Find research datasets worth reusing

Impacts of ecological restoration on the genetic diversity of plant species: A global meta-analysis

1. In contrast to the depth of knowledge available for the enhancement of plant species diversity and ecosystem services through ecological restoration, our understanding of how ecological restoration impacts genetic diversity (GD) of plant species has not yet been synthesized. 2. We performed a global meta-analysis to examine whether ecological restoration improved GD of plant species in restored populations. First, we compared the GD of restored populations with reference or degraded populations. Second, we explored whether the influence of ecological restoration on plant GD varies between species with different characteristics (life form and threat status), between different restoration strategies (active/passive, seeding/planting, mixture/non-mixture) or between different restoration times (<50 and ≥50 years; with an average of 29.3 years). 3. The GD of restored populations was significantly lower (HE, 1.06%; PPB, 5.10%, and SWI, 4.95%) than in reference populations but was comparable to degraded populations. The inbreeding coefficient (FIS, the proportion by which the heterozygosity of an individual is reduced by inbreeding) was consistently comparable between restored populations and reference or degraded populations. 4. Woody species but not herbs had significantly lower GD in restored populations than in reference populations. Forest but not grassland ecosystem had significantly lower GD in restored populations than in reference populations. Passive but not active restoration, seeding rather than planting, and mixing materials from different sources rather than using a single source, all significantly increased the GD of restored populations. When the restoration time was ≥50 years, in contrast to <50 years, GD was comparable between the restored and reference populations. 5. Synthesis and applications. In general, ecological restoration did not significantly improve the GD of plant species compared to reference or degraded populations. This might be due in part to the relatively short restoration time. Using passive restoration, seeding, and mixed sources could significantly increase the GD of restored populations. We emphasize that GD should not be treated as a minor cobenefit of ecological restoration for other purposes and that the recovery of GD should be listed as a vital goal in future ecological restoration with plant species.

Data for: Who defines the "personal utility" of genetic and genomic testing?

<div> <div> <div> Importance: Expansion in the clinical use of genetic and genomic testing has led to a recognition that these tests provide personal as well as clinical utility to patients and families. It is essential to ensure that members of diverse sociodemographic backgrounds are included in defining and measuring personal utility. Objective: To determine the demographics of participants contributing to the development of a definition of personal utility for genetic and genomic testing. Evidence Review: We searched PubMed, Scopus, Web of Science, and Embase for peer-reviewed literature published between 2003 and January 2022 on the personal utility of genetic or genomic sequencing. Our review included both qualitative and quantitative studies with samples that included patients, their family members, or the general public. Eligible studies could examine any clinical genetic or genomic test and required the use of the term "utility." Authors extracted and reviewed study and participant characteristics including number of participants, study location (U.S. or international), primary methodology (qualitative or quantitative), race and ethnicity, gender, income, and education data. Findings: Our final review included 53 studies and 13,315 total participants. Gender was provided for 95.6% of participants (n=12,724), of whom 61.5% were female (n=7,823). Race and/or ethnicity was provided for 83.0% of participants (n=11,048), of whom 82.2% (n=9,083) were White. The remaining participants were identified as Hispanic/Latinx (5.5%, n=607), Asian American and Pacific Islander (3.8%, n=421), Black (3.5%, n=387), multiracial (0.2%, n=27), and various other racial or ethnic categories (3.7%, n=412). Educational attainment was reported for 82.6% of participants. Among these participants, 71.2% (n=7,830) had a bachelor's degree or higher. Income was reported for 66.5% of participants (n=8,857), and 66% of these participants (n=5,831) reported income above the U.S. median. Conclusions and Relevance: Our results suggest that the concept of personal utility in genetic and genomic testing in the U.S. is disproportionately defined by the perspectives of a narrow subset of the population – specifically non-Hispanic White, well-educated women with above-average household incomes. If we are to provide equitable care in the areas of genomics and genetics, we will need to expand research to include more diverse and representative samples. </div> </div> </div>

Genetic insights into the age-specific biological mechanisms governing human ovarian ageing

There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modelling framework, which determines the time-dependency of DNA variant-age-at-onset associations, without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the sign of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages, and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age-dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modelling of large-scale biobank data.

Data from: Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild

The vast variation in floral traits across angiosperms is often interpreted as the result of adaptation to pollinators. However, studies in wild populations often find no evidence of pollinator-mediated selection on flowers. Evolutionary theory predicts this could be the outcome of periods of stasis under stable conditions, followed by shorter periods of pollinator change that provide selection for innovative phenotypes. We asked if periods of stasis are caused by stabilizing selection, absence of other forms of selection, or by low trait ability to respond even if selection is present. We studied a plant predominantly pollinated by one bee species across its range. We measured heritability and evolvability of traits, using genome-wide relatedness in a large wild population, and combined this with estimates of selection on the same individuals. We found evidence for both stabilizing selection and low trait heritability as potential explanations for stasis in flowers. The area of the standard petal is under stabilizing selection, but the variability is not heritable. A separate trait, floral weight, presents high heritability, but is not currently under selection. We show how a simple pollination environment coincides with the absence of current prerequisites for adaptive evolutionary change, while heritable variation remains to respond to future selection pressures.

Genetic variation in sexual size dimorphism is associated with variation in sex-specific plasticity in Drosophila

The difference in body size between females and males, or sexual size dimorphism (SSD), is ubiquitous, and yet we have a poor understanding of the developmental-genetic mechanisms that generate it, and how these mechanisms may vary within and among species. Such an understanding of the genetic architecture of SSD is important if we are to evaluate alternative models of SSD evolution, but is difficult to describe because SSD is a characteristic of populations, not individuals. Here, we overcome this challenge by using isogenic lineages of Drosophila to measure SSD for 196 genotypes. We demonstrate extensive genetic variation for SSD, primarily driven by higher levels of genetic variation for body size among females than males. While we observe a general increase in SSD with sex-averaged body size (pooling for sex) among lineages, the vast majority of variation in SSD is independent of sex-averaged body size, and shows a strong genetic correlation with sex-specific plasticity, such that increased female-biased SSD is associated with increased body-size plasticity in females. Our data are consistent with the condition-dependence hypothesis of sexual dimorphism, and suggest that SSD in Drosophila is a consequence of selection on the developmental-genetic mechanisms that regulate the plasticity of body size.

opencc-by-4.0Feb 2022View details →

Recurrent, founder and hypomorphic variants contribute to shaping the genetic landscape of Joubert syndrome

Introduction: This database includes the raw data linked with the paper “Recurrent, founder and hypomorphic variants contribute to the genetic landscape of Joubert syndrome”. In this paper we reported eleven recurrent variants in seven distinct JS genes occurring in our large European JS cohort, including a previously unreported variant in KIAA0586 (c.1006C>T). Methods: We evaluated the frequencies of these variants in our cohort of >500 European JS patients and compared them with controls (from three large Italian non-JS cohorts and from the gnomAD database), and with an independent cohort of about 600 JS probands from the United States. Results: All variants were markedly enriched in the European JS cohort compared to all controls. When comparing allele frequencies in the two JS cohorts, the Ashkenazi Jewish founder variant (TMEM216 c.218G>T) was significantly enriched in American JS compared to European JS patients, while the MKS1 c.1476T>G variant was about ten times more frequent among European JS. Frequencies of all remaining variants were comparable in the two cohorts. Genotyping of several microsatellite markers across the gene loci in carriers of seven variants identified four novel founder haplotypes. Of note, MKS1 c.1476T>G was consistently detected in compound heterozygosity with deleterious variants in JS patients, while it was found in homozygosity in an unaffected parent. Functional studies on fibroblasts from this healthy carrier and her affected son showed a similarly reduced percentage of ciliated cells compared to unaffected controls, but much shorter cilia in the patient than in the unaffected homozygous parent, consistent with a hypomorphic effect.

Genetic dissection of triplicated chromosome 21 orthologs yields varying skeletal traits in Down syndrome model mice

Down syndrome (DS) phenotypes result from triplicated genes, but effects of three copy genes are not well known. A mouse mapping panel genetically dissecting human chromosome 21 (Hsa21) syntenic regions was used to investigate the contributions and interactions of triplicated Hsa21 orthologous genes on mouse chromosome 16 (Mmu16) on skeletal phenotypes. Skeletal structure and mechanical properties were assessed in femurs of male and female Dp9Tyb, Dp2Tyb, Dp3Tyb, Dp4Tyb, Dp5Tyb, Dp6Tyb, Ts1Rhr, and Dp1Tyb;Dyrk1a+/+/- mice. Dp1Tyb mice, with the entire Hsa21 homologous region of Mmu16 triplicated, display bone deficits similar to those of humans with DS and served as a baseline for other strains in the panel. Bone phenotypes varied based on triplicated gene content, sex, and bone compartment. Three copies of Dyrk1a played a sex-specific, essential role in trabecular deficits and may interact with other genes to influence cortical deficits related to DS. Triplicated genes in Dp9Tyb and Dp2Tyb mice improved some skeletal parameters. As triplicated genes can both improve and worsen bone deficits, it is important to understand the interaction between and molecular mechanisms of skeletal alterations affected by these genes.

Genetic determinants of atherogenic indexes

Genetic determinants of atherogenic indexes

Genetic Characterization of the Norwegian Apple Collection

Commercial fruit production in Norway is located at around latitude 60° north, demanding careful choice of adapted cultivars. The most comprehensive collection of apple genetic resources in Norway is being kept in the Norwegian Apple Collection (NAC) at Njøs Fruit and Berry Centre (NJØS). The collection contains around 350 accessions and was recently genotyped with a single nucleotide polymorphism (SNP) array. Curated SNP data were used for structure assessment, diversity analysis, pedigree confirmation, and core collection development. In the subsequent SNP analysis, we identified several duplicates and parent–offspring relationships. The collection was equally diverse across the geographic regions represented. Different methods for analyzing population structure were applied. K-means clustering and a Bayesian modeling approach with prior assumptions of the data revealed five subpopulations associated with geographic breeding centers. The collection has a distinct genetic structure and low relatedness among the accessions; hence, two 100 accession core collections were created. These new core collections will allow breeders and researchers to use the NAC efficiently. The results from this study suggest that several of the accessions in the Norwegian Apple Collection could be of high importance for breeding programs.

Data from: Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in sage grouse Centrocercus urophasianus

Sex ratio, and the extent to which it varies over time, is an important factor in the demography, management, and conservation of wildlife populations. We estimated pre-breeding sex ratio of greater sage-grouse (Centrocercus urophasianus) in a peripheral, geographically isolated population in northwestern Colorado during two consecutive winters using closed-population, robust-design, multi-state, genetic mark-recapture models in program MARK (White and Burnham 1999). This data release includes the data files (.inp format) used in those models, as described in Shyvers et al. 2023. The data include capture histories and auxiliary data for individual greater sage-grouse collected during two study seasons: Season 1 (winter 2012-2013) and Season 2 (winter 2013-2014) and are readable using program MARK or notepad. Each data row includes the unique bird identification number (GMR-ID); the bird's encounter history for n= sampling occasions coded as a static state (M = male, F = female); the group ID; and a region covariate (0 = North, 1 = South). The data were adapted from those originally developed for Shyvers et al. 2020 and applied using Closed Robust Design Multi-state (CRDMS) Huggins' p and c w/state probabilities in program MARK to obtain estimates of Omega, enabling estimation of sex ratio with associated confidence intervals (see Shyvers et al. 2023). References: Shyvers, J.E., Walker, B.L., Oyler-McCance, S.J., Fike, J.A. and Noon, B.R. 2023. Genetic mark-recapture analysis reveals large annual variation in pre-breeding sex ratio of greater sage-grouse. Wildlife Biology (https://doi.org/10.1002/wlb3.01085) Shyvers, J.E., Walker, B.L., Oyler‐McCance, S.J., Fike, J.A. and Noon, B.R., 2020. Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in Sage Grouse Centrocercus urophasianus. Ibis, 162(3), pp.749-765. White, G. C., and K. P. Burnham. 1999. Program Mark: survival estimation from populations of marked animals. – Bird Study 46:120–139.

Conditional indirect genetic effects of caregivers on brood in the clonal raider ant

Caregivers shape the rearing environment of their young. Consequently, offspring traits are influenced by the genes of their caregivers via indirect genetic effects (IGEs). However, the extent to which IGEs are modulated by environmental factors, other than the genotype of social partners (i.e., intergenomic epistasis), remains an open question. Here we investigate how broods are influenced by the genotype of their caregivers in the clonal raider ant, Ooceraea biroi, a species in which the genotype, age, and number of both caregivers and brood can be experimentally controlled. First, we used four clonal lines to establish colonies that differed only in the genotype of caregivers and measured effects on foraging activity, as well as IGEs on brood phenotypes. In a second experiment, we tested whether these IGEs are conditional on the age and number of caregivers. We found that caregiver genotype affected the feeding and foraging activity of colonies, and influenced the rate of development, survival, body size, and caste fate of brood. Caregiver genotype interacted with other factors to influence the rate of development and survival of brood, demonstrating that IGEs can be conditional. Thus, we provide an empirical example of phenotypes being influenced by IGE-by-environment interactions beyond intergenomic epistasis, highlighting that IGEs of caregivers/parents are alterable by factors other than their brood's/offspring's genotype.

Life on the edge: a changing genetic landscape within an iconic American pika metapopulation over the last half century

Declines and extirpations of American pika (Ochotona princeps) populations at historically occupied sites started being documented in the literature during the early 2000s. Commensurate with global climate change, many of these losses at peripheral and lower elevation sites have been associated with changes in ambient air temperature and precipitation regimes. Here, we report on a decline in available genetic resources for an iconic American pika metapopulation, located at the southwestern edge of the species distribution in the Bodie Hills of eastern California, USA. Composed of a highly fragmented habitat created by hard rock mining, the ore dumps at this site were likely colonized by pikas at the end of the 19th century from nearby natural talus outcrops. Genetic data extracted from both contemporary samples and archived natural history collections allowed us to track population and patch-level genetic diversity for Bodie pikas across three distinct sampling points during the last half-century (1948, 1988-1991, 2013-2015). In addition to declines in within-population allelic diversity and expected heterozygosity, we observed an increase in population structure and a reduction in effective population size from more extensive sampling of extant patches during 1988-1991 and 2013-2015, respectively. Furthermore, census records from the last 50 years as well as archived museum samples collected in 1947 from a nearby pika population in the Wassuk range (NV, USA) provide further support for the increasing isolation and genetic coalescence occurring in this region. This study highlights the importance of museum samples and long-term monitoring in contextualizing our understanding of population viability.

Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution

Supplementary Tables for article "Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution"

DaRT-seq raw data of Eucalyptus spp for the genetic assessment of the value of restoration planting within an endangered eucalypt woodland

Assessment of woodland restoration often focusses on stand demographics, but genetic factors likely influence long-term stand viability. We examined the genetic composition of Yellow Box (Eucalyptus melliodora) trees in endangered Box-Gum Grassy Woodland in SE Australia, some 30 years after planting with seeds of reportedly local provenance. Using DArT sequencing for 1406 SNPs, we compared genetic diversity and population structure of planted E. melliodora trees with remnant bushland trees, paddock trees, and natural recruits. Genetic patterns imply that natural stands and paddock trees had historically high gene flow (among group pairwise FST = 0.04–0.10). Genetic diversity was highest among relictual paddock trees (He = 0.17), while diversity of revegetated trees was identical to natural bushland trees (He = 0.14). Bayesian clustering placed the revegetated trees into six genetic groups with four corresponding to genotypes from paddock trees, indicating that revegetated stands are mainly of genetically diverse, local provenance. Natural recruits were largely derived from paddock trees with some contribution from planted trees. A few trees have likely hybridised with other local eucalypt species which are unlikely to compromise stand integrity. We show that paddock trees have high genetic diversity and capture historic genetic variety and provide important foci for natural recruitment of genetically diverse and outcrossed seedlings.

Dog guardians and genetic testing: Survey textbox responses & human-animal bond influences

Project was exported from Atlas.ti version 23, data analysis was completed using version 9. This subset data was derived from Wisdom PanelTM consumers in which participants provided qualitative responses and answered HAB related questions (see <a href="https://doi.org/10.3390/ani12233360">https://doi.org/10.3390/ani12233360</a>). Qualitative data were obtained via open-ended textboxes. In light of a number of participants providing meaningful data, a post-hoc analysis was added to report central themes present and provide further characterization of potential human-dog relationship influences. Please contact the author directly with any questions about the data.

Genomic tools for comparative conservation genetics among three recently diverged stag beetles (Lucanus, Lucanidae)

We are witnessing a rapid decline in global biodiversity. International protocols and local conservation laws have been installed to counter such an unprecedented rate of decline. However, quantitatively evaluating how much biodiversity has been lost due to climatic and anthropogenic effects and how much biodiversity has been restored due to conservation efforts remain challenging. We applied a comparative conservation genomic approach to statistically and quantitatively address these questions using three geographical taxa from a stag beetle species complex. We found that the three sky-island taxa formed three independently evolving units without detectable post-divergence gene flow; furthermore, the three taxa, which have been divergent from each other since the mid-Pleistocene, have experienced episodes of demographic decline in the past. More importantly, even though idiosyncratic anthropogenic exploitations have been hypothesized to impact the recent demographic history (< 100 years) differently, we found a shared pattern of continuous decline in effective population size among the three geographical taxa. We argue that future empirical studies should include more taxa, in addition to the focal species, that may or may not be affected by the focal historical events to avoid making biased conservation plans.

Data set: genetic variants related to SARS-CoV-2 viremia

Data set generated to evaluate the association between SNPs from genes related to SARS-CoV-2 pathogenesis and the presence of viremia.

opencc-zeroMay 2023View details →

Dataset for: Plasticity and genetic effects contribute to different axes of neural divergence in a community of mimetic Heliconius butterflies

Changes in ecological preference, often driven by spatial and temporal variation in resource distribution, can expose populations to environments with divergent information content. This can lead to adaptive changes in the degree to which individuals invest in sensory systems and downstream processes, to optimize behavioural performance in different contexts. At the same time, environmental conditions can produce plastic responses in nervous system development and maturation, providing an alternative route to integrating neural and ecological variation. Here, we explore how these two processes play out across a community of Heliconius butterflies. Heliconius communities exhibit multiple Mullerian mimicry rings, associated with habitat partitioning across environmental gradients. These environmental differences have previously been linked to heritable divergence in brain morphology in parapatric species pairs. They also exhibit a unique dietary adaptation, known as pollen feeding, that relies heavily on learning foraging routes, or trap-lines, between resources, which implies an important environmental influence on behavioural development. By comparing brain morphology across 133 wild-caught and insectary reared individuals from seven Heliconius species, we find strong evidence for interspecific variation in patterns of neural investment. These largely fall into two distinct patterns of variation; first, we find consistent patterns of divergence in the size of visual brain components across both wild and insectary reared individuals, suggesting genetically encoded divergence in the visual pathway. Second, we find interspecific differences in mushroom body size, a central component of learning and memory systems, but only among wild caught individuals. The lack of this effect in common-garden individuals suggests an extensive role for developmental plasticity in interspecific variation in the wild. Finally, we illustrate the impact of relatively small-scale spatial effects on mushroom body plasticity by performing experiments altering the cage size and structure experienced by individual H. hecale. Our data provide a comprehensive survey of community level variation in brain structure, and demonstrate that genetic effects and developmental plasticity contribute to different axes of interspecific neural variation.

opencc-zeroMay 2023View details →

Data from: A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea

Conjugative plasmids (CP) are self-transmissible mobile genetic elements which transfer DNA between host cells via Type IV Secretion Systems (T4SS). While T4SS-mediated conjugation has been well-studied in bacteria, information is sparse in Archaea and known representatives exist only in the Sulfolobales order of Crenarchaeota. Here we present the first self-transmissible plasmid identified in a Euryarchaeon, Thermococcus sp. 33-3. The 103 kbp plasmid, pT33-3, is seen in CRISPR-spacers throughout the Thermococcales order. We demonstrate that pT33-3 is a bona fide conjugative plasmid that requires cell-to-cell contact, and is dependent upon canonical, plasmid-encoded T4SS-like genes. Under laboratory conditions pT33-3 transfers to various Thermococcales, and transconjugants propagate at 100°C. Using pT33-3, we developed a genetic toolkit which allows modification of phylogenetically diverse Archaeal genomes. We demonstrate pT33-3–mediated plasmid mobilization and subsequent targeted genome modification in previously untransformable Thermococcales species, and extend this process to interphylum transfer to a Crenarchaeon.