Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota.

To explain differences in gut microbial communities we must determine how processes regulating microbial community assembly (colonization, persistence) differ among hosts and affect microbiota composition. We surveyed the gut microbiota of threespine stickleback (Gasterosteus aculeatus) from 10 geographically clustered populations and sequenced environmental samples to track potential colonizing microbes and quantify the effects of host environment and genotype. Gut microbiota composition and diversity varied among populations. These among-population differences were associated with multiple covarying ecological variables: habitat type (lake, stream, estuary), lake geomorphology and food- (but not water-) associated microbiota. Fish genotype also covaried with gut microbiota composition; more genetically divergent populations exhibited more divergent gut microbiota. Our results suggest that population level differences in stickleback gut microbiota may depend more on internal sorting processes (host genotype) than on colonization processes (transient environmental effects).

Covarying variances: more morphologically variable populations also exhibit more diet variation.

Many ecologically generalized populations are composed of relatively specialized individuals that selectively consume a subset of their population's diet, a phenomenon known as 'individual specialization'. The Niche Variation Hypothesis posits that this individual specialization can arise during ecological release if niche expansion occurs mainly through diet divergence among individuals, leading to greater morphological variation. Most tests of this hypothesis have searched for correlations between niche width and morphological variance, but this approach rests on the untested assumption that within-population morphological diversity is highly correlated with ecological diversity. Here, we test whether intrapopulation diet variation is correlated with intrapopulation morphological variation, across 12 lacustrine populations of three-spine stickleback. First, we use behavioral observations, isotopes, and gut contents to show that, within populations, individuals differ in microhabitat use and diet. Second, we show that some populations exhibit more diet variation than others, as evidenced by differences in both isotopic and gut content variation among individuals. Finally, we confirm that populations with greater dietary variation are more morphologically variable. However, this relationship is only significant when total morphological variance is examined, not for individual morphological traits. This discordance may reflect among-population differences in the relationship between individual morphology and diet. Because morphology-diet relationships can differ among populations, morphological variance may be a poor predictor of actual diet variation when diverse populations are being compared.

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.

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.

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.