Uninformative polymorphisms bias genome scans for signatures of selection

[ This post is by Marius Roesti; I'm just putting it up.  -B. ]

Current adaptation research is increasingly employing genome scans to search for signatures of selection in the form of markers displaying relatively elevated divergence (typically quantified by Fst) between populations in ecologically distinct habitats. While performing such a study using RADseq in threespine stickleback (see Roesti et al. 2012, Mol. Ecol.), we came across an analytical issue crucial to genome scans, but largely ignored so far.

The point is that polymorphisms with a low minor allele frequency (MAF) are not informative in inferring genetic differentiation between populations and can thus bias the outcome and interpretation of genome scans. Such low-MAF polymorphisms obviously arise easily from technical problems (e.g. sequencing or PCR errors), but theory predicts clearly that a high frequency of low-MAF polymorphisms (especially singletons) is a natural feature of biological samples. No matter how low-MAF polymorphisms arise, we argue in our just-published BMC Evolutionary Biology paper (Roesti et al. 2012, in press) that genetic markers with a low MAF can bias any study – not only genome scans – that involves Fst calculation or any other divergence metric.

The reason why low-MAF markers should be discarded is that researchers conducting genome scans make the tacit assumption that genetic markers adequately capture two key processes – hitchhiking with a selected locus, and drift. The markers used for a genome scan thus need to adequately mirror these historical processes. However, this is not the case for low-MAF polymorphisms because they mostly represent short-lived mutations without historical depth, and their highly imbalanced allele frequencies prevent them from displaying the genetic footprints of selective sweeps. In other words, genetic markers with a low MAF simply lack the potential to capture possible frequency shifts at close-by genomic regions. The best way to think about this is to toy around with this idea even further: if a monomorphic locus was included in a genome scan study, there would be a clear bias in the outcome because this locus obviously cannot capture hitchhiking and drift even if these processes occur! For exactly that reason, nobody thinks about using monomorphic loci for genome scans, but it is generally overlooked that low-MAF markers are nearly as uninformative as fully monomorphic loci.

Again, low-MAF polymorphisms are predicted to be very common in any study system. Marker numbers reported in genome scans studies that do not exclude uninformative polymorphisms are thus likely massively inflated, and divergence patterns and outliers potentially inaccurate. For instance, in our recent genome scans, we applied a minimum threshold of 25% for the minor allele. This leads to a marker loss of 60-70%. However, the remaining markers were really informative. In the BMC paper we make suggestions how this problem can be addressed.

Overall, our study highlights the major need to carefully handle and interpret molecular data, especially in the current golden age of evolutionary genetics and genomics.

Reference:

Roesti M, Salzburger W and Berner D: Uninformative polymorphisms bias genome scans for signatures of selection. BMC Evolutionary Biology 2012, 12:94.  http://www.biomedcentral.com/1471-2148/12/94/abstract

Evolution 2012: Ottawa

Evolution 2012 is coming to Ottawa!  It promises to be utter mayhem — up to 18 parallel sessions at any given time.  The Hendry Lab will be there in force; to help you watch every one of our talks (you know you want to!) here they are, assembled in one place:


Eco-evolutionary dynamics: How ecological and evolutionary process influence one another.  CSEE-sponsored symposium.  Organizers: Andrew Hendry (McGill) and Dolph Schluter (UBC).  Sunday July 8, 1:15 - 4:45, Canada Hall 2-3.  (Andrew Hendry will introduce the symposium from 1:15 - 1:45).

Linking macro-theories with micro-rates: micro-evolutionary support for Cope's rule?
Kiyoko Gotanda, Cristián Correa, Martin Turcotte, Andrew Hendry.  Monday July 9th, 8:45 - 9:00, Room 204.  (Kiyoko and Cristián are both PhD students in the lab.)

Hybridization between genetically-modified Atlantic salmon and wild brown trout results in novel ecological interactions and potential genetic introgression.  Krista Oke, Peter Westley, Darek Moreau, Ian Fleming.  Saturday July 7, 9:30 - 9:45, Room 213.  (Krista is a PhD student in the lab.)

Solving the paradox of stasis: Stabilizing selection and the limits of detection.  Ben Haller, Andrew Hendry.  Sunday July 8th, 4:00 - 4:15, Room 204.  (Ben is a PhD student in the lab.)

The balance between selection and gene flow evaluated in threespine stickleback.  Shahin Muttalib and Andrew Hendry.  Saturday July 7, 3:30 - 3:45, Room 202.  (Shahin is a Master's student in the lab.)


  Hendry Lab in the house, y'all!
  And there are a bunch more talks by people associated with the lab:


The evolution of habitat preference in ecological speciation.  Xavier Thibert-Plante, Daniel Berner.  Monday July 9, 2:15 - 2:30, Room 206.  (Both are lab alumni.)

Rapid evolution of parasite resistance under enemy release in a Guppy-Gyrodactylus host-parasite system.  Felipe Dargent, Marilyn Scott, Andrew Hendry, Gregor Fussmann.  Monday July 9, 1:30 - 1:45, Room 208.  (Felipe is co-supervised by Andrew).

Exploring anthropogenic vs. natural influences on the evolution of Darwin's finches.  Joost Raeymaekers, Luis Fernando De León, Jaime Chaves, Jeffrey Podos, Andrew Hendry, Karl Cottenie.  Sunday July 8, 4:15 - 4:30, Room 201.  (Joost and Luis are both lab alumni.)

Genome divergence during evolutionary diversification in replicate lake-stream stickleback population pairs.  Marius Roesti, Andrew Hendry, Walter Salzburger, Daniel Berner.  Tuesday July 10, 9:45 - 10:00, Room 207.  (Daniel is a lab alumnus.)

Spatiotemporal divergence of threespine stickleback in a dynamic natural system - Lake Myvatn, Iceland.  Katja Räsänen, Antoine Millet, Arni Einarsson, Bjarni Kristjansson.  Monday July 9, 11:45 - 12:00, Room 204.  (Katja is a lab alumna.)

When continents divide: Comparative phylogeography of reef fishes from the Red Sea and Indian Ocean.  Joseph DiBattista, Michael Berumen, Michelle Gaither, Luiz Rocha, Derek Skillings, Brian Bowen.  Saturday July 7, 3:15 - 3:30, Room 210.  (Joseph is a lab alumnus.)


  I think that might be just about it.  Sheesh.  Times/rooms are subject to change, of course, so check the schedule to avoid getting tears in your beer later.  And if you're giving a talk at the conference related to eco-evolutionary dynamics, post it in the comments!  See you in Ottawa!

Factors influencing progress toward ecological speciation: a special issue.

I recently helped Marianne Elias, Rui Faria, and Zach Gompert to edit a special issue on the topic of Ecological Speciation for the International Journal of Ecology. The special issue is now online and is entirely free to download. The issue includes19 papers from many of the leading authors in ecological speciation.

All of the papers in the special issue can viewed here:
http://www.hindawi.com/journals/ijeco/si/213683/

And the entire issue can be downloaded as a single PDF here: http://downloads.hindawi.com/journals/specialissues/213683.pdf

Happy reading.

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Here is a paragraph from our introduction to the special issue that summarizes it's contents. I follow that with a list of the paper titles and authors.

"This special issue on ecological speciation puts snapshots of progress toward speciation sharply in focus and then investigates this topic from several angles. First, several papers provide conceptual or theoretical models for how to consider progress toward ecological speciation (Funk; Heard; Lenormand; Liancourt et al.; Agrawal et al.). Second, several papers highlight the noninevitability of ecological speciation through investigations where ecological speciation seems to be strongly constrained (Räsänen et al.; Bolnick) or at least lacking definitive evidence (Ostevik et al.; Scholl et al.). Some of these papers also uncover specific factors that seem particularly important to ecological speciation, such as the combination of geographic isolation and habitat differences (Surget-Groba et al.), the strength of disruptive selection and assortative mating (Bolnick), and host-plant adaptation (Scholl et al.). Third, several particularly important factors emerge as a common theme across multiple papers, particularly parasites/pollinators (Xu et al.; Karvonen and Seehausen), habitat choice (Webster et al.; Feder et al.; Carling and Thomassen; Egan et al.), and phenotypic plasticity (Fitzpatrick; Vallin and Qvarnström)."

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Ecological Speciation

Guest Editors: Marianne Elias, Rui Faria, Zachariah Gompert, and Andrew Hendry

Factors Influencing Progress toward Ecological Speciation, Marianne Elias, Rui Faria, Zachariah Gompert, and Andrew Hendry
Volume 2012 (2012), Article ID 235010, 7 pages

The Role of Parasitism in Adaptive Radiations—When Might Parasites Promote and When Might They Constrain Ecological Speciation?, Anssi Karvonen and Ole Seehausen
Volume 2012 (2012), Article ID 280169, 20 pages

Parallel Ecological Speciation in Plants?, Katherine L. Ostevik, Brook T. Moyers, Gregory L. Owens, and Loren H. Rieseberg
Volume 2012 (2012), Article ID 939862, 17 pages

From Local Adaptation to Speciation: Specialization and Reinforcement, Thomas Lenormand
Volume 2012 (2012), Article ID 508458, 11 pages

Testing the Role of Habitat Isolation among Ecologically Divergent Gall Wasp Populations, Scott P. Egan, Glen R. Hood, and James R. Ott
Volume 2012 (2012), Article ID 809897, 8 pages

Underappreciated Consequences of Phenotypic Plasticity for Ecological Speciation, Benjamin M. Fitzpatrick
Volume 2012 (2012), Article ID 256017, 12 pages

Ecological Adaptation and Speciation: The Evolutionary Significance of Habitat Avoidance as a Postzygotic Reproductive Barrier to Gene Flow, Jeffrey L. Feder, Scott P. Egan, and Andrew A. Forbes
Volume 2012 (2012), Article ID 456374, 15 pages

Larval Performance in the Context of Ecological Diversification and Speciation in Lycaeides Butterflies, Cynthia F. Scholl, Chris C. Nice, James A. Fordyce, Zachariah Gompert, and Matthew L. Forister
Volume 2012 (2012), Article ID 242154, 13 pages

Divergent Selection and Then What Not: The Conundrum of Missing Reproductive Isolation in Misty Lake and Stream Stickleback, Katja Räsänen, Matthieu Delcourt, Lauren J. Chapman, and Andrew P. Hendry
Volume 2012 (2012), Article ID 902438, 14 pages

How Facilitation May Interfere with Ecological Speciation, P. Liancourt, P. Choler, N. Gross, X. Thibert-Plante, and K. Tielbörger
Volume 2012 (2012), Article ID 725487, 11 pages

Use of Host-Plant Trait Space by Phytophagous Insects during Host-Associated Differentiation: The Gape-and-Pinch Model, Stephen B. Heard
Volume 2012 (2012), Article ID 192345, 15 pages

Habitat Choice and Speciation, Sophie E. Webster, Juan Galindo, John W. Grahame, and Roger K. Butlin
Volume 2012 (2012), Article ID 154686, 12 pages

The Role of Environmental Heterogeneity in Maintaining Reproductive Isolation between Hybridizing Passerina (Aves: Cardinalidae) Buntings, Matthew D. Carling and Henri A. Thomassen
Volume 2012 (2012), Article ID 295463, 11 pages

Pollinator-Driven Speciation in Sexually Deceptive Orchids, Shuqing Xu, Philipp M. Schlüter, and Florian P. Schiestl
Volume 2012 (2012), Article ID 285081, 9 pages

Synergy between Allopatry and Ecology in Population Differentiation and Speciation, Yann Surget-Groba, Helena Johansson, and Roger S. Thorpe
Volume 2012 (2012), Article ID 273413, 10 pages

Of “Host Forms” and Host Races: Terminological Issues in Ecological Speciation, Daniel J. Funk
Volume 2012 (2012), Article ID 506957, 8 pages

Learning the Hard Way: Imprinting Can Enhance Enforced Shifts in Habitat Choice, Niclas Vallin and Anna Qvarnström
Volume 2011 (2011), Article ID 287532, 7 pages

Sympatric Speciation in Threespine Stickleback: Why Not?, Daniel I. Bolnick
Volume 2011 (2011), Article ID 942847, 15 pages

Ecological Divergence and the Origins of Intrinsic Postmating Isolation with Gene Flow, Aneil F. Agrawal, Jeffrey L. Feder, and Patrik Nosil
Volume 2011 (2011), Article ID 435357, 15 pages

Darwin in the genome

(I am posting a press release from McGill related to a paper that has just officially come out.)

A current controversy raging in evolutionary biology is whether adaptation to new environments is the result of many genes, each of relatively small effect, or just a few genes of large effect. A new study published in Molecular Ecology strongly supports the first "many-small" hypothesis. McGill University professor Andrew Hendry, from the Department of Biology and the Redpath Museum, and evolutionary geneticists at Basel University in Switzerland, studied how threespine stickleback fish adapted to lake and stream environments in British Columbia, Canada.

The authors used cutting-edge genomic methods to test for genetic differences at thousands of positions ("loci") scattered across the stickleback genome. Very large genetic differences between lake and stream stickleback were discovered at more than a dozen of these loci, which is considerably more than expected under the alternative "few-large" hypothesis.

By examining four independently evolved lake-stream population pairs, the researchers were further able to show that increasing divergence between the populations involved genetic differences that were larger and present at more and more loci.

As these results were obtained using new high-resolution genetic methods, it is conceivable that previous perceptions of adaptation as being a genetically simple process are simply the result of a bias resulting from previous lower-resolution genomic methods.

"I suspect that as more and more studies use these methods, the tide of opinion will swerve strongly to the view that adaptation is a complex process that involves many genes spread across diverse places in the genome," says Prof. Hendry.

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Source:

Roesti, M., A.P. Hendry, W. Salzburger, and D. Berner. 2012. Genome divergence during evolutionary diversification revealed in replicate lake-stream stickleback population pairs. Molecular Ecology 21:2852-2862. [Cover Article]. Link: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2012.05509.x/abstract

A News and Views about the article:

Nosil, P., and J.L. Feder. 2012. Widespread yet heterogeneous genomic divergence. Molecular Ecology 21:2829-2832. [Perspective]. Link: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2012.05580.x/abstract

Another paper employing SNP genome scans in lake-stream stickleback:

Deagle, B.C., F.C. Jones, Y.F. Chan, D.M. Absher, D.M. Kingsley, and T.E. Reimchen. 2012. Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions. Proceedings of the Royal Society B. Biological Sciences 279 1732 1277-1286. Link: http://rspb.royalsocietypublishing.org/content/279/1732/1277.abstract?sid=cc0e3784-2fc0-41ea-ac1d-a5dd3919d5fd

Carnival of Evolution #48

So, it's Carnival of Evolution time again, and Carnival #48 is up at Pharyngula!  (For more information on the Carnival itself, check out the Carnival of Evolution blog.)

We've got two posts in this Carnival (since we missed the previous edition due to a software glitch).  One piece is by Kiyoko Gotanda, writing about fish, oxygen, and local adaptation.  The other is by Emily Drummond, writing on dandelions, intraspecific genetic diversity, and ecology.  But of course you've read those already, so now you should go enjoy the other posts in the Carnival!

PZ has chosen an Icelandic theme for this month.  I don't have any photos from Iceland, since I've never  been there myself; but here's a photo I took in Yellowstone National Park, which is kind of a mini-Iceland in the middle of the U.S.:

Photo credit: Ben Haller, 2009.

Late-breaking news: my parents were recently in Iceland, so here's a photo they took of Arctic terns in a stiff wind, against a panoramic Icelandic backdrop near Snaefellsness.  No doubt, it being Iceland, the whole scene is about to be engulfed by floods of molten lava.

Photo credit: Helen Haller, 2010.

Team Pinzones IMAX 3D

If you are going to have your research filmed, you might as well go the whole hog: high definition 3D shown in an IMAX theater with Sir David Attenborough narrating. In theory, that is what will happen with Team Pinzones, our hard working and long suffering research team studying the evolution of Darwin’s finches (pinzones). This week I was back in Galapagos with team member Jaime Chaves to recreate our fascinating and exciting procedure for the cameras: setting nets, catching birds, putting on bands, measuring wings, measuring legs, measuring  beaks, measuring heads, photographing, weighing, and releasing (no blood samples this time). It was quite an adventure.

Team Pinzones goes before the (3D) camera. (Photo by Aspen Hendry.)

First, the permits weren’t approved until the very last minute – after the last minute actually. Not only did the film crew (Colossus Productions filming for BBC) need permits to film our work but we also needed permits to speak to them about our work. That achieved the day after we arrived, filming was set to occur in a few days. The next problem, however, was that the filming equipment was delayed – 5 tons of it! Customs in Guayaquil had taken every single part of the equipment and removed it from the packaging and photographed it. This delayed things for a few days but then the equipment was finally shipped – except the batteries, which were deemed hazardous cargo. This battery delay pushed us past the official filming date, and so we had to change our flights by two more days. Having done so, the batteries arrived the next day but one piece was still missing – the base for the crane. Yes, the crane. They needed a crane to film our work. So it came down to one final day for filming before we really needed to leave Galapagos. Would the crane base come in time?

It's not your mother's camera. (Photo by Jaime Chaves.)

Indeed it did, just in time for filming on that last day.  The next worry – for us at least – was that the 3D camera, the crane, and all the other equipment would be so heavy and cumbersome and finnicky that the whole procedure would be very slow. It takes a long time to move the stuff around and they wanted to film several locations along the El Garrapatero beach – itself a decent walk from the parking lot. The equipment was all ferried down the day before and then we all arrived at first light on the filming day. But would there be enough time to film all the bird sequences before it got too hot for the birds – normally about 10 am? The answer normally would be an emphatic no because it generally gets really sunny and baking around that time. But fortune smiled upon us beyond all expectation and it was cloudy and windy all day. The next concern was whether we could catch enough birds at the right times? Sometimes at El Garrapatero, we can go a long time without catching birds and that might be a problem since we didn’t want to hold any individual bird for too long. We started with one net and, within half an hour, we had a male and female fuliginosa (small ground finch), a male and female fortis (medium ground finch), and a female scandens (cactus finch) – each of the species we might reasonably expect to catch here. Let’s start filming.

Getting a finch ready for its close-up. (Photo by Jaime Chaves.)

First we did the close-ups with the huge camera nestled right up next to our hands (I had to bend my neck around the camera to see what I was measuring). At the end of this close-up period, we suggested it would be good to film the large and small beaked morphs of the fortis – the phenomenon we study at this site – but we didn’t have a small morph bird already captured. So we started filming a medium bird alongside a very large one but, as I was holding the birds for the camera, Jaime ran off to see if he could set the net again and catch a smaller bird. Five minutes later he was back with the perfect bird. After that minor miracle the crew needed wider angle shots of the same thing but most of the birds had been held in their bags for an hour already and they should be set free. So we went back to the net, set it again, and had 5 birds of all three species in half an hour. It was almost like we could just “dial a finch” and place our order, having it delivered at a pace that would shame pizza delivery.

Even the banding equipment gets a close-up.

Then it was time for even wider shots – and now the crane would be called into action. We were to walk from the net with birds in their bags to our banding station and the 3D camera would swoop around us presumably giving everyone vertigo in the theater. So we did this a few times for practice and then did the actual sequence. As we sat down on this first take and started to process the birds, we noticed that there were 4 or 5 finches hopping around not 2 meters from where we were processing. “Hey you guys should film those birds,” we said. Yeah right. What are the chances that they could set this complicated camera up on a huge crane, have some birds hop down at random at just the perfect distance, swoop the camera on the crane 180 degrees, and have it plop down in front of the finches without them leaving. Well, not only did that happen but as soon as the camera came near to the birds a bunch more arrived until nine of them were all hopping around right in front of the camera. They filmed this for a minute and then swooped around to show us processing finches right beside the free-flying finches in one continuous sequence. Dial a finch indeed.

Moments before the finches arrived.

Next it was time to film us taking a bird from the net. As we did this, the entire crane was moved about 40 meters to a rock promontory between two patches of sandy beach and reconstituted on a wooden platform that had been constructed just that day as the other filming was going on. This platform was quite substantial because it also had a rail on it so that the entire crane could be rolled along smoothly as it swooped around a cactus and could then be pulled back to show us walking across the beach and then the lava toward our net. We got to watch them practice their crane moves with one "grip" holding the counterweight at one end and swooping it around and the other grip rolling the entire apparatus along the rail. Then we had to go off and perform our walk for the real filming. After that, with the light just petering out, it was time for an interview at yet another location – sitting on some (reasonably comfortable) lava beside the beach. Then 5 tons had to be carried back up to the parking lot. It was a good thing 24 people were involved.

The camera on the crane on the rails on the platform.

This experience taught me several things. First, 3D is much much much more complicated than 2D – the camera is huge and needs to be calibrated before every shot. Second, those shots you see in BBC videos require an immense amount of work – and now I know what a “grip” really does, although I forgot to ask what made one of the grips the “best boy grip” that you often see acknowledged in film credits. Third, film makers may often be unlucky with the elements or animals – as you so often see in the behind-the-scenes stuff for BBC videos – but the opposite can also be true. The weather we had was perfect – beyond perfect. It was literally the best possible weather for working with birds ALL DAY LONG. And the birds were incredibly accommodating. With a single net we could catch exactly what we wanted within 15 minutes at any time of the day, which is definitely not typical. And then a whole gaggle of finches shows up right in the perfect place for the camera already on a crane. I am pretty sure the film makers don’t realize how incredibly lucky we all were. And maybe those extra birds we captured and measured will be the ones that make all our statistical tests significant.

Now we just have to wait a year  or so to see how it looks in IMAX 3D with narration by you know who (of course, our stuff will be only a tiny fraction of the entire movie). In the meantime, we need to interest someone in Team Stickleback IMAX 3D and Team Guppy IMAX 3D.

Note: Special thanks to key recent Team Pinzones members Jeff Podos, Luis Fernando De Leon, and Joost Raeymaekers.

Black Out Speak Out

Today, our blog joins the Black Out Speak Out movement to protest the Canadian government's Bill C-38 which would severely cripple many of Canada's important environmental laws. For more information about what the bill will do, more information is here.

For more information, please visit Black Out Speak Out