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