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344 results for “genetic testing”
Data from: Genetic patterns across an invasion's history: a test of change versus stasis for the Eurasian round goby in North America
Biological invasions comprise accidental evolutionary experiments, whose genetic compositions underlie relative success, spread, and persistence in new habitats. However, little is known about whether, or how, their population genetic patterns change temporally and/or spatially across the invasion's history. Theory predicts that most would undergo founder effect, exhibit low genetic divergence across the new range, and gain variation over time via new arriving propagules. To test these predictions, we analyze population genetic diversity and divergence patterns of the Eurasian round goby Neogobius melanostomus across the two decades of its North American invasion in the Laurentian Great Lakes, comparing results from 13 nuclear DNA microsatellite loci and mitochondrial DNA cytochrome b sequences. We test whether "genetic stasis", "genetic replacement", and/or "genetic supplement" scenarios have occurred at the invasion's core and expansion sites, in comparison to its primary native source population in the Dnieper River, Black Sea. Results reveal pronounced genetic divergence across the exotic range, with population areas remaining genetically distinct and statistically consistent across two decades, supporting "genetic stasis" and "founder takes most". The original genotypes continue to predominate, whose high population growth likely outpaced the relative success of later arrivals. The original invasion core has stayed the most similar to the native source. Secondary expansion sites indicate slight allelic composition convergence towards the core population over time, attributable to some early "genetic supplementation". The geographic and temporal coverage of this investigation offers a rare opportunity to discern population dynamics over time and space in context of invasion genetic theory versus reality.
Data from: Testing the species–genetic diversity correlation in the Aegean archipelago: towards a haplotype-based macroecology?
A positive correlation between species and genetic diversity (SGDC) has been proposed, consistent with neutral predictions in macroecology. We assessed the SGDC in tenebrionid beetle communities of the Aegean archipelago on fifteen islands of different sizes, distances to mainland, and ages of isolation. Alpha- and beta-diversity of species and haplotypes were assessed using sequences of >1000 individuals (mitochondrial Cytochrome Oxidase I and nuclear Muscular Protein 20) to test the SGDC. We show that: (i) there is a strong species-area and haplotype-area relationship; (ii) species richness in island communities is correlated with intraspecific genetic diversity in the constituent species except when island size or distance to mainland are factored out in partial correlations; (iii) community similarity declines exponentially at an increasing rate when calculated based on species, nuclear and mtDNA haplotypes; and (iv) distance decay of community similarity is slower in dispersive sand-dwelling lineages compared to less dispersive lineages that are not sand-obligate. Taken together, these correlated patterns at the species and haplotype level are consistent with individual-based stochastic dispersal proposed by neutral theories of biodiversity. The results also demonstrate the utility of haplotype data for exploring macroecological patterns in poorly known biota and predicting large-scale biodiversity patterns based on genetic inventories of local samples.
Data from: A test of the "flexible stem" model of evolution: ancestral plasticity, genetic accommodation, and morphological divergence in the threespine stickleback radiation
If an ancestral stem group repeatedly colonizes similar environments, developmental plasticity specific to that group should consistently give rise to similar phenotypes. Parallel selection on those similar phenotypes could lead to the repeated evolution of characteristic ecotypes, a property common to many adaptive radiations. A key prediction of this "flexible stem" model of adaptive radiation is that patterns of phenotypic divergence in derived groups should mirror patterns of developmental plasticity in their common ancestor. The threespine stickleback radiation provides an excellent opportunity to test this prediction because the marine form is representative of the ancestral stem group, which has repeatedly given rise to several characteristic ecotypes. We examined plasticity of several aspects of shape and trophic morphology in response to diets characteristic of either the derived benthic or limnetic ecotypes. When marine fish were reared on alternative diets, plasticity of head and mouth shape paralleled phenotypic divergence between the derived ecotypes, supporting the flexible stem model. Benthic and limnetic fish exhibited patterns of plasticity similar to the marine population; however, some differences in population means were present, as well as subtle differences in shape plasticity in the benthic population, indicating a role for genetic accommodation in this system.
Data from: A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)
The central-marginal hypothesis (CMH) predicts that population size, genetic diversity, and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core-to-edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size, and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core-to-edge genetic patterns. These results suggest that multiple processes may influence a species' distribution based on the heterogeneity of habitat across a species' range and that replicated sampling may be needed to accurately test the CMH. Our work also emphasizes the importance of identifying the geographic range core with methods other than using the Euclidean center on a map, which may help to explain discrepancies among other empirical tests of the CMH. Assessing core to edge population genetic patterns across an entire species' range accompanied with ENM can inform our general understanding of the mechanisms leading to species' geographic range limits.
Data from: What caused over a century of decline in general intelligence? Testing predictions from the genetic selection and neurotoxin hypotheses
Several converging lines of evidence indicate that general intelligence (g) has declined in Western populations. The causes of these declines are debated. Here, two hypotheses are tested: (1) selection acting against genetic variants that promote g causes the decline and (2) the presence of neurotoxic pollution in the environment causes the decline. A linear mixed model was devised to test (1) and (2), in which the secular decline in a "heritable g" (g.h) chronometric factor (comprised of convergent indicators of simple reaction time, working memory, utilization frequencies of high difficulty and also social-intelligence-indicating vocabulary items and per capita macro-innovation rates) was predicted using a neurotoxin chronometric factor (comprised of convergent secular trends among measures of lead, mercury and dioxin + furan pollution, in addition to alcohol consumption) and a polygenic score chronometric factor (comprised of polygenic score means for genetic variants predictive of g, sourced from US and Icelandic age-stratified cohorts). Bivariate correlations revealed that (other than time) only the polygenic score factor was significantly associated with declining g.h (r = .393, p < .05 vs. .033, ns for the neurotoxin factor). Using a hierarchical linear mixed model approach incorporating 25 year lags between the predictors and g.h, time period, operationalized categorically as fifths of a century, accounted for the majority of the variance in the decline in g.h (partial η^2 = .584, p < .05). Net of time period and neurotoxins, changing levels of polygenic scores also significantly predicted variance in the decline in g.h (partial η^2 = .253, p < .05); however, changing levels of neurotoxins did not significantly predict variance in g.h net of time (partial η^2 = .027 ns). Within-period analysis indicates that the independent significant positive effect of the polygenic score factor on g.h was restricted to the third fifth of a century period (β = .202, p < .05).
Data for: Global frequency analyses of canine progressive rod-cone degeneration–progressive retinal atrophy and collie eye anomaly using commercial genetic testing data
<p>Hundreds of genetic variants associated with canine traits and disorders have been identified, with commercial tests offered. However, the geographic distributions and changes in allele and genotype frequencies over prolonged, continuous periods of time are lacking. This study utilized a large set of genotypes from dogs tested for the progressive rod-cone degeneration–progressive retinal atrophy (prcd-PRA) G>A missense PRCD variant (n = 86,667) and the collie eye anomaly (CEA)-associated NHEJ1 deletion (n = 33,834) provided by the commercial genetic testing company (Optigen/Wisdom Panel, Mars Petcare Science & Diagnostics). These data were analyzed using the chi-square goodness-of-fit test, time-trend graphical analysis, and regression modeling in order to evaluate how test results changed over time. The results span fifteen years, representing 82 countries and 67 breeds/breed mixes. Both diseases exhibited significant differences in genotype frequencies (p = 2.7 × 10−152 for prcd-PRA and 0.023 for CEA) with opposing graphical trends. Regression modeling showed time progression to significantly affect the odds of a dog being homozygous or heterozygous for either disease, as do variables including breed and breed popularity. This study shows that genetic testing informed breeding decisions to produce fewer affected dogs. However, the presence of dogs homozygous for the disease variant, especially for prcd-PRA, was still observed fourteen years after test availability, potentially due to crosses of unknown carriers. This suggests that genetic testing of dog populations should continue.</p>
A pilot study evaluating consumer motivations, perceptions, and responses to direct-to-consumer (DTC) canine genetic test results
<p>Survey responses exported from Qualtrics XM platform used for data analysis. The objectives of the study were to evaluate the user experience of current Wisdom Panel customers and evaluate their motivations to pursue canine genetic services, their perceptions of the services and test(s) used, and their response to the canine genetic test results. The file format provided is for Excel. Data analysis was completed using SPSS version 28. Please contact the author directly with any questions about the data.</p>
Data from: Parapatric genetic introgression and phenotypic assimilation: testing conditions for introgression between Hercules beetles (Dynastes, Dynastinae)
The prevalence and consequences of genetic introgression between species have been intensively debated. I used Hercules beetles as examples to test for conditions that may be associated with the occurrence of introgression. RADseq data were used to reconstruct the species tree and history of introgression between Hercules beetles. Image data from museum specimens were used to investigate the phenotypic similarity of two adaptive traits between species from two distinct climatic realms (Nearctic vs. Neotropical). Genetic introgression was identified between Hercules beetles living in geographic proximity (parapatric). Phylogenetic relatedness and phenotypic similarity did not predict nor preclude genetic introgression between species. Phenotypic assimilation in body coloration was evident between distantly related Hercules beetles codistributed in Central America, where directional introgression was also statistically supported from the putative donor to receiver lineages. The number of introgressed loci was significantly higher between species with than without phenotypic similarity. I discuss the implications of recent studies on adaptive genetic introgression by providing supporting evidence from the Hercules beetle system.
Data from: Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing
Migration traits are presumed to be complex and to involve interaction among multiple genes, thus we employed both univariate analyses and multivariate Random Forest (RF) machine learning algorithm to conduct association mapping of 15,239 single nucleotide polymorphisms (SNPs) for adult migration-timing phenotype in steelhead (Oncorhynchus mykiss). Our study focused on a model natural population of steelhead that exhibits two distinct migration-timing life histories with high levels of admixture in nature. Neutral divergence was limited between fish exhibiting summer- and winter-run migration owing to high levels of interbreeding, but a univariate mixed linear model found three SNPs from a major effect gene to be significantly associated with migration-timing (p < 0.000005) that explained 46% of trait variation. Alignment to the annotated S. salar genome provided evidence that all three SNPs localize within a 46 kb region overlapping GREB1-like (an estrogen target gene) on chromosome Ssa03. Additionally, multivariate analyses with RF identified that these 3 SNPs plus 15 additional SNPs explained up to 60% of trait variation. These candidate SNPs may provide the ability to predict adult migration-timing of steelhead to facilitate conservation management of this species and this study demonstrates the benefit of multivariate analyses for association studies.
Data for: A selfish genetic element and its suppressor causes abnormalities to testes in a fly
<p class="MsoNormal">Selfish genetic elements (SGEs), specifically X-chromosome meiotic drive (XCMD), create huge conflicts within a host's genome and can have profound effects on fertility. Suppressors are a common evolutionary response to XCMD to negate its costs. However, whether suppressors themselves can cause negative non-target effects remains understudied. Here, we examine whether the intragenomic conflicts created by XCMD and its suppressor affect gonad morphology in <em>Drosophila subobscura. </em>We found significant differences in testes, seminal vesicle, and accessory gland size depending on whether a male carried a non-driving X chromosome, an XCMD, and if the XCMD was suppressed. We also found the first evidence of abnormal testes development that is specifically associated with a suppressor of XCMD. Unlike other studies, our evidence suggests that XCMD in <em>D. subobscura </em>creates major abnormalities to male gonads. These abnormalities are most frequent if both XCMD and its suppressor are both present. While costs of suppression have importance in theoretical models, they have largely been ignored in empirical XCMD systems. Overall, this study highlights that genetic conflict, created by SGEs and their suppressors, is a potent evolutionary force that can have major impacts on gonad development and gametogenesis. <span><br></span></p>
APOL1 Genetic Testing Program for Living Donors
ClinicalTrials.gov study NCT04910867. IPD Sharing: NO. Countries: 1. Publications: 1.
Personalised Therapy for Metastatic ADPC Determined by Genetic Testing and Avatar Model Generation
ClinicalTrials.gov study NCT02795650. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
APOL1 Genetic Testing in African Americans
ClinicalTrials.gov study NCT05656261. IPD Sharing: UNDECIDED. Countries: 1. Publications: 6.
Testing Spanish-language Genetic Literacy
ClinicalTrials.gov study NCT01610583. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Genetic of Response to Acute Saline Load Test in Hypertension (Naload)
ClinicalTrials.gov study NCT04625569. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Testing of NBIA Genes: Analysis of Genetic Heterogeneity and Validation of Mitochondrial Markers for Assessing Causality of Sequence Variants.
ClinicalTrials.gov study NCT05615571. IPD Sharing: NO. Countries: 1. Publications: 1.
Genetic Testing or Clinical Assessment in Determining the Need for Chemotherapy in Women With Breast Cancer That Involves No More Than 3 Lymph Nodes
ClinicalTrials.gov study NCT00433589. IPD Sharing: Not stated. Countries: 1. Publications: 11.
Stand up to Cancer: MAGENTA (Making Genetic Testing Accessible)
ClinicalTrials.gov study NCT02993068. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Genetic Testing in Primary Congenital Glaucoma Patients
ClinicalTrials.gov study NCT01136460. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Choices About Genetic Testing And Learning Your Risk With Smart Technology
ClinicalTrials.gov study NCT06184867. IPD Sharing: NO. Countries: 1. Publications: 0.
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Allen Brain Atlas
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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.