Monday, June 30, 2014

A polymorphism persists in panmixia despite unfit heterozygotes

Discovering the genes that underlie phenotypic variation within species is increasingly common, but figuring out how they respond to natural selection is a major challenge. Stickleback researchers have been particularly successful at identifying genes or genomic regions of major phenotypic effect. The Pitx1 gene, for example, is known to influence pelvic girdle and spine development. QTL studies have revealed genomic regions underlying variation in phenotypes ranging from juvenile growth rate, gill rakers, pigmentation, schooling, and sensory systems. The Ectodysplasin gene (Eda) is particularly interesting, because of its strong effect on the number of bony lateral plates in stickleback (Colosimo et al. 2004). Multiple freshwater stickleback populations have a reduced number and/or size of lateral plates relative to their marine ancestors, suggesting that natural selection has repeatedly acted on Eda following the colonization of freshwaters by stickleback.

Stickleback plate morphs found in Kennedy Lake (Marchinko and Schluter 2007), where the partial morph is surprisingly rare (Marchinko et al. 2014).

Over a decade has passed since the discovery of Eda, and numerous speculative hypotheses have emerged about what selective forces affect Eda to control armor plate evolution in wild stickleback populations. In 2008, Barrett and colleagues did a selection experiment with the aim of observing how colonization of freshwater could drive phenotypic evolution of stickleback armor (Barrett et al. 2008). They introduced marine stickleback, heterozygous at the Eda locus, into freshwater ponds and found strong positive selection for the low-plated Eda allele. As predicted, the low-plated phenotypes had a fitness advantage once lateral plates had developed, possibly due to enhanced growth in freshwater environments (Marchinko and Schluter 2007). However, in early life stages (prior to plate development) selection favored the high-armor (“complete”) allele, suggesting that the strength and direction of selection varied among life stages. They concluded that Eda was potentially having either direct or epistatic effects on other phenotypic traits affecting fitness. As simple as this experiment was, it revealed considerable complexities about how natural selection drives phenotypic evolution, even when the phenotype has a relatively simple genetic basis.

Prior to this experiment, Marchinko and colleagues had begun to investigate a polymorphism in body armor of a population of stickleback in Kennedy Lake on Vancouver Island. Plate polymorphisms are not unique to Kennedy Lake, but in the Pacific basin it is relatively uncommon to have a high frequency of both completely plated and low-plated individuals. Typically, freshwater populations are either low-plated or fully plated. In some cases, a polymorphism is present transiently, as the frequency of plates changes over time in response to changing selection pressures (Kitano et al. 2008). In Kennedy Lake, however, this plate polymorphism has been stable since at least 1965.

Typically, polymorphisms are thought to be maintained either by heterozygote advantage (when the fitness of Aa is higher than that of both AA and aa genotypes), or more commonly by spatially varying selection (whereby each of AA and aa have highest fitness in different parts of the population). In contrast, population genetic theory indicates that a polymorphism is highly unlikely to persist when heterozygotes have a disadvantage (when the fitness of Aa is lower than AA or aa). This is because in the absence of assortative mating, a higher fraction of copies of whichever allele is rarest (A or a) end up in low-fitness heterozygotes. Selection is expected to drive the common allele to a frequency of p = 1, eliminating the polymorphism. With the discovery of Eda’s effects on lateral plates, the Kennedy population became an attractive system to test the role of natural selection in maintaining a polymorphism.

The first hint that something interesting was going on in the Kennedy Lake stickleback population came from our first sampling campaign in 2004. We found that the vast majority of individuals were low-plated or completely plated, whereas intermediates were scarce. Low-plated and completely plated morphs differed both in their morphology (head shape) and stable isotopes (reflecting diet/habitat choice). The results were difficult to interpret, as we had no strong a priori prediction about how diet or morphology might differ between the morphs.

Sampling Kennedy Lake

The story became much more interesting when we started genotyping. Over multiple years of sampling the adults in the population, we repeatedly found a deficit of Eda heterozygotes that was not associated with population structure. This indicated that the polymorphism was unlikely to result from either heterozygote advantage or gene flow between locally adapted populations. Maybe assortative mating could explain the heterozygote deficit? Not so. We raided egg clutches from stickleback nests and found they were in Hardy-Weinberg equilibrium.

Really?!? No assortative mating?

Without evidence for assortative mating, the most likely explanation was that every year disruptive natural selection regenerated the heterozygote deficiency in the adult population. We estimated that heterozygotes were 20–30% less fit than individuals with the fully plated homozygous genotype, and up to 80% less fit than the low-plated homozygous genotype. The low fitness of the heterozygotes has been observed only once before, in a previously published experiment by Zeller et al. (2012). The superior fitness of the low-plated homozygous genotype was consistent with an observed growth advantage of this genotype in a previous study (Marchinko and Schluter 2007).

At this point we had some nice patterns from a single stickleback population, but why is this interesting to non-stickleback folk? First, evidence for stable genetic polymorphisms with heterozygote disadvantage are extremely rare, even though theory suggests that they might arise under a wide range of ecological conditions. Second, the polymorphism appears to be maintained under a seemingly worst-case scenario. As we described above, maintenance of a polymorphism with heterozygote disadvantage is theoretically difficult. However, the solution might be frequency-dependent selection: each allele might have an advantage overall as it becomes rare. Third, such a polymorphism can lead to a wide range of evolutionary outcomes, including the evolution of dominance, assortative mating (and possibly sympatric speciation), or the loss of the polymorphism. Although the specific outcome is difficult to predict, Kennedy Lake sticklebacks are well suited for studying how frequency-dependent selection can maintain genetic and phenotypic diversity within a population.

Kennedy Lake is the largest lake on Vancouver Island, and definitely worth a visit.

Our study also adds another chapter to the Eda story. The mere existence of the stable polymorphism means that fully plated and low-plated populations are not the only options. However, we still know very little about the agents of selection that affect Eda in natural populations, and so we can only speculate about the forces driving disruptive selection (and rare-allele advantage, if it exists) in the Kennedy Lake population. Hopefully our study has exposed our ignorance and will inspire further experimental tests and new comparative studies of polymorphic stickleback populations.

Cited work

Barrett, R. D. H., Rogers, S. M., & Schluter, D. (2008). Natural selection on a major armor gene in threespine stickleback. Science, 322(5899), 255–257. doi:10.1126/science.1159978

Colosimo, P. F., Peichel, C. L., Nereng, K., Blackman, B. K., Shapiro, M. D., Schluter, D., & Kingsley, D. M. (2004). The Genetic Architecture of Parallel Armor Plate Reduction in Threespine Sticklebacks. PLoS Biology, 2(5), e109. doi:10.1371/journal.pbio.0020109

Kitano, J., Bolnick, D. I., Beauchamp, D. A., Mazur, M. M., Mori, S., Nakano, T., & Peichel, C. L. (2008). Reverse Evolution of Armor Plates in the Threespine Stickleback. Current Biology, 18(10), 769–774. doi:10.1016/j.cub.2008.04.027

Marchinko, K. B., & Schluter, D. (2007). Parallel evolution by correlated response: lateral plate reduction in threespine stickleback. Evolution, 61(5), 1084–1090. doi:10.1111/j.1558-5646.2007.00103.x

Marchinko, K. B., Matthews, B., Arnegard, M. E., Rogers, S. M., & Schluter, D. (2014). Maintenance of a Genetic Polymorphism with Disruptive Natural Selection in Stickleback. Current Biology, 1–4. doi:10.1016/j.cub.2014.04.026

Zeller, M., Lucek, K., Haesler, M., Seehausen, O., & Sivasundar, A. (2012). Little evidence for a selective advantage of armour-reduced threespined stickleback individuals in an invertebrate predation experiment. Evolutionary Ecology, 26(6), 1293–1309. doi:10.1007/s10682-012-9566-2

Tuesday, June 24, 2014

Add it up: the genetic basis of ecological adaptation

[This post is by Katie Peichel. I am just putting it up.]

What are the genetic and genomic changes that underlie adaptation to divergent environments? How do these changes lead to the formation of new species? These two questions have driven my research for the past 15 years - and it’s been an exciting time to be asking them! The field of evolutionary genetics has begun to make great progress in identifying specific genetic changes that underlie phenotypes thought to be important for adaptation to particular environments. Yet there usually isn’t just one "magic" phenotype important for adaptation to a complex environment, and many different phenotypes need to work together for an organism to be successful in a new environment. Importantly, we still don’t have a clear idea of how the genetic changes that underlie specific phenotypes contribute to whole-organism performance or fitness in a particular environment. Also, we know very little about how these genetic changes lead to the evolution of reproductive isolation between species that have adapted to divergent environments.

To address these questions, I have had the good fortune to work with Matt Arnegard and Dolph Schluter on the benthic-limnetic stickleback species pairs – the poster children for the study of ecological speciation. These two species have evolved within the past 12,000 years as a consequence of adaptation to divergent trophic habitats. First discovered and characterized by Don McPhail (University of British Columbia - UBC), the benthic-limnetic species pairs have independently evolved in several lakes in British Columbia, including Paxton Lake on Texada Island. A body of work by Dolph and his group has led to our understanding of the ecological factors that have driven divergence between the species and of the isolating barriers that maintain them in the face of gene flow.

Dolph Schluter explaining his quest to understand the origin of species using the benthic-limnetic species pairs at the Texada Island Stickleback meeting in 2010.

Matt, Dolph and I decided to investigate the genetic basis of the traits responsible for adaptation to the two trophic niches (benthic and limnetic) found in Paxton Lake, as well as the traits that contribute to reproductive isolation. Many of these traits, such as foraging naturally on different food resources, female mate preference, or male nest site preference are either difficult or impossible to measure in the laboratory. Thus, we took advantage of Dolph’s amazing new pond facility at UBC. These ponds were established in 2008, and we conducted the first experiments in this new facility. Matt worked hard to establish the environments in these ponds using material from Paxton Lake, and multiple lines of evidence suggest that they approximate the two habitats found within the lake.

Photo of experimental pond 4 at UBC in fall 2008, when we collected the F2 juveniles used in our study. The pond has both a benthic habitat (shallow littoral zone) and a limnetic habitat (deep open-water zone), approximating the two environments present within Paxton Lake. (Figure from Arnegard et al. 2014)

We designed a novel approach that would allow us to uncover the genetic basis of whole-organism feeding performance in the contrasting habitats. To do so, we first made F1 hybrids between Paxton benthics and limnetics in the lab. In the spring of 2008, we put 40 of these F1s into one pond (pond 4) and allowed them to mate freely. The F2 intercross population that resulted thus spent their entire lives in the pond, where they were free to choose their habitat and diet. We collected 633 F2s as juveniles in the fall of 2008, when we measured the consequences of these choices on the performance of the fish, measured as body size. In addition, we measured the diet of the F2s using both stable isotope analyses and gut contents, with help from Blake Matthews (EAWAG). We also measured the morphological traits that are expected to contribute to performance in the two trophic habitats, including functional morphological traits that Matt McGee (UC Davis) has shown to be important for prey capture and retention in the benthics and limnetics.

Matt Arnegard and Katie Peichel looking for the Paxton benthic-limnetic F1 hybrids in spring 2008, just after 40 F1s were released into pond 4. These F1s mated freely to create the large F2 population used for genetic mapping in our study.

Amazingly, we found strong evidence for a performance landscape within the pond! When we mapped body size of the F2s onto their position in stable isotope space, we found two peaks of F2s with large body size, separated by a saddle of F2s with smaller body size, as well as a valley of F2s with very small body size. One group of large F2s (group B) was eating mostly benthic resources and had more benthic-like functional morphology, whereas the other group of large F2s (group L) was eating mostly limnetic resources and had more limnetic-like functional morphology. The F2s with smaller body size were intermediate in both diet and morphology. The really small F2s (group A) were eating an alternative food resource not usually consumed by benthics or limnetics in the wild (we think it blew into the pond) and had a strong phenotypic mismatch in two oral jaw traits previously shown by Matt McGee to be key for feeding on zooplankton, a major food resource of limnetics. Importantly, these results showed that there is not one “magic” trait that allows sticklebacks to feed on these alternative food resources and that whole-organism performance is driven by integrated suites of phenotypic traits.

Performance landscape in pond 4. The positions of individual F2s are plotted based on their stable isotope values, overlain with contours of loess-smoothed body size. Individuals in the three groups with the most extreme body sizes are shown in black symbols (group B, downward triangles; group L, upward triangles; group A, squares), and the remaining individuals are shown in gray circles. PC1 represents the major axis of isotope variation in the F2s and is consistent with the major axis of niche divergence between the benthics and limnetics in the wild. (Figure from Arnegard et al. 2014)

We then determined the genetic basis of performance in this trophic landscape. First, we genotyped the F2s with a panel of single nucleotide polymorphism (SNP) markers developed by David Kingsley, Felicity Jones and Frank Chan (Stanford). We then performed genetic linkage mapping of all the morphological traits that we measured, with a particular focus on the “component” traits that contributed to variation in performance. We found that over half of the 21 stickleback chromosomes had at least one genetic locus that contributed to variation in these component traits. We then asked how the genetic loci that underlie individual component traits combine to determine the performance of an F2 in niche space. Figuring out how to robustly conduct these genetic analyses was probably one of the most challenging parts of the study. Matt, Dolph and I had many discussions about how to do best do these analyses; I think our final breakthrough occurred during a break from skiing during the Peichel-Schluter Lab retreat at Mt Baker! Matt persevered through many iterations of the analyses, and in the end, we demonstrated that the genetic basis of niche divergence is largely polygenic and additive. That is, the addition of a benthic allele at any of the loci for individual morphological traits moves a fish in isotope space by the same amount as at any other locus. We did find evidence that epistatic interactions between loci have an effect on niche divergence, but the core genetic architecture is largely additive.

I personally was quite surprised by our findings that such a complex and distributed genetic architecture has arisen in such a short evolutionary time, especially in the face of gene flow! Perhaps naively, I had originally expected that we would find a few clusters of loci with relatively strong effects on performance in the divergent habitats. The genetic architecture we instead uncovered could be a consequence of strong and multifarious selection on multiple traits. It is also possible that this complex genetic architecture did not arise de novo in the past 12,000 years but is the reassembly of ancestral variation that was segregating in the marine ancestors of the benthic and limnetic species. I would love to test these ideas in the future.

The work also has implications for the genetic basis of speciation in this system. Multiple lines of evidence indicate that hybrids do not perform well in either parental environment in Paxton Lake and that ecological selection against hybrids contributes to reproductive isolation. Clearly, some F2 hybrids in our study performed better than others and some performed particularly poorly (the group A fish). If the slower growth of intermediate hybrids in the pond would lead to lower fitness (and in sticklebacks, growth has been associated with fitness), then our results suggest that the genetic architecture of extrinsic hybrid inviability might be largely additive. This is a very different genetic architecture than the epistatic genetic interactions that underlie intrinsic hybrid incompatibilities. Nonetheless, the group A F2 hybrids have combinations of traits from the parent species that are badly mismatched. Thus, our data suggest a parallel between the genetic mismatch found in intrinsic incompatibilities under “mutation-order” speciation and the phenotypic mismatch found in extrinsic incompatibilities under ecological speciation.

Our genetic mapping results are consistent with recent genome scans in sticklebacks and several other systems showing that many regions distributed across the genome can show high levels of divergence between even young species. As Patrik Nosil’s group nicely demonstrated using experimental population genomics in stick insects, at least some of these genomic regions of high divergence can result from divergent selection. Both of these studies further highlight the need to perform experimental genetic and genomic studies in natural or semi-natural conditions in order to identify loci associated with fitness and performance in the wild. In the future, it will be important to combine the results of our phenotype-driven genetic mapping studies with population genomic studies in order to obtain an integrated view of the genotypes and phenotypes that contribute to ecological adaptation and speciation in the wild.

Arnegard ME, McGee MD, Matthews BW, Marchinko KB, Conte GL, Kabir S, Bedford N, Bergek S, Chan YF, Jones FC, Kingsley DM, Peichel CL*, and Schluter D* (2014) Genetics of ecological divergence during speciation. Nature. doi:10.1038/nature13301

Saturday, June 14, 2014

Evolution Bucket List - alpha 1

Humans have a penchant for making “best of” (Top 10, Top 5, anything from Buzzfeed, ...) lists. David Letterman’s Top 10 lists are, of course, a long-standing classic. Many magazines and websites have Best Of lists for the year: best photos, best movies, etc. And now we have “best of” YouTube collections for pretty much anything that might interest you. It seems to be human nature to make such lists – although the characters in the movie High Fidelity argue it is a tendency more common or more enhanced in men than women.

The ultimate best-of lists are Bucket Lists – the things you need to see/do before you die. Presumably these are the 100 (or whatever number of) things that would enrich your life experience more than any other. The things that – if you didn’t do them – would have you looking back from the grave and thinking “Damn, I never went cave diving” or “Why didn’t I ever see a Broadway Play?” or whatever. Sometimes we see global bucket lists presumably applicable to all humanity (or perhaps the “average” human), but other times we see more targeted Bucket Lists for things such as Sporting Events, Fishing, Skiing, Reading, Dining, Sex, and so on. This got me to thinking: what would be an Evolution Bucket List? A Google search suggests no such list exists and so I figure we should develop one.

I will start the ball rolling with some initial ideas. I hope folks will suggest additional options in the comments. Perhaps with a few versions of the list batted around, we can develop the optimal set. What should be on such a list? Several categories stand out. (1) Locations where organisms are particularly special, such as Galápagos. (2) Particular organisms of evolutionary significance or novelty, such as the platypus. (3) Locations of historical/contemporary importance to the study of evolution, such as Darwin’s home. (4) Amazing interactions between organisms, such honey guides and honey badgers or the parasitic isopod that replaces the tongue of some marine fish. (5) Specific dramatic or important fossils or fossil sites, such as the Burgess Shale. So I will start our group effort by suggesting some items for the Evolution Bucket List: some I have already experienced, some I expect to experience, and some that would be great to experience but that I probably never will. 

Things already in my bucket

1. Galápagos Islands. For me, Galápagos is the single most iconic and inspirational location for someone interested in evolution. Not only did it inspire Darwin and many evolutionary biologists since, but it is home to some of the world’s most unique and interesting organisms: marine iguanas, Darwin’s finches, flightless cormorants, tropical penguins, and many others. Of course, we could easily list each of these organisms as separate items on the bucket list but – given that one can knock all of them off in a relatively short time in a relatively small area – I think they are better encompassed as a location. I have been fortunate enough to visit Galápagos many times, although I still haven’t seen a flightless cormorant. BLOG POST

Darwin called them "imps of darkness."
2. Down, EnglandNo location was more instrumental in the development and exposition of Darwin’s theory. It was here that Darwin did nearly all of the work that led us to our modern understanding of life on earth and how it came to be. The most obvious thing to see is Down House (especially his study) and its grounds (especially the Sandwalk). However, what was even more exciting for me was Darwin’s Pub. BLOG POST

Having a pint in Darwin's Pub.
3. ArchaeopteryxDiscovered soon after Darwin published his magnum opus, Archaeopteryx made flesh the intermediate forms between extant groups (birds and reptiles) and was thus a crucial contributor to acceptance of Darwin’s theory. Simply put, Archaeopteryx is the most famous fossil in the world: it is even in MS Word’s spell-check dictionary which, I have just discovered, knows how to spell it better than me. It is also the world’s most beautiful fossil – and spectacular versions can be seen in many museums. I have seen them in the Berlin Natural History Museum and the British Natural History Museum.

The Berlin Archaeopteryx
4. OilbirdsOne of the most exciting things for an evolutionary biologist is evolutionary novelties – species that just stick out in ways that set them apart from even the most closely related species. That is, they are the sorts of species that might not be imaginable if they didn’t actually exist. Oilbirds are my current favorite. They nest in caves and feed on fruit at night, and they echolocate! They are also huge outliers on the evolutionary tree of birds. And they live in spectacular settings in tropical forests. I have seen them in Trinidad both in caves and clicking their way along river corridors at night. BLOG POST

Me shooting pictures of oilbirds. (Photo by Felipe Perez-Jvostov)
5. Carnivorous plantsI was sorely tempted to list another cool animal (mudskippers or leafcutter ants) but I suppose plants might also be important and interesting – at least to some. Being an animal guy, the plants that are most fascinating to me are the ones that seem almost like animals – the predatory plants. Most iconically, this category (actually several independent evolutionary lineages) jncludes pitcher plants, sundews, and Venus flytraps. It is one of life’s guilty pleasure, at least for kids, to catch and “feed” insects to these plants. And, of course, it helps that Darwin was a big fan, even writing a book about them. Indeed, various carnivorous plants are featured to this day in the greenhouse at Down House (PHOTO).

Sundew in British Columbia.

Things reasonably likely to end up in my bucket

6. MadagascarAnother evolutionary marvel. A place, like Galapagos or New Zealand, long cut off from the rest of the world and so able to embark on an independent evolutionary trajectory. In the case of Madagascar, what I would most like to see are lots of lemurs: ring-tailed lemurs, mouse lemurs, and – most importantly – aye-ayes. Surely the aye-aye is one of the most bizarre and amazing mammals in existence – my kids think so anyway. Check out this awesome video True Facts about the Aye-Aye (3.5 million views and counting).

7. Burgess ShaleOne of the most important fossil finds was in the Canadian Rockies where, 500 million years ago, a large mudslide covered an almost intact fauna from the Cambrian Explosion, a period during which animal life exploded in diversity. This site has told us most of what we know about this time, half a billion years age. In fact, I am shocked that I have not already been to the Burgess Shale, given that I grew up only a few hours away (What the hell were my parents thinking not taking me there?) and I still drive through the area all the time. You can even get a guided tour. What could be simpler? Surely, I will soon check it off.

8. Chimpanzees – in the wildOur closest relative, and popularly consider 95+% genetically similar to us – to me! I am captivated watching them in any of the countless BBC videos. It is like a window into the past, in the sense that our common ancestor probably looked a lot more like a chimp than a human. I am pretty confident I will soon knock this one off too, given that I have collaborators working in Kibale National Park, Uganda, where chimpanzees are abundant and easily seen. Yet another reason to do some work there.

9. Platypus – in the wildOK, I suppose some other monotreme, like the echidna, would do in a pinch but the platypus just seems so much more bizarre. In fact, it bedeviled scientists for almost a century, as playfully described in the book titled, wait for it… Platypus. Of course, I envision my encounter will be like the one in David Attenborough’s Life of Mammals – me sitting peacefully on the edge of a pool while a platypus swims playfully (or at least indifferently) about my feet in crystal-clear water. I have already been to Australia but didn’t seek out a platypus at the time, dammit. Yet I will surely be back to Australia soon. In the meantime, I will have to be satisfied with the dusty old male platypus moldering away in the basement of the Redpath Museum. Not quite the same, but inspirational nonetheless.

10. Flying herpsThey don’t really fly, of course: flying has evolved only four times (bats, birds, insects, pterosaurs), but these gliders can be just as amazing. I grew up watching flying squirrels, which were cool enough, but what about flying snakes (VIDEO), flying lizards (VIDEO), or flying frogs (VIDEO)? The snakes can dramatically change direction in mid-air. The lizards extend their ribs until they look like a kite. The frogs were described by Alfred Russell Wallace – the co-discover of natural selection.

Things with varying degrees of unlikeness.

11. Bolas spider in actionLooks like a bird turd. Gives off a moth pheromone. Spins a ball of sticky web on a string and swings it around to catch sexed-up moths in flight (VIDEO). This sight should be the most accessible of these relatively inaccessible bucket list options, given that bolas spiders are widespread, seemingly even near my house. I just don’t know where or how to start looking. (OK. so maybe this one actually is achievable and I should have picked some rarer but equally cool spider.)

Many spiders could make the list. 
How cool is this crab spider waiting for dinner to fly up?
12. Antarctic breeding coloniesAlbatrosses. Elephant seals. Penguins. By the millions. South Georgia Island. The Kerguelen Islands. One of life’s great spectacles. Ironically, I once passed up a chance to go to the Kerguelen Islands. I probably won’t get another.

Penguin (check - Galapagos), Elephant Seal (check - California). Millions of each on a beach in (or near) Antarctica (pending).
13. Killer whales swimming onto the beach to get at sea lionsI must have watched videos of this behavior hundreds of times – truly amazing stuff. Here is one of those VIDEOS – 12 million views. In reality, this spectacle should be reasonably accessible (at least in relation to those that follow) but I am betting the chances are still remote because it happens in only a few places (Península Valdés, Argentina) for only part of the year (Feb–Apr – and episodically even then) and access seems to be strictly controlled.

Just need to get this orca and this sea lion on the beach in the same picture!
14. Hydrothermal vent communitiesEntire communities that thrive independently of energy from the sun. First seen in 1979, these communities of tube worms, crabs, fish, and other critters were too bizarre and unpredicted to be believed – except that we could actually see them on VIDEO. For this I just need a submarine.

15. TylacineIf one is to see a cool marsupial, one couldn’t do better than a Thylacine – the Tasmanian Tiger, in colloquial terms. OK, I know you’re saying well, duh, it’s extinct. But not everyone is convincedand a few of these critters might still be hanging out in the woods of Tasmania. To give a hint of what you might see, check out this chilling VIDEO of the last one alive in a zoo – viewed more than 2 million times. For this I might just need a time machine.

I would trade several thousand kangaroos for one (OK, maybe two) thylacines.

So, there’s my first attempt at an alpha version of an Evolution Bucket List. Please send me some new ideas so we can make a definitive list. If you have actually knocked off the item, then a tiny description like those above would be great – with a video or picture, ideally one you took yourself.

Have at ’er.

Friday, June 6, 2014

Genomic islands: analyzing a metaphor

[ This post is by Patrik Nosil, Zach Gompert, and Victor Soria Carrasco; I am just putting it up. –B. ]

It is well appreciated that some regions of the genome are more differentiated between populations or species than others. Indeed, a study of genomic divergence in 2005 found that significant genetic differentiation between M and S forms of the mosquito Anopheles gambiae was primarily restricted to just three regions of the genome, and these regions were dubbed ‘genomic islands of speciation’ (see Turner et al. 2005, PLoS Biology). It was initially assumed that these genomic islands harbored loci under divergent selection or those that generate reproductive isolation, and thus that they were central to speciation. Evolutionary biologists enthusiastically set out to find genomic islands in other species, and the genomic islands metaphor became an organizing concept in speciation research.

However, the initial intellectual excitement provided by the concept of genomic islands has progressively cooled down in the face of increasing scrutiny. First, whereas genomic islands have been identified in some species, apparently other species lack them. Strikingly, even the case for a small number of genomic islands in Anopheles gambiae has been questioned because whole-genome sequencing revealed many more genetic differences than found by earlier studies examining a subset of the genome (e.g., see Lawniczak et al. 2010, Science). Second, there is also some discrepancy among biologists about what does or doesn’t constitute a genomic island. Third, it has been argued that genomic islands are not necessarily evidence of divergent selection or differential gene flow, since they can occur for many other reasons, and that they might often be incidental, rather than instrumental, to speciation. A recent review article that also re-analyzes existing genomic data highlights all these issues to argue that genomic islands may often be indicative of post-speciation processes, rather than differential gene flow between taxa caused by divergent selection (see Cruikshank and Hahn, Mol. Ecol. 2014).

In this context, we embarked on a search for genomic islands between host-associated ecotypes of the stick-insect Timema cristinae so that we could quantify the role of divergent natural selection in generating any islands we might find. These stick insects are a nice system to do this in (see previous posts about eco-evolutionary dynamics in Timema and experimental genomics in Timema), because they provide several tractable avenues to ask about selection’s effects on genome divergence. Timema cristinae populations have repeatedly adapted to two different host plants, Adenostoma and Ceanothus (see drawings below), which in turn has lead to the repeated evolution of reproductive isolation (a process dubbed ‘parallel speciation’). This parallelism could result in parallel genomic islands, which would strengthen the argument that genomic islands are a product of divergent selection and key to speciation. Importantly, these host ecotypes are in the early stages of speciation and still undergo substantial gene flow, making post-speciation processes an unlikely explanation for any observed genomic islands. These stick insects can also be used to execute field experiments; they can be moved from one host plant to another, providing another avenue to test selection’s role in generating genomic islands.

Figure 1. The host plant ecotypes of Timema cristinae. Credit: Rosa Marin Ribas.

But before we could ask if genomic islands hold the key to understanding speciation in T. cristinae, we had to figure out whether they existed, and so we set out in search of islands of divergence between the T. cristinae ecotypes. As with most genomic projects, one of the first steps was creating a reference genome. This was done by sequencing libraries of various insert sizes and carrying out a de novo assembly of the resulting sequencing reads (done by Alex Buerkle), followed by linkage mapping to order the scaffolds onto linkage groups (done by Zach Gompert). The genome was then annotated by Victor Soria-Carrasco, a computational biologist in the lab at the University of Sheffield. Upon obtaining this annotated genome, we conducted whole genome re-sequencing of 160 individuals from four replicate pairs of the Adenostoma and Ceanothus ecotypes of T. cristinae.

Population genomic analyses then ensued, led by Zach Gompert. We used a Hidden Markov model to search for genomic islands. This is a cool approach that has only recently been used to search for genomic islands (in humans), and that really lets the data speak for itself. We found that there were indeed thousands of differentiated genetic regions between the population pairs. When we examined these regions in more detail, we found that even the most differentiated ones were not extremely differentiated (e.g., contained no fixed differences). This doesn’t really fit the original view of genomic islands, but rather suggests ‘riffles’ or ‘bumps’ of differentiation along a genomic landscape characterized by fine-scale heterogeneity in divergence. Nonetheless, these ‘bumps’ on the genomic landscape could still be central to speciation...

Thus, we looked for evidence that the same regions showed elevated divergence across multiple population pairs. We found that most (>80%) regions of accentuated divergence between ecotypes were unique to individual population pairs. However, we also found regions of repeated, parallel divergence regions across ecotype pairs, and more of these than expected by chance. However, even parallel divergence might not necessarily be affected by divergent selection. We thus tested if these parallel divergence regions correspond to regions showing parallel real-time allele-frequency changes between host species in the field. Specifically, we conducted a field transplant experiment using host-associated populations of the stick-insect T. cristinae. The idea was rather simple: If divergence in these regions is in truth driven by selection, then regions exhibiting pronounced allele frequency changes in experimental field transplants between hosts should correspond to regions of accentuated divergence between natural population pairs. This is the result we found.

Figure 2. Tim Farkas, a PhD student in the Nosil lab, setting up a field transplant experiment.

The experiment provided evidence that these high divergence regions are, at least in part, created by divergent selection. Luck was on our side and we were able to publish the findings in Science. We even graced the cover with a fantastic photo of Timema taken by Moritz Muschick. Our findings provide evidence that the metaphor of genomic islands might not be fundamentally flawed – there are regions of accentuated divergence in the genome which can be subject to divergent selection, and thus are also likely subject to differential gene flow. However, the results also highlight that the process of genomic divergence and the patterns created during this process can be nuanced. Only with further studies, including experimental tests of selection and unbiased quantification of genome-wide differentiation, will the true nature of speciation become better understood.

The full paper can be found here:

V. Soria-Carrasco, Z. Gompert, A. A. Comeault, T. E. Farkas, T. L. Parchman, J. S. Johnston, C. A. Buerkle, J. L. Feder, J. Bast, T. Schwander, S. P. Egan, B. J. Crespi, and P. Nosil. (2014). Stick insect genomes reveal natural selection’s role in parallel speciation. Science 344(6185), 738-742. DOI: 10.1126/science.1252136

Wednesday, June 4, 2014

Carnival of Evolution #72

Hi everybody!  Carnival of Evolution #72 is now up!  Our contribution is Kiyoko Gotanda’s post about  spatiotemporal variation in guppy color; check it out for an interesting tale of how guppies have evolved over time in different locations, and what these patterns tell us about selection in the wild.

Guppies!  Photo: Paul Bentzen.

The Carnival has lots of other interesting posts in it, but it doesn’t really have a theme this month, so instead of my usual theme-based picture, I will leave you with a post by Alex Wild that I particularly enjoyed:

Alex Wild, Compound Eye