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1.
Daniel I. Bolnick Lisa K. Snowberg J. Gregory Caporaso Chris Lauber Rob Knight William E. Stutz 《Molecular ecology》2014,23(19):4831-4845
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. 相似文献
2.
Sean M. Rogers 《Molecular ecology》2012,21(21):5155-5158
The hunt for the genes underlying ecological speciation has now closed in on a number of candidates, but making the link from genotype to phenotype continues to pose a significant challenge. This is partly because genetic studies in many systems remain impeded by long generation times or an inability to perform controlled crosses. Now, in this issue of Molecular Ecology, Malek et al. (2012) demonstrate the utility of a novel admixture mapping approach that can be used to identify genomic regions contributing to adaptive trait divergence between natural populations. Remarkably, they validate their approach by mapping traits associated with mate choice in a wild limnetic and benthic threespine stickleback (Gasterosteus aculeatus) species pair, finding several loci associated with male nuptial coloration and shape. While this study benefited from tried‐and‐true microsatellites in a well‐characterized species with a detailed genetic map (and genome sequence), the field is quickly moving towards the use of next‐generation sequencing, especially for nonmodel systems. The ability to characterize molecular polymorphisms for any system suggests that molecular ecologists working on virtually any species may benefit from applying Malek et al.'s approach, if naturally admixed populations are available. 相似文献
3.
Jacquelin DeFaveri Heidi Viitaniemi Erica Leder Juha Merilä 《Molecular ecology resources》2013,13(3):377-392
The implications of transitioning to single nucleotide polymorphism (SNPs) from microsatellite markers (MSs) have been investigated in a number of population genetics studies, but the effect of genomic location on the amount of information each type of marker reveals has not been explored in detail. We developed novel SNP markers flanking 1 kb regions of 13 genic (within gene or <1 kb away from gene) and 13 nongenic (>10 kb from annotated gene) MSs in the threespine stickleback genome to obtain comparable data for both types of markers. We analysed patterns of genetic diversity and divergence on various geographic scales after converting the SNP loci within each genomic region into haplotypes. Marker type (SNP haplotype or MS) and location (genic or nongenic) significantly affected most estimates of population diversity and divergence. Between‐lineage divergence was significantly higher in SNP haplotypes (genic and nongenic), however, within‐lineage divergence was similar between marker types. Most divergence and diversity measures were uncorrelated between markers, except for population differentiation which was correlated between MSs and SNP haplotypes (both genic and nongenic). Broad‐scale population structure and assignment were similarly resolved by both marker types, however, only the MSs were able to delimit fine‐scale population structuring, particularly when genic and nongenic markers were combined. These results demonstrate that estimates of genetic variability and differentiation among populations can be strongly influenced by marker type, their genomic location in relation to genes and by the interaction of these two factors. This highlights the importance of having an awareness of the inherent strengths and limitations associated with different molecular tools to select the most appropriate methods for accurately addressing various ecological and evolutionary questions. 相似文献
4.
Karen E. Sullam Blake Matthews Thierry Aebischer Ole Seehausen Helmut Bürgmann 《Ecology and evolution》2017,7(5):1572-1582
The presence of predators can impact a variety of organisms within the ecosystem, including microorganisms. Because the effects of fish predators and their phenotypic differences on microbial communities have not received much attention, we tested how the presence/absence, genotype, and plasticity of the predatory three‐spine stickleback (Gasterosteus aculeatus) influence aquatic microbes in outdoor mesocosms. We reared lake and stream stickleback genotypes on contrasting food resources to adulthood, and then added them to aquatic mesocosm ecosystems to assess their impact on the planktonic bacterial community. We also investigated whether the effects of fish persisted following the removal of adults, and the subsequent addition of a homogenous juvenile fish population. The presence of adult stickleback increased the number of bacterial OTUs and altered the size structure of the microbial community, whereas their phenotype affected bacterial community composition. Some of these effects were detectable after adult fish were removed from the mesocosms, and after juvenile fish were placed in the tanks, most of these effects disappeared. Our results suggest that fish can have strong short‐term effects on microbial communities that are partially mediated by phenotypic variation of fish. 相似文献
5.
Daniel I. Bolnick Lisa K. Snowberg Philipp E. Hirsch Christian L. Lauber Rob Knight J. Gregory Caporaso Richard Svanbäck 《Ecology letters》2014,17(8):979-987
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. 相似文献
6.
In the threespine stickleback Gasterosteus aculeatus model system, phenotypes are often classified into three morphs according to lateral plate number. Morph identity has been shown to be largely genetically determined, but substantial within‐morph variation in plate number exists. In this study, we test whether plate number has a plastic component in response to salinity in the low‐plated morph using a split‐clutch experiment where families were split in two, one half raised in water at 0 and the other at 30 ppt salt. We find a small salinity‐induced plastic effect on plate number in an unexpected direction, opposite to what we predicted: Fish raised in freshwater on average have slightly more plates than fish raised in saltwater. Our results confirm that heritability of plate number is high. Additionally, we find that variance in plate number at the family level can be predicted from other family level traits, which might indicate that epistatic interactions play a role in creating the observed pattern of lateral plate number variation. 相似文献
7.
Anurag Chaturvedi Joost A. M. Raeymaekers Filip A. M. Volckaert 《Molecular ecology resources》2014,14(4):768-777
An intriguing question in biology is how the evolution of gene regulation is shaped by natural selection in natural populations. Among the many known regulatory mechanisms, regulation of gene expression by microRNAs (miRNAs) is of critical importance. However, our understanding of their evolution in natural populations is limited. Studying the role of miRNAs in three‐spined stickleback, an important natural model for speciation research, may provide new insights into adaptive polymorphisms. However, lack of annotation of miRNA genes in its genome is a bottleneck. To fill this research gap, we used the genome of three‐spined stickleback to predict miRNAs and their targets. We predicted 1486 mature miRNAs using the homology‐based miRNA prediction approach. We then performed functional annotation and enrichment analysis of these targets, which identified over‐represented motifs. Further, a database resource (GAmiRdb) has been developed for dynamically searching miRNAs and their targets exclusively in three‐spined stickleback. Finally, the database was used in two case studies focusing on freshwater adaptation in natural populations. In the first study, we found 44 genomic regions overlapping with predicted miRNA targets. In the second study, we identified two SNPs altering the MRE seed site of sperm‐specific glyceraldehyde‐3‐phosphate gene. These findings highlight the importance of the GAmiRdb knowledge base in understanding adaptive evolution. 相似文献
8.
Tanja K. Kleinhappel Oliver H. P. Burman Elizabeth A. John Anna Wilkinson Thomas W. Pike 《Ethology : formerly Zeitschrift fur Tierpsychologie》2016,122(9):712-716
Chemical information is used in a variety of contexts including habitat recognition, foraging and predator avoidance, and a plethora of studies have shown that an individual's distinct chemical profile can mediate interactions with conspecifics. Interestingly, recent work has revealed that diet alone is sufficient to change the chemical profile of individuals, and with it, the way other individuals perceive and interact with them. Free amino acids are known to be utilised across species in a range of contexts, including during predator–prey and host–parasite interactions, and have been widely postulated to underpin diet‐mediated social interactions, especially in fish. However, so far no empirical evidence has been presented to support this suggestion. Using an established behavioural assay in three‐spined sticklebacks (Gasterosteus aculeatus), we aimed to assess association preferences in groups of fish fed experimental diets which differed by a single free amino acid. Our results demonstrate that free amino acids alone are sufficient to mediate interindividual association preferences, raising the possibility that such a mechanism may be widespread among aquatic animals. 相似文献
9.
Simon Pearish Miles K. Bensky Alison M. Bell 《Ethology : formerly Zeitschrift fur Tierpsychologie》2019,125(12):855-862
Populations of animals are composed of individuals that differ in ecologically relevant behaviors. Building evidence also suggests that individuals occupy different social niches. Here, in a mark–recapture experiment, we show evidence of an interacting effect of behavior and social niche on survival in the wild: Bold individuals had higher survival if they were initially captured in groups, while shy, inactive individuals had higher survival if they were initially captured when alone. These findings provide support for the hypothesis that behavioral type–environment correlations can be favored by natural selection. 相似文献
10.
Carl Smith Rowena Spence Iain Barber Mirosław Przybylski Robert J. Wootton 《Ecology and evolution》2014,4(18):3550-3554
While the genetic basis to plate morph evolution of the three‐spined stickleback (Gasterosteus aculeatus) is well described, the environmental variables that select for different plate and spine morphs are incompletely understood. Using replicate populations of three‐spined sticklebacks on North Uist, Scotland, we previously investigated the role of predation pressure and calcium limitation on the adaptive evolution of stickleback morphology and behavior. While dissolved calcium proved a significant predictor of plate and spine morph, predator abundance did not. Ecol. Evol., xxx, 2014 and xxx performed a comparable analysis to our own to address the same question. They failed to detect a significant effect of dissolved calcium on morphological evolution, but did establish a significant effect of predation; albeit in the opposite direction to their prediction. 相似文献
11.
Rowena Spence Robert J. Wootton Iain Barber Mirosław Przybylski Carl Smith 《Ecology and evolution》2013,3(6):1717-1726
The central assumption of evolutionary theory is that natural selection drives the adaptation of populations to local environmental conditions, resulting in the evolution of adaptive phenotypes. The three‐spined stickleback (Gasterosteus aculeatus) displays remarkable phenotypic variation, offering an unusually tractable model for understanding the ecological mechanisms underpinning adaptive evolutionary change. Using populations on North Uist, Scotland we investigated the role of predation pressure and calcium limitation on the adaptive evolution of stickleback morphology and behavior. Dissolved calcium was a significant predictor of plate and spine morph, while predator abundance was not. Stickleback latency to emerge from a refuge varied with morph, with populations with highly reduced plates and spines and high predation risk less bold. Our findings support strong directional selection in three‐spined stickleback evolution, driven by multiple selective agents. 相似文献
12.
The light environment influences an animal's ability to forage, evade predators, and find mates, and consequently is known to drive local adaptation of visual systems. However, the light environment may also vary over fine spatial scales at which genetic adaptation is difficult. For instance, in aquatic systems, the available wavelengths of light change over a few metres depth. Do animals plastically adjust their visual system to such small‐scale environmental light variation? Here, we show that in three‐spine stickleback (Gasterosteus aculeatus), opsin gene expression (an important determinant of colour vision) changes over a 2‐m vertical gradient in nest depth. By experimentally altering the light environment using light filters to cover enclosures in a lake, we found that opsin expression can be adjusted on a short time frame (weeks) in response to the local light environment. This is to our knowledge the smallest spatial scale on which visual adjustments through opsin expression have been recorded in a natural setting along a continuously changing light environment. 相似文献
13.
Mathew Seymour Katja Räsänen Rolf Holderegger Bjarni K. Kristjánsson 《Ecology and evolution》2013,3(3):492-502
Neutral genetic structure of natural populations is primarily influenced by migration (the movement of individuals and, subsequently, their genes) and drift (the statistical chance of losing genetic diversity over time). Migration between populations is influenced by several factors, including individual behavior, physical barriers, and environmental heterogeneity among populations. However, drift is expected to be stronger in populations with low immigration rate and small effective population size. With the technological advancement in geological information systems and spatial analysis tools, landscape genetics now allows the development of realistic migration models and increased insight to important processes influencing diversity of natural populations. In this study, we investigated the relationship between landscape connectivity and genetic distance of threespine stickleback (Gasterosteus aculeatus) inhabiting a pond complex in Belgjarskógur, Northeast Iceland. We used two landscape genetic approaches (i.e., least-cost-path and isolation-by-resistance) and asked whether gene flow, as measured by genetic distance, was more strongly associated with Euclidean distance (isolation-by-distance) or with landscape connectivity provided by areas prone to flooding (as indicated by Carex sp. cover)? We found substantial genetic structure across the study area, with pairwise genetic distances among populations (DPS) ranging from 0.118 to 0.488. Genetic distances among populations were more strongly correlated with least-cost-path and isolation-by-resistance than with Euclidean distance, whereas the relative contribution of isolation-by-resistance and Euclidian distance could not be disentangled. These results indicate that migration among stickleback populations occurs via periodically flooded areas. Overall, this study highlights the importance of transient landscape elements influencing migration and genetic structure of populations at small spatial scales. 相似文献
14.
Marius Roesti Sergey Gavrilets Andrew P. Hendry Walter Salzburger Daniel Berner 《Molecular ecology》2014,23(16):3944-3956
Parallel adaptation is common and may often occur from shared genetic variation, but the genomic consequences of this process remain poorly understood. We first use individual‐based simulations to demonstrate that comparisons between populations adapted in parallel to similar environments from shared variation reveal a characteristic genomic signature around a selected locus: a low‐divergence valley centred at the locus and flanked by twin peaks of high divergence. This signature is initiated by the hitchhiking of haplotype tracts differing between derived populations in the broader neighbourhood of the selected locus (driving the high‐divergence twin peaks) and shared haplotype tracts in the tight neighbourhood of the locus (driving the low‐divergence valley). This initial hitchhiking signature is reinforced over time because the selected locus acts as a barrier to gene flow from the source to the derived populations, thus promoting divergence by drift in its close neighbourhood. We next empirically confirm the peak‐valley‐peak signature by combining targeted and RAD sequence data at three candidate adaptation genes in multiple marine (source) and freshwater (derived) populations of threespine stickleback. Finally, we use a genome‐wide screen for the peak‐valley‐peak signature to discover additional genome regions involved in parallel marine‐freshwater divergence. Our findings offer a new explanation for heterogeneous genomic divergence and thus challenge the standard view that peaks in population divergence harbour divergently selected loci and that low‐divergence regions result from balancing selection or localized introgression. We anticipate that genome scans for peak‐valley‐peak divergence signatures will promote the discovery of adaptation genes in other organisms. 相似文献
15.
Kay Lucek Bjarni K. Kristjánsson Skúli Skúlason Ole Seehausen 《Ecology and evolution》2016,6(15):5256-5272
Cases of evolutionary diversification can be characterized along a continuum from weak to strong genetic and phenotypic differentiation. Several factors may facilitate or constrain the differentiation process. Comparative analyses of replicates of the same taxon at different stages of differentiation can be useful to identify these factors. We estimated the number of distinct phenotypic groups in three‐spine stickleback populations from nine lakes in Iceland and in one marine population. Using the inferred number of phenotypic groups in each lake, genetic divergence from the marine population, and physical lake and landscape variables, we tested whether ecosystem size, approximated by lake size and depth, or isolation from the ancestral marine gene pool predicts the occurrence and the extent of phenotypic and genetic diversification within lakes. We find intralacustrine phenotypic diversification to be the rule rather than the exception, occurring in all but the youngest lake population and being manifest in ecologically important phenotypic traits. Neutral genetic data further indicate nonrandom mating in four of nine studied lakes, and restricted gene flow between sympatric phenotypic groups in two. Although neither the phenotypic variation nor the number of intralacustrine phenotypic groups was associated with any of our environmental variables, the number of phenotypic traits that were differentiated was significantly positively related to lake size, and evidence for restricted gene flow between sympatric phenotypic groups was only found in the largest lakes where trait specific phenotypic differentiation was highest. 相似文献
16.
17.
William E. Stutz Matthew Schmerer Jessica L. Coates Daniel I. Bolnick 《Molecular ecology》2015,24(18):4629-4646
Geographic variation in parasite communities can drive evolutionary divergence in host immune genes. However, biotic and abiotic environmental variation can also induce plastic differences in immune function among populations. At present, there is little information concerning the relative magnitudes of heritable vs. induced immune divergence in natural populations. We examined immune gene expression profiles of threespine stickleback (Gasterosteus aculeatus) from six lakes on Vancouver Island, British Columbia. Parasite community composition differs between lake types (large or small, containing limnetic‐ or benthic‐like stickleback) and between watersheds. We observed corresponding differences in immune gene expression profiles among wild‐caught stickleback, using a set of seven immune genes representing distinct branches of the immune system. To evaluate the role of environmental effects on this differentiation, we experimentally transplanted wild‐caught fish into cages in their native lake, or into a nearby foreign lake. Transplanted individuals' immune gene expression converged on patterns typical of their destination lake, deviating from their native expression profile. Transplant individuals' source population had a much smaller effect, suggesting relatively weak genetic underpinning of population differences in immunity, as viewed through gene expression. This strong environmental regulation of immune gene expression provides a counterpoint to the large emerging literature documenting microevolution and genetic diversification of immune function. Our findings illustrate the value of studying immunity in natural environmental settings where the immune system has evolved and actively functions. 相似文献
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19.
Adam M. M. Stuckert Sara Drury Christopher M. Anderson Tyler B. T. Bowling Jeffrey S. Mckinnon 《Journal of fish biology》2019,94(3):520-525
We compared the colour patterns of free swimming, reproductively active male threespine stickleback Gasterosteus aculeatus of the anadromous and stream ecotypes from three geographically distinct regions. Consistent with the hypothesis of environmentally mediated selection, our results indicate ecologically replicated differences in G. aculeatus coloration between anadromous and stream-resident populations, and that G. aculeatus probably have the visual acuity to discriminate colour pattern differences between anadromous and stream-resident fish. 相似文献
20.
Laura K. Helenius Anna Aymà Padrós Elina Leskinen Hannu Lehtonen Leena Nurminen 《Ecology and evolution》2015,5(10):2021-2035
Planktivorous fish can exert strong top‐down control on zooplankton communities. By incorporating different feeding strategies, from selective particulate feeding to cruising filter feeding, fish species target distinct prey. In this study, we investigated the effects of two species with different feeding strategies, the three‐spined stickleback (Gasterosteus aculeatus (L.)) and roach (Rutilus rutilus (L.)), on a low‐diversity brackish water zooplankton community using a 16‐day mesocosm experiment. The experiment was conducted on a small‐bodied spring zooplankton community in high‐nutrient conditions, as well as a large‐bodied summer community in low‐nutrient conditions. Effects were highly dependent on the initial zooplankton community structure and hence seasonal variation. In a small‐bodied community with high predation pressure and no dispersal or migration, the selective particulate‐feeding stickleback depleted the zooplankton community and decreased its diversity more radically than the cruising filter‐feeding roach. Cladocerans rather than copepods were efficiently removed by predation, and their removal caused altered patterns in rotifer abundance. In a large‐bodied summer community with initial high taxonomic and functional diversity, predation pressure was lower and resource availability was high for omnivorous crustaceans preying on other zooplankton. In this community, predation maintained diversity, regardless of predator species. During both experimental periods, predation influenced the competitive relationship between the dominant calanoid copepods, and altered species composition and size structure of the zooplankton community. Changes also occurred to an extent at the level of nontarget prey, such as microzooplankton and rotifers, emphasizing the importance of subtle predation effects. We discuss our results in the context of the adaptive foraging mechanism and relate them to the natural littoral community. 相似文献