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opencc-zeroDec 2020View details →

Genotype data from: Restoration of transborder connectivity for Fennoscandian brown bears (Ursus arctos)

Knowledge about the connectivity among natural populations is essential to identify management units for effective conservation actions. Conservation-minded management has led to the recovery of large carnivore populations in northern Europe, possibly restoring connectivity between the two separated, but expanding brown bear (Ursus arctos) populations on the Scandinavian peninsula to the west and Karelia, a part of the large Eurasian population, to the east. The degree of connectivity between these populations has been poorly understood, therefore we investigated the extent of connectivity between the two populations using autosomal microsatellites and Y chromosome haplotypes in 924 male bears (the dispersing sex), sampled during a period of 12 years (2005-2017) across the transborder area where these two populations meet. Our results showed that the two populations are not genetically isolated as reported in earlier studies. We detected recent asymmetrical gene flow at a rate (individuals per generation) of 4.6-5.5 (1%) from Karelia into Scandinavia, whereas the rate was approximately 27.1-34.5 (8%) in the opposite direction. We estimated historical gene flow of effective number of migrants to be between 1.7 and 2.5 between the populations. Analyses of Y chromosome markers supported these results. Successful recovery and expansion of both populations led to the restoration of connectivity, however, it is asymmetric, possibly due to different recovery histories and population densities. By aligning monitoring between neighboring countries, we were able to better understand the biological processes across the relevant spatial scale.

Data from: Effect of craniofacial genotype on the relationship between morphology and feeding performance in cichlid fishes

The relationship between morphology and performance is complex, but important for understanding the adaptive nature of morphological variation. Recent studies have sought to better understand this system by illuminating the interconnectedness of different functional systems; however, the role of genetics is often overlooked. In this study, we attempt to gain insights into this relationship by examining the effect of genotypic variation at putative craniofacial loci on the relationship between morphology and feeding performance in cichlids. We studied two morphologically disparate species, as well as a morphologically intermediate hybrid population. We assessed feeding performance, jaw protrusion, and general facial morphology for each fish. We also genotyped hybrid animals at six previously identified craniofacial loci. Cichlid species were found to differ in facial geometry, kinematic morphology, and performance. Significant correlations were also noted between these variables; however, the explanatory power of facial geometry in predicting performance was relatively poor. Notably, when hybrids were grouped by genotype, the relationship between shape and performance improved. This relationship was especially robust in animals with the specialist allele at sox9b, a well-characterized regulator of craniofacial development. These data suggest a novel role for genotype in influencing complex relationships between form and function.

Data from: Phenotypic and genotypic variation across a stable white-eye (Zosterops sp.) hybrid zone in central South Africa

The interbreeding of two species after a period of separation (secondary contact) most often results in stable areas of hybridization or tension zones characterized by selection against hybrid individuals. Three plumage forms of Zosterops meet and interbreed in central South Africa. Here we examine how phenotypic measures (biometric and plumage) and genotypic markers (mitochondrial and nuclear DNA) change through a putative hybrid zone located in the area where the ranges of the Orange River white-eye Zosterops pallidus and a subspecies of the Cape white-eye Zosterops virens capensis meet. Four of the five sequenced loci (i.e. ATP6, MUSK, GADPH and TGF-β2) showed strong divergence and differentiation between allopatric parental populations, whereas the sex-linked CHD1Z locus exhibited high homogeneity. Microsatellite data also distinguished between pure Z. pallidus and Z. v. capensis populations. Together, the nuclear data (introns and microsatellites) identified at least 12 hybrid individuals as later generation hybrids (i.e. F2 or backcrosses), and no F1 hybrids were detected. As genetic incompatibility does not appear to play a role in restricting this stable hybrid zone, it is likely that environmental conditions including biome type and edge effect are constraining hybrid zone movement.

Data from: Testing genotypic variation of an invasive plant species in response to soil disturbance and herbivory

Herbivores, competitors, and predators can inhibit biological invasions ("biotic resistance" sensu Elton 1959), while disturbance typically promotes biological invasions. Although biotic resistance and disturbance are often considered separately in the invasion literature, these two forces may be linked. One mechanism by which disturbance may facilitate biological invasions is by decreasing the effectiveness of biotic resistance. The effects of both disturbance and biotic resistance may vary across invading genotypes, and genetic variation in the invasive propagule pool may increase the likelihood that some genotypes can overcome biotic resistance or take greater advantage of disturbance. We conducted an experimental field trial in which we manipulated soil disturbance (thatch removal and loosening soil) and the presence of insect herbivores and examined their effects on the invasion success of 44 Medicago polymorpha genotypes. As expected, insecticide reduced leaf damage and increased Medicago fecundity, suggesting that insect herbivores in this system provide some biotic resistance. Soil disturbance increased Medicago fecundity, but did not alter the effectiveness of biotic resistance by insect herbivores. We found significant genetic variation in Medicago in response to disturbance, but not in response to insect herbivores. These results suggest that the ability of Medicago to invade particular habitats depends on the amount of insect herbivory, the history of disturbance in the habitat, and how the specific genotypes in the invader pool respond to these factors.

Data from: Phylogenetic relationships, breeding implications, and cultivation history of Hawaiian taro (Colocasia esculenta) through genome-wide SNP genotyping

Taro, Colocasia esculenta, is one of the world's oldest root crops and of particular economic and cultural significance in Hawai'i, where historically more than 150 different landraces were grown. We developed a genome-wide set of more than 2400 high-quality single nucleotide polymorphism (SNP) markers from 70 taro accessions of Hawaiian, South Pacific, Palauan, and mainland Asian origins, with several objectives: (a) uncover the phylogenetic relationships between Hawaiian and other Pacific landraces, (b) shed light on the history of taro cultivation in Hawai'i, and (c) develop a tool to discriminate among Hawaiian and other taros. We found that almost all existing Hawaiian landraces fall into five monophyletic groups that are largely consistent with the traditional Hawaiian classification based on morphological characters, e.g., leaf shape and petiole color. Genetic diversity was low within these clades but considerably higher between them. Population structure analyses further indicated that the diversification of taro in Hawai'i most likely occurred by a combination of frequent somatic mutation and occasional hybridization. Unexpectedly, the South Pacific accessions were found nested within the clades mainly composed of Hawaiian accessions, rather than paraphyletic to them. This suggests that the origin of clades identified here preceded the colonization of Hawai'i, and that early Polynesian settlers brought taro landraces from different clades with them. In the absence of a sequenced genome, this marker set provides a valuable resource towards obtaining a genetic linkage map, and to study the genetic basis of phenotypic traits of interest to taro breeding such as disease resistance.

opencc-zeroDec 2017View details →

Data from: Genotyping by sequencing and genome–environment associations in wild common bean predict widespread divergent adaptation to drought

Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome–environment associations in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using Genotyping by Sequencing (GBS) to discover single-nucleotide-polymorphisms (SNPs). The wild beans represented Mesoamerica, Guatemala, Colombia, Ecuador/Northern Peru and Andean groupings. We found high polymorphism with a total of 22,845 SNPs across the 86 accessions loci that confirmed genetic relationships for the groups. As a second objective, we quantified allelic associations with a bioclimatic-based drought index using 10 different statistical models that accounted for population structure. Based on the optimum model, 115 SNPs in 90 regions, widespread in all 11 common bean chromosomes, were associated with the bioclimatic-based drought index. A gene coding for an Ankyrin repeat-containing protein and a phototropic-responsive NPH3 gene were identified as potential candidates. Genomic windows of 1Mb containing associated SNPs had more positive Tajima's D scores than windows without associated markers. This indicates that adaptation to drought, as estimated by bioclimatic variables, has been under natural divergent selection, suggesting that drought tolerance may be favorable under dry conditions but harmful in humid conditions. Our work exemplifies that genomic signatures of adaptation are useful for germplasm characterization, potentially enhancing future marker-assisted selection and crop improvement.

opengpl-2.0Feb 2016View details →

Raw hexaploid genotype data

Raw microarray data from an F1 population of hexaploid chrysanthemum. The file is tab-separated and has sample names in columns and probe names in rows.

opencc-by-4.0Apr 2024View details →

Soybean Root Phenotype and Genotype Data from the Piney Purdue Agricultural Center (PPAC), Indiana

This data repository contains records of root phenotypes collected in the Pinney Purdue Agricultural Center (PPAC) (Wanatah, Indiana, USA) on 24 soybean genotypes in 2022 along with their genotype information from the intersection of the BARCSoySNP6K and SoySNP50K assays. The repository contains the following files: Bogati_soybean_root_phenotype_data1.xlsx 6k_and_50k_geno.map 6k_and_50k_geno.ped The map file contains chromosome number, SNP ID, Genetic Distance, and Base pair position. The ped file contains sample name (first two columns) with genotype data corresponding to the .map file beginning in column 7.   Acknowledgements:  To-Chia Ting, Luis Vargas, and Sajad Jamshidi assisted in the collection of root phenotype data. Chance Clark helped extract DNA for genotyping.

opencc-by-4.0Oct 2023View details →

Mingrelian SNP Genotype Data

This dataset contains data from 645,337 single nucleotide polymorphisms (SNPs) that were genotyped on GenoChip 2+ microarrays. The SNP data were ascertained from the mtDNA, Y-chromosome and autosomes for each individual, depending on their biological sex. In total, 5,205 mtDNA and 10,272 Y-chromosome SNPs were extracted from the array data. These data files have been uploaded as .csv files and also be uploaded as plink-formatted files. Details about the analysis of the SNP data can be found in the associated manuscript:Theodore G Schurr, Ramaz Shengelia, Michel Shamoon-Pour, David Chitanava, Shorena Laliashvili, Irma Laliashvili, Redate Kibret, Yanu Kume-Kangkolo, Irakli Akhvlediani, Lia Bitadze, Iain Mathieson, Aram Yardumian, Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus), Genome Biology and Evolution, 2023; evad198, <a href="https://doi.org/10.1093/gbe/evad198">https://doi.org/10.1093/gbe/evad198</a>

opencc-zeroDec 2023View details →

Data for: A diverse parasite pool can improve effectiveness of biological control constrained by genotype-by-genotype interactions

The outcomes of biological control programs can be highly variable, with natural enemies often failing to establish or spread in pest populations. This variability has posed a major obstacle in use of the bacterial parasite Pasteuria penetrans for biological control of Meloidogyne species, economically devastating plant-parasitic nematodes for which there are limited management options. A leading hypothesis for this variability in control is that infection is successful only for specific combinations of bacterial and nematode genotypes. Under this hypothesis, failure of biological control results from the use of P. penetrans genotypes that cannot infect local Meloidogyne genotypes. We tested this hypothesis using isofemale lines of M. arenaria derived from a single field population and multiple sources of P. penetrans from the same and nearby fields. In strong support of the hypothesis, susceptibility to infection depended on the specific combination of host line and parasite source, with lines of M. arenaria varying substantially in which P. penetrans source could infect them. In light of this result, we tested whether using a diverse pool of P. penetrans could increase infection and thereby control. We found that increasing the diversity of the P. penetrans inoculum from one to eight sources more than doubled the fraction of M. arenaria individuals susceptible to infection and reduced variation in susceptibility across host lines. Together, our results highlight genotype-by-genotype specificity as an important cause of variation in biological control and call for the maintenance of genetic diversity in natural enemy populations.

opencc-zeroDec 2023View details →

Data from: Evaluating genotyping-in-thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non-invasive and archival samples

Genetic tools for wildlife monitoring can provide valuable information on spatiotemporal population trends and connectivity, particularly in systems experiencing rapid environmental change. Though many DNA sequencing approaches still require high quality and quantity of DNA obtained from traditional sources (e.g. blood and tissue), rapid genotyping tools such as Genotyping-in-Thousands by sequencing (GT-seq) have improved our ability to make use of degraded and less concentrated DNA commonly obtained from non-invasive and archival samples. Here, we developed a multi-purpose GT-seq panel (307 single nucleotide polymorphisms) for a climate sentinel mammal (the American pika, Ochotona princeps) for use as a genetic tool for monitoring populations in the Canadian Rocky Mountains. We optimized the panel using contemporary tissue samples (n = 77) and subsequently applied it to archival tissue (n = 17) and contemporary fecal pellet samples (n = 129) to evaluate its effectiveness at identifying individuals and sex, estimating relatedness, and inferring population structure. The panel demonstrated high efficacy with contemporary and archival tissue samples (94.7% and 90.5% genotyping success, respectively) and negligible genotyping error (0.001% and 0.0%, respectively). Despite relatively high genotyping success for fecal pellet samples (79.7%), high genotyping error (28.4%) limited its power as a monitoring tool to assess genetic variation using non-invasive samples and highlighted the need for further optimization around sample and data collection.

opencc-zeroMar 2024View details →

Original genotype data of 159 wheat samples

This dataset contains all 55K SNP original genotype data from 159 wheat samples used in the study, including SNP site IDs, chromosomes and positions, allele information, and genotype information for each material at each SNP site.

opencc-by-4.0Jun 2024View details →

Supplementary data: Effect of genotype by environment interaction (GEI) analysis for potato tuber yield and their quality traits in organic multi-environment domains of Poland

Climate and raw data supplementary to the related publication in the journal Agriculture (ISSN 2077-0472).

opencc-zeroOct 2021View details →

Genotype data of 1970 Pedunculate oak trees (Quercus robur L.) in 13 European countries at 381 gene loci covering the nuclear and organelle genome

The data set is the result of genetic inventory on 1970 Pedunculate oak trees from 197 locations in Europe. The samples are from the countries: Belarus, Bosnia, Bulgaria, Croatia, Finland, France, Germany, Hungary, Italy, Latvia, Poland, Russia and Ukraine. At each location ten individual trees were collected. The data set includes the location ID and geographic coordinates of each sampled tree (longitude and latitude in decimal degrees) and the genotype data. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs and five mitochondrial SNPs). The genotype of each individual is one row in the csv-file "genotypes". The genotypes at the nuclear markers are diploid and represented by two columns per gene marker. The genetic information at the organelle genome is haploid. For each of these gene markers one column is used. Genotypes are coded by Arabic numbers. The meaning of the numbers is explained in the table "coding genotypes" in a second csv-file.

opencc-zeroNov 2021View details →

Data from: Host-parasite dynamics shaped by temperature and genotype: quantifying the role of underlying vital rates

1. Global warming challenges the persistence of local populations, not only through heat-induced stress, but also through indirect biotic changes. We study the interactive effects of temperature, competition and parasitism in the water flea Daphnia magna. 2. We carried out a common garden experiment monitoring the dynamics of Daphnia populations along a temperature gradient. Halfway through the experiment, all populations became infected with the ectoparasite Amoebidium parasiticum, enabling us to study interactive effects of temperature and parasite dynamics. We combined Integral Projection Models with epidemiological models, parameterized using the experimental data on the performance of individuals within dynamic populations. This enabled us to quantify the contribution of different vital rates and epidemiological parameters to population fitness across temperatures and Daphnia clones originating from two latitudes. 3. Interactions between temperature and parasitism shaped competition, where Belgian clones performed better under infection than Norwegian clones, mainly due to higher survival. Infected Daphnia populations performed better at higher than at lower temperatures, mainly due to an increased host capability of reducing parasite loads. Temperature strongly affected individual vital rates, but effects largely cancelled out on a population-level. In contrast, parasitism strongly reduced fitness through consistent negative effects on all vital rates. As a result, temperature-mediated parasitism was more important than the direct effects of temperature in shaping population dynamics. Both the outcome of the competition treatments and the observed extinction patterns support our modeling results. 4. Our study highlights that shifts in biotic interactions can be equally or more important for responses to warming than direct physiological effects of warming, emphasizing that we need to include such interactions in our studies to predict the competitive ability of natural populations experiencing global warming.

opencc-by-4.0Dec 2021View details →

Supplementary Table 1. Raw data of egg quality parameters for 990 egg samples with ATOL (Animal Trait Ontology for Livestock) descriptors, as function of hen age, pen no. and genotype in 15 replicates.

Data table of egg quality parameters

opencc-by-4.0Dec 2021View details →

Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities: validation cohort meta data and parsed TCR repertoire data

Meta data corresponding the the validation cohort for the paper, "Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities" by Magdalena L Russell, Aisha Souquette, David M Levine, Stefan A Schattgen, E Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G Thomas, Frederick A Matsen IV, and Philip Bradley. These meta data include:  (1) SNP genotypes for the two SNPs which overlap with the discovery cohort          - (nicaragua_snp_genotypes_ints.tsv) -- SNP genotypes as integers          - (nicaragua_snp_genotypes_strings.tsv) -- SNP genotypes as allele strings  (2) the ancestry PCs for each individual in the validation cohort (nicaragua_snp_ancestry_PCA.tsv) (3) a file including IMGT genes and sequences used for parsing TCRB repertoire data (human_vj_allele_cdr3_nucseqs.tsv) (4) a file including IMGT genes used for parsing TCRA repertoire data (human_vj_alleles_alpha.tsv) (5) Parsed TCRA repertoire data (nicaragua_parsed_TCRA.tgz) (6) Parsed TCRB repertoire data (nicaragua_parsed_TCRB.tgz)  Corresponding raw validation cohort TCR repertoire data is available here: https://www. ncbi.nlm.nih.gov/bioproject/PRJNA762269 (The BioProject database, accession number: PRJNA762269) Software tools designed to work with these data are available here: https://github.com/phbradley/tcr-gwas

opencc-zeroDec 2021View details →

Microsatellite genotype data from: Male-biased dispersal in a fungus-gardening ant symbiosis (Matthews et al, Ecology and Evolution)

For nearly all organisms, dispersal is a fundamental life history trait that can shape their ecology and evolution. Variation in dispersal capabilities within a species exists and can influence population genetic structure and ecological interactions. In fungus-gardening (attine) ants, co-dispersal of ants and mutualistic fungi is crucial to the success of this obligate symbiosis. Female-biased dispersal (and gene flow) may be favored in attines because virgin queens carry the responsibility of dispersing the fungi, but a paucity of research has made this conclusion difficult. Here, we investigate dispersal of the fungus-gardening ant Trachymyrmex septentrionalis using a combination of maternally- (mitochondrial DNA) and biparentally-inherited (microsatellites) markers. We found three distinct, spatially isolated mitochondrial DNA haplotypes; two were found in the Florida panhandle and the other in the Florida peninsula. In contrast, biparental markers illustrated significant gene flow across this region and minimal spatial structure. The differential patterns uncovered from mitochondrial DNA and microsatellite markers suggest that most long-distance ant dispersal is male-biased and that females (and concomitantly the fungus) have more limited dispersal capabilities. Consequently, the limited female dispersal is likely an important bottleneck for the fungal symbiont. This bottleneck could slow fungal genetic diversification, which has significant implications for both ant hosts and fungal symbionts regarding population genetics, species distributions, adaptive responses to environmental change, and coevolutionary patterns.

opencc-zeroJan 2022View details →

C porosus genotype data

We collected 714 tissue samples of non-captive saltwater crocodiles Crocodylus porosus from Australia and its neighbouring countries and got them genotyped by Diversity Arrays Technology (Canberra, Australia) between 2016 and 2019. The folder contains two files named 'Report_DCroc19-4196_4_moreOrders_SNP_mapping_2.csv' and 'IDpop_sample_data_.csv'. The former contains the single-nucleotide polymorphism (SNP) data and latter has attributes (population ID, GPS coordinates, species, country) of each sample.