The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes.

Organisms well suited for the study of ecotype formation have wide distribution ranges, where they adapt to multiple drastically different habitats repeatedly over space and time. Here we study such ecotypes in a Crustacean model, Asellus aquaticus, a commonly occurring isopod found in freshwater habitats as diverse as streams, caves and lakes. Previous studies focusing on cave vs. surface ecotypes have attributed depigmentation, eye loss and prolonged antennae to several south European cave systems. Likewise, surveys across multiple Swedish lakes have identified the presence of dark-pigmented "reed" and light-pigmented "stonewort" ecotypes, which can be found within the same lake. In this study, we sequenced the first draft genome of A. aquaticus, and subsequently use this to map reads and call variants in surface stream, cave and two lake ecotypes. In addition, the draft genome was combined with a RADseq approach to perform a quantitative trait locus (QTL) mapping study using a laboratory bred F2 and F4 cave × surface intercross. We identified genomic regions associated with body pigmentation, antennae length and body size. Furthermore, we compared genome-wide differentiation between natural populations and found several genes potentially associated with these habitats. The assessment of the cave QTL regions in the light-dark comparison of lake populations suggests that the regions associated with cave adaptation are also involved with genomic differentiation in the lake ecotypes. These demonstrate how troglomorphic adaptations can be used as a model for related ecotype formation.

Rapid adaptive divergence between ecotypes of an aquatic isopod inferred from F-Q analysis.

Divergent natural selection is often thought to be the principal factor driving phenotypic differentiation between populations. We studied two ecotypes of the aquatic isopod Asellus aquaticus which have diverged in parallel in several Swedish lakes. In these lakes, isopods from reed belts along the shores colonized new stonewort stands in the centre of the lakes and rapid phenotypic changes in size and pigmentation followed after colonization. We investigated if selection was likely to be responsible for these observed phenotypic changes using indirect inferences of selection (F(ST)-Q(ST) analysis). Average Q(ST) for seven quantitative traits were higher than the average F(ST) between ecotypes for putatively neutral markers (AFLPs). This suggests that divergent natural selection has played an important role during this rapid diversification. In contrast, the average Q(ST) between the different reed ecotype populations was not significantly different from the mean F(ST). Genetic drift could therefore not be excluded as an explanation for the minor differences between allopatric populations inhabiting the same source habitat. We complemented this traditional F(ST)-Q(ST) approach by comparing the F(ST) distributions across all loci (n = 67-71) with the Q(ST) for each of the seven traits. This analysis revealed that pigmentation traits had diverged to a greater extent and at higher evolutionary rates than size-related morphological traits. In conclusion, this extended and detailed type of F(ST)-Q(ST) analysis provides a powerful method to infer adaptive phenotypic divergence between populations. However, indirect inferences about the operation of divergent selection should be analyzed on a per-trait basis and complemented with detailed ecological information.

Habitat-specific pigmentation in a freshwater isopod: adaptive evolution over a small spatiotemporal scale.

Pigmentation in the freshwater isopod Asellus aquaticus (Crustacea) differed between habitats in two Swedish lakes. In both lakes, isopods had lighter pigmentation in stands of submerged vegetation, consisting of stoneworts (Chara spp.), than in nearby stands of reed (Phragmites australis). Experimental crossings of light and dark isopods in a common environment showed that pigmentation had a genetic basis and that genetic variance was additive. Environmental effects of diet or chromatophore adjustment to the background had minor influence on pigmentation, as shown by laboratory rearing of isopods on stonewort or reed substrates, as well as analyses of stable isotope ratios for isopods collected in the field. In both study lakes, the average phenotype became lighter with time (across generations) in recently established stonewort stands. Taken together, these results indicate that altered phenotype pigmentation result from evolutionary responses to local differences in natural selection. Based on the assumption of two generations per year, the evolutionary rate of change in pigmentation was 0.08 standard deviations per generation (haldanes) over 20 generations in one lake and 0.22 haldanes over two generations in the other lake. This genetic change occurred during an episode of population growth in a novel habitat, a situation known to promote adaptive evolution. In addition, stonewort stands constitute large and persistent patches, characteristics that tend to preserve local adaptations produced by natural selection. Results from studies on selective forces behind the adaptive divergence suggest that selective predation from visually oriented predators is a possible selective agent. We found no indications of phenotype-specific movements between habitats. Mating within stonewort stands was random with respect to pigmentation, but on a whole-lake scale it is likely that mating is assortative, as a result of local differences in phenotype distribution.

Effects of pH, humic substances and animal interactions on survival and physiological status of Asellus aquaticus L. and Gammarus pulex (L.) : A field experiment.

The mortality and physiological status (body water content) of Asellus aquaticus (Isopoda) and Gammarus pulex (Amphipoda) were measured after 25 days exposure in 20 natural streams with a pH range of 4.3-7.5 and a colour range of 8-280 mg Pt L-1. In addition, the effects of keeping the animals as single species or together were studied. The response of Gammarus to low pH was an increased mortality and lower physiological status of surviving individuals in streams with a pH lower than 6.0. In Asellus the physiological status was correlated with pH, while the mortality was not pH dependent. The effects of humus on the physiological status of Asellus was significant when fitted to a second order polynomial function. The influence of humus can, however, be regarded as small relative to pH. The interactions between the species could be described as asymmetric under optimal conditions of high pH and low humus concentrations, where the presence of Gammarus decreased the survival and physiological status of Asellus. Acid stress did not seem to reverse the direction of this asymmetry, but the presence of Gammarus improved the physiological status of Asellus at pH lower than 6.0. Since the presence of Asellus did not increase the mortality or decrease the physiological status of Gammarus, this could be explained by Asellus feeding on Gammarus that died from physiological stress solely. This mechanism suggests that food quality, and thus effects of diffuse competition, can be important for the ability to withstand acid stress. The results, though, give no support for the hypothesis that competition from Asellus is important for the disappearance of Gammarus during the acidification of streams.

The role of different reproductive barriers during phenotypic divergence of isopod ecotypes.

The question of how diverging populations become separate species by restraining gene flow is a central issue in evolutionary biology. Assortative mating might emerge early during adaptive divergence, but the role of other types of reproductive barriers such as migration modification have recently received increased attention. We demonstrate that two recently diverged ecotypes of a freshwater isopod (Asellus aquaticus) have rapidly developed premating isolation, and this isolation barrier has emerged independently and in parallel in two south Swedish lakes. This is consistent with ecological speciation theory, which predicts that reproductive isolation arises as a byproduct of ecological divergence. We also find that in one of these lakes, habitat choice acts as the main barrier to gene flow. These observations and experimental results suggest that migration modification might be as important as assortative mating in the early stages of ecological speciation. Simulations suggest that the joint action of these two isolating barriers is likely to greatly facilitate adaptive divergence, compared to if each barrier was acting alone.