some 40 million years ago in South America, following the arrival of the common ancestor of caviomorph rodents from the Old World, big changes were afoot.

Specifically, the caviomorph colonists were beginning to give rise to an extant evolutionary progeny of nearly 250 species and 13 families of endemic South American rodents, which show notable diversity in morphology, ecology, and life history (think New World porcupines, chinchillas, and guinea pigs). Interestingly, caviomorphs are also the bearers of notable genomic changes (i.e., evolution of genome size and structure; like the number, form, and arrangement of chromosomes). Functional numbers of chromosomes vary widely from 10-118; moreover, the most extreme instances of genomic evolution in caviomorphs tend to be found in clades with highest diversification rates. That pattern (correlated rates of speciation and genomic evolution) is not uncommon in mammals, and its presence in caviomorphs reiterates persistent holes in our understanding of the links between genomic evolution, speciation, and molecular adaptation.

Present (and prominent) within this milieu of caviomorph chromosomal combinatorics is a species named Tympanoctomys barrerae, or the red vizcacha rat (Figure 1). Red vizcacha rats are small rodents (if you’re a North American desert dweller, think kangaroo rat size) that inhabit the high-latitude, cis-Andean deserts of western Argentina, where they eke out a living largely on low-hanging saltbush fruits. Amazingly, the cells of T. berrarae host nuclear genomes that are more than double the size of an average mammal, and nearly three times that of the human genome. This mass of DNA is packaged into a whopping 102 chromosomes that, while failing to comprise the largest known mammalian karyotype (an honor that belongs to the Bolivian bamboo rat), are still double that of most of its closest living relatives. Possession of the largest known mammalian genome is plenty sufficient for status as an ‘evolutionary curiosity’; however, there are still major questions related to how and why the red vizcacha rat’s genome became so large.

“Evolutionary relationships, chromosome number (2n), and genome size in picograms (C-value) of vizcacha rats and other members of the family Octodontidae (left). Red vizcacha rat T. barrerae in El Nihuil, Mendoza, Argentina (photo credit: Fernanda Cuevas).” Caption from Evans et al. 2017.

In a new paper in Genome Biology and Evolution, Ben Evans, Nate Upham, and colleagues bring whole-genome and whole-transcriptome data to bear on those questions. Their analysis compares and contrasts genomic properties of T. barrerae with those of one of its closest relatives, the mountain vizcacha rat (Octomys mimax). Geologically speaking, these 2 lineages are relatively recently diverged (earliest Pliocene), but the genome of the red vizcacha rat is still twice as large and comprised of nearly double the number of chromosomes. It is worth noting that new specimens of T. barrerae were collected specifically for this work, hard-fought during recent expeditions to the Argentinian high desert. (That part of the study is nicely chronicled here, allowing lots of room for vicarious experience!).

Evans et al. use a variety of tests to understand whether red vizcacha rat genome expansion might be the result of whole genome duplication (polyploidy is extremely rare in vertebrates), but also if accumulation of repetitive elements may have played a role. As an experimental control in the test for polyploidy, the authors subjected genomes of 2 African clawed frogs (Xenopus; 1 of which is a confirmed tetraploid) to the same battery of tests.

The preponderance of their results reject polyploidization in T. barrerae, instead suggesting significant accumulation of repetitive regions as the cause for genome expansion. Interestingly, however, only a few of the repetitive elements BLAST to regions of known biological function in related rodent species. The rest either find their match in regions of unknown function (satellite or micro satellite DNA) or simply lack a clear match at all. According to the authors, their results “support that 1) [the genome of T. barrerae] evolved by expansion of a diverse mosaic of repetitive sequences, and 2) the genomic distribution of these elements is not uniform.”

Still an open question is whether these repetitive genomic elements serve actual biological function(s), and whether those functions were involved in the speciation process. One hypothesis is that the repetitive regions (which make up a whopping 1/2 of the genome of T. barrerae) are somehow involved in adaptation to desert environments and processing of desert food sources. T. barrerae inhabits regions of high-latitude South America that, due to a sizable Andean rain shadow, receive among the lowest rainfall of anywhere in the New World. The species has also evolved an ability to survive on diets made up largely of saltbush fruits. Continuing to pinpoint the causes and consequences of genome expansion in T. berrarae will likely teach us much more about genome evolution, adaptation, and diversification and their links in endemic South American rodents.

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Genomes are coming: Sequence libraries from the honey bee reflect associated microbial diversity

One of the coolest of reasons that cheap sequencing is nifty, in my opinion, is that it has allowed researchers to study individual eukaryotic organisms, and their associated microbes (their microbiome). Let’s be real, we are in the midst of identifying essential interactions between eukaryotes and their microbes, which are key in driving evolution. If you’ve any doubt about that, feel free to check out this great read, or take a glance at this article.

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TME Chat: That #NewPI life

This post is a new format for The Molecular Ecologist: a group chat. Sometimes there are multiple TME contributors who have interesting takes on the same topic, and it’d be nice to hear from them all, and sometimes a conversation is better than a formalized essay. We’re trying this out with a chat about life as new PIs — two of the regular TME contributors are starting their second year as tenure-track faculty, and I’m about to start my first. So we got together on the TME Slack channel to talk about that #NewPI life for an hour. What follows is a transcript of our chat, lightly edited for clarity and grammar and with the odd hyperlink added for context. Enjoy!

— Jeremy

Jeremy Yoder: Hi, everyone! The last year or so has seen some major career transitions for TME contributors — including, now, three new professorships. Stacy Krueger-Hadfield and Arun Sethuraman both started tenure-track positions in the last year, and I’m getting read to move to Los Angeles to start my own. So it seemed like a good time to round up the three of us for a chat about life as new PIs. As the newest one, I’ll mostly moderate and ask questions. Honestly, I want to know everything Arun and Stacy can tell me about getting started.

Let’s start with full introductions: your career stage, a little about what you do, scientifically, and the campus and department where you’re faculty. Maybe Stacy first?

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This new review explains why soft sweeps are the bane — and the baseline — of ecological genetics

(Flickr: andrew)

If you’ve done ecological genetics research in the last decade, you’ve almost certainly cited a series of papers by Pleuni Pennings and Joachim Hermisson, which broke down the problem of soft selective sweeps. Pennings and Hermisson have revisited soft sweeps in a big, detailed new review article for Methods in Ecology and Evolution, which pulls together more than a decade of research following the original studies, and makes a good case that everyone’s favorite excuse for a less-than-dramatic genome scan result is not going away any time soon.

First, what exactly is a soft sweep? Well, it’s a selective sweep that is … not hard. The original papers addressed a couple different ways that natural selection might fail to produce the classic signature of a “hard” selective sweep — in which a single advantageous genetic variant spreads through a population over a few generations, eventually becoming the only variant present — but didn’t quite line them up for comparison. In the new review, Hermisson and Pennings do this very explicitly.

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No, I don’t write for the Genetic Literacy Project (and I never will)

So yesterday I got a notification on Twitter that the Genetic Literacy Project had posted about my pushback on an account of scientific racism published by NPR. Well, nifty, I guess. I’d encountered the GLP before — it’s a news site covering “the intersection of DNA research and real world applications of genetics with the media and policy worlds in order to disentangle science from ideology”. So, great, they wrote something about my post? When I clicked through, though, it turned out to be a ham-fisted edit of my post extracting the gist … annoying, but bog-standard blog-aggregation, no value added. But something about the layout of page caught my attention.

Screenshot from the GLP page. (Google cached version)

That’s my name under the GLP post title, where any respectable news site puts a byline. There’s no other authorial or editorial name on the GLP post page. The date, July 11, is the date of the GLP post, not my original. It does say “Molecular Ecologist”, but there’s no explanation what that indicates from the page layout. If you click on my name, you get an “author” page explaining that GLP posts may be original writing for the GLP, or aggregation-posts. And at the end of the GLP post, there’s a disclaimer to the effect that GLP aggregated the post from The Molecular Ecologist, with a link to the original — but it still doesn’t clarify who did the aggregation. There is no indication, on the post page or elsewhere, as to what human being or algorithm is responsible for the bowdlerized “excerpt” of my TME post … except me.

Call me crazy, but I happen to think my byline has some value, and that it means something — specifically, that when it appears on a post on a website, I had some authorial or editorial role in the creation of that post. (For a post about scientific racism, in particular, I want to be in control of what’s attached to my name!) GLP’s site design obscures that — and after an extended e-mail exchange with the site’s editor, I’m inclined to think that’s deliberate. GLP appears to be quite happy to make it look as though writers all over the web are contributing material for them, without any prior consultation with those writers or the sites where their work is posted.

I’ve lodged my complaints on Twitter and on the comments on the GLP post and in that e-mail back-and-forth, and I will not go on at further length. There’s not a lot more I can do, anyway. A DMCA takedown notice is not really appropriate because, as I noted above, the excerpting of my post itself is pretty standard practice, and probably not a violation of fair use — and some sort of injunction against the use of my name in connection with material I didn’t create seems like overkill, and is beyond both my legal ken and budget. So I’ll simply close out by saying: The Genetic Literacy Project doesn’t understand how authorship and web design works, and any post you see there with my name on it was created without my authorization and against my express wishes.

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#Evol2017 catch-up — or remember that time when someone stole your field gear?

To borrow from our lead in paragraph for post-Evol2017 wrap-ups:

Two weeks after the closing day of the 2017 Evolution Meetings, the Molecular Ecologists have all dispersed from Portland, though items from the Krueger-Hadfield lab didn’t make the return journey! Still, the conference was so big that there’s a lot we missed the first time around — many great talks were scheduled against each other. Fortunately, hundreds of talks were recorded on video and posted online, so it’s possible to go back and catch up with them all. Be sure to check out the great videos on the conference’s well-organized YouTube channel, but, here, I’ll tell a tale of woe …

In the month leading up to #Evol2017, my lab had embarked on some ambitious field sampling down the Pacific coast of North America. It was mostly a reccy to facilitate new lines of inquiry based on natural history. Maybe a few small natural history papers could even come out of it.

If you caught Stephanie Meirmans’ talk (Doing research in the wild: Why does it matter?) on the final day of #Evol2017, she highlighted exactly what this trip was about:

We went out, hoping to stumble over something cool (we did, more about that in the future).

We went to almost 70 sites over 15 days of low tides. That sounds like a ton, but in reality, many sites had nothing for which we were searching or they were very close to one another making it possible to hit several sites in the space of a few hours.

It was amazing, good fun and facilitated by my longest-serving seaweed roadies (my mom and dad), and during the second leg, a grad student at UAB (Sabrina Heiser wrote a post for TME as a #SciComm student).

As I hadn’t planned on attending #Evol2017 this year due to prior commitments to other conferences, I returned to Birmingham for two days before venturing out west again for another few sites of algal adventuring. Field + jet lag can make you sick …

Nevertheless, whither we went, so did the dissecting microscope with which to identify reproductive structures, boots, Falcon tubes, and an herbarium press!

At many other stops along the first legs before the serendipitous #Evol2017 sampling, we’d left the Pelican case (complete with stickers attesting to the scope’s first, of what I’d assumed to be many, outings) and other suitcases in the back of our rental minivan. So, we did the same thing in Portland in what we assumed was a secure hotel parking lot.

Well, you know what happens when you assume …

The Friday night, or technically early Saturday morning, blissfully unaware, we got a good night’s rest before the first full day of #Evol2017. Simultaneously, someone was relieving us of our duffle bag filled with all the goodies, including precious herbarium specimens, and the Pelican case complete with microscope

The next morning, unaware, I went to see some talks. Then, I headed over to the train station to hang out with a colleague who happened to be transiting through Portland.

Then, I found out …

Burglarized …

Microscope, gone.

Pelican case, gone.

Herbarium press, gone.

Boots, gone.

Brand new waders, gone.

Cool drawstring backpack from the Tour of California with pre-labeled Falcon tubes, gone.

Sense of security and opinion of humanity … severely dented.

It was all caught on video … the thief brazenly walked along “casing” cars. Popped the window (it turns out some minivans are dead easy to break into …), climbed in, took our things and went off into the night.

I imagine when he popped the Pelican case open and saw a Leica scope, he was bitterly disappointed to have committed a felony for a scope and some boots and some stinky seaweed drying on paper.

Honestly, I was most upset about the Pelican case. I’d begun to populate the case with stickers of places we’d been. Like, the most amazing fish and chips in Oregon that incidentally has the most amazing stickers. Tangible memories that are not replaceable …

As I thought of the sticker loss (silly as it was), I immediately thought of the herbarium samples. Luckily, I’d had the genetic samples in silica gel in my other luggage. All wasn’t completely lost.

However, those herbarium specimens were destined for my lab’s herbarium, along with the University Herbarium at Berkeley and the Natural History Museum in London once we’d completed some genetic and morphological analyses completed. There were quite a few talks on using herbarium specimens at #Evol2017, such as the talks by Lua Lopez or Kathryn Turner, so the loss of these for future reference was saddening. And, it was such a waste!

It was only a few sites lost in the end, but I’m still angry that someone had the audacity to brazenly take things that weren’t theirs!

The microscope can be replaced.

New stickers will decorate my new Pelican case.

But, the herbarium samples cannot be replaced. They are forever lost in presumably a Portland dumpster somewhere … or maybe now a landfill.

So, if you see these items:

Get in touch … I’ve replaced the scope, but I’d quite like the herbarium samples back!

At least, I’ve progressed to acceptance. I can even find humor in the situation.

And, we’ve learned a lesson … never leave anything in a car, or at the very least as a friend told me today, chain it to the seats.

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