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194 results for “Evolutionary adaptation”
A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years
<p>The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950's, opossum shrimp (<em>Mysis diluviana</em>) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Shrimp were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity and test for genetic divergence between populations and for evidence of adaptive evolution within the introduced populations in Colorado. We found overall very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was also little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that the population in Gross Reservoir is of hybrid origin, with an earlier founding population from an unknown source being later supplemented from another population. Despite the overall low genetic diversity we observed, F<sub>ST</sub> outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments.</p>
Data from: The spotted parrotfish genome provides evolutionary insight into the ecological adaptation of a keystone dietary specialist
<p>With over 600 valid species, the wrasses (family Labridae) are among the largest and most successful of the marine teleosts. They feature prominently on coral reefs where they are known not only for their impressive diversity in colouration and form, but also in their functional specialization and ability to occupy a wide variety of trophic guilds. Among the wrasses, the parrotfishes (tribe Scarini) display some one of the most dramatic examples of trophic specialization. Using abrasion-resistant biomineralized teeth, parrotfishes are able to mechanically extract protein-rich micro-photoautotrophs growing in and amongst reef carbonate material, a dietary niche that is inaccessible to most other teleost fishes. This ability to exploit an otherwise untapped trophic resource is thought to have played a role in the diversification and evolutionary success of the parrotfishes. In order to better understand the key evolutionary innovations leading to the success of these dietary specialists, we sequenced and analysed the genome of a representative species, the spotted parrotfish (<em>Cetoscarus ocellatus</em>). We find significant expansion, selection, and duplication within several detoxification gene families and a novel poly-glutamine expansion in the enamel protein ameloblastin, and we consider their evolutionary implications. Our genome provides a useful resource for comparative genomic studies investigating the evolutionary history of this highly specialized teleostean radiation.</p>
Evolutionary footprints of cold adaptation in arctic-alpine Cochlearia (Brassicaceae) – evidence from freezing experiments and electrolyte leakage
<p><span>As </span><span>global warming progresses, plants may be forced to adapt to drastically changing environmental conditions. Arctic-alpine plants have been among the first to experience the effects of climate change. As a result, cold acclimation and freezing tolerance may become increasingly crucial for the survival as winter warming events and earlier snowmelt will cause increased exposure to occasional frost. The tribe </span><span>Cochlearieae in the mustard family (Brassicaceae) </span><span>offers an instructive system for studying cold adaptation in evolutionary terms, as the two sister genera </span><em><span>Ionopsidium</span></em> <span>and </span><em><span>Cochlearia</span></em> <span>are distributed among different ecological habitats throughout the European continent and the far north into circumarctic regions. By applying an electrolyte leakage assay to leaves obtained from plants cultivated under controlled temperature regimes in growth chambers, the freezing tolerance of different </span><em><span>Ionopsidium</span></em> <span>and </span><em><span>Cochlearia</span></em> <span>species was assessed measuring lethal freezing temperature values (</span><em><span>LT</span><span>50</span></em> <span>and </span><em><span>LT</span><span>100</span></em><span>), thereby allowing for a comparison across different species and accessions in their responses to cold. We hypothesized that, owing to varying selection pressures, geographically distant species would differ in freezing tolerance. Despite </span><em><span>Ionopsidium</span></em> <span>occurring under warm and dry Mediterranean conditions and </span><em><span>Cochlearia</span></em> <span>species distributed often at cold habitats, all accessions exhibited similar cold responses. The results may indicate that physiological adaptations of primary metabolic pathways to different stressors, such as salinity and drought, may confer an additional tolerance to cold; this is because all these stressors induce osmotic challenges. </span></p>
Genomic features for adaptation and evolutionary dynamics of four Asian domestic carps
<p><span>The four major Asian domestic carps, namely grass carp, black carp, bighead carp, and silver carp, belonging to <span>Cypriniformes, <span>and are among the most important aquaculture species and sources of animal protein in China. they <span>have similar habitats, closely phylogenetic relationships, and large body sizes. However, they differ in their diet preferences, behavior, and physical traits. Here, to better understand their evolution, we generated the chromosome-level genomes of the four domestic carps. We uploaded the assembled genomes of four carps, the gene annotation files in gff format of four carps, the protein sequences files of four carps, and the analysis code or pipeline used in the article, and the readme file. This study <span>shed light on the genomic bases</span><span> driving species divergence and adaptation, providing valuable insights for future research in this field.</span></span></span></span></span></p>
Data and code from: Longevity hinders evolutionary rescue through slower growth but not necessarily slower adaptation
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Genomic features for adaptation and evolutionary dynamics of four Asian domestic carps
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A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years
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Data from: Maintaining local adaptation is key for evolutionary rescue and long-term persistence of populations experiencing habitat loss and a changing environment
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Evolutionary footprints of cold adaptation in arctic-alpine Cochlearia (Brassicaceae) – evidence from freezing experiments and electrolyte leakage
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Data from: The spotted parrotfish genome provides evolutionary insight into the ecological adaptation of a keystone dietary specialist
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Data from: Plasticity versus evolutionary divergence: what causes habitat partitioning in urban-adapted birds?
<p>Habitat partitioning can facilitate the coexistence of closely related species, and often results from competitive interference inducing plastic shifts of subordinate species in response to aggressive, dominant species (plasticity), or the evolution of ecological differences in subordinate species that reduce their ability to occupy habitats where the dominant species occurs (evolutionary divergence). Evidence consistent with both plasticity and evolutionary divergence exist, but the relative contributions of each to habitat partitioning have been difficult to discern. Here we use a global dataset on the breeding occurrence of birds in cities to test predictions of these alternative hypotheses to explain previously described habitat partitioning associated with competitive interference. Consistent with plasticity, the presence of behaviorally dominant congeners in a city was associated with a 65% reduction in occurrence of subordinate species, but only when the dominant was a widespread breeder in urban habitats. Consistent with evolutionary divergence, increased range-wide overlap with dominant congeners was associated with a 56% reduction in occurrence of subordinates in cities, even when the dominant was absent from the city. Overall, our results suggest that both plasticity and evolutionary divergence play important, concurrent roles in habitat partitioning among closely related species in urban environments.</p>
Data from: Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene
<p>Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions. Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong. We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus <i>Capreolus</i>, speciation within this genus during the Quaternary and during divergence among European roe deer (<i>C. capreolus</i>) populations. Our analyses were facilitated by the generation of a new high-coverage reference genome for the Siberian roe deer (<i>Capreolus pygargus</i>). We find progressive reductions in effective population size (<i>Ne</i>), despite very large census sizes in modern <i>C. capreolus</i> populations and show that low <i>Ne</i> has impacted the <i>C. capreolus</i> genome, reducing diversity and increasing linkage disequilibrium. Even so, we find evidence for natural selection shared among <i>C. capreolus</i> populations, including a population that has been through a severe bottleneck. During each period of transition there is evidence for selection, including at loci associated with diapause (delayed embryonic development), a phenotype restricted to this genus among the even-toed ungulates. Together these data allow us to assess expectations for the origin and diversification of a mammalian genus during a period of extreme environmental change.</p>
Data from: The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish
Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor–based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediating genes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversity has likely been a crucial substrate for selective sweeps to propel rapid adaptation.
Data from: Disentangling evolutionary, environmental and morphological drivers of plant anatomical adaptations to drought and cold in Himalayan graminoids
Understanding what determine plants ability to survive drought and cold is crucial for predicting how plants may respond to ongoing climate change. Plant survival strategies are usually characterized by morphological and physiological adaptations, while their underlying anatomical settings are largely unknown. Woody angiosperms and herbaceous dicots have repeatedly evolved small water transporting conduits and large storage parenchyma tissues at colder or drier places to cope with freezing- and drought-induced damages. However, whether these adaptations are also valid for graminoids remains unclear. Here we show that stem anatomical variations in grasses, sedges and rushes dominating in western Himalayan grasslands are driven by elevation and soil moisture via control over aboveground plant stature and belowground clonal growth, while phylogenetic constraints have only a weak effect. Phylogenetic comparative analyses controlling for confounding factors showed that the elevation-related cooling controls the conductive system through reduced vessel diameter and extended assimilatory and storage tissues with more chlorenchyma and less sclerenchyma around vessels. The soil moisture deficit, on the other hand, determines stabilization structures by promoting short-rhizomatous turf graminoids with hollow stems, thicker epidermis and deep adventitious roots in dry steppes and semi-deserts. Saline wetlands and moist alpine pastures promote long-rhizomatous short-stature plants with lower need for mechanical support (absence of hollow stem) and exposure to high evaporative forcing (thinner epidermis). Observed trends of decreasing vessel sizes and lignification rate with elevation supports the existing knowledge that narrower vessels and extensive parenchyma assist plants to grow in cold environments by avoiding freezing-induced cavitation. Our results bring novel information on ecological drivers influencing the evolution of anatomical adaptations in high mountain graminoids. Distinct grassland types, covering elevations from 2650 to 6150 m, harbor unrelated species with different evolutionary histories that have converged towards similar anatomical structures.
Data from: Cross-biome patterns in soil microbial respiration predictable from evolutionary theory on thermal adaptation
Climate warming may stimulate microbial metabolism of soil carbon, causing a carbon cycle-climate feedback whereby carbon is redistributed from soil to atmospheric CO2. The magnitude of this feedback is uncertain, in part because warming-induced shifts in microbial physiology and/or community composition could retard or accelerate soil carbon losses. Here, we measure microbial respiration rates for soils collected from 22 sites in each of three years, at locations spanning boreal to tropical climates. Respiration was measured in the laboratory with standard temperatures, moisture and excess carbon substrate, to allow physiological and community effects to be detected independent from the influence of these abiotic controls. Patterns in respiration for soils collected across the climate gradient are consistent with evolutionary theory on physiological responses that compensate for positive effects of temperature on metabolism. Respiration rates per unit microbial biomass were as much as 2.6-times higher for soils sampled from sites with a mean annual temperature (MAT) of -2.0 versus 21.7ºC. Subsequent 100-day incubations suggested differences in the plasticity of the thermal response among microbial communities, with communities sampled from sites with higher MAT having a more plastic response. Our findings are consistent with adaptive metabolic responses to contrasting thermal regimes that are also observed in plants and animals. These results may help build confidence in soil carbon-climate feedback projections by improving understanding of microbial processes represented in biogeochemical models.
Demographic feedbacks during evolutionary rescue can slow or speed adaptive evolution
<p>Populations declining toward extinction can persist via genetic adaptation in a process called evolutionary rescue. Predicting evolutionary rescue has applications ranging from conservation biology to medicine, but requires understanding and integrating the multiple effects of a stressful environmental change on population processes. Here we derive a simple expression for how generation time, a key determinant of the rate of evolution, varies with population size during evolutionary rescue. Change in generation time is quantitatively predicted by comparing how intraspecific competition and the source of maladaptation each affect the rates of births and deaths in the population. Depending on the difference between two parameters quantifying these effects, the model predicts that populations may experience substantial changes in their rate of adaptation in both positive and negative directions, or adapt consistently despite severe stress. These predictions were then tested by comparison to the results of individual-based simulations of evolutionary rescue, which validated that the tolerable rate of environmental change varied considerably as described by analytical results. We discuss how these results inform efforts to understand wildlife disease and adaptation to climate change, evolution in managed populations, and treatment resistance in pathogens.</p>
Data from: The evolutionary genomics of adaptation to stress in wild rhizobium bacteria
<p>Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. In vitro experiments demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry variation. We find discordance between inferred evolutionary histories of the core genome and nreAXY genes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, different nre alleles confer distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use.</p>
Exo-Metabolomics Data for "Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile"
<p>Exo-Metabolomics Data for "<em>Phocaeicola vulgatus</em> shapes the long-term growth dynamics and evolutionary adaptations of <em>Clostridioides difficile</em>"</p>
Illumina Sequencing Data for "Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile"
<p>Illumina Sequencing Data for "<em>Phocaeicola vulgatus</em> shapes the long-term growth dynamics and evolutionary adaptations of <em>Clostridioides difficile</em>"</p>
Data from: The evolution of egg shape in birds: Evolutionary constraints and adaptations
<p>Using accurate measures of size and shape, we studied the eggs of 955 extant species across the avian phylogeny, including 39 of the 40 orders, and 78% of the 249 families. We show that the elongation component of egg shape is largely the result of constraints imposed by the female's anatomy during egg formation, whereas asymmetry is mainly an adaptation to conditions during the incubation period. Thus, egg elongation is related to the size of the egg in relation to the size of the female's oviduct and also to either the shape of her pelvis or general body conformation associated with her mode of locomotion. Egg asymmetry is related mainly to clutch size and the structure of the incubation site, factors that influence thermal efficiency during incubation and the risk of breakage. Importantly, general patterns across the phylogeny do not always reflect the trends within families and orders. We argue that the analysis of avian egg shape is most profitably conducted within taxa where all species share similar life histories and ecologies, as there is no single factor that influences egg shape in the same way in all birds.</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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.