Specialization of trophic position and habitat use by sticklebacks in an adaptive radiation

Non-random mating behaviour between diverging littoral and pelagic three-spined sticklebacks in an invasive population from Upper Lake Constance

Adaptive divergence and increased genetic differentiation among populations can lead to reproductive isolation. In Lake Constance, Germany, a population of invasive three-spined stickleback (Gasterosteus aculeatus) is currently diverging into littoral and pelagic ecotypes, which both nest in the littoral zone. We hypothesized that assortative mating behaviour contributes to reproductive isolation between these ecotypes and performed a behavioural experiment in which females could choose between two nest-guarding males. Behaviour was recorded, and data on traits relevant to mate choice were collected. Both females of the same and different ecotypes were courted with equal vigour. However, there was a significant interaction effect of male and female ecotypes on the level of aggression in females. Littoral females were more aggressive towards pelagic males, and pelagic females were more aggressive towards littoral males. This indicates rejection of males of different ecotypes in spite of the fact that littoral males were larger, more intensely red-coloured and more aggressive than the pelagic males-all mating traits female sticklebacks generally select for. This study documents the emergence of behavioural barriers during early divergence in an invasive and rapidly diversifying stickleback population and discusses their putative role in facilitating reproductive isolation and adaptive radiation within this species.

Associations Between Gut Microbiota Diversity and a Host Fitness Proxy in a Naturalistic Experiment Using Threespine Stickleback Fish

The vertebrate gut microbiota is a critical determinant of organismal function, yet whether and how gut microbial communities affect host fitness under natural conditions remains largely unclear. We characterised associations between a fitness proxy-individual growth rate-and bacterial gut microbiota diversity and composition in threespine stickleback fish introduced to large semi-natural ponds. We detected a 63% higher richness of bacterial taxa (α-diversity) in the guts of high-fitness fish compared to low-fitness fish, which might be driven by stronger bacterial dispersal among high-fitness fish according to the fit of a neutral community model. Further, microbial communities of high-fitness fish were more similar to one another (i.e., exhibited lower β-diversity) than those of low-fitness fish. The lower β-diversity found to be associated with higher host fitness is consistent with the Anna Karenina principle-that there are fewer ways to have a functional microbiota than a dysfunctional microbiota. Our study links differences in α- and β-diversity to a fitness-related trait in a vertebrate species reared under naturalistic conditions and our findings provide a basis for functional tests of the fitness consequences of host-microbiota interactions.

Gut microbiota as a sensor of autoimmune response and treatment for rheumatoid arthritis

Rheumatoid arthritis (RA) is considered a multifactorial condition where interaction between the genetic and environmental factors lead to immune dysregulation causing autoreactivity. While among the various genetic factors, HLA-DR4 and DQ8, have been reported to be the strongest risk factors, the role of various environmental factors has been unclear. Though events initiating autoreactivity remain unknown, a mucosal origin of RA has gained attention based on the recent observations with the gut dysbiosis in patients. However, causality of gut dysbiosis has been difficult to prove in humans. Mouse models, especially mice expressing RA-susceptible and -resistant HLA class II genes have helped unravel the complex interactions between genetic factors and gut microbiome. This review describes the interactions between HLA genes and gut dysbiosis in sex-biased preclinical autoreactivity and discusses the potential use of endogenous commensals as indicators of treatment efficacy as well as therapeutic tool to suppress pro-inflammatory response in rheumatoid arthritis.

Historical Field Records Reveal Habitat as an Ecological Correlate of Locomotor Phenotypic Diversity in the Radiation of Neotropical Geophagini Fishes

AbstractPhenotypic macroevolutionary studies provide insight into how ecological processes shape biodiversity. However, the complexity of phenotype-ecology relationships underscores the importance of also validating phenotype-based ecological inference with direct evidence of resource use. Unfortunately, macroevolutionary-scale ecological studies are often hindered by the challenges of acquiring taxonomically and spatially representative ecological data for large and widely distributed clades. The South American cichlid fish tribe Geophagini represents a continentally distributed radiation whose early locomotor morphological divergence suggests habitat as one ecological correlate of diversification, but an association between locomotor traits and habitat preference has not been corroborated. Field notes accumulated over decades of collecting across South America provide firsthand environmental records that can be mined for habitat data in support of macroevolutionary ecological research. In this study, we applied a newly developed method to transform descriptive field note information into quantitative habitat data and used it to assess habitat preference and its relationship to locomotor morphology in Geophagini. Field note-derived data shed light on geophagine habitat use patterns and reinforced habitat as an ecological correlate of locomotor morphological diversity. Our work emphasizes the rich data potential of museum collections, including often-overlooked material such as field notes, for evolutionary and ecological research.

Designing eco-evolutionary experiments for restoration projects: Opportunities and constraints revealed during stickleback introductions

Eco-evolutionary experiments are typically conducted in semi-unnatural controlled settings, such as mesocosms; yet inferences about how evolution and ecology interact in the real world would surely benefit from experiments in natural uncontrolled settings. Opportunities for such experiments are rare but do arise in the context of restoration ecology-where different "types" of a given species can be introduced into different "replicate" locations. Designing such experiments requires wrestling with consequential questions. (Q1) Which specific "types" of a focal species should be introduced to the restoration location? (Q2) How many sources of each type should be used-and should they be mixed together? (Q3) Which specific source populations should be used? (Q4) Which type(s) or population(s) should be introduced into which restoration sites? We recently grappled with these questions when designing an eco-evolutionary experiment with threespine stickleback (Gasterosteus aculeatus) introduced into nine small lakes and ponds on the Kenai Peninsula in Alaska that required restoration. After considering the options at length, we decided to use benthic versus limnetic ecotypes (Q1) to create a mixed group of colonists from four source populations of each ecotype (Q2), where ecotypes were identified based on trophic morphology (Q3), and were then introduced into nine restoration lakes scaled by lake size (Q4). We hope that outlining the alternatives and resulting choices will make the rationales clear for future studies leveraging our experiment, while also proving useful for investigators considering similar experiments in the future.

Host ecotype and rearing environment are the main drivers of threespine stickleback gut microbiota diversity in a naturalistic experiment

Host-microbiota interactions play a critical role in the hosts' biology, and thus, it is crucial to elucidate the mechanisms that shape gut microbial communities. We leveraged threespine stickleback fish (Gasterosteus aculeatus) as a model system to investigate the contribution of host and environmental factors to gut microbiota variation. These fish offer a unique opportunity for experiments in naturalistic conditions; we reared benthic and limnetic ecotypes from three different lakes in experimental ponds, allowing us to assess the relative effects of shared environment (pond), geographic origin (lake-of-origin), trophic ecology and genetics (ecotype) and biological sex on gut microbiota α- and β-diversity. Host ecotype had the strongest influence on α-diversity, with benthic fish exhibiting higher diversity than limnetic fish, followed by the rearing environment. β-diversity was primarily shaped by rearing environment, followed by host ecotype, indicating that environmental factors play a crucial role in determining gut microbiota composition. Furthermore, numerous bacterial orders were differentially abundant across ponds, underlining the substantial contribution of environmental factors to gut microbiota variation. Our study illustrates the complex interplay between environmental and host ecological or genetic factors in shaping the stickleback gut microbiota and highlights the value of experiments conducted under naturalistic conditions for understanding gut microbiota dynamics.

Foraging-induced craniofacial plasticity is associated with an early, robust and dynamic transcriptional response

Phenotypic plasticity is the ability of a single genotype to vary its phenotype in response to the environment. Plasticity of the skeletal system in response to mechanical input is widely studied, but the timing of its transcriptional regulation is not well understood. Here, we used the cichlid feeding apparatus to examine the transcriptional dynamics of skeletal plasticity over time. Using three closely related species that vary in their ability to remodel bone and a panel of 11 genes, including well-studied skeletal differentiation markers and newly characterized environmentally sensitive genes, we examined plasticity at one, two, four and eight weeks following the onset of alternate foraging challenges. We found that the plastic species exhibited environment-specific bursts in gene expression beginning at one week, followed by a sharp decline in levels, while the species with more limited plasticity exhibited consistently low levels of gene expression. This trend held across nearly all genes, suggesting that it is a hallmark of the larger plasticity regulatory network. We conclude that plasticity of the cichlid feeding apparatus is not the result of slowly accumulating gene expression difference over time, but rather is stimulated by early bursts of environment-specific gene expression followed by a return to homeostatic levels.

Elemental content of a host-parasite relationship in the threespine stickleback

Parasite infections are ubiquitous and their effects on hosts could play a role in ecosystem processes. Ecological stoichiometry provides a framework to study linkages between consumers and their resource, such as parasites and their host, and ecosystem process; however, the stoichiometric traits of host-parasite associations are rarely quantified. Specifically, it is unclear whether parasites' elemental ratios closely resemble those of their host or if infection is related to host stoichiometry, especially in vertebrate hosts. To answer such questions, we measured the elemental content (%C, %N, and %P) and molar ratios (C:N, C:P, and N:P) of parasitized and unparasitized Gasterosteus aculeatus (three-spined stickleback) and their cestode parasite, Schistocephalus solidus. Host and parasite elemental content were distinct from each other, and parasites were generally higher in %C and lower in %N and %P. Parasite infections were related to host C:N, with infected hosts being lower in C:N. Parasite elemental content was independent of their host, but parasite body mass and parasite density were important drivers of parasite stoichiometry. Overall, these potential effects of parasite infections on host stoichiometry along with parasites' distinct elemental compositions suggest parasites may further contribute to differences in how individual hosts store and recycle nutrients.

Pelvic spine reduction affects diet but not gill raker morphology in two polymorphic brook stickleback (Culaea inconstans) populations

Pelvic spine polymorphism occurs in several species in the stickleback family (Gasterosteidae). Given the similar phenotypic polymorphisms in multiple stickleback species, we sought to determine the extent of parallelism in the ecological correlates of pelvic spine reduction. Based on a metabarcoding analysis of brook stickleback gut contents in two polymorphic populations, we found that significant diet differences were associated with pelvic spine reduction, but we found no clear or consistent trend supporting a tendency for benthic feeding in pelvic-reduced brook sticklebacks. These results contrast with those found in threespine sticklebacks where pelvic spine reduction is often associated with a benthic diet. Hence, we found non-parallel consequences of spine polymorphism across species. Furthermore, a difference in gill raker morphology has been frequently observed between ecomorphs with different diets in many fish species. However, we found no evidence of any difference in gill raker morphology associated with pelvic spine polymorphism in brook sticklebacks.

Trophic Position of the Species and Site Trophic State Affect Diet Niche and Individual Specialization: From Apex Predator to Herbivore

Intra-species variability in isotopic niches, specifically isotopic total niche width (ITNW), isotopic individual niche width (IINW), and isotopic individual specialization (IIS), was studied using an innovative approach without sacrificing the vertebrates. Stable isotopes (δ13C, δ15N) in four body tissues differing in isotopic half-life were analyzed from four freshwater fish species representing different trophic positions. ITNW was widest for the apex predator (European catfish) and narrowest for the obligate predator (Northern pike). IINW exhibited a polynomial trend for the European catfish, Northern pike, and Eurasian perch (mesopredator), decreasing with body mass and increasing again after exceeding a certain species-dependent body mass threshold. Thus, for ectotherms, apex predator status is linked rather to its size than to the species. In herbivores (rudd), IINW increased with body mass. The IIS of predators negatively correlated with site trophic state. Therefore, eutrophication can significantly change the foraging behavior of certain species. We assume that the observed trends will occur in other species at similar trophic positions in either aquatic or terrestrial systems. For confirmation, we recommend conducting a similar study on other species in different habitats.

Species divergence under competition and shared predation

Species competing for resources also commonly share predators. While competition often drives divergence between species, the effects of shared predation are less understood. Theoretically, competing prey species could either diverge or evolve in the same direction under shared predation depending on the strength and symmetry of their interactions. We took an empirical approach to this question, comparing antipredator and trophic phenotypes between sympatric and allopatric populations of threespine stickleback and prickly sculpin fish that all live in the presence of a trout predator. We found divergence in antipredator traits between the species: in sympatry, antipredator adaptations were relatively increased in stickleback but decreased in sculpin. Shifts in feeding morphology, diet and habitat use were also divergent but driven primarily by stickleback evolution. Our results suggest that asymmetric ecological character displacement indirectly made stickleback more and sculpin less vulnerable to shared predation, driving divergence of antipredator traits between sympatric species.

Quantifying (non)parallelism of gut microbial community change using multivariate vector analysis

Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have limited knowledge of whether parallel evolution of host organisms is accompanied by parallel changes of their associated microbial communities (i.e., microbiotas), which are crucial for their hosts' ecology and evolution. Determining the extent of microbiota parallelism in nature can improve our ability to identify the factors that are associated with (putatively adaptive) shifts in microbial communities. While it has been emphasized that (non)parallel evolution is better considered as a quantitative continuum rather than a binary phenomenon, quantitative approaches have rarely been used to study microbiota parallelism. We advocate using multivariate vector analysis (i.e., phenotypic change vector analysis) to quantify direction and magnitude of microbiota changes and discuss the applicability of this approach for studying parallelism, and we compiled an R package for multivariate vector analysis of microbial communities ('multivarvector'). We exemplify its use by reanalyzing gut microbiota data from multiple fish species that exhibit parallel shifts in trophic ecology. We found that multivariate vector analysis results were largely consistent with other statistical methods, parallelism estimates were not affected by the taxonomic level at which the microbiota is studied, and parallelism might be stronger for gut microbiota function compared to taxonomic composition. This approach provides an analytical framework for quantitative comparisons across host lineages, thereby providing the potential to advance our capacity to predict microbiota changes. Hence, we emphasize that the development and application of quantitative measures, such as multivariate vector analysis, should be further explored in microbiota research in order to better understand the role of microbiota dynamics during their hosts' adaptive evolution, particularly in settings of parallel evolution.

Characterizing phenotypic diversity in marine populations of the threespine stickleback

The threespine stickleback (Gasterosteus aculeatus) is an important model for studying the evolution of vertebrate morphology. Sticklebacks inhabit freshwater, brackish, and marine northern hemisphere waters. Anadromous and marine populations (hereafter marine) are assumed to have remained unchanged morphologically from ancestral marine sticklebacks, despite marine environments varying on regional and local scales. Recent studies suggest that genetic and phenotypic structure exists in marine populations, yet the scale of this variation, and its ecological causes remain unclear. Our goal was to assess morphological trait variation in marine stickleback populations around Southern British Columbia (BC) and determine if oceanographic and habitat characteristics were associated with this variation. Between May-July 2019, we sampled 534 sticklebacks from 15 sites around Vancouver Island, a region characterized by a large diversity of oceanographic and habitat features. We characterized trait variation using two-dimensional (2D) geometric morphometric analysis, comparing individuals between oceanographic regions and habitats. We focused on head and body shape. We found that marine sticklebacks varied morphologically among and between regions and habitats, but the variation did not appear to be related to environmental variation. Sexual dimorphism was the largest source of variation, but oceanographic and habitat variables influenced differences between sexes. We concluded that marine sticklebacks offer abundant opportunities for expanding our knowledge of drivers of morphology.

Sick of eating: Eco-evo-immuno dynamics of predators and their trophically acquired parasites

When predators consume prey, they risk becoming infected with their prey's parasites, which can then establish the predator as a secondary host. A predator population's diet therefore influences what parasites it is exposed to, as has been repeatedly shown in many species such as threespine stickleback (Gasterosteus aculeatus) (more benthic‐feeding individuals obtain nematodes from oligocheate prey, whereas limnetic‐feeding individuals catch cestodes from copepod prey). These differing parasite encounters, in turn, determine how natural selection acts on the predator's immune system. We might therefore expect that ecoevolutionary dynamics of a predator's diet (as determined by its ecomorphology) should drive correlated evolution of its immune traits. Conversely, the predator's immunity to certain parasites might alter the relative costs and benefits of different prey, driving evolution of its ecomorphology. To evaluate the potential for ecological morphology to drive evolution of immunity, and vice versa, we use a quantitative genetics framework coupled with an ecological model of a predator and two prey species (the diet options). Our analysis reveals fundamental asymmetries in the evolution of ecomorphology and immunity. When ecomorphology rapidly evolves, it determines how immunity evolves, but not vice versa. Weak trade‐offs in ecological morphology select for diet generalists despite strong immunological trade‐offs, but not vice versa. Only weak immunological trade‐offs can explain negative diet‐infection correlations across populations. The analysis also reveals that eco‐evo‐immuno feedbacks destabilize population dynamics when trade‐offs are sufficiently weak and heritability is sufficiently high. Collectively, these results highlight the delicate interplay between multivariate trait evolution and the dynamics of ecological communities.

On the evolution of trophic position

The trophic structure of food webs is primarily determined by the variation in trophic position among species and individuals. Temporal dynamics of food web structure are central to our understanding of energy and nutrient fluxes in changing environments, but little is known about how evolutionary processes shape trophic position variation in natural populations. We propose that trophic position, whose expression depends on both environmental and genetic determinants of the diet variation in individual consumers, is a quantitative trait that can evolve via natural selection. Such evolution can occur either when trophic position is correlated with other heritable morphological and behavioural traits under selection, or when trophic position is a target of selection, which is possible if the fitness effects of prey items are heterogeneously distributed along food chains. Recognising trophic position as an evolving trait, whose expression depends on the food web context, provides an important conceptual link between behavioural foraging theory and food web dynamics, and a useful starting point for the integration of ecological and evolutionary studies of trophic position.

The interaction of resource use and gene flow on the phenotypic divergence of benthic and pelagic morphs of Icelandic Arctic charr (Salvelinus alpinus)

Conceptual models of adaptive divergence and ecological speciation in sympatry predict differential resource use, phenotype-environment correlations, and reduced gene flow among diverging phenotypes. While these predictions have been assessed in past studies, connections among them have rarely been assessed collectively. We examined relationships among phenotypic, ecological, and genetic variation in Arctic charr (Salvelinus alpinus) from six Icelandic localities that have undergone varying degrees of divergence into sympatric benthic and pelagic morphs. We characterized morphological variation with geometric morphometrics, tested for differential resource use between morphs using stable isotopes, and inferred the amount of gene flow from single nucleotide polymorphisms. Analysis of stable isotopic signatures indicated that sympatric morphs showed similar difference in resource use across populations, likely arising from the common utilization of niche space within each population. Carbon isotopic signature was also a significant predictor of individual variation in body shape and size, suggesting that variation in benthic and pelagic resource use is associated with phenotypic variation. The estimated percentage of hybrids between sympatric morphs varied across populations (from 0% to 15.6%) but the majority of fish had genotypes (ancestry coefficients) characteristic of pure morphs. Despite evidence of reduced gene flow between sympatric morphs, we did not detect the expected negative relationship between divergence in resource use and gene flow. Three lakes showed the expected pattern, but morphs in the fourth showed no detectable hybridization and had relatively low differences in resource use between them. This coupled with the finding that resource use and genetic differentiation had differential effects on body shape variation across populations suggests that reproductive isolation maintains phenotypic divergence between benthic and pelagic morphs when the effects of resource use are relatively low. Our ability to assess relationships between phenotype, ecology, and genetics deepens our understanding of the processes underlying adaptive divergence in sympatry.

Individual Prey Specialization Drives PCBs in Icelandic Killer Whales

Interindividual variation in prey specialization is an essential yet overlooked aspect of wildlife feeding ecology, especially as it relates to intrapopulation variation in exposure to toxic contaminants. Here, we assessed blubber concentrations of an extensive suite of persistent organic pollutants in Icelandic killer whales (Orcinus orca). Polychlorinated biphenyl (PCB) concentrations in blubber were >300-fold higher in the most contaminated individual relative to the least contaminated, ranging from 1.3 to 428.6 mg·kg^-1 lw. Mean PCB concentrations were 6-to-9-fold greater in individuals with a mixed diet including marine mammals than in fish specialist individuals, whereas males showed PCB concentrations 4-fold higher than females. Given PCBs have been identified as potentially impacting killer whale population growth, and levels in mixed feeders specifically exceeded known thresholds, the ecology of individuals must be recognized to accurately forecast how contaminants may threaten the long-term persistence of the world's ultimate marine predator.

Intraspecific variation and energy channel coupling within a Chilean kelp forest

The widespread importance of variable types of primary production, or energy channels, to consumer communities has become increasingly apparent. However, the mechanisms underlying this "multichannel" feeding remain poorly understood, especially for aquatic ecosystems that pose unique logistical constraints given the diversity of potential energy channels. Here, we use bulk tissue isotopic analysis along with carbon isotope (δ13 C) analysis of individual amino acids to characterize the relative contribution of pelagic and benthic energy sources to a kelp forest consumer community in northern Chile. We measured bulk tissue δ13 C and δ15 N for >120 samples; of these we analyzed δ13 C values of six essential amino acids (EAA) from nine primary producer groups (n = 41) and 11 representative nearshore consumer taxa (n = 56). Using EAA δ13 C data, we employed linear discriminant analysis (LDA) to assess how distinct EAA δ13 C values were between local pelagic (phytoplankton/particulate organic matter), and benthic (kelps, red algae, and green algae) endmembers. With this model, we were able to correctly classify nearly 90% of producer samples to their original groupings, a significant improvement on traditional bulk isotopic analysis. With this EAA isotopic library, we then generated probability distributions for the most important sources of production for each individual consumer and species using a bootstrap-resampling LDA approach. We found evidence for multichannel feeding within the community at the species level. Invertebrates tended to focus on either pelagic or benthic energy, deriving 13-67% of their EAA from pelagic sources. In contrast, mobile (fish) taxa at higher trophic levels used more equal proportions of each channel, ranging from 19% to 47% pelagically derived energy. Within a taxon, multichannel feeding was a result of specialization among individuals in energy channel usage, with 37 of 56 individual consumers estimated to derive >80% of their EAA from a single channel. Our study reveals how a cutting-edge isotopic technique can characterize the dynamics of energy flow in coastal food webs, a topic that has historically been difficult to address. More broadly, our work provides a mechanism as to how multichannel feeding may occur in nearshore communities, and we suggest this pattern be investigated in additional ecosystems.

Variation in the Sensory Space of Three-spined Stickleback Populations

The peripheral sensory systems, whose morphological attributes help determine the acquisition of distinct types of information, provide a means to quantitatively compare multiple modalities of a species' sensory ecology. We used morphological metrics to characterize multiple sensory modalities-the visual, olfactory, and mechanosensory lateral line sensory systems-for Gasterosteus aculeatus, the three-spined stickleback, to compare how sensory systems vary in animals that evolve in different ecological conditions. We hypothesized that the dimensions of sensory organs and correlations among sensory systems vary in populations adapted to marine and freshwater environments, and have diverged further among freshwater lake-dwelling populations. Our results showed that among environments, fish differed in which senses are relatively elaborated or reduced. When controlling for body length, littoral fish had larger eyes, more neuromasts, and smaller olfactory tissue area than pelagic or marine populations. We also found differences in the direction and magnitude of correlations among sensory systems for populations even within the same habitat type. Our data suggest that populations take different trajectories in how visual, olfactory, and lateral line systems respond to their environment. For the populations we studied, sensory modalities do not conform in a predictable way to the ecological categories we assigned.

The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback

The repeated occurrence of similar phenotypes in independent lineages (i.e., parallel evolution) in response to similar ecological conditions can provide compelling insights into the process of adaptive evolution. An intriguing question is to what extent repeated phenotypic changes are underlain by repeated changes at the genomic level and whether patterns of genomic divergence differ with the geographic context in which populations evolve. Here, we combined genomic, morphological and ecological data sets to investigate the genomic signatures of divergence across populations of threespine stickleback (Gasterosteus aculeatus) that adapted to contrasting ecological niches (benthic or limnetic) in either sympatry or allopatry. We found that genome-wide differentiation (F_ST ) was an order of magnitude higher and substantially more repeatable for sympatric benthic and limnetic specialists compared to allopatric populations with similar levels of ecological divergence. We identified genomic regions consistently differentiated between sympatric ecotypes that were also differentiated between or associated with benthic vs. limnetic niche in allopatric populations. These candidate regions were enriched on three chromosomes known to be involved in the benthic-limnetic divergence of threespine stickleback. Some candidate regions overlapped with QTL for body shape and trophic traits such as gill raker number, traits that strongly differ between benthic and limnetic ecotypes. In summary, our study shows that magnitude and repeatability of genomic signatures of ecological divergence in threespine stickleback highly depend on the geographic context. The identified candidate regions provide starting points to identify functionally important genes for the adaptation to benthic and limnetic niches.

Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish

BACKGROUND

Recent increases in understanding the ecological and evolutionary roles of microbial communities have underscored the importance of their hosts' biology. Yet, little is known about gut microbiota dynamics during the early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of Nicaraguan Midas cichlid fish (Amphilophus cf. citrinellus). Specifically, we tested the hypothesis that parallel divergence in trophic ecology in extremely young adaptive radiations from two crater lakes is associated with parallel changes of their gut microbiota.

RESULTS

Bacterial communities of fish guts and lake water were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Among individuals of the same crater lake, differentiation in trophic ecology was weakly associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across the two crater lakes, we could not detect conclusive evidence for parallel changes of the gut microbiota associated with trophic ecology.

CONCLUSIONS

A lack of clearly differentiated niches during the early stages of ecological diversification might result in non-parallel changes of gut microbial communities, as observed in our study system as well as in other recently diverged fish species. Video Abstract.

A test of the Niche Variation Hypothesis in a ruminant herbivore

Despite the shared prediction that the width of a population's dietary niche expands as food becomes limiting, the Niche Variation Hypothesis (NVH) and Optimal Foraging Theory (OFT) offer contrasting views about how individuals alter diet selection when food is limited. Classical OFT predicts that dietary preferences do not change as food becomes limiting, so individuals expand their diets as they compensate for a lack of preferred foods. In contrast, the NVH predicts that among-individual variation in cognition, physiology or morphology create functional trade-offs in foraging efficiency, thereby causing individuals to specialize on different subsets of food as food becomes limiting. To evaluate (a) the predictions of the NVH and OFT and (b) evidence for physiological and cognitive-based functional trade-offs, we used DNA microsatellites and metabarcoding to quantify the diet, microbiome and genetic relatedness (a proxy for social learning) of 218 moose Alces alces across six populations that varied in their degree of food limitation. Consistent with both the NVH and OFT, dietary niche breadth increased with food limitation. Increased diet breadth of individuals-rather than increased diet specialization-was strongly correlated with both food limitation and dietary niche breadth of populations, indicating that moose foraged in accordance with OFT. Diets were not constrained by inheritance of the microbiome or inheritance of diet selection, offering support for the little-tested hypothesis that functional trade-offs in food use (or lack thereof) determine whether populations adhere to the predictions of the NVH or OFT. Our results indicate that both the absence of strong functional trade-offs and the digestive physiology of ruminants provide contexts under which populations should forage in accordance with OFT rather than the NVH. Also, because dietary niche width increased with increased food limitation, OFT and the NVH provide theoretical support for the notion that plant-herbivore interaction networks are plastic rather than static, which has important implications for understanding interspecific niche partitioning. Lastly, because population-level dietary niche breadth and calf recruitment are correlated, and because calf recruitment can be a proxy for food limitation, our work demonstrates how diet data can be employed to understand a populations' proximity to carrying capacity.

Morphological and physiological traits of Mediterranean sticklebacks living in the Camargue wetland (Rhone river delta)

Three-spined sticklebacks (Gasterosteus aculeatus L.) living at the southern limit of the species distribution range could possess specific morphological and physiological traits that enable these fish to live at the threshold of their physiological capacities. Morphological analysis was carried out on samples of sticklebacks living in different saline habitats of the Camargue area (Rhone delta, northern Mediterranean coast) obtained from 1993 to 2017. Salinity acclimation capacities were also investigated using individuals from freshwater-low salinity drainage canals and from mesohaline-euryhaline lagoons. Fish were maintained in laboratory conditions at salinity values close to those of their respective habitats: low salinity (LS, 5‰) or seawater (SW, 30‰). Fish obtained from a mesohaline brackish water lagoon (BW, 15‰) were acclimated to SW or LS. Oxygen consumption rates and branchial Na⁺ /K⁺ -ATPase (NKA) activity (indicator of fish osmoregulatory capacity) were measured in these LS or SW control fish and in individuals subjected to abrupt SW or LS transfers. At all the studied locations, only the low-plated "leiurus" morphotype showed no spatial or temporal variations in their body morphology. Gill rakers were only longer and denser in fish sampled from the LS-freshwater (FW) drainage canals. All fish presented similar physiological capacities. Oxygen consumption rates were not influenced by salinity challenge except in SW fish transferred to LS immediately and 1 h after transfer. However, and as expected, gill NKA activity was salinity dependent. Sticklebacks of the Camargue area sampled from habitats with contrasted saline conditions are homogenously euryhaline, have low oxygen consumption rates and do not appear to experience significantly greater metabolic costs when challenged with salinity. However, an observed difference in gill raker length and density is most probably related to the nutritional condition of their habitat, indicating that individuals can rapidly acclimatize to different diets.

Resource diversity promotes among-individual diet variation, but not genomic diversity, in lake stickleback

Many generalist species consist of specialised individuals that use different resources. This within-population niche variation can stabilise population and community dynamics. Consequently, ecologists wish to identify environmental settings that promote such variation. Theory predicts that environments with greater resource diversity favour ecological diversity among consumers (via disruptive selection or plasticity). Alternatively, niche variation might be a side-effect of neutral genomic diversity in larger populations. We tested these alternatives in a metapopulation of threespine stickleback. Stickleback consume benthic and limnetic invertebrates, focusing on the former in small lakes, the latter in large lakes. Intermediate-sized lakes support generalist stickleback populations using an even mixture of the two prey types, and exhibit greater among-individual variation in diet and morphology. In contrast, genomic diversity increases with lake size. Thus, phenotypic diversity and neutral genetic polymorphism are decoupled: trophic diversity being greatest in intermediate-sized lakes with high resource diversity, whereas neutral genetic diversity is greatest in the largest lakes.

Striving for population-level conservation: integrating physiology across the biological hierarchy

The field of conservation physiology strives to achieve conservation goals by revealing physiological mechanisms that drive population declines in the face of human-induced rapid environmental change (HIREC) and has informed many successful conservation actions. However, many studies still struggle to explicitly link individual physiological measures to impacts across the biological hierarchy (to population and ecosystem levels) and instead rely on a 'black box' of assumptions to scale up results for conservation implications. Here, we highlight some examples of studies that were successful in scaling beyond the individual level, including two case studies of well-researched species, and using other studies we highlight challenges and future opportunities to increase the impact of research by scaling up the biological hierarchy. We first examine studies that use individual physiological measures to scale up to population-level impacts and discuss several emerging fields that have made significant steps toward addressing the gap between individual-based and demographic studies, such as macrophysiology and landscape physiology. Next, we examine how future studies can scale from population or species-level to community- and ecosystem-level impacts and discuss avenues of research that can lead to conservation implications at the ecosystem level, such as abiotic gradients and interspecific interactions. In the process, we review methods that researchers can use to make links across the biological hierarchy, including crossing disciplinary boundaries, collaboration and data sharing, spatial modelling and incorporating multiple markers (e.g. physiological, behavioural or demographic) into their research. We recommend future studies incorporating tools that consider the diversity of 'landscapes' experienced by animals at higher levels of the biological hierarchy, will make more effective contributions to conservation and management decisions.

Parallel changes in gut microbiome composition and function during colonization, local adaptation and ecological speciation

The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from the repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we use three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

Assessing Feeding Preferences of a Consumer Guild: Partitioning Variation Among versus Within Species

Interspecific variation in resource use is critical to understanding species diversity, coexistence, and ecosystem functioning. A growing body of research describes analogous intraspecific variation and its potential importance for population dynamics and community outcomes. However, the magnitude of intraspecific variation relative to interspecific variation in key dimensions of consumer-resource interactions remains unknown, hampering our understanding of the importance of this variation for population and community processes. In this study, we examine feeding preference through repeated laboratory choice feeding assays of 444 wild-caught individuals of eight invertebrate grazer species on rocky reefs in northern California. Between-species variation accounted for 25%-33% of the total variation in preference for the preferred resource, while between-individual variation accounted for 4%-5% of total variation. For two of the eight species, between-individual variation was significantly different from zero and on average contributed 14% and 17% of the total diet variation, even after accounting for differences due to size and sex. Therefore, even with clearly distinguishable between-species differences in mean preference, diet variation between and within individuals can contribute to the dietary niche width of species and guilds, which may be overlooked by focusing solely on species' mean resource use patterns.

Genetic Coupling of Female Mate Choice with Polygenic Ecological Divergence Facilitates Stickleback Speciation

Ecological speciation with gene flow is widespread in nature [1], but it presents a conundrum: how are associations between traits under divergent natural selection and traits that contribute to assortative mating maintained? Theoretical models suggest that genetic mechanisms inhibiting free recombination between loci underlying these two types of traits (hereafter, "genetic coupling") can facilitate speciation [2-4]. Here, we perform a direct test for genetic coupling by mapping both divergent traits and female mate choice in a classic model of ecological speciation: sympatric benthic and limnetic threespine stickleback (Gasterosteus aculeatus). By measuring mate choice in F2 hybrid females, we allowed for recombination between loci underlying assortative mating and those under divergent ecological selection. In semi-natural mating arenas in which females had access to both benthic and limnetic males, we found that F2 females mated with males similar to themselves in body size and shape. In addition, we found two quantitative trait loci (QTLs) associated with female mate choice that also predicted female morphology along the benthic-limnetic trait axis. Furthermore, a polygenic genetic model that explains adaptation to contrasting benthic and limnetic feeding niches [5] also predicted F2 female mate choice. Together, these results provide empirical evidence that genetic coupling of assortative mating with traits under divergent ecological selection helps maintain species in the face of gene flow, despite a polygenic basis for adaptation to divergent environments.

Stable isotope ecology of a hyper-diverse community of scincid lizards from arid Australia

We assessed the utility of stable isotope analysis as a tool for understanding community ecological structure in a species-rich clade of scincid lizards from one of the world's most diverse lizard communities. Using a phylogenetic comparative framework, we tested whether δ¹⁵N and δ¹³C isotopic composition from individual lizards was correlated with species-specific estimates of diet and habitat use. We find that species are highly divergent in isotopic composition with significant correlations to habitat use, but this relationship shows no phylogenetic signal. Isotopic composition corresponds to empirical observations of diet for some species but much variation remains unexplained. We demonstrate the importance of using a multianalytical approach to questions of long-term dietary preference, and suggest that the use of stable isotopes in combination with stomach content analysis and empirical data on habitat use can potentially reveal patterns in ecological traits at finer scales with important implications for community structuring.

Adaptation to an invasive host is driving the loss of a native ecotype

Locally adapted populations are often used as model systems for the early stages of ecological speciation, but most of these young divergent populations will never become complete species. The maintenance of local adaptation relies on the strength of natural selection overwhelming the homogenizing effects of gene flow; however, this balance may be readily upset in changing environments. Here I show that soapberry bugs (Jadera haematoloma) have lost adaptations to their native host plant (Cardiospermum corindum) and are regionally specializing on an invasive host (Koelreuteria elegans), collapsing a classic and well-documented example of local adaptation. All populations that were adapted to the native host-including those still found on that host today-are now better adapted to the invasive host in multiple phenotypes. Weak differentiation remains in two traits, suggesting that homogenization across the region is incomplete. This study highlights the potential for adaptation to invasive species to disrupt native communities by swamping adaptation to native conditions through maladaptive gene flow.

The temporal window of ecological adaptation in postglacial lakes: a comparison of head morphology, trophic position and habitat use in Norwegian threespine stickleback populations

Background

Studying how trophic traits and niche use are related in natural populations is important in order to understand adaptation and specialization. Here, we describe trophic trait diversity in twenty-five Norwegian freshwater threespine stickleback populations and their putative marine ancestor, and relate trait differences to postglacial lake age. By studying lakes of different ages, depths and distance to the sea we examine key environmental variables that may predict adaptation in trophic position and habitat use. We measured trophic traits including geometric landmarks that integrated variation in head shape as well as gillraker length and number. Trophic position (Tpos) and niche use (α) were estimated from stable isotopes (δ¹³C, δ¹⁵N). A comparison of head shape was also made with two North American benthic-limnetic species pairs.

Results

We found that head shape differed between marine and freshwater sticklebacks, with marine sticklebacks having more upturned mouths, smaller eyes, larger opercula and deeper heads. Size-adjusted gillraker lengths were larger in marine than in freshwater stickleback. Norwegian sticklebacks were compared on the same head shape axis as the one differentiating the benthic-limnetic North American threespine stickleback species pairs. Here, Norwegian freshwater sticklebacks with a more “limnetic head shape” had more and longer gillrakers than sticklebacks with “benthic head shape”. The “limnetic morph” was positively associated with deeper lakes. Populations differed in α (mean ± sd: 0.76 ± 0.29) and Tpos (3.47 ± 0.27), where α increased with gillraker length. Larger fish had a higher Tpos than smaller fish. Compared to the ecologically divergent stickleback species pairs and solitary lake populations in North America, Norwegian freshwater sticklebacks had similar range in Tpos and α values, but much less trait divergences.

Conclusions

Our results showed trait divergences between threespine stickleback in marine and freshwater environments. Freshwater populations diverged in trophic ecology and trophic traits, but trophic ecology was not related to the elapsed time in freshwater. Norwegian sticklebacks used the same niches as the ecologically divergent North American stickleback species pairs. However, as trophic trait divergences were smaller, and not strongly associated with the ecological niche, ecological adaptations along the benthic-limnetic axis were less developed in Norwegian sticklebacks.

Investment in boney defensive traits alters organismal stoichiometry and excretion in fish

Understanding how trait diversification alters ecosystem processes is an important goal for ecological and evolutionary studies. Ecological stoichiometry provides a framework for predicting how traits affect ecosystem function. The growth rate hypothesis of ecological stoichiometry links growth and phosphorus (P) body composition in taxa where nucleic acids are a significant pool of body P. In vertebrates, however, most of the P is bound within bone, and organisms with boney structures can vary in terms of the relative contributions of bones to body composition. Threespine stickleback populations have substantial variation in boney armour plating. Shaped by natural selection, this variation provides a model system to study the links between evolution of bone content, elemental body composition, and P excretion. We measure carbon:nitrogen:P body composition from stickleback populations that vary in armour phenotype. We develop a mechanistic mass-balance model to explore factors affecting P excretion, and measure P excretion from two populations with contrasting armour phenotypes. Completely armoured morphs have higher body %P but excrete more P per unit body mass than other morphs. The model suggests that such differences are driven by phenotypic differences in P intake as well as body %P composition. Our results show that while investment in boney traits alters the elemental composition of vertebrate bodies, excretion rates depend on how acquisition and assimilation traits covary with boney trait investment. These results also provide a stoichiometric hypothesis to explain the repeated loss of boney armour in threespine sticklebacks upon colonizing freshwater ecosystems.

Habitat-related specialization of lateral-line system morphology in a habitat-generalist and a habitat-specialist New Zealand eleotrid

An investigation of intraspecific habitat-related patterns of variation in oculoscapular lateral-line superficial neuromasts (SN) identified a decrease in the ratio of total SNs to pores, and a trend towards decreased asymmetry in SNs in the habitat-generalist common bully Gobiomorphus cotidianus from fluvial habitats compared to lacustrine habitats, suggesting habitat-related phenotypic variability. A greater ratio of pores to SNs, as well as less variation in the total number and asymmetry of SNs observed in the fluvial habitat-specialist redfin bully Gobiomorphus huttoni may provide further evidence of variations in the oculoscapular lateral-line morphology of fluvial habitat G. cotidianus individuals serving as adaptations to more turbulent environments.

Speciation, Ecological Opportunity, and Latitude (American Society of Naturalists Address)

Evolutionary hypotheses to explain the greater numbers of species in the tropics than the temperate zone include greater age and area, higher temperature and metabolic rates, and greater ecological opportunity. These ideas make contrasting predictions about the relationship between speciation processes and latitude, which I elaborate and evaluate. Available data suggest that per capita speciation rates are currently highest in the temperate zone and that diversification rates (speciation minus extinction) are similar between latitudes. In contrast, clades whose oldest analyzed dates precede the Eocene thermal maximum, when the extent of the tropics was much greater than today, tend to show highest speciation and diversification rates in the tropics. These findings are consistent with age and area, which is alone among hypotheses in predicting a time trend. Higher recent speciation rates in the temperate zone than the tropics suggest an additional response to high ecological opportunity associated with low species diversity. These broad patterns are compelling but provide limited insights into underlying mechanisms, arguing that studies of speciation processes along the latitudinal gradient will be vital. Using threespine stickleback in depauperate northern lakes as an example, I show how high ecological opportunity can lead to rapid speciation. The results support a role for ecological opportunity in speciation, but its importance in the evolution of the latitudinal gradient remains uncertain. I conclude that per capita evolutionary rates are no longer higher in the tropics than the temperate zone. Nevertheless, the vast numbers of species that have already accumulated in the tropics ensure that total rate of species production remains highest there. Thus, tropical evolutionary momentum helps to perpetuate the steep latitudinal biodiversity gradient.

Widespread positive but weak assortative mating by diet within stickleback populations

Assortative mating - correlation between male and female traits - is common within populations and has the potential to promote genetic diversity and in some cases speciation. Despite its importance, few studies have sought to explain variation in the extent of assortativeness across populations. Here, we measure assortative mating based on an ecologically important trait, diet as inferred from stable isotopes, in 16 unmanipulated lake populations of three-spine stickleback. As predicted, we find a tendency toward positive assortment on the littoral-pelagic axis, although the magnitude is consistently weak. These populations vary relatively little in the strength of assortativeness, and what variation occurs is not explained by hypothesized drivers including habitat cosegregation, the potential for disruptive selection, costs to choosiness, and the strength of the relationship between diet and body size. Our results support recent findings that most assortative mating is positive, while suggesting that new approaches may be required to identify the environmental variables that drive the evolution of nonrandom mating within populations.

Immunogenetic control of the intestinal microbiota

All vertebrates contain a diverse collection of commensal, symbiotic and pathogenic microorganisms, such as bacteria, viruses and fungi, on their various body surfaces, and the ecological community of these microorganisms is referred to as the microbiota. Mucosal sites, such as the intestine, harbour the majority of microorganisms, and the human intestine contains the largest community of commensal and symbiotic bacteria. This intestinal community of bacteria is diverse, and there is a significant variability among individuals with respect to the composition of the intestinal microbiome. Both genetic and environmental factors can influence the diversity and composition of the intestinal bacteria with the predominant environmental factor being diet. So far, studies have shown that diet-dependent differences in the composition of intestinal bacteria can be classified into three groups, called enterotypes. Other environmental factors that can influence the composition include antibiotics, probiotics, smoking and drugs. Studies of monozygotic and dizygotic twins have proven that genetics plays a role. Recently, MHC II genes have been associated with specific microbial compositions in human infants and transgenic mice that express different HLA alleles. There is a growing list of genes/molecules that are involved with the sensing and monitoring of the intestinal lumen by the intestinal immune system that, when genetically altered, will significantly alter the composition of the intestinal microflora. The focus of this review will be on the genetic factors that influence the composition of the intestinal microflora.

Predicting species' vulnerability in a massively perturbed system: the fishes of Lake Turkana, Kenya

Background and Trophic Diversity Study

Lake Turkana is an understudied desert lake shared by Kenya and Ethiopia. This system is at the precipice of large-scale changes in ecological function due to climate change and economic development along its major inflowing river, the Omo River. To anticipate response by the fish community to these changes, we quantified trophic diversity for seven ecological disparate species (Alestes baremose, Hydrocynus forskalli, Labeo horie, Lates niloticus, Oreochromis niloticus, Synodontis schall, and Tilapia zillii) using stable isotopes. Based on their marked morphological differentiation, we postulated that dietary niches of these species would be similar in size but show little overlap. The degree of trophic diversity varied greatly among the species studied, refuting our hypothesis regarding dietary niche size. Oreochromis niloticus and L. niloticus had the highest trophic diversity and significantly larger dietary niches than T. zillii, A. baremose and H. forskalli. Low overlap among the dietary niches of the seven species, with the exception of the synodontid catfish S. schall, is consistent with our second hypothesis.

Predicting Species’ Vulnerability

Breeding vulnerability was highest among those species with the lowest trophic diversity. We predict that in suffering two strikes against them, A. baremose, H. forskalli, T. zillii, and L. horie will be most affected by the highly altered Lake Turkana ecosystem and that O. niloticus, L. niloticus and S. schall will be least affected. Low vulnerability among O. niloticus and L. niloticus is promising for the future of the lake’s fishery, but the third most important fishery species (L. horie) will be highly vulnerable to impending ecosystem change. T. zillii should be treated as separate from O. niloticus in the fishery given higher sensitivity and a different ecological role. We see potential for expansion of the fishery for S. schall but don’t recommend the development of a fishery for A. baremose and H. forskalli.

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).