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

Posted on 18 Jul, 2017 by Jeremy Yoder

(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)

Posted on 12 Jul, 2017 by Jeremy Yoder

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?

Posted on 12 Jul, 2017 by Stacy Krueger-Hadfield

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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#Evol2017 catch-up — Effects of range expansions on mating system

Posted on 11 Jul, 2017 by Stacy Krueger-Hadfield

Two weeks (more about that in a post I’ve written for Wednesday!) after the closing day of the 2017 Evolution Meetings, the Molecular Ecologists have all dispersed from Portland, though some may have left things behind! 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. Over the next few days, we’ll highlight some recommendations from the conference’s well-organized YouTube channel. 
Matthew Koski’s talk on mating system evolution (The effects of historic range expansion on drift load, inbreeding depression, and autonomous selfing) is one I somehow missed.

Patterns of historical migration can influence geographic structuring of the magnitude of inbreeding depression and genetic drift, both of which are correlated with the evolution of mating systems. For example, low costs of inbreeding can facilitate the evolution of selfing, and small populations that experience strong drift are more likely to evolve elevated self-fertilization. Here, we identify clinal patterns of autonomous self-fertilization across 24 populations of the short-lived herb, Campanula americana. Specifically, autonomous fruit set is elevated at the leading range edges, but is low in populations near glacial refugia. We predict that the populations further from glacial refugia that display elevated autonomy also express higher drift load, and have reduced inbreeding depression. In each population we estimated the amount of inbreeding depression and heterosis (drift load) by conducting controlled hand-pollinations, and evaluating the fitness of progeny. We explore geographic patterns of inbreeding depression and drift load, and associate each parameter with the observed spatial variation in autonomous selfing. Our study highlights how genetic structuring following range expansion can affect the evolution of mating systems.

Koski presented work done with Jeremiah Busch and Laura Galloway on when we might expect selfing to evolve. The benefits include the automatic transmission of genes, but the costs include inbreeding depression.
By studying migration from glacial refugia, we can explore how migration may structure genetic loads and mating system variation. At the leading edges, we should expect increased selfing as a form of reproductive assurance (aka Baker’s Law). Thus, we may expect a cline in mating system patterns. As we get further away from the refugium, we should expect to see increasing frequency of selfing.
They studied 24 populations of Campanula americana, the American bellflower, across the North American range.

This species spread from the southeastern part of the continent following the last glacial maximum.

Screen grab of migration schematic for C. americana      © Matthew Koski


They posited three hypotheses:

  1. The leading edge should have an increased capability of selfing
  • They found the northwestern populations exhibited more autonomous fruit set in a common garden with no pollinators. There was, therefore, latitudinal and longitudinal clines in selfing, occurring farther away from the glacial refugium.
  1. The leading edge should have increased drift load
  • Looking at the variation in flower production, the northwestern populations showed evidence of increased drift load, consistent with migration route and selfing capability. However, when they looked at the cumulative drift load and not focused solely on germination, bolting or flower production, the longitudinal pattern dissolved. So, for this hypothesis, Koski gave it a “luke warm” check mark!
  1. The leading edge should have decreased inbreeding depression
  • There was no evidence for inbreeding depression for those leading edge populations.

Thus, the genetic underpinnings of inbreeding depression and drift load may differ. Importantly, the evolution of mating systems will depend on the magnitude of selection for reproductive assurance and inbreeding depression. We can forget to asses the historical processes and their effects on mating system evolution.
Here’s the video with some pretty cool heat maps of selfing!

Posted in conferences, evolution, mating system, natural history, phylogeography, plants, selection | Tagged , , , , , | Leave a comment

NPR's muddled take on scientific racism and direct-to-consumer genetics

Posted on 7 Jul, 2017 by Jeremy Yoder

NPR’s science blog Cosmos & Culture has a post up about a new book on scientific racism and population genetics, particularly in connection with personal genetic ancestry reconstruction like that offered by 23andMe and other “direct-to-consumer” (DTC) genetic testing outfits. Now, these are important and complex issues, and we have some interest in them right here at TME, so it was only sensible to take a look. But the post, in which biological anthropologist Barbara King reviews the new book Is Science Racist by anthropologist Jonathan Marks, starts off with a premise that took me aback:
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#Evol2017 catch-up — Wing shape evolution in non-migrating monarch butterflies

Posted on 5 Jul, 2017 by Jeremy Yoder

A week after the closing day of the 2017 Evolution Meetings, the Molecular Ecologists have all dispersed from Portland. 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. Over the next few days, we’ll highlight some recommendations from the conference’s well-organized YouTube channel.
Micah Freedman’s “Contemporary evolution of monarch butterflies in their introduced range” is a good example of a talk I’d have been excited to see if I weren’t double-booked elsewhere — monarchs have some fascinating natural history, including cool tripartite interactions with their hosts plants and damaging microbial parasites, and recent rapid evolution is a topic that’s been on my radar for a while. Here’s the abstract, with the video following:

Monarch butterflies are best known from their North American range, where they migrate extremely long distances–up to 4,000 km over the lifetime of an individual–to track seasonally available milkweed host plants. Over the past 200 years, monarch butterflies have achieved a nearly global distribution, and can now be found on every major Pacific island group. These introduced island populations are almost all residents (i.e. they breed year-round and do not migrate seasonally). Because each Pacific island population is derived from the ancestrally migratory North American population, these isolated island populations can be treated as replicate exeriments for investigating phenotypic evolution associated with the loss of migration.
Here, I present evidence suggesting that Pacific island monarch butterflies are undergoing contemporary evolution associated with the loss of migration. Using a combination of contemporary wild-caught individuals and museum specimens dating back to 1871, I show that monarch forewing morphology is changing predictably across multiple island groups. Specifically, time series data indicate that Pacific island monarch forewings have become both signifcantly smaller and signficantly more round through time. These findings are consistent with (1) relaxation of selection previously imposed by the demands of long-distance migration and/or (2) directional selection for smaller, rounder wings to promote maneuverability. Results are discussed in the context of functional tradeoffs associated with divergent wing morphologies and recently published genomic data that compares migratory and resident populations of monarch butterflies.

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#Evol2017 catch-up: Biome turnover and body size evolution in Australian vertebrates

Posted on 4 Jul, 2017 by Rob Denton

A week after the closing day of the 2017 Evolution Meetings, the Molecular Ecologists have all dispersed from Portland. 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. Over the next few days, we’ll highlight some recommendations from the conference’s well-organized YouTube channel.
I didn’t see Ian Brennan’s “Late Miocene biome turnover constrained body size evolution across Australian vertebrates” at the meeting, but I really liked the video (clear and beautiful). It’s totally not my field, but I found it super cool. Here’s the abstract from the online program, and then the video.

Climatic trends may influence macroevolutionary trajectories via abiotic and biotic paths. Evidence from mass extinction events suggest rapid climatic oscillations can influence ecological diversification by opening niche space and precipitating adaptive radiation. However, dramatic climatic events represent infrequent deviations from extended periods of protracted climate change and biome turnover. Our understanding of the macroevolutionary impacts of the intervening periods of gradual change remain limited. In contrast to rapid perturbations, gradual climatic change may constrain ecological diversification by making conditions favorable for allopatric and nonadaptive speciation. The degree to which this response is congruent among ecologically different groups also remains unknown. I tested these concepts using a series of fossil-calibrated, species-level phylogenies, and continuous morphological and discrete ecological data for six diverse Australian vertebrate radiations encompassing mammals, birds, and reptiles. To observe temporal trends in the frequency and timing of cladogenetic dispersal events among biomes, and investigate a Late Miocene shift in dispersal patterns, I used a likelihood method for reconstructing ancestral states and modelling cladogenetic dispersal event types (sympatry, allopatry, vicariance). I then compiled body size data for each group, and using maximum likelihood, modelled the temporal trend in body size evolution by comparing standard evolutionary models against novel models which account for a shift in the mode of size evolution in the Miocene. I compared the results of biogeographic and body size modelling, principally temporal shifts in trends, and suggest that coincident timing of changes indicate that Miocene cooling and aridification restricted niche diversification of these diverse radiations. Bounded morphological divergence during the late Miocene coincided with elevated rates of allopatric, particularly vicariant, speciation, characterizing a shift from adaptive to nonadaptive processes during a period of considerable biome transition. These findings suggest that niche evolution can be constrained not only by biotic interactions, but also by gradual abiotic change.

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Easily aggregate bioinformatic sample output with one tool

Posted on 3 Jul, 2017 by Elin Videvall

Today I’m going to write about one of my favorite bioinformatic tools, MultiQC. If you’ve used it, you know why, and if you haven’t, prepare to be amazed.
Many bioinformatic software produce output on a per-sample basis. That is, you may be quality-filtering, trimming, blasting, and mapping your sequence reads to a genome separately for each and every sample. And if you have more than 3 samples (who hasn’t?) going through the output for all samples can become quite tedious and time-consuming.
A single paired-end Illumina MiSeq run can yield 386 separate samples, and bigger genome, transcriptome, and amplicon projects can these days aggregate hundreds or thousands of separate samples.
This is where MultiQC comes in. This tool will first take all the output files from your favorite quality-screening program, and aggregate the results into one simple and pretty report. With FastQC, for example, you normally retrieve a couple of quality plots per sample. MultiQC uses its magic (almost) to compile all samples into combined plots.

Example plot from running FastQC followed by MultiQC. Each line represents one sample.

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Still alive from #Evol2017 – Tuesday highlights

Posted on 28 Jun, 2017 by Jeremy Yoder

My phone battery bought the farm at the entrance to the Oregon Zoo, so in lieu of photos from the terrific final Super Social, here’s someone else’s image of one of the zoo’s bald eagles, looking concerned. (Flickr: Tamara)


A subset of the Molecular Ecologist team is attending this year’s Evolution meeting in Portland, Oregon. As part of our coverage of the meeting, we’ve been recapping the highlights of each day here on the blog, and occasionally previewing upcoming presentations. You can find all of the TME contributors on Twitter using the sidebar on the right or compiled in a handy Twitter list here, check in on meeting news using the hashtag #Evol2017>. You can also view a still-expanding list of video recordings of presentations at the meeting on the Evolution 2017 YouTube channel.
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Live from #Evol2017 – Monday highlights

Posted on 27 Jun, 2017 by Rob Denton

A subset of the Molecular Ecologist team is attending this year’s Evolution meeting in Portland, Oregon. As part of our coverage of the meeting, we will recapping the highlights of each day here on the blog, and occasionally previewing upcoming presentations. You can find all of the TME contributors on Twitter using the sidebar on the right or compiled in a handy Twitter list here; follow along with all meeting news using the hashtag #Evol2017.
Jeremy
Joachim Hermisson — Footprints of Adaptive Introgression
Identifies a “volcano” profile of nucleotide diversity flanking an adaptive locus that introgressed from another species (or population, I think), and some variation in the shape of the volcano depending on the fitness effects of linked variants. A formal method to test for these effects is provided in VolcanoFinder, which does not appear to be released yet (or is not visible to Google, anyway), so that’s a publication to watch out for.
Miranda Sinnott-Armstrong — Evolutionary transitions in fruit colors with respect to climate
Cool first results from a big dataset of data on fruit morphologies and color in plant communities from about a hundred different sites worldwide. It looks like the diversity of fruit color is greater in the tropics than at higher latitudes (though the southern hemisphere looks more “tropical” than the north, which is odd), and frequency of transitions to particular fruit colors may be correlated with transitions to particular climate regimes.
Ailene MacPheson — Finding disease genes in the face of the Red Queen
Genome-wide association is pretty dependent on variation in the population studied; if a locus isn’t variable, by definition GWAS  can’t identify it as associated with a given trait. In the case of disease resistance, we know that negative frequency-dependent selection can create sequential sweeps that remove variation from host and pathogen populations at resistance and virulence loci. MacPherson develops a method of GWAS based on both host and pathogen allele frequencies that can maybe overcome this limitation. (Disclaimer: She’s at UBC, my current institution, and is working with a member of my PhD committee)
Stacy
Sally Chang – Genomic signatures of asexual and sexual reproduction within the colonial hydrozoan Ectopleura larynx
Anything with clonality is pretty much guaranteed to be a major draw for me! Sally is one of the first talks I’ve seen that has used RClone to look at clonality among colonies of the cnidarian Ectopleura. RClone is the fantastic R update to GenClone (the old Excel-like macro that required individual analyses per population!!) led by the work of Sophie Arnaud-Haond’s lab. It’s something that we’ve struggled with … with so many SNPs, you’re not going to get matching genotypes in the way you would with microsatellites. So, where do you draw that line? What’s a clonal lineage? Interesting to see Sally’s work on using called genotypes (20x per our subsequent meeting over coffee trading war stories of working with clonal species) and looking at super close genotypes (likely MLLs), different ones that are clearly the product of sex, and those that so different … totally unrelated polyps? Excited for her work to come out and more studies using RClone and SNPs!
Maurine Neiman – Genomic consequences of asexuality
Maurine described a ton of work out of their group on the snail Potamopyrgus antipodarum. It’s native to New Zealand lakes and populations vary in frequency of sexual and asexual. This snail could be a lovely, modern model for understanding when to have sex and when to maybe be asexual. The coolest thing I found was the fact that radical changes persist for a whole lot longer in asexuals!
Sally Otto – Evolution of sex, evolution of ploidies (SSE Presidential address)
… need I say anymore?
Finally, I neglected to add an awesome poster from Sunday night in my wrap up yesterday!
Kazuhiro Bessho presented work on the evolution of energy from haploid gametophytes to diploid sporophtyes. He used my favorite red algae as a model. Red algae are thought to have poor fertilization success since the female gamete doesn’t disperse at all and male gametes have no flagella. They found if the female totally controls the development of the sporophyte, then an ESS exists and females can maximize their fitness. In contrast, if there is increasing paternal control and fewer sporophytes, then parental care may be favored … this is an excellent model and I look forward to talking more to Bessho-San about this in terms of red algal fertilization success that is actually quite high!
Ethan
Leonardo Campagna – Repeated divergent selection on pigmentation genes in a rapid finch radiation
A number of bird speciation studies from the last few years have shown that recently diverged lineages differ in little beyond genes associated with plumage. Campagna’s talk contributed to this growing consensus, showing that in a species complex of South American birds known as the capuchino seedeaters, divergence peaks in genome scans from different pairwise comparisons are primarily associated with coloration.
Marc Tollis – The tuatara genome sheds light on phylogenetics and rates of evolution during the amniote radiation
It turns out the tuatara genome is about as cool as you’d expect it to be.

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