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267 results for “genetic change”
Genetic Diversity, Ecological Niches, and Climate Change Vulnerability of Aspens in the Upper Midwest:Leaf phenology
Quaking aspen (Populus tremuloides) is the most cosmopolitan tree species in North America and an important native at Cedar Creek and across the Midwest. Aspen stands are quite common through eastern, central, and northern Minnesota, and occur sporadically in cool, wet microclimates across the Great Plains. Currently, these stands are in decline, are poorly reproducing in the wild, and are suffering from a range of stresses. Climate change associated phenomena, drought and altered freeze-thaw cycles, have contributed to massive aspen dieback, especially in the American West. We have received funding from the National Park Service to assess the genetic diversity and hybrid status, age structure and health, ecological niche and historical rate of range contraction, and drought and freezing tolerance physiology of an aspen stand of interest at the Niobrara National Scenic River (NNSR) in northern Nebraska. As part of this project, we are also studying genetic diversity and physiological vulnerability to climate change in quaking and bigtooth (P. grandidentata) aspen populations in Minnesota, Wisconsin, Iowa, South Dakota, and Nebraska. We will use genetic markers to identify genetically unique stands and compare growth and survival of these to populations of the parent species under different drought and freeze-thaw conditions. This study will allow us to better pinpoint the causes of decline in the NNSR aspen stands and aspen stands across the upper Midwest, and potentially provide guidance to managers on the prioritization of particular stands for conservation or in identifying genetic sources for any ex situ conservation or assisted migration.
Supplementary material 8 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Table S1. Number of macroinvertebrate individuals per sample and season
Ancestral genetic variation in phenotypic plasticity underlies rapid evolutionary changes in resurrected populations of waterfleas
<p>The role that phenotypic plasticity plays in adaptive evolution has been debated for decades. This is because the strength of natural selection is dependent upon the direction and magnitude of phenotypic responses to environmental signals. Therefore, the connection between plasticity and adaptation will depend on the patterns of plasticity harbored by ancestral populations prior to a change in the environment. Yet, few studies have directly assessed ancestral variation in plasticity and tracked phenotypic changes over time. Here we resurrected historic propagules of <i>Daphnia</i> spanning multiple species and lakes in Wisconsin following the invasion and proliferation of a novel predator (spiny waterflea, <i>Bythotrephes</i> <i>longimanus</i>)<i>. </i>This approach revealed extensive genetic variation in predator-induced plasticity in ancestral populations of <i>Daphnia</i>. It is unlikely that the standing patterns of plasticity shielded <i>Daphnia</i> from selection to permit long-term coexistence with a novel predator. Instead, this variation in plasticity provided the raw materials for <i>Bythotrephes</i>-mediated selection to drive rapid shifts in <i>Daphnia</i> behavior and life history. Surprisingly, there was little evidence for the evolution of trait plasticity as genetic variation in plasticity was maintained in the face of a novel predator. Such results provide new insights into the link between plasticity and adaptation and highlight the importance of quantifying genetic variation in plasticity when evaluating the drivers of evolutionary change in the wild. </p>
Data from: The genetic architecture of fitness drives population viability during rapid environmental change
<p>The rapid global loss of biodiversity calls for improved predictions of how populations will evolve and respond demographically to ongoing environmental change. The heritability (<i>h</i><sup>2</sup>) of selected traits has long been known to affect evolutionary and demographic responses to environmental change. However, effects of the genetic architecture underlying the <i>h</i><sup>2</sup> of a selected trait on population responses to selection are less well understood. We use deterministic models and stochastic simulations to show that the genetic architecture underlying <i>h</i><sup>2</sup> can dramatically affect population viability during environmental change. Polygenic trait architectures (many loci, each with a small phenotypic effect) conferred higher population viability than genetic architectures with the same initial <i>h</i><sup>2</sup> and large-effect loci under a wide range of scenarios. Population viability also depended strongly on the initial frequency of large-effect beneficial alleles, with moderately low initial allele frequencies conferring higher viability than rare or already-frequent large-effect alleles. Greater population viability associated with polygenic architectures appears to be due to higher short term evolutionary potential compared to architectures with large-effect loci. These results suggest that integrating information on the trait genetic architecture into quantitiative genetic analysis will substantially improve our understanding and prediction of evolutionary and demographic responses to environmental change.</p>
Data from: Testing mechanisms of Bergmann's rule: phenotypic but no genetic change in body size in three passerine bird populations
Bergmann's rule predicts a decrease in body size with increasing temperature and has much empirical support. Surprisingly, we know very little about whether 'Bergmann size clines' are due to a genetic response or is a consequence of phenotypic plasticity. Here we use data on body size (mass and tarsus length) from three long-term (1979-2008) study populations of great tits (Parus major), in which there has been a temperature increase, to examine mechanisms behind Bergmann's rule. We show that adult body mass decreased over the study period in all populations and that tarsus length increased in one population. Both body mass and tarsus length were heritable and under weak positive directional selection, predicting an increase, rather than decrease, in body mass. There was no support for micro-evolutionary change and thus the observed declines in body mass were a result of phenotypic plasticity. Interestingly, this plasticity was not in direct response to temperature changes but seemed to be due to changes in prey dynamics. Our results caution against interpreting recent phenotypic body size declines as an adaptive evolutionary response to temperature changes and highlight the importance of considering alternative environmental factors when testing size clines.
Data from: Adaptive genetic potential and plasticity of trait variation in the foundation prairie grass Andropogon gerardii across the US Great Plains' climate gradient: Implications for climate change and restoration
<p>Plant response to climate depends on a species' adaptive potential. To address this, we used reciprocal gardens to detect genetic and environmental plasticity effects on phenotypic variation and combined with genetic analyses. Four reciprocal garden sites were planted with three regional ecotypes of <i>Andropogon gerardii</i>, a dominant Great Plains prairie grass, using dry, mesic, wet ecotypes originating from western KS to Illinois that span 500 to 1,200 mm rainfall year<sup>-1</sup>. We aimed to answer: (1) What is the relative role of genetic constraints and phenotypic plasticity in controlling phenotypes? 2) When planted in the home site, is there a trait syndrome for each ecotype? 3) How are genotypes and phenotypes structured by climate? (4) What are implications of these results for response to climate change and use of ecotypes for restoration? Surprisingly, we did not detect consistent local adaptation. Rather, we detected co-gradient variation primarily for most vegetative responses. All ecotypes were stunted in western KS. Eastward, the wet ecotype was increasingly robust relative to other ecotypes. In contrast, fitness showed evidence for local adaptation in wet and dry ecotypes with wet and mesic ecotypes producing little seed in western KS. Earlier flowering time in the dry ecotype suggests adaptation to end of season drought. Considering ecotype traits in home site, the dry ecotype was characterized by reduced canopy area and diameter, short plants, and low vegetative biomass and putatively adapted to water limitation. The wet ecotype was robust, tall with high biomass and wide leaves putatively adapted for the highly competitive, light-limited Eastern Great Plains. Ecotype differentiation was supported by random forest classification and PCA. We detected genetic differentiation and outlier genes associated primarily with precipitation. We identified candidate gene GA1 for which allele frequency associated with plant height. Sourcing of climate adapted ecotypes should be considered for restoration.</p>
Data from: Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation
We tested the hypothesis that the rate of marsupial cranial evolution is dependent on the distribution of genetic variation in multivariate space. To do so, we carried out a genetic analysis of cranial morphological variation in laboratory strains of Monodelphis domestica and used estimates of genetic covariation to analyze the morphological diversification of the Monodelphis brevicaudata species group. We found that within-species genetic variation is concentrated in only a few axes of the morphospace and that this strong genetic covariation influenced the rate of morphological diversification of the brevicaudata group, with between-species divergence occurring fastest when occurring along the genetic line of least resistance. Accounting for the geometric distribution of genetic variation also increased our ability to detect the selective regimen underlying species diversification, with several instances of selection only being detected when genetic covariances were taken into account. Therefore, this work directly links patterns of genetic covariation among traits to macroevolutionary patterns of morphological divergence. Our findings also suggest that the limited distribution of Monodelphis species in morphospace is the result of a complex interplay between the limited dimensionality of available genetic variation and strong stabilizing selection along two major axes of genetic variation.
Data from: Predictability and irreversibility of genetic changes associated with flower color evolution in Penstemon barbatus
Two outstanding questions in evolutionary biology are whether, and how often, the genetic basis of phenotypic evolution is predictable; and whether genetic change constrains evolutionary reversibility. We address these questions by studying the genetic basis of red flower color in Penstemon barbatus. The production of red flowers often involves the inactivation of one or both of two anthocyanin pathway genes, Flavonoid 3',5'-hydroxylase (F3'5'h) and Flavonoid 3'-hydroxylase (F3'h). We used gene expression and enzyme function assays to determine that redundant inactivating mutations to F3'5'h underlie the evolution of red flowers in P. barbatus. Comparison of our results to previously characterized shifts from blue to red flowers suggests that the genetic change associated with the evolution of red flowers is predictable: when it involves elimination of F3'5'H activity, functional inactivation or deletion of this gene tends to occur; however, when it involves elimination of F3'H activity, tissue-specific regulatory substitutions occur and the gene is not functionally inactivated. This pattern is consistent with emerging data from physiological experiments indicating that F3'h may have pleiotropic effects and is thus subject to purifying selection. The multiple, redundant inactivating mutations to F3'5'h suggest that reversal to blue-purple flowers in this group would be unlikely.
Data from: Temporal changes in genetic variability in three bumblebee species from Rio Grande do Sul, South Brazil
[No abstract entered]
SNP data: Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high-transmission
<p>Genetic diversity and population structure of <em>Plasmodium falciparum</em> are assessed here using three established methods (i) SNP barcoding (panel of 24-biallelic loci), (ii) microsatellite genotyping (panel of 12-multiallelic loci), and (iii) varcoding (fingerprinting var gene diversity, akin to microhaplotyping) to identify changes in parasite population genetics in response to a short-term indoor residual spraying (IRS) intervention. Typical of high seasonal transmission in Africa, multiclonal infections were found in <span>82.3% (median 3; range 1–18) and 57.8% (median 2; range 1–12) of asymptomatic individuals pre- and post-IRS, respectively, in Bongo District, Ghana. </span>Since directly phasing multilocus haplotypes for population genetic analysis is not possible for biallelic SNPs and microsatellites, we chose 200 low-complexity infections for analysis. Each genotyping method presented a different pattern of change in population diversity and structure as a consequence of variability in usable data and the relative polymorphism of the molecular markers (<a>SNPs < microsatellites < var</a>). In terms of neutral variation, the 24-SNP barcode was the least informative, largely due to the bi-allelic nature of SNPs leading to a high proportion of double-allele calls (<a>DACs</a>), whereas multiallelic microsatellites showed high haplotype diversity with ten markers but no measurable change in population structure after IRS. Varcoding provided the most informative and nuanced description of changes in population structure, showing high diversity with a subtle but measurable change to less related var repertoires as a result of the IRS intervention. Relative performance, suitability, and cost-effectiveness of the methods relevant to local malaria elimination in high-transmission endemic areas are discussed. </p>
Data from: Tracking changes in chromosomal arrangements and their genetic content during adaptation
There is considerable evidence for an adaptive role of inversions, but how their genetic content evolves and affects the subsequent evolution of chromosomal polymorphism remains controversial. Here, we track how life-history traits, chromosomal arrangements and 22 microsatellites, within and outside inversions, change in three replicated populations of Drosophila subobscura for 30 generations of laboratory evolution since founding from the wild. The dynamics of fitness-related traits indicated adaptation to the new environment concomitant with directional evolution of chromosomal polymorphism. Evidence of selective changes in frequency of inversions was obtained for seven of 23 chromosomal arrangements, corroborating a role for inversions in adaptation. The evolution of linkage disequilibrium between some microsatellites and chromosomes suggested that adaptive changes in arrangements involved changes in their genetic content. Several microsatellite alleles increased in frequency more than expected by drift in targeted inversions in all replicate populations. In particular, there were signs of selection in the O3+4 arrangement favouring a combination of alleles in two loci linked to the inversion and changing along with it, although the lack of linkage disequilibrium between these loci precludes epistatic selection. Seven other alleles increased in frequency within inversions more than expected by drift, but were not in linkage disequilibrium with them. Possibly these alleles were hitchhiking along with alleles under selection that were not specific to those inversions. Overall, the selection detected on the genetic content of inversions, despite limited coverage of the genome, suggests that genetic changes within inversions play an important role in adaptation.
Data from: Environmentally induced changes in correlated responses to selection reveal variable pleiotropy across a complex genetic network
Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of covariation in the evolutionary response between phenotypes or across environments differed depending on the environment in which selection occurred, including asymmetrical responses to selection in some cases. These results indicate that variation in pleiotropy across the stress response network is highly sensitive to the external environment. Our findings highlight the complexity of the interaction between genes and environment that influences the ability of organisms to acclimate to novel environments. They also make clear the need to identify the underlying genetic basis of genetic correlations in order understand how patterns of pleiotropy are distributed across complex genetic networks.
Testing GSK2636771 as a Potential Targeted Treatment in Cancers With PTEN Genetic Changes (MATCH-Subprotocol N)
ClinicalTrials.gov study NCT04439149. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Genetic Epidemiology of Change in CVD Risk Factors
ClinicalTrials.gov study NCT00037440. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Testing AZD9291 as Potentially Targeted Treatment in Cancers With EGFR Genetic Changes (MATCH-Subprotocol E)
ClinicalTrials.gov study NCT06303167. IPD Sharing: YES. Countries: 1. Publications: 0.
Testing Ado-Trastuzumab Emtansine as a Potential Targeted Treatment in Cancers With HER2 Genetic Changes (MATCH-Subprotocol Q)
ClinicalTrials.gov study NCT04439110. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Testing Binimetinib as a Potential Targeted Treatment in Cancers With NRAS Genetic Changes (MATCH-Subprotocol Z1A)
ClinicalTrials.gov study NCT04439344. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Testing Trametinib as a Potential Targeted Treatment in Cancers With BRAF Genetic Changes (MATCH-Subprotocol R)
ClinicalTrials.gov study NCT04439279. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Genetic Information as a Life Style Change Motivator
ClinicalTrials.gov study NCT03794141. IPD Sharing: NO. Countries: 0. Publications: 1.
Testing GDC-0032 (Taselisib) as a Potential Targeted Treatment in Cancers With PIK3CA Genetic Changes (MATCH-Subprotocol I)
ClinicalTrials.gov study NCT04439175. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.