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Microsatellite genotypes for adult and seedlings of the temperate seagrass (ribbon weed), Posidonia australis, from four meadows at Rottnest Island, Western Australia

Adult shoots and seedings of the ribbon weed (Posidonia australis Hook.f.), a widespread temperate seagrass, were sampled from four meadows around Rottnest Island, Western Australia. The data set contains multilocus genotypes for adult shoots from four meadows and seedlings from three meadows over two consecutive years. The metadata file contains: Pop number (1 – 10), Sample site, Latitude (S), Longitude (E), individual sample code, year of sampling, life stage (adult shoot or seedling), genotypes (2 columns per locus). The seven polymorphic microsatellite loci are: PaA1, PaA105, PaA120, PaB6, PaB8, PaB112, PaD113. Most genotypes are diploid, however, 3N genotypes are included.

Raw data containing microsatellite genotypes and otolith microchemistry data for Lutjanus argentiventris individuals from Galapagos (Ecuador) and the Gulf of California (Mexico)

The dataset contains the raw microsatellite genotypes and otolith microchemistry data for yellow snapper (Lutjanus argentiventris) individuals from Galapagos (Ecuador) and the Gulf of California (Mexico), described in the journal publication: Cavole LM, Munguia-Vega A, Miller JA, Salinas-de-Leon P, Marin Jarrin JR, Johnson AF, Laplane ER, Giron-Nava A, Aburto-Oropeza O (2023) Combining otolith chemistry and genetics to infer the population structure of yellow snapper Lutjanus argentiventris. Ecosphere.

Stage-specific genotype-by-environment interactions determine yield components in wheat

The tables (climate_data.csv, and Yield_data.csv) include the recorded climatic and measured yield components data from multi-environment field trails (2014-2017). The table (soil_water_data.csv) presents the simulated water content for the experiments. The tables (Coefficients_data.csv, and multiple_regression_coefficients_data.csv) present the log p-values of comparing models M1, M2, and M3 and their coefficients. All the necessary information to read these datasets is provided in the table (read_me.csv).

Development and application of a qPCR-based genotyping assay for Ophidiomyces ophidiicola to investigate the epidemiology of ophidiomycosis

Ophidiomycosis (snake fungal disease) is an infectious disease caused by the fungus Ophidiomyces ophidiicola to which all snake species appear to be susceptible. Significant variation has been observed in clinical presentation, progression of disease, and response to treatment, which may be due to genetic variation in the causative agent. Recent phylogenetic analysis based on whole-genome sequencing identified that O. ophidiicola strains from the United States formed a clade distinct from European strains, and that multiple clonal lineages of the clade are present in the United States. The purpose of this study was to design a qPCR-based genotyping assay for O. ophidiicola, then apply that assay to swab-extracted DNA samples to investigate whether the multiple O. ophidiicola clades and clonal lineages in the United States have specific geographic, taxonomic, or temporal predilections. To this end, six full genome sequences of O. ophidiicola representing different clades and clonal lineages were aligned to identify genomic areas shared between subsets of the isolates. Eleven hydrolysis-based Taqman primer-probe sets were designed to amplify selected gene segments and produce unique amplification patterns for each isolate, each with a limit of detection of 10 or fewer copies of the target sequence and an amplification efficiency of 90–110%. The qPCR-based approach was validated using samples from strains known to belong to specific clades and applied to swab-extracted O. ophidiicola DNA samples from multiple snake species, states, and years. When compared to full-genome sequencing, the qPCR-based genotyping assay assigned 75% of samples to the same major clade (Cohen's kappa = 0.360, 95% Confidence Interval = 0.154–0.567) with 67–77% sensitivity and 88–100% specificity, depending on clade/clonal lineage. Swab-extracted O. ophidiicola DNA samples from across the United States were assigned to six different clonal lineages, including four of the six established lineages and two newly defined groups, which likely represent recombinant strains of O. ophidiicola. Using multinomial logistic regression modeling to predict clade based on snake taxonomic group, state of origin, and year of collection, state was the most significant predictor of clonal lineage. Furthermore, clonal lineage was not associated with disease severity in the most intensely sampled species, the Lake Erie watersnake (Nerodia sipedon insularum). Overall, this assay represents a rapid, cost-effective genotyping method for O. ophidiicola that can be used to better understand the epidemiology of ophidiomycosis.

BioGraph Quality Score and Genotype Classifer Models

BioGraph Quality Score and Genotype Classifer Models v7.1.0 for use with BioGraph software available at https://github.com/spiralgenetics/biograph

Harnessing genotype-phenotype nonlinearity to accelerate biological prediction

Description: We are sharing phenotypic data sets used in the pub <a href="http://doi.org/10.57844/arcadia-5953-995f">“Harnessing genotype-phenotype nonlinearity to accelerate biological prediction”</a>. Contained within are a set of publicly available empirical phenotype data sets, synthetic phenotypes we generated, and the output of an autoencoder model trained on them. Walkthroughs for all analyses using these data are available on <a href="http://doi.org/10.5281/zenodo.8371249">GitHub</a>. Files:  <ul> <li>“ail_cleaned_phenos.RDS”: .RDS file of mouse phenotypes from Bogue et al. 2015</li> <li>“all_autoencoder_phenotype_predictions.csv“: .csv file containing accuracy statistics for all phenotype-phenotype autoencoder models analyzed in the pub</li> <li>“arapheno_cleaned_phenos.RDS“: .RDS file of Arabidopsis phenotypes from Exposito-Alonso et al. 2019</li> <li>“autoencoder_phenos.zip“: directory of synthetic phenotype sets used to train the autoencoder models</li> <li>“dgrp_cleaned_phenos.RDS”: .RDS file of DGRP fruit fly phenotypes compiled from multiple sources, originally reported in Mackay et al. 2012</li> <li>“jax_cleaned_phenos.RDS”: .RDS file of mouse phenotypes from Gonzales et al. 2018</li> <li>“nematode_cleaned_phenos.RDS”: .RDS file of nematode phenotypes from Snoek et al. 2019</li> <li>“phen_pleio_int_01_0_1.pk”: pickle of all synthetic phenotypes analyzed in the pub</li> <li>“yeast_cleaned_phenos.RDS”: .RDS file of yeast phenotypes from Bloom et al. 2019</li> </ul> A full description of how the synthetic phenotypes and autoencoder predictions were generated is available in the associated <a href="http://doi.org/10.57844/arcadia-5953-995f">pub</a>.

Data for: A predominant role of genotypic variation in both expression of sperm competition genes and paternity success in Drosophila melanogaster

The study focuses on investigating the impact of both environmental and genotypic variations on the expression of sperm competition genes and relative paternity success (i.e. second male paternity; P2) in Drosophila melanogaster. To address this, the research leverages the Drosophila Genetic Reference Panel (DGRP) inbred lines and introduces manipulation of developmental population density, specifically larval density. This experimental design allows for the examination of the effects of genotype, environment, and potential genotype-environment interactions (GEI) on the expression of seminal fluid genes, namely Sex Peptide, Acp36DE, and CG9997 and sperm competitiveness. In light of the observed genotypic influence on genes' expression, a genome-wide association study (GWAS) was also conducted for Sex Peptide and Acp36DE.

Data for: The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype

Through developmental plasticity, an individual organism integrates influences from its immediate environment with those due to the environment of its parents. While both effects on phenotypes are well documented, their relative impact has been little studied in natural systems, especially at the level of gene expression. We examined this issue in four genotypes of the annual plant Persicaria maculosa by varying two key resources light and soil moisture in both generations. Transcriptomic analyses showed that the relative effects of parent and offspring environment on gene expression (i.e., the number of differentially expressed transcripts, DETs) varied both for the two types of resource stress and among genotypes. For light, immediate environment induced more DETs than parental environment for all genotypes (although the precise proportion of parental versus immediate DETs varied among genotypes). By contrast, the relative effect of soil moisture varied dramatically among genotypes, from 8-fold more DETs due to parental than immediate conditions to 10-fold fewer. These findings provide evidence at the transcriptome level that the relative impacts of parental and immediate environment on the developing organism may depend on the environmental factor and vary strongly among genotypes, providing potential for the interplay of these developmental influences to evolve.

Microsatellite genotypes of Japanese abies species: Insights from population genetics and SDM

Range shifts during the Pleistocene shaped the unique phylogeographical structures of many species. Pleistocene range shifts gave currently allopatric species opportunities to occur in sympatry, likely resulting in ancient introgressions between related taxa. In our study, we investigate the range shifts and introgression patterns of three Japanese Abies species (A. firma, A. homolepis, and A. veitchii) by employing an extensive survey of 43 populations. This survey includes comprehensive analysis of both mitochondrial (mtDNA) and nuclear (18 microsatellites) genomes, in combination with species distribution modeling (SDM). It is important to note that these two types of markers provide distinct and complementary information, as they have different modes of inheritance and mutation rates. Bayesian clustering analysis indicates that the three species were clearly separated, with the exception of the A. homolepis var. umbellata population, which is considered a natural hybrid between A. homolepis and A. firma. However, mtDNA haplotypes of the four northern populations of A. firma were entirely replaced by two major haplotypes of A. homolepis and A. veitchii. The results of Neighbor-net, NewHybrids, STRUCTURE analyses, and SDM suggest that historical introgression between species occurred in each geographic region, with mtDNA capture being the likely mechanism. However, contrary to these findings, the ABC coalescent analysis did not support an ancient introgression. Therefore, further validation with genome-wide level data is needed to clarify this issue. Our conclusion is that climate-induced range shifts during the Pleistocene/Holocene likely played a crucial role in the observed patterns of introgression in these species.

Genotype likelihood (beagle file) and genotype (vcf) files of North Atlantic and Black Sea Harbour porpoises (Phocoena phocoena)

The Harbour porpoise (Phocoena phocoena) is a highly mobile cetacean species primarily occurring in coastal and shelf waters across the Northern hemisphere. It inhabits heterogeneous seascapes broadly varying in salinity and temperature. Here we produced 74 whole genomes at intermediate coverage to study Harbour porpoise's evolutionary history and investigate the role of local adaptation in the diversification into subspecies and populations. We identified ~6 million high-quality SNPs sampled at 8 localities across the North Atlantic and adjacent waters, which we used for population structure, demographic, and genotype-environment association analyses. Our results suggest a genetic differentiation between three subspecies (P.p. relicta, P.p. phocoena, and the recently proposed P.p meridionalis), and three distinct populations within the subspecies P.p. phocoena: Atlantic, Belt Sea, and Proper Baltic Sea. Effective population size and Tajima's D levels suggest a population contraction in Black Sea and Iberian porpoises, but a population expansion in the P.p. phocoena populations. Phylogenetic trees indicate a post-glacial colonization from a southern refugium. Genotype-environment association analysis identified salinity as a major driver in genomic variation and we identified candidate genes putatively underlying adaptation to different salinity levels. Our study highlights the value of whole genome resequencing to unravel subtle population structure in highly mobile species, shows how strong environmental gradients and local adaptation may lead to population differentiation and how neutral and adaptive markers give different perspectives on population subdivision. The results have great conservation implications as we found inbreeding and low genetic diversity in the endangered Black Sea subspecies and identified the critically endangered Proper Baltic Sea porpoises as a separate population.

opencc-by-4.0Feb 2022View details →

Data from: Evaluating predator control using two non-invasive population metrics: a camera trap activity index and density estimation from scat genotyping

Includes datasets from the Wimmera and Mallee, Victoria, Australia: - Fox camera trap data used to model activity - Fox scat SECR capture and trap files used to model density

Data From: Effects of measurement methods and growing conditions on phenotypic expression of photosynthesis in seven diverse rice genotypes

Introduction: Light response curves are widely used to quantify phenotypic expression of photosynthesis by measuring a single sample and sequentially altering light intensity within a chamber (sequential method) or by measuring different samples that are each acclimated to a different light level (nonsequential method). Both methods are often conducted in controlled environments to achieve steady-state results, and neither method involves equilibrating the entire plant to the specific light level. Methods: Here, we compare sequential and non-sequential methods in controlled (greenhouse), semi-controlled (plant grown in growth chamber and acclimated to field conditions 2-3 days before measurements), and field environments. We selected seven diverse rice genotypes (five genotypes from the USDA rice minicore collection: 310588, 310723, 311644, 311677, 311795; and 2 additional genotypes: Nagina 22 and Zhe 733) to understand (1) the limitations of different methods, and (2) phenotypic plasticity of photosynthesis in rice grown under different environments. Results: Our results show that the non-sequential method was time-efficient and captured more variability of field conditions than the sequential method, but the model parameters were generally similar between the two methods except for the maximum photosynthesis rate (Amax). Amax was significantly lower across all genotypes under greenhouse conditions compared to the growth chamber and field conditions consistent with prior work, but surprisingly the apparent quantum yield (α) and the mitochondrial respiration (Rd) were generally not different among growing environments or measurement methods. Discussion: Our results suggest that field conditions are best suited to quantify phenotypic differences across different genotypes, and the nonsequential method was better at capturing the variability in photosynthesis.

Supergene genotypes and associated phenotypes in Formica cinerea samples

Antagonistic selection has long been considered a major driver of the formation and expansion of sex chromosomes. For example, sexually antagonistic variation on an autosome can select for suppressed recombination between that autosome and the sex chromosome, leading to a neo-sex chromosome. Autosomal supergenes, chromosomal regions containing tightly linked variants affecting the same complex trait, share similarities with sex chromosomes, raising the possibility that sex chromosome evolution models can explain the evolution of genome structure and recombination in other contexts. We tested this premise in a Formica ant species wherein we identified four supergene haplotypes on chromosome 3 underlying colony social organization and sex ratio. We discovered a novel rearranged supergene variant (9r) on chromosome 9 underlying queen miniaturization. The 9r is in strong linkage disequilibrium with one chromosome 3 haplotype (P2) found in multi-queen (polygyne) colonies. We suggest that queen miniaturization is strongly disfavored in the single queen (monogyne) background, and thus socially antagonistic. As such, divergent selection experienced by ants living in alternative social 'environments' (monogyne and polygyne) may have contributed to the emergence of a genetic polymorphism on chromosome 9 and associated queen-size dimorphism. Consequently, an ancestral polygyne-associated haplotype may have expanded to include the polymorphism on chromosome 9, resulting in a larger region of suppressed recombination spanning two chromosomes. This process is analogous to the formation of neo-sex chromosomes and consistent with models of expanding regions of suppressed recombination. We propose that miniaturized queens, 16-20% smaller than queens without 9r, could be incipient intraspecific social parasites.

Data from: Coinfection with chytrid genotypes drives divergent infection dynamics reflecting regional distribution patterns

By altering the abundance, diversity, and distribution of species — and their pathogens — globalization may inadvertently select for more virulent pathogens. In Brazil's Atlantic Forest, a hotspot of amphibian biodiversity, the global trade has facilitated the co-occurrence of previously isolated enzootic and panzootic lineages of the pathogenic amphibian-chytrid (Batrachochytrium dendrobatidis, 'Bd') and generated new virulent recombinant genotypes ('hybrid'). Epidemiological data indicate that amphibian declines are most severe in hybrid zones, suggesting that coinfections are causing more severe infections or selecting for higher virulence. We investigated how coinfections involving these genotypes shaped virulence and transmission. Overall, coinfection favored the more virulent and competitively superior panzootic genotype, despite dampening its transmission potential and overall virulence. However, for the least virulent and least competitive genotype, coinfection increased both overall virulence and transmission. Thus, by integrating experimental and epidemiological data, our results provide a mechanistic insight into how globalization can select for, and propel, the emergence of introduced hypervirulent lineages, such as the globally distributed panzootic lineage of Bd.

Genotype data for: Demographic and genetic consequences of a steelhead supplementation program

Supplementation of naturally-spawning populations by the addition of hatchery-spawned individuals is commonly conducted for recovery of threatened and endangered populations and to support harvest opportunities. We present an analysis of steelhead, the anadromous form of Rainbow Trout (Oncorhynchus mykiss), returning to an integrated supplemented population in Southwest Washington over the course of 15 years. The goal of the supplementation program was to evaluate whether use of a juvenile captive broodstock and an integrated paradigm could be used to increase adult returns while avoiding negative genetic impacts to the population. Estimates of relative reproductive success (RRS) for fish spawned in the hatchery ranged from 2.4 for hatchery-origin females to 6.4 for natural-origin males, indicating that fish spawned in the hatchery produced more returning adult progeny than did fish allowed to spawn in the natural environment. We observed a slight reduction in reproductive success (RS) for hatchery-origin (relative to natural-origin) fish when spawning in the natural environment, but the difference was non-significant for males and marginally significant for females. In contrast to the relatively weak relationship between RS and origin (male P = 0.347, η2 = 0.008; female P = 0.066, η2 = 0.037), we observed a strong relationship between RS and return year (male P < 0.001, η2 = 0.896; female P < 0.001, η2 = 0.867) (i.e., hatchery- and natural-origin fish did well or poorly together each year). Hatchery-origin fish exhibited reduced genetic diversity, as well as evidence of increased temporal population structure among hatchery fish. We suspect the latter is an artifact of cultural practices that reduce diversity in age at smoltification. We conclude that the program was successful in achieving an increase in adult return, but not in avoiding negative genetic effects on the population, and that any lasting impacts of supplementation remain to be determined.

opencc-zeroOct 2023View details →

Genotype data of Philippine native pigs, Duroc, Landrace, Large White and Berkshire, using 20 ISAG-FAO recommended microsatellite markers

Microsatellite genotyping is a cost-effective method for the genetic diversity analysis of under-studied populations, such as the Philippine native pigs. We genotyped n = 196 pigs representing 7 Philippine native pig populations (n = 20 to 27 for each population) and 4 commercial transboundary breeds (n = 9 to 11 for each population). Twenty microsatellite markers, recommended by the International Society of Animal Genetics (ISAG)-FAO, were used to generate the dataset for population analysis (S0005, S0155, S0026, S0355, Sw830, Sw2410, Swr1941, Sw632, Sw24, S0228, Sw936, S0097, Sw857, Sw122, Sw2406, IGF1, Sw240, S0090, S0226, Sw72). S0218 was used as a sex marker (data not shown). All loci, except Sw24, did not deviate from Hardy Weinberg equilibrium. Each marker showed an average PIC of 0.779. A total of 260 alleles of length 86 to 272 bp were obtained. Using this dataset, we determined population structure and conservation priorities in the Philippine native pigs. This dataset contains both the raw files (.fsa) and the processed file (.txt). This dataset can be used by colleagues to increase their research coverage and achieve multi-population and multi-country comparisons, especially among Asian indigenous pigs.

restrictedIPD-UNDECIDEDFeb 2026View details →

Sofosbuvir With Pegylated Interferon and Ribavirin Hepatitis C Virus (HCV) Genotypes 1,4,5,6

ClinicalTrials.gov study NCT01329978. IPD Sharing: Not stated. Countries: 2. Publications: 2.

controlledIPD-YESFeb 2026View details →

Safety and Efficacy of Ledipasvir/Sofosbuvir Fixed Dose Combination Administered in Patients Infected With Chronic Genotype 1 or 4 HCV for Use in the Peri-Operative Liver Transplantation Setting

ClinicalTrials.gov study NCT02350569. IPD Sharing: YES. Countries: 1. Publications: 1.

controlledIPD-YESFeb 2026View details →

Safety and Efficacy of LDV/SOF Fixed-Dose Combination (FDC) ± Ribavirin in HCV Genotype 1 Subjects

ClinicalTrials.gov study NCT01726517. IPD Sharing: YES. Countries: 1. Publications: 1.