Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

Animals harbour diverse communities of symbiotic bacteria, which differ dramatically among host individuals. This heterogeneity poses an immunological challenge: distinguishing between mutualistic and pathogenic members of diverse and host-specific microbial communities. We propose that Major Histocompatibility class II (MHC) genotypes contribute to recognition and regulation of gut microbes, and thus, MHC polymorphism contributes to microbial variation among hosts. Here, we show that MHC IIb polymorphism is associated with among-individual variation in gut microbiota within a single wild vertebrate population of a small fish, the threespine stickleback. We sampled stickleback from Cedar Lake, on Vancouver Island, and used next-generation sequencing to genotype the sticklebacks' gut microbiota (16S sequencing) and their MHC class IIb exon 2 sequences. The presence of certain MHC motifs was associated with altered relative abundance (increase or decrease) of some microbial Families. The effect sizes are modest and entail a minority of microbial taxa, but these results represent the first indication that MHC genotype may affect gut microbiota composition in natural populations (MHC-microbe associations have also been found in a few studies of lab mice). Surprisingly, these MHC effects were frequently sex-dependent. Finally, hosts with more diverse MHC motifs had less diverse gut microbiota. One implication is that MHC might influence the efficacy of therapeutic strategies to treat dysbiosis-associated disease, including the outcome of microbial transplants between healthy and diseased patients. We also speculate that macroparasite-driven selection on MHC has the potential to indirectly alter the host gut microbiota, and vice versa.

Individual diet has sex-dependent effects on vertebrate gut microbiota

Vertebrates harbour diverse communities of symbiotic gut microbes. Host diet is known to alter microbiota composition, implying that dietary treatments might alleviate diseases arising from altered microbial composition ('dysbiosis'). However, it remains unclear whether diet effects are general or depend on host genotype. Here we show that gut microbiota composition depends on interactions between host diet and sex within populations of wild and laboratory fish, laboratory mice and humans. Within each of two natural fish populations (threespine stickleback and Eurasian perch), among-individual diet variation is correlated with individual differences in gut microbiota. However, these diet-microbiota associations are sex dependent. We document similar sex-specific diet-microbiota correlations in humans. Experimental diet manipulations in laboratory stickleback and mice confirmed that diet affects microbiota differently in males versus females. The prevalence of such genotype by environment (sex by diet) interactions implies that therapies to treat dysbiosis might have sex-specific effects.

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)

Vertebrates' diets profoundly influence the composition of symbiotic gut microbial communities. Studies documenting diet-microbiota associations typically focus on univariate or categorical diet variables. However, in nature individuals often consume diverse combinations of foods. If diet components act independently, each providing distinct microbial colonists or nutrients, we expect a positive relationship between diet diversity and microbial diversity. We tested this prediction within each of two fish species (stickleback and perch), in which individuals vary in their propensity to eat littoral or pelagic invertebrates or mixtures of both prey. Unexpectedly, in most cases individuals with more generalised diets had less diverse microbiota than dietary specialists, in both natural and laboratory populations. This negative association between diet diversity and microbial diversity was small but significant, and most apparent after accounting for complex interactions between sex, size and diet. Our results suggest that multiple diet components can interact non-additively to influence gut microbial diversity.

Partitioning the effects of spatial isolation, nest habitat, and individual diet in causing assortative mating within a population of threespine stickleback

Assortative mating is measured as a phenotypic or genotypic correlation between mates. Although biologists typically view assortative mating in terms of mate preference for similar partners, correlations between mates can also arise from phenotypic spatial structure arising from spatial isolation or habitat preferences. Here, we test whether diet-assortative mating within an ecologically variable population of threespine stickleback results from small-scale geographic isolation or microhabitat preference. We find evidence for assortative mating in the form of a positive correlation between mated pairs' diets (measured using stable isotopes). Stable isotopes reveal diet differences between different nesting areas and among individuals using different nest habitat within a nesting area. This spatial segregation of diet types should generate some assortative mating, but is insufficient to explain the observed assortment strength. Significant male-female isotope correlations remain after controlling for spatial variables. We therefore conclude that sticklebacks' diet-assortative mating arises from additional behavioral preference. More generally, our results illustrate the point that spatial segregation can only drive appreciable levels of phenotypic assortative mating when environment-phenotype correlations are parallel and strong in both sexes. Consequently, intraspecific assortative mating may typically entail mating preferences rather than just spatial cosegregation of phenotypes.

Ecological release from interspecific competition leads to decoupled changes in population and individual niche width

A species's niche width reflects a balance between the diversifying effects of intraspecific competition and the constraining effects of interspecific competition. This balance shifts when a species from a competitive environment invades a depauperate habitat where interspecific competition is reduced. The resulting ecological release permits population niche expansion, via increased individual niche widths and/or increased among-individual variation. We report an experimental test of the theory of ecological release in three-spine stickleback (Gasterosteus aculeatus). We factorially manipulated the presence or absence of two interspecific competitors: juvenile cut-throat trout (Oncorhynchus clarki) and prickly sculpin (Cottus asper). Consistent with the classic niche variation hypothesis, release from trout competition increased stickleback population niche width via increased among-individual variation, while individual niche widths remained unchanged. In contrast, release from sculpin competition had no effect on population niche width, because increased individual niche widths were offset by decreased between-individual variation. Our results confirm that ecological release from interspecific competition can lead to increases in niche width, and that these changes can occur on behavioural time scales. Importantly, we find that changes in population niche width are decoupled from changes in the niche widths of individuals within the population.

Phenotype-dependent native habitat preference facilitates divergence between parapatric lake and stream stickleback

Adaptive divergence between adjoining populations reflects a balance between the diversifying effect of divergent selection and the potentially homogenizing effect of gene flow. In most models of migration-selection balance, gene flow is assumed to reflect individuals' inherent capacity to disperse, without regard to the match between individuals' phenotypes and the available habitats. However, habitat preferences can reduce dispersal between contrasting habitats, thereby alleviating migration load and facilitating adaptive divergence. We tested whether habitat preferences contribute to adaptive divergence in a classic example of migration-selection balance: parapatric lake and stream populations of three-spine stickleback (Gasterosteus aculeatus). Using a mark-transplant-recapture experiment on morphologically divergent parapatric populations, we showed that 90% of lake and stream stickleback returned to their native habitat, reducing migration between habitats by 76%. Furthermore, we found that dispersal into a nonnative habitat was phenotype dependent. Stream fish moving into the lake were morphologically more lake-like than those returning to the stream (and the converse for lake fish entering the stream). The strong native habitat preference documented here increases the extent of adaptive divergence between populations two- to fivefold relative to expectations with random movement. These results illustrate the potential importance of adaptive habitat choice in driving parapatric divergence.

Mate choice based on a key ecological performance trait

Mate preference for well-adapted individuals may strengthen divergent selection and thereby facilitate adaptive divergence. We performed mate choice experiments in which we manipulated male red crossbill (Loxia curvirostra complex) feeding rates. Using association time as a proxy for preference, we found that females preferred faster foragers, which reinforces natural selection because poorly adapted males would be less likely to obtain a mate as well as less likely to survive. Although theoretical models predict direct preference for adaptation and performance, to the best of our knowledge this experiment provides the first evidence of individuals directly assessing feeding performance in mate choice. In species where assessing the ecological adaptation of potential mates is possible, females may gain fitness benefits from choosing a well-adapted mate directly or indirectly, promoting the use of information about ecological adaptation in mate choice.

Assortative mating by diet in a phenotypically unimodal but ecologically variable population of stickleback

Speciation with gene flow may be driven by a combination of positive assortative mating and disruptive selection, particularly if selection and assortative mating act on the same trait, eliminating recombination between ecotype and mating type. Phenotypically unimodal populations of threespine stickleback (Gasterosteus aculeatus) are commonly subject to disruptive selection due to competition for alternate prey. Here we present evidence that stickleback also exhibit assortative mating by diet. Among-individual diet variation leads to variation in stable isotopes, which reflect prey use. We find a significant correlation between the isotopes of males and eggs within their nests. Because egg isotopes are derived from females, this correlation reflects assortative mating between males and females by diet. In concert with disruptive selection, this assortative mating should facilitate divergence. However, the stickleback population remains phenotypically unimodal, highlighting the fact that assortative mating and disruptive selection do not guarantee evolutionary divergence and speciation.

The role of marker traits in the assortative mating within red crossbills,Loxia curvirostracomplex

We conducted mate choice experiments to determine whether differences in calls or bill morphology might influence assortative mating between call types of red crossbills (Loxia curvirostra complex) that have diverged in bill structure to specialize on different species of conifers. Females preferred males that gave calls that matched their own type, but did not prefer males that more closely approximated the average or optimal bill size of the female's call type. These results were consistent with our breeding simulations, which showed that females gained an indirect fitness benefit by choosing a male of her own call type because this reduced the production of offspring with morphologies that fell between adaptive peaks. However, choice based on bill morphology within a call type provided no further benefit. Calls, which crossbills learn from their parents, likely act as a marker trait indicative of the morphological adaptations of the group, allow for easy assessment of potential mates and facilitate rapid divergence under ecological selection.