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184 results for “threespine stickleback”
Data from: Inferring the evolution of reproductive isolation in a lineage of fossil threespine stickleback, Gasterosteus doryssus
<p>Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr's peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould's original punctuated equilibrium model combined Darwin's conjecture, Mayr's model, and 124 years of unsuccessfully sampling the fossil record for transitions. Observing such divergence, however, could illustrate the tempo and mode of evolution during early speciation. Here, we investigate peripatric divergence in a Miocene stickleback fish, <em>Gasterosteus doryssus</em>. This lineage appeared and, over ~8,000 generations, evolved significant reduction of twelve of sixteen traits related to armor, swimming, and diet, relative to its ancestral population. This was greater morphological divergence than we observed between reproductively isolated, benthic-limnetic ecotypes of extant <em>Gasterosteus aculeatus</em>. Therefore, we infer that reproductive isolation was evolving. However, local extinction of low-armoured <em>G. doryssus</em> lineages shows how young isolate populations often disappear, supporting Darwin's explanation for missing evidence and revealing a mechanism behind morphological stasis. Exctinction may also account for limited sustained divergence within the stickleback species complex and help reconcile speciation rate variation observed across time scales.</p>
Data for the manuscript: Demographic basis of spatially structured fluctuations in a threespine stickleback metapopulation
<p>Uncovering the demographic basis of population fluctuations is a central goal of population biology. This is particularly challenging for spatially structured populations, which require disentangling synchrony in demographic rates from coupling via immigration. In this study, we fit a stage-structured metapopulation model to a 29-year times series of threespine stickleback abundance in the heterogeneous and productive Lake Myvatn, Iceland. The lake comprises two basins (North and South) connected by a channel through which the stickleback disperse. The model includes time-varying demographic rates, allowing us to assess the potential contributions of recruitment and survival, spatial coupling via immigration, and demographic transience to the population's large fluctuations in abundance. Our analyses indicate that recruitment was only modestly synchronized between the two basins, whereas survival probabilities of adults were more strongly synchronized, contributing to cyclic fluctuations in the lake-wide population size with a period of approximately six years. The analyses further show that the two basins are coupled through immigration, with the North Basin subsidizing the South Basin and playing a dominant role in driving the lake-wide dynamics. Our results show that cyclic fluctuations of a metapopulation can be explained in terms of the combined effects of synchronized demographic rates and spatial coupling.</p>
Scripts and sample information for: Molecular mechanisms of Eda-mediated adaptation to freshwater in threespine stickleback
<p><span>A main goal of evolutionary biology is to understand the genetic basis of adaptive evolution. Although the genes that underlie some adaptive phenotypes are now known, the molecular pathways and regulatory mechanisms mediating the phenotypic effects of those genes often remain a black box. Unveiling this black box is necessary to fully understand the genetic basis of adaptive phenotypes, and to understand why particular genes might be used during phenotypic evolution. Here, we investigated which genes and regulatory mechanisms are mediating the phenotypic effects of the <em>Eda</em> haplotype, a locus responsible for the loss of lateral plates and changes in the sensory lateral line of freshwater threespine stickleback (<em>Gasterosteus aculeatus</em>) populations. Using a combination of RNAseq and a cross design that isolated the Eda haplotype on a fixed genomic background, we found that the Eda haplotype affects both gene expression and alternative splicing of genes related to bone development, neuronal development and immunity. These include genes in conserved pathways, like the BMP, netrin and bradykinin signalling pathways, known to play a role in these biological processes. Furthermore, we found that differentially expressed and differentially spliced genes had different levels of connectivity and expression, suggesting that these factors might influence which regulatory mechanisms are used during phenotypic evolution. Taken together, these results provide a better understanding of the mechanisms mediating the effects of an important adaptive locus in stickleback and suggest that alternative splicing could be an important regulatory mechanism mediating adaptive phenotypes.</span></p>
Repeated parallel differentiation of social learning differences in benthic and limnetic threespine stickleback fish
<p>Individuals can reduce sampling costs and increase foraging efficiency by using information provided by others. One simple form of social information use is delayed local enhancement, or increased interest in a location because of the past presence of others. We tested for delayed local enhancement in two ecomorphs of stickleback fish, benthic and limnetic, from three different lakes with putative independent evolutionary origins. Two of these lakes have reproductively isolated ecomorphs ('species-pairs'), whereas in the third a previously intact species-pair recently collapsed into a hybrid swarm. Benthic fish in both intact species-pair lakes were more likely to exhibit delayed local enhancement despite being more solitary than limnetic fish. Their behaviour and morphology suggest their current perceived risk and past evolutionary pressure from predation did not drive this difference. In the hybrid swarm lake, we found a reversal in patterns of social information use, with limnetic-looking fish showing delayed local enhancement rather than benthic-looking fish. Together, our results strongly support parallel differentiation of social learning differences in recently evolved fish species, although hybridization can apparently erode and possibly even reverse these differences.</p>
Local adaptation and the evolution of genome architecture in threespine stickleback
<p class="MsoNormal"><span>Theory predicts that local adaptation should favour the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine vs. freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harbouring multiple quantitative trait loci (QTL) for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these "genomic islands" is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a <em>de novo</em> assembly of the closely-related tubesnout (<em>Aulorhyncus flavidus</em>) genome and compared this to the genomes of threespine stickleback and two other closely related species. We found that small rearrangements, within-chromosome duplications, and Lineage-Specific Genes (LSGs) were enriched around genomic islands, and that all three chromosomes harbouring large genomic islands have experienced macro-rearrangements. We also found that duplicates and micro-rearrangements are 9.9x and 2.9x more likely to involve genes differentially expressed between marine and freshwater genotypes. While not conclusive, these results are consistent with the explanation that strong divergent selection on candidate genes drove the recruitment of rearrangements to yield clusters of locally adaptive loci.</span></p>
Local adaptation and the evolution of genome architecture in threespine stickleback
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Data for the manuscript: Demographic basis of spatially structured fluctuations in a threespine stickleback metapopulation
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Scripts and sample information for: Molecular mechanisms of Eda-mediated adaptation to freshwater in threespine stickleback
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Data from: Repeated parallel differentiation of social learning differences in benthic and limnetic threespine stickleback fish
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Data from: Is phenotypic plasticity use-it-or-lose-it? Exploring genetic assimilation of salinity-plastic traits across threespine stickleback (<em>Gasterosteus aculeatus</em>) populations
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Data from: Inferring the evolution of reproductive isolation in a lineage of fossil threespine stickleback, Gasterosteus doryssus
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Does motility-restricting fibrosis influence dispersal? An experiment in nature with threespine stickleback
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Data from: The temporal window of ecological adaptation in postglacial lakes: a comparison of head morphology, trophic position and habitat use in Norwegian threespine stickleback populations
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Prickly postglacial pioneers: freshwater plankton community composition influences fatty acid desaturase (FADS2) copy number in Southern Greenland threespine sticklebacks
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Genetic structure and historic demography of endangered unarmored threespine stickleback at southern latitudes signals a need for new management directives
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Data from: Predator life history and prey ontogeny limit natural selection on the major armour gene, Eda, in threespine stickleback
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Data from: The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback
<p>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 combine genomic, morphological and ecological datasets to investigate the genomic signatures of divergence across populations of threespine stickleback (<i>Gasterosteus aculeatus</i>) that adapted to contrasting ecological niches (benthic or limnetic) in either sympatry or allopatry. We found that genome-wide differentiation (F<sub>ST</sub>) 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 sum, 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.</p>
Microhabitat contributes to microgeographic divergence in threespine stickleback
<p><span><span><span><span><span><span><span><span><span><span><span>Since the New Synthesis, most migration-selection balance theory predicted that there should be negligible differentiation over small spatial scales (relative to dispersal), because gene flow should erode any effect of divergent selection. Nevertheless, there are classic examples of microgeographic divergence, which theory suggests can arise under specific conditions: exceptionally strong selection, phenotypic plasticity in philopatric individuals, or non-random dispersal. Here, we present evidence of microgeographic morphological variation within lake and stream populations of threespine stickleback (<i>Gasterosteus aculeatus</i>). It seems reasonable to assume, and most researchers have, that a given lake or stream population of fish is well-mixed. However, we found this assumption to be untenable. We examined trap-to-trap variation in 34 morphological traits measured on stickleback from 16 lakes and 16 streams. Most traits varied appreciably among traps within populations. Both between-trap distance and microhabitat characteristics like depth and substrate explained some of the within-population morphological variance. Microhabitat was also associated with genotype at particular loci but there was no genetic isolation by distance, implying that heritable habitat preferences may contribute to microgeographic variation. Our study adds to growing evidence that microgeographic divergence can occur across small spatial scales within individuals' daily dispersal neighborhood where gene flow is expected to be strong. </span></span></span></span></span></span></span></span></span></span></span></p>
Characterizing contemporary evolutionary change in a recently isolated population of Threespine Stickleback (Gasterosteus aculeatus L.)
<p>Parallel evolution of lateral plates and body shape in threespine stickleback (Gasterosteus aculeatus) is an iconic example of adaptation. We test a case of contemporary evolutionary transition in a recently isolated population of marine G. aculeatus in British Columbia, Canada. We investigate Ectodysplasin (Eda) genotypes, plate counts, neutral genetic divergence and whole-body phenotypes to determine genetic and phenotypic distance between this population and nearby comparative populations. Our focal population is in the process of adapting both genetically and phenotypically to a freshwater environment and we provide an example of the genetic basis for parallel evolutionon a contemporary timescale. The frequency of Eda genotypes and lateral plate phenotypes in our focal population are not consistent with those of marine or fully freshwater populations. Although our focal population is genetically distinct from nearby marine populations, these fish still more closely resemble marine populations in overall body shape while demonstrating an intriguing intermediate phenotype. Eda frequency and lateral plate phenotype change faster than body shape in response to freshwater conditions, suggesting that the pace of adaptation differs across traits in response to the same environmental conditions. Our results further bolster the case for G. aculeatus as a key model of contemporary evolution.</p>
Shedding light on the threespine stickleback circadian clock
<p>The circadian clock is an internal timekeeping system shared by most organisms, and knowledge about its functional importance and evolution in natural environments is still needed. Here, we investigated the circadian clock of wild-caught threespine sticklebacks (<i>Gasterosteus aculeatus</i>) at the behavioural and molecular levels. While their behaviour, ecology, and evolution are well studied, information on their circadian rhythms are scarce. We quantified the daily locomotor activity rhythm under a light-dark cycle (LD) and under constant darkness (DD). Under LD, all fish exhibited significant daily rhythmicity, while under DD, only 18% of individuals remained rhythmic. This interindividual variation suggests that the circadian clock controls activity only in certain individuals. Moreover, under LD, some fish were almost exclusively nocturnal, while others were active around the clock. Furthermore, the most nocturnal fish were also the least active. These results suggest that light masks activity (i.e. suppresses activity without entraining the internal clock) more strongly in some individuals than others. Finally, we quantified the expression of five clock genes in the brain of sticklebacks under DD using qPCR. We did not detect circadian rhythmicity, which could either indicate that the clock molecular oscillator is highly light-dependent, or that there was an oscillation but that we were unable to detect it. Overall, our study suggests that a strong circadian control on behavioural rhythms may not necessarily be advantageous in a natural population of sticklebacks and that the daily phase of activity varies greatly between individuals because of a differential masking effect of light.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.