Friday, January 31, 2014

‘Experimental genomics’ reveals selection’s role in genome evolution

[ I am posting this on behalf of the authors, Zach Gompert and Patrik Nosil.  -B. ]

Biologists agree that natural selection is the mechanism responsible for adaptation. In contrast, debates persist about the relative contributions of selection, randomness, and historical contingency to molecular evolution and biological diversification. The context of this debate has shifted some in recent years with an increased emphasis on genetic drift in declining populations, contemporary natural selection, and evolution on ecological time scales. An understanding of recent and short-term evolution is of course important if we hope to predict or alter how populations will respond to rapid global change. These issues prompted us to think about how one might experimentally measure genetic drift and natural selection over short time scales. We were particularly interested in the genomic consequences of these processes, in other words, how much of the genome is affected by selection in a given generation and how much might drift alter allele frequencies across the genome.

Our study was catalyzed by conversations between Patrik and Jeff Feder in the dark bars of Berlin, Germany (in 2008 and 2009) concerning their growing dissatisfaction with inferring evolutionary process based solely on patterns of genomic variation. These discussions led to the idea that natural selection and drift could be measured directly by combining a field transplant experiment with genome-wide DNA sequencing of the organisms involved in the experiment.

Trying to figure out how to measure selection directly at the genomic level, circa 2009, in Berlin, Germany.

We quickly decided on a species of stick insect (Timema cristinae) as an ideal focal species for our experimental genomics study. This was driven in part by the natural history of this species – host specialization and low dispersal ability allow for ecologically relevant mark-recapture studies – but also in part by it being the main system Patrik knows how to work with. In terms of natural history, two specialized ecotypes of this species have evolved and are adapted to different host plant species: Adenostoma fasciculatum (a small, shrubby Rose) and Ceanothus spinosus (a larger, tree-like Buckthorn). These ecotypes differ in several ways, with the most obvious difference being the presence versus absence of a highly heritable white dorsal stripe, distinguishing the ‘green striped’ and ‘green unstriped’ morphs (see this earlier post by Tim Farkas). Striped individuals are better camouflaged and suffer less predation on Adenostoma whereas green individuals are better camouflaged on Ceanothus. Thus, we would expect stick insects transplanted from their native host plant to the alternative host to experience stronger effects of natural selection (higher rates of mortality due to selection) that would affect more of the genome, compared to insects transplanted to their native host.

Patrik and his students set off for southern California in 2011 to test this prediction (with Patrik feeling more lucid and healthy, and less of an ‘urban biologist’, than the year in Berlin). Our basic plan was to collect hundreds of stick insects, move them to experimental Adenostoma and Ceanothus bushes, and measure evolutionary (i.e., allele frequency) change across the genome caused by mortality of the transplanted stick insects over about a week's time. A key difficulty with this design was that we needed to be able to match the DNA of the stick insects we released with those that were recaptured at the end of the experiment, so that we would know the genotypes of both the founders and the subset of them that survived. We considered several possibilities, including raising the founders in the lab to collect DNA from their feces or discarded exoskeletons. In fact, this was attempted, but the DNA quantity and quality was poor. So, we finally decided to simply remove a portion of a leg from each stick insect before its release. With that the field experiment was underway and 500 stick insects were captured, had their tissue sampled, were released to the wild, and then the subset (140 to be exact) of them that survived were recaptured. The tissues from the survivors and all the initial founding individuals were then ground up for next-generation DNA sequencing.

The design of the transplant experiment used to measure the effects of selection and drift on genomic change within a generation.

We were rewarded a few months later with hundreds of millions of DNA sequences. Zach and his colleagues (primarily Alex Buerkle and Tom Parchman) then went to work processing and trying to make sense of the sequence data. This required assembling sequences to an early draft of the Timema genome, trying to match stick insect legs with bodies based on the sequence data, and developing the computational statistical methods to analyze the contributions of genetic drift and natural selection to evolutionary change during the experiment. After months of analyses we finally had some answers to our questions and wrote an initial draft of the paper. Thus began the biggest trials and tribulations we experienced over the course of this study.

Time and time again it seemed as though reviewers did not appreciate or accept our results and our paper was turned down at journal after journal. The key problem was that our findings were multifaceted, complicated, and nuanced and we didn't really know how to effectively communicate them to our readers. While tiring at times, this experience taught us that as data and analyses continue to grow in complexity it will become ever more important to present and frame scientific results in a manner that allows readers to see the connections and key results that we have identified, while at the same time embracing the complexity that might often simply represent biological reality. We learned from our initial mistakes and were able to close the paper with what is a new record for us: “We thank... 10 anonymous reviewers for comments on previous versions of the manuscript” (the paper is Open Access at Ecology Letters).

So, besides how to be better communicators, what did we learn from our study? First, we came to grips with the importance of both direct and indirect selection as drivers of genomic change. Phenotypic selection is transmitted to causal genetic variants that affect fitness (this is direct selection) and to additional genetic loci correlated with these functional variants (this is indirect selection). This distinction has long been emphasized at the phenotypic level, but has been mostly thought of only for tightly linked genes at the genetic level. But statistical correlations are not restricted to physically linked loci (in fact, in our study over 97% of loci were most correlated with distant genetic loci), and given the enormous number of variable genetic loci in genomes the opportunities for correlations and indirect selection are vast. This simple fact means that it will be incredibly difficult to catalog the targets of direct selection. But we can readily estimate total selection experienced by a locus, which is the driver of evolutionary change anyway (particularly over short time scales). Along these lines, we found evidence that hundreds of loci were affected by potentially strong host-associated selection, particularly when stick insects were moved from their native host plant to the novel one.

Thus, we detected host plant-associated selection with stronger effects of selection on novel host plants. This natural selection was caused in part by variation in the stripe phenotype, but that wasn’t the whole story. In fact, the genetic loci that were most likely affected by host plant-specific selection were not associated with the stripe phenotype. Moreover, we uncovered genomic evidence that the strength of the effect of selection varied with the elevation of the experimental populations. We think that this nicely demonstrates how genomic analyses can help identify previously underappreciated sources or targets of selection.

Finally, whereas we documented rapid and detectable genomic change from natural selection, this was not the sole or even main source of genomic change. Genetic drift was rampant during the eight day experiment. Thus, neutral divergence between the founders and survivors over eight days was similar in magnitude to the genetic differences among natural T. cristinae populations. We think this really highlights how rapidly evolution can occur (by selection and drift), particularly in small populations that move into new environments (our founder populations began with 50 individuals). These conditions might be common when species ranges shift or are fragmented.

The paper:

Gompert, Z., A.A. Comeault, T.E. Farkas, J.L. Feder, T.L. Parchman, C. A. Buerkle, and P. Nosil. (2014). Experimental evidence for ecological selection on genome variation in the wild. Ecology Letters 17(3), 369–379. DOI: 10.1111/ele.12238

Thursday, January 23, 2014

Future Earth is a singles bar

It began at a restaurant. Six of us were halfway through dinner and were discussing climate change and biodiversity. I was trying to argue that one of the key things we need to know about organisms in a changing world is their movement ability. This realization starts from the fact that changing environments are expected to render organisms poorly suited for their current locations, which could cause population declines, extirpation, and extinction. It continues with the recognition that a potential solution to this problem is for organisms to simply move from their current “bad” location to a new “good” location. Indeed, past climate change is known to have caused massive changes in the geographical distributions of species. In the context of current climate change, then, we really need to know the ability of organisms to move to new places (including through seed dispersal). Of course, not all organisms will be able to move at the same rate and so we will end up with new mixed-up communities that vary from place to place, with some species in some places encountering species with which they have no previous experience – generating what are sometimes called “non-analog communities.” Immediately prior to this discussion about organisms moving with climate change, we had been talking about how “species” are rather porous entities – for instance, I argued (without any quantitative data) that most species hybridize successfully in nature with at least one other species. Then, nimbly linking these two ideas (non-analog communities and promiscuous species), Alan Mix observed: “So what you are saying is that climate change is a singles bar.”

Indeed. Climate change is a singles bar! What a cool phrase – I will have to use that in a blog post, I thought. The trouble was that I had just done a post about climate change and I didn’t want to be too obviously repetitive. Fortunately, I soon realized that the climate change as a singles bar metaphor extended to the entire endeavor in which we were engaged.

We were all in Washington, DC, at the first-ever meeting of all the core projects that are joining the new uber-NGO Future Earth. In the past, these core projects were divided amongst a number of independent environmental and sustainability NGOs, such as DIVERSITAS, IGBP (International Geosphere-Biosphere Programme), IHDP (International Human Dimension Programme on Global Environmental Change), WCRP (World Climate Research Programme), and ESSP (Earth System Science Partnership). Governments and their national funding agencies, such as NSF and NERC, had been supporting these programs separately and had decided this was inefficient and that these “global change” NGOs should unite into one uber-NGO (Future Earth), which they would then fund. This meant that all of the 20+ individual core projects of the original NGOs would need to transition to Future Earth while their original parent organizations went extinct. For DIVERSITAS, the NGO with which I am associated, this included projects such as bioGENESIS, bioDISCOVERY, ecoSERVICES, ecoHealth, freshwaterBIODIVERSITY, and the Global Mountain Biodiversity Assessment.

Me spotting the world's largest Darwin's finch - on the wall at the Keck Centre, where the meeting was held. Photo by Dan Faith.
Quite understandably, each of the core projects from each of the NGOs was quite concerned about what would happen to them and their initiatives under the new governance and funding structure of Future Earth. The Washington meeting was intended to get all of these projects together for the first time (definitely a non-analog NGO community!) to interact with each other and with Future Earth. Two important themes were emphasized regarding how we should proceed in the future. First, different core projects were expected to work jointly toward shared goals and, second, projects within Future Earth should be “co-designed” with stakeholders, such as industry, governments, and other NGOs.

To facilitate this melting pot, the moderator immediately had us rotating among tables so as to meet as many people from as many projects as possible – partly to consider who might be profitable partners for endeavors with Future Earth. It was singles bar for core projects – and it could come with a payoff! In particular, Future Earth had recently secured a million dollars to fund approximately 10 Fast Track Initiatives that would bring the core projects together to develop initiatives that embraced the above ideals. 

After our initial singles bar experience, we were encouraged to quickly propose projects to the entire group and then break out onto different tables where interested individuals/projects could discuss the development of joint proposals. But not too long for any one table/proposal – we soon had to rotate to a new table and project. So the singles bar had morphed into a speed-dating game – but we didn’t have to pick only one core project to date. We were encouraged to be promiscuous!

It ended at a bar – a real one this time. On the last night, a group of us were talking about how several social scientists had (during the speed dating round) been listening to discussions about a particular proposal by natural scientists: a global georeferenced database of organismal traits. The social scientists were struck by how we seemed to have designed a proposal that allowed no room for social scientists. So they – partly in fun – went to another table and came up with a social science project that seemed to have no room for natural scientists. And yet here we now were on the last night together at the same table in the same bar: some natural scientists who had (obliviously) spurned social scientists who had then (intentionally) spurned them back. But it all had a happy ending – we spent the next hour figuring out how the spatial trait database could be integrated with a spatial human behavior database to simultaneously better predict both human endeavors and biodiversity. Singles bar becomes speed-dating game becomes swinger’s club.

It was a very interesting experience. I was introduced to several nice single core projects, became convinced during the speed dating round to set up future dates with several of them, and happily helped to form a swinger’s club. To increase the fun at our next meeting, let’s bring even more of our friends, and a bunch of stakeholders too. I can already think of a great analogy.

Sunday, January 19, 2014

Wine and World Leaders I: Dinner with the Clintons

For five or so years, I have been part of the bioGENESIS core project of the NGO DIVERSITAS. DIVERSITAS "is an international research programme aiming at integrating biodiversity science for human well-being." Within DIVERSITAS, the specific goal of bioGENESIS is to provide an evolutionary framework for biodiversity science. DIVERSITAS is soon ending as an independent identity and its core projects (as well as those of other NGOs) are transitioning to the new uber-NGO Future Earth

I just arrived a few hours ago in Washington, DC, for a meeting of Future Earth and the many projects that are joining it. I couldn't help but remember that last time I traveled to DC, which was also under the auspices of bioGENESIS. I had quite a strange experience at the time that, in combination with another experience soon thereafter, spurred me to write a narrative called "Wine and World Leaders." I will here provide the first part of that story and give the second part in a later  post. 


Feb. 12, 2009, was Darwin’s 200th birthday and the year of the 150th anniversary of the publication of his On the Origin of Species. It was also Abe Lincoln’s 200th birthday - wonderful coincidence, perhaps, or maybe cosmic convergence. Either birthday would have been a great occasion to visit Washington DC – and many folks were doing so for Abe – but I was there for Darwin. The occasion was a National Academy of Sciences symposium, organized by the NGO DIVERSITAS, and held at the theater of the American Association for the Advancement of Science. The title of the symposium was Twenty-first Century Ecosystems: Systemic Risk and the Public Good – but, really, it was a celebration of Darwin’s birthday in hopes of influencing government policy with respect to biodiversity conservation. My purpose was to talk about how rapid evolution was occurring all around us at all times and therefore needed to be considered in conservation planning. 

I left  home in Napa, CA, where I was on sabbatical, for the San Francisco Airport on a shuttle – Evan’s Airport Express. I had deliberated the night before as to whether or not I should bring some wine. Now that we were living on the vineyard, I could bring wine wherever I went, but I had no specific plan for it in DC. I could always come up with a reason, I thought, and so I put a couple of bottles in the bag. The shuttle schedule was a bit awkward and so I got to the airport a few hours early and checked my bag – because of the wine. If I hadn’t brought the wine, I would have just carried my small bag onto the plane. Instead, the small act of bringing two bottles of Hendry wine  started a series of coincidences that, for me at least, rivaled those of Abe L. and Chuck D. taking their first breaths a few hours apart. Well, maybe not, but the concurrence of events was still amazing.

 Passing through security, I noticed that there were several earlier flights to DC. I went to the gate agent and asked if I could get on this earlier flight. “Certainly” she said, “as long as you didn’t check any bags.” Oh well – damn wine. With several hours to spare, I got out my computer, plugged it into the wall outlet in the airport and started working. After the plane boarded, I worked on my computer almost all the way to DC. Arriving in DC., I checked into my hotel (Palomar) and got out my computer to check email. Noticing I was very low on batteries, I dug in my pack for my power cord. Oops – it was still plugged into an outlet in the San Francisco Airport. Damn it – and I did actually NEED computer power. I spent the next hour or so calling various electronic supply companies (Radio Shack, etc.) to see if they had a power cord. Strangely, all were open (at least according to their phone menu) but wouldn’t answer their phones - bizarre.

So what was I to do now? I figured why not walk down to the hotel restaurant and see if any other folks from my symposium were there – something I probably wouldn't have done if my computer still had power. I walked into the hotel restaurant and looked around for my colleagues. The first person I set my eyes on looked exactly like Hillary Clinton – amazingly so, but I quickly averted my eyes in awkwardness. I continued round the restaurant thinking, “Could that really have been Hillary. I know this is DC but really, what are the chances?” None of my colleagues were in the restaurant so I took another swing back around the restaurant to see if it really was her. This time I saw who she was with – a guy who looked exactly like Bill Clinton. Oh s**t! It really was them.

Shocked by how normal the whole situation seemed, I walked back to the hostess and said, “You know, I think I will have dinner here tonight.” She seemed to know what I was thinking and smiled. I continued, “Do you have table with a view of the Clintons?” She laughed and said she had several and wondered if I would like to evaluate the sight lines. I said I would, and we picked a table that was one table away from Bill and Hillary, with reasonable gaps between the tables, and me sitting facing them. Cool. “Is this typical,” I asked, “having sitting Secretaries of State and former Presidents stop by for dinner?” “Not really,” she responded, “but Ted Danson comes here frequently.” Huh? I hadn’t even notice that Bill and Hillary were having dinner with a guy in a toupee who played a bartender on TV – along with his lady friend.

For the next hour, Bill and Hillary (and Ted) and I shared a waiter, a water pitcher, and the air we were breathing. I bonded a bit with the waiter, who introduced me to some nice beers, and we talked a bit about the absurdity of it all. “I am just trying not to pee my pants,” was his  observation. “Well, they’re having dinner with Ted Danson,” I said, “it isn’t like they are talking about foreign policy.” “Oh they are, actually,” he said. It is amazing who has the ear of the Secretary of State of the most powerful country in the world.

It was a fun time. Hillary and I exchanged glances a few times – perhaps I occupied the thoughts of the Secretary of State for a few seconds. Hillary laughed raucously. Bill smiled that irascible smile and drawled that down-home southern drawl that won the hearts of voters and interns. And the Secret Service was nowhere in sight – until the Clintons stood up to leave, that is. And then it was over. I bonded with the waiter some more, brought him some Hendry wine, and stopped by the next night to drink it with the wait staff. Too bad I couldn’t get some wine into the hands of the Clintons. But the cool thing was that NOBODY disturbed them – standard etiquette in DC, I guess – or maybe the Secret Service would have materialized and tackled anyone who tried.

So, if I hadn’t brought Hendry wine, I wouldn’t have taken my scheduled flight, and so I wouldn’t have used my computer in the airport, and so I wouldn’t have left my power cord behind, and so I wouldn’t have ended up in the restaurant to have dinner “with” the Clintons.

Dinner the next night was in the biodiversity gallery of the Smithsonian.

Other posts about my experiences with bioGENESIS:

Wednesday, January 15, 2014

Climate change and evolution - or not?

The world is changing at an unprecedented rate. This change renders populations (and sometimes entire species) maladapted for the new conditions. This maladaptation can decrease fitness, which can cause population declines, extirpation, and extinction. The world is going to hell in a hand-basket.

Populations can arrest their declines and thereby prevent extirpation through changes that better match their phenotypes for the new conditions. These changes might be most easily achieved by moving to a better location: if it is getting too warm, simply move to a colder place. Indeed, changes in geographic ranges are a common feature of species’ responses to climate change in Earths past and present. In many instances, however, such movement is not possible, such as when barriers hinder movement between locations or when organisms have restricted movements, such as in plants with limited seed dispersal.

When organisms cannot move to better locations, they must alter their phenotypes in situ to better suit the new conditions. Perhaps the easiest way to do so is through phenotypic plasticity, where changing environmental conditions induce new adaptive phenotypes without evolution. Indeed, many instances are known of induced changes in traits, such as breeding time, that better suit organisms for altered conditions. Plasticity is not a panacea, however, because it has limits and costs. Sustainability in the face of environmental change will therefore often also require evolutionary change.

Populations and species currently found in different environments clearly have traits that are well suited for (adapted to) those different conditions – as extremes, think of Emperor penguins in the Antarctic (and Galapagos!) and camels in the Sahara (and Mongolia!). Evolution can thus accomplish a remarkable diversity of adaptations to different climates. These existing differences, however, usually evolved over very long time frames, whereas current climate change is occurring much faster. For this reason, the classic perception has been that evolution will not have a noteworthy ability to rescue populations that are otherwise likely to be extirpated under rapid climate change.

This classic expectation of the separation of ecological and evolutionary time began to wane with the publication of a number of instances where organisms were seen to have evolved on very short time scales, variously called “contemporary evolution,” “evolution on ecological time scales,” or “rapid evolution.” I was involved in the early stages of this realization through my own empirical work on introduced salmon and through several review papers that I wrote with Mike Kinnison and others (1999, 2001, 2003, 2008). Tantalizingly, a number of the emerging examples of contemporary evolution seemed related to climate change. And thus, a solution to climate change seemed to have emerged (evolution to the rescue!), with a large number of review papers beginning to tout this possibility. Moreover, many examples of phenotypic change were appearing in the literature and evolution was often advanced as a likely cause. Problem solved.

A compilation of images of some of the species shown to have evolved on short time scales in response to environmental change.
Or not. Examining the published work, Juha Merilä (and others) came to the conclusion that very few studies had employed methodologies sufficient for revealing evolutionary response – and, of the few studies that had used robust methods, most found no evolutionary change. Annoyed by the seemingly lax standards in the literature, Juha wrote several papers (20082012arguing that evolution in response to climate change was rare – or at best, still largely undocumented.

At an Evolutionary Applications editorial board meeting at the European Society for Evolutionary Biology in 2011, Juha and I got into a spirited argument about climate change and evolution. Juha argued that it had not been demonstrated. I argued that, while this might well be so, evolution is almost certainly occurring given many examples of contemporary evolution in response to local environmental change. What we could both agree on was that a serious appraisal of the methodology and literature had not been attempted and was sorely needed. Given the venue for our argument, the solution was right at hand: Juha and I should write a perspective piece on the problem for Evolutionary Applications and use this article as a springboard for a special issue – which has just been published.

In the perspective that opens the special issue, Juha and I critically evaluate the different methods for inferring (1) evolution versus plastic responses to environmental change, (2) whether any such changes are adaptive or not, and (3) whether changes are specifically the result of climate change (as opposed to some other environmental factor). After drafting the perspective, we sent it to experts on the topic in particular taxa (plants, fish, birds, mammals, amphibians and reptiles, terrestrial invertebrates, freshwater invertebrates, marine animals and plants, marine phytoplankton) and encouraged them to write review papers evaluating published examples of phenotypic change for the strength of evidence relating to the above three topics. In addition, we asked other experts for a review of Bergmanns Rule (larger body size at higher latitudes) in the context of climate change and of theoretical models of evolution (and plasticity) under environmental change.

Although the individual papers (see below) should be consulted for details, a few key points can be summarized here:

1. A diversity of methods exist for assessing evolutionary and plastic responses to climate change. These methods vary in the strength of inferences they provide. Some of the best methods include “animal models,” common-garden experiments, and reciprocal transplants.

2. Many studies have documented phenotypic changes associated with climate change. In the vast majority of such cases, strong inferential methods have not been employed, and so the relative contributions of evolution and plasticity are unknown. In such cases, neither plasticity nor evolution should be considered a “null” model – that is, both remain in play until appropriate methods are implemented.

3. Studies of at least 26 species have employed strong inferential methods to test for evolutionary responses to climate change. Studies of birds and mammals – often using “animal model” approaches – usually do not find evolutionary responses. Studies of plants and insects – often using common-garden approaches – usually do find evolutionary responses.

4. Evolution clearly occurs in response to climate change. Plasticity also plays a role in many instances. For the vast majority of cases, however, inferential methods are as yet insufficient to conclude the relative contributions of these two types of response.

Red squirrels – a mammal that has evolved in response to climate change (although even this example is controversial). Photo: Andrew P. Hendry.
“To sum up, this perspective and the accompanying eleven articles have focused on methods and quality of evidence for genetic and phenotypic changes in response to climate change in nature. While the current picture emerging from all of this work might not seem particularly encouraging, it should provide guidelines, avenues, and inspiration for research to come. Identification of the challenges and knowledge gaps can be viewed as a first step toward progress in improving our understanding of the relative roles of genetic change and plasticity in mediating adaptive organismal responses to changing climatic conditions.” (From the concluding paragraph.)

Pink salmon - a fish that has evolved in response to climate change. Photo: Andrew P. Hendry
The Evolutionary Applications special issue:

Juha Merilä and Andrew P. Hendry.

Anne Charmantier and Phillip Gienapp

Stan Boutin and Jeffrey E. Lane

Robby Stoks, Aurora N. Geerts and Luc De Meester

Menno Schilthuizen and Vanessa Kellermann

Lisa G. Crozier and Jeffrey A. Hutchings

Mark C. Urban, Jonathan L. Richardson and Nicole A. Freidenfelds

Thorsten B. H. Reusch

Steven J. Franks, Jennifer J. Weber and Sally N. Aitken

Sinéad Collins, Björn Rost and Tatiana A. Rynearson

Celine Teplitsky and Virginie Millien

Michael Kopp and Sebastian Matuszewski

Friday, January 3, 2014

Carnival of Evolution #67

The latest Carnival of Evolution (#67) is up!  Our main contribution is Steven Brady’s recent post on wood frogs and misfit toys; check it out if you haven’t already, it’s both entertaining and fascinating.  We also contributed Andrew’s post on Epic Wrap Battles of Christmas; don’t miss the photo at the end, of Andrew’s latest hairstyle (if that is the proper word for what he has done to his hair)!

As usual, the Carnival has lots of other interesting posts in it, too.  This month’s Carnival celebrates Alfred Russel Wallace, co-discoverer of evolution by natural selection.  Although the end of 2013 marks the end of the centennial of Wallace’s death, I hope that doesn’t mean the world will forget about him until 2023, which will be the bicentennial of his birth!

Alfred Russel Wallace, whose beard rivalled Charles Darwin’s.

A 25-year quest for the Holy Grail of evolutionary biology

When I started my postdoc in 1998, I think it is safe to say that the Holy Grail (or maybe Rosetta Stone) for many evolutionary biologists w...