Find research datasets worth reusing

opencc-zeroJun 2023View details →

A case of forensic genomics in Uganda reveals animal ownership and low exotic genetic introgression in indigenous cattle

The cattle industry contributes to Uganda's agricultural output. It however faces challenges that include theft and parentage ascertainment. These challenges can benefit from recent developments in genomics and bioinformatics technologies. In the current study, we provided a proof-of-concept conflict resolution method based on the available bovine genomic tools. Briefly, two farmers we refer to as A and B contested for ownership of a group of 9 cattle. To offer objective and data-based guidance to resolving this conflict, we sampled hair samples of the 9 contested cattle as well as 7 and 2 cattle from farmers A and B respectively that were identified by these farmers as the closest relatives of the contested animals. DNA was extracted from each of the collected hair samples and subsequently genotyped on the Illumina BovineSNP50-24 version 3 BeadChip for 53218 DNA Single Nucleotide Polymorphisms (SNP) variants. Upon genotype data cleaning we retained ~30,000 SNPs which were used for different genomic analyses including principal component analysis, identity by state (IBS) analysis, and hierarchical clustering analysis, to establish the genetic relationships within and between the investigated animal groups.

opencc-zeroJun 2023View details →

Additive genetic effects in interacting species jointly determine the outcome of caterpillar herbivory

Plant-insect interactions are common and important in basic and applied biology. Trait and genetic variation can affect the outcome and evolution of these interactions, but the relative contributions of plant and insect genetic variation and how these interact remain unclear and are rarely subject to assessment in the same experimental context. Here we address this knowledge gap using a recent host range expansion onto alfalfa by the Melissa blue butterfly. Common garden rearing experiments and genomic data show that caterpillar performance depends on plant and insect genetic variation, with insect genetics contributing to performance earlier in development and plant genetics later. Our models of performance based on caterpillar genetics retained predictive power when applied to a second common garden. Much of the plant genetic effect could be explained by heritable variation in plant phytochemicals, especially saponins, peptides, and phosphatidyl cholines, providing a possible mechanistic understanding of variation in the species interaction. We find evidence of polygenic, mostly additive effects within and between species, with consistent effects of plant genotype on growth and development across multiple butterfly species. Our results inform theories of plant-insect coevolution and the evolution of diet breadth in herbivorous insects and other host-specific parasites.

opencc-by-4.0May 2019View details →

Patterns of genetic variation reflect multiple introductions and pre-admixture sources of common ragweed (Ambrosia artemisiifolia) in China

Informations about the locations and genetic diversity of Ambrosia artemisiifolia populations in published paper "Patterns of genetic variation reflect multiple introductions and pre-admixture sources of common ragweed (Ambrosia artemisiifolia) in China".

opencc-by-4.0Mar 2023View details →

Additional data and code for "You can move, but you can't hide: identification of mobile genetic elements with geNomad"

<ul> <li>benchmark_data: Data used to train and evaluate the classification models.</li> <li>giant_virus_data: Sequences and metadata of giant viruses identified in public metagenomes.</li> <li>neural_network_training: Code used to train geNomad's neural network-based classification model.</li> <li>provirus_data: Data used to train and evaluate the conditional random field model employed by geNomad to identify provirus regions.</li> <li>reference_sequences: Sequences of chromosomes, plasmids, and viruses that were used to build geNomad's marker dataset and to generate the training data for the classification models.</li> </ul>

opencc-by-4.0Mar 2023View details →

Figure 1 in Genetic diversity, phylogenetic and phylogeographic analyses of Oncideres impluviata (Germar, 1823) (Coleoptera: Cerambycidae) in Rio Grande do Sul state, Brazil

Figure 1 Adult specimen of O. impluviata - Dorsal view.

Data for: Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow (Ammospiza caudacuta)

Determining factors that shape a species' population genetic structure is beneficial for identifying effective conservation practices. We assessed population structure and genetic diversity for Saltmarsh Sparrow (Ammospiza caudacuta), an imperiled tidal marsh specialist, using 13 microsatellite markers and 964 individuals sampled from 24 marshes across the breeding range. We show that Saltmarsh Sparrow populations are structured regionally by isolation-by-distance, with gene flow occurring among marshes within ~110-135 km of one another. Isolation-by-resistance and isolation-by-environment also shape genetic variation; several habitat and landscape features are associated with genetic diversity and genetic divergence among populations. Human development in the surrounding landscape isolates breeding marshes, reducing genetic diversity and increasing population genetic divergence, while surrounding marshland and patch habitat quality (proportion high marsh and sea-level-rise trend) have the opposite effect. The distance of the breeding marsh to the Atlantic Ocean also influences genetic variation, with marshes farther inland being more divergent than coastal marshes. In northern marshes, hybridization with Nelson's Sparrow (A. nelsoni) strongly influences Saltmarsh Sparrow genetic variation, by increasing genetic diversity in the population; this has a concomitant effect of increasing genetic differentiation of marshes with high levels of introgression. From a conservation perspective, we found that the majority of population clusters have low effective population sizes, suggesting a lack of resiliency. To conserve the representative breadth of genetic and ecological diversity and to ensure redundancy of populations, it will be important to protect a diversity of marsh types across the latitudinal gradient of the species range, including multiple inland, coastal and urban populations, which we have shown to exhibit signals of genetic differentiation. It will also require maintaining connectivity at a regional level, by promoting high marsh habitat at the scale of gene flow (~130 km), while also ensuring "stepping stone" populations across the range.

Genetic erosion in an endangered desert fish during a multi-decadal megadrought despite long-term supportive breeding

Human water use combined with a recent megadrought have reduced river and stream flow through the Southwestern United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande Silvery Minnow. This species experiences 'boom-and-bust' population dynamics where large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We leveraged demographic and genetic data from wild and hatchery individuals to understand the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d=1.34) and remains low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size (NeD) were positively associated (r=0.53) with wild/total abundance, but as the proportion of hatchery-origin spawners increased, NeD was reduced (NeD r= -0.55). Megadrought limits wild spawner abundance and precludes refreshment of hatchery brood stocks with wild fish, hence we predict an increasingly hatchery-dominated population, and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.

opencc-by-4.0Mar 2023View details →

Figure 3 in Genetic diversity, phylogenetic and phylogeographic analyses of Oncideres impluviata (Germar, 1823) (Coleoptera: Cerambycidae) in Rio Grande do Sul state, Brazil

Figure 3 Physiographic regions of Rio Grande do Sul state, Brazil.

Data from: Testing concordance and conflict in spatial replication of landscape genetics inferences

The degree to which landscape genetics findings can be extrapolated to different areas of a species range is poorly understood. Here, we used a broadly distributed ectothermic lizard (Sceloporus occidentalis, Western Fence lizard) as a model species to evaluate the full role of topography, climate, vegetation, and roads on dispersal and genetic differentiation. We conducted landscape genetics analyses in five areas within the Sierra Nevada mountain range. Genetic distances calculated from thousands of ddRAD markers were used to optimize landscape resistance surfaces and infer the effects of landscape and topographic features. Across study areas, we found a great deal of consistency in the primary environmental gradients impacting genetic connectivity, along with some site-specific differences, and a range in the proportion genetic variance explained by environmental factors across study sites. High-elevation colder areas were consistently found to be barriers to gene flow, as were areas of high ruggedness and slope. High temperature seasonality and high precipitation during the winter wet season also presented a substantial barrier to gene flow in a majority of study areas. The effect of other landscape variables on genetic differentiation was more idiosyncratic and depended on specific attributes at each site. Across study areas, canyon valleys were always implicated as facilitators to dispersal and key features linking populations and maintaining genetic connectivity, though the relative importance varied in different areas. We emphasize that spatial data layers are complex and multidimensional, and careful consideration of spatial data correlation structure and robust analytic frameworks will be critical to our continued understanding of spatial genetics processes.

Low genetic diversity and shallow population structure in the broom hare, Lepus castroviejoi (Lagomorpha:Leporidae)

Microsatellite dataset of 322 hare samples from five species: 76 samples from the broom hare (Lepus castroviejoi); 81 for the European hare (L. europaeus); 68 for the Iberian hare (L. granatensis); 77 for the mountain hare (L. timidus); and 20 for the Italian hare (L. corsicanus).

Data from: Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes:Leuciscidae)

We used Nextera-tagmented reductively amplified DNA (nextRAD) sequencing data to discover SNPs in Rio Grande silvery minnow samples of known and unknown sex; and we produced two contig level genomes from Nanopore long-read sequencing. Raw NextRAD was aligned to each of the genomes. Subsequent SNP calling and filtering were repeated independently to obtain two datasets, one using the female genome as reference (female-referenced dataset) and another using the male genome (male-referenced dataset). The SNP calling identified 4.46 M raw variants in female-referenced dataset and of these 16,714 biallelic SNPs were retained after all filtering steps. For this set of SNPs, the average depth of coverage for the retained 64 females was 35.81 (ranging from 8.94 to 86.88) and 33.14 for the retained 53 males (ranging from 18.93 to 65.56). When using the male genome as reference we obtained 3.77 M raw variants and 17,920 biallelic SNPs. In this case the average depth of coverage for the same 64 females was 36.01 (ranging from 8.99 to 87.34) and for the same 53 males was 33.36 (ranging from 19.23 to 66.27).

opencc-by-4.0Nov 2022View details →

The impact of genetically controlled splicing on exon inclusion and protein structure

This repository contains raw and processed files used in Einson et. al 2022. Code used to generate these files can be found here: https://github.com/jeinson/sqtl_manuscript Descriptions of files contained within each sub directory 01_raw_psi <ul> <li>{GTEx_tissue_id}_v8.psi.tsv.gz: Unfiltered PSI output from IPSA-nf, per tissue. See methods for details about how files were created. </li> <li>gtex_v8_exon_id_map.tsv: Mapping file between exon coordinates and Ensembl gene IDs, with suffix used in GTEx v8 gencode annotation. </li> </ul> 02_qtl_results <ul> <li>cross_tissue <ul> <li>top_sQTLs_MAF05.tsv: List of top GTEx v8 sQTLs across tissues, with one exon and top variant per tissue. See methods for details. See matching file for column descriptions. </li> <li>top_sQTLs_median_psi.tsv: The median, mean, and standard deviation of PSI of each significant exon from the previous file, taken across all individuals from GTEx with data available.</li> <li>top_sQTLs_MAF05_w_anc_allele.tsv: List of top sQTLs across tissues, with additional columns for the top ψQTL ancestral and derived alleles, where available. </li> </ul> </li> <li>per_tissue <ul> <li>{GTEx_tissue_id}_combined_sQTLs.tsv.gz: Raw output of ψQTL calling using QTLtools in grouped permutational mode per tissue, with groups specified by gene. See methods for more details, and https://qtltools.github.io/qtltools/ for column descriptions. </li> </ul> </li> </ul> 03_qtl_credible_sets <ul> <li> GTEx_psi_{GTEx_tissue_id}.collapsed.txt.gz: Output of the QTL catalog fine mapping pipeline (https://github.com/eQTL-Catalogue/qtlmap), run on all exons and tissues, and collapsed using the procedure described in Methods. </li> </ul> 04_qtl_coloc <ul> <li>combined_coloc_results_full.tsv.gz: Combined output of running coloc on ψQTLs from the 18 GTEx tissues against 87 sets of GWAS summary statistics. This file contains all results, including non-significant associations. A nominal QTLtools pass was used as input. We do not include these files in this repository due to size limitations, but contact the authors if you need access to nominal QTL calls. </li> <li>top_sQTLs_with_top_coloc_event.tsv: The QTLs in top_sQTLs_MAF05.tsv with additional columns for the GWAS with the highest posterior probability of a colocalization event. Importantly, the tissue and top variant may not match the main top_sQTLs_MAF05.tsv file for every gene. </li> </ul> 05_exon_features: See matching files for description of each column.  <ul> <li>cross_tissue_constitutive_exons_with_AF.tsv: Detailed features of cross tissue constitutive exons. See methods for definition of constitutive exons. </li> <li>cross_tissue_nonsignificant_genes_with_AF.tsv: Detailed features of sufficiently variable exons with no significant variant across tissues. See methods for more details. </li> <li>top_sQTLs_MAF05_with_AF.tsv: Detailed features of top sQTLs. </li> <li>top_sQTLs_with_top_coloc_with_AF.tsv: Detailed features of sQTLs that colocalize with at least one GWAS trait. Contains columns for Euclidean distances between PAE matrices and RMSD between isoforms, among genes with a significant GWAS colocalization event. </li> </ul> 06_predicted_structures: Each prediction was run 5 times, and we report the best model in the manuscript.  <ul> <li>{protein.id}[_mutant].result <ul> <li>{protein.id}[_mutant]{_run.id}_coverage.png.gz: Plot of the number of sequences per position in MSA</li> <li>{protein.id}[_mutant]{_run.id}_PAE.png.gz: PAE matrix plots for each model</li> <li>{protein.id}[_mutant]{_run.id}_plddt.png.gz: pLDDT plots for each model</li> <li>{protein.id}[_mutant]{_run.id}_predicted_aligned_error_v1.json.gz: A PAE matrix for the best model using <a href="https://alphafold.ebi.ac.uk/faq#faq-7">AlphaFold-DB's format</a></li> <li>{protein.id}[_mutant]{_run.id}_unrelaxed_rank_{rank.num}_model_{model.num}_scores.json.gz: Per model array (list of lists) with PAE, a list of the average pLDDT and the pTM score. </li> <li>{protein.id}[_mutant]{_run.id}_unrelaxed_rank_{rank.num}_model_{model.num}_pdb.gz: Per model predicted structure in pd format</li> <li>{protein.id}[_mutant]{_run.id}.a3m.gz: A3M formatted input MSA</li> <li>cite.bibtex: BibTex file with citations for all used tools and databases</li> <li>config.json: Model input parameters</li> </ul> </li> </ul> 07_other_data <ul> <li>cross_tissue_constitutive_exons.tsv: List of exons that are constitutively spliced across multiple tissues. See methods for details. </li> <li>cross_tissue_nonsignificant_genes.tsv: List variably spliced exons with no significant sVariant in any tissue. See methods for details. </li> <li>gtex_v8_exon_id_map.rds: rds representation of a map between exon IDs, as used in the modified version of gencode v26, and exon hg38 coordinates. </li> <li>gtex_v8_n_exons_per_gene.tsv: Number of exons per gene, as annotated in the modified version of gencode v26 used in GTEx v8. </li> </ul> 08_geuvadis <ul> <li>geuvadis_psi.tsv.gz: Unfiltered PSI output from IPSA-nf, run on Geuvadis BAM files. See methods for details. (Raw data was downloaded from ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEUV)</li> <li>geuvadis_sQTLs.tsv.gz: Raw output of ψQTL calling using QTLtools in grouped permutational mode for geuvadis data, with groups specified by gene. See methods for more details, and https://qtltools.github.io/qtltools/ for column descriptions. </li> <li>remapped_gencode.v26.GRCh37.GTEx_v8.nochr.genes.gtf.gz: Lifted over version of the gencode v26 gtf file, used to define exons for PSI and qtl mapping in the geuvadis analysis. The original version that was used in the GTEx analysis is based on GRCh38, and is available here: https://storage.googleapis.com/gtex_analysis_v8/reference/gencode.v26.GRCh38.genes.gtf</li> </ul>

Genetic differentiation and evolution of broad-leaved evergreen shrub and tree varieties of Daphniphyllum macropodum (Daphniphyllaceae)

Tree form evolution is an important ecological specialization for woody species, but its evolutionary process with adaptation is poorly understood, especially on the microevolutionary scale. Daphniphyllum macropodum comprises two varieties: a tree variety growing in a warm temperate climate with light snowfall and a shrub variety growing in a cool temperate climate with heavy snowfall of Japan. Chloroplast DNA variations and genome-wide single nucleotide polymorphisms across D. macropodum populations and D. teijsmannii as an outgroup were used to reveal evolutionary process of the shrub variety. Population genetic analysis indicated that the two varieties diverged but were weakly differentiated. Approximate Bayesian computation analysis supported a scenario, which assumed migration between the tree variety and the southern populations of the shrub variety. We found migration between the two varieties where the distributions of the two varieties are in contact, it is concordant with higher tree height in the southern populations of the shrub variety than the northern populations. The genetic divergence between the two varieties was associated with snowfall. The heavy snowfall climate is considered to have developed since the middle Quaternary in this region. The estimated divergence time between the two varieties suggests that the evolution of the two varieties may be concordant with such paleoclimatic change.

Data from: Genetic variation in reproductive investment across an Ephemerality gradient in Daphnia pulex

Species across the tree of life can switch between asexual and sexual reproduction. In facultatively sexual species, the ability to switch between reproductive modes is often environmentally dependent and subject to local adaptation. However, the ecological and evolutionary factors that influence the maintenance and turnover of polymorphism associated with facultative sex remain unclear. We studied the ecological and evolutionary dynamics of reproductive investment in the facultatively sexual model species, Daphnia pulex. We found that patterns of clonal diversity, but not genetic diversity varied among ponds consistent with the predicted relationship between ephemerality and clonal structure. Reconstruction of a multi-year pedigree demonstrated the coexistence of clones that differ in their investment into male production. Mapping of quantitative variation in male production using lab-generated and field-collected individuals identified multiple putative quantitative trait loci (QTL) underlying this trait, and we identified a plausible candidate gene. The evolutionary history of these QTL suggests that they are relatively young, and male limitation in this system is a rapidly evolving trait. Our work highlights the dynamic nature of the genetic structure and composition of facultative sex across space and time and suggests that quantitative genetic variation in reproductive strategy can undergo rapid evolutionary turnover.

Genetic and morphological data from two bird genera (Cranioleuca and Geospiza) showing continuous variation

Extinction is a dominant force shaping patterns of biodiversity through time however its role as a catalyst of speciation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of 'speciation-by-extinction' in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature, indicating that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism.

opencc-by-4.0Jul 2023View details →

Additional Files for "Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank"

Additional files for the article entitled "Assessing the potential of germplasm collections for managing genetic diversity: the case of the French National Cryobank". Additional file 1: Table S1 Title: Report on the output of material since the creation of the French National Cryobank Additional file 2: Figure S1 Title: Summary of material outputs from the French National Cryobank since 1999 Additional file 3: Table S2 Title: Descriptors from the French National Cryobank data for six species Additional file 4: Figure S2 Title: Distribution of data and definition of intervals regarding breed diffusion (A), donor birth-year classes (B), and classes of donor’s age at 1st collection (C) Additional file 5: Table S3 Title: Statistics of the number of effective donors (De) according to species Additional file 6: Table S4 Title: Distribution of donors and doses across breeds Description: In green, the breeds for which the FNC collections meet FAO conditions for reconstitution of an extinct breed. In blue, the breeds for which the collections of the FNC do not yet meet FAO conditions for reconstitution of an extinct breed. In gray, FAO recommendations not available. Based on the 2012 FAO report, with 100 founder females for ruminants and horses, or 30 founder females for pigs (with a pregnancy rate of 0.6). Additional file 7: Figure S3 Title: Evolution of genetic contributions of sires and their production of direct descendants in the French National Cryobank over the period 2011–2020 for three livestock species Description: Two breeds of pigs are represented in pink (a, b), three breeds of sheep are represented in blue (c, d, e), and five breeds of cattle are represented in ochre (f, g, h, i, j). Additional file 8: Figure S4 Title: Distribution of individual IDIs of cryopreserved sires for the 17 breeds analyzed Description: Pig breeds are represented in pink, sheep breeds are represented in blue, and cattle breeds are represented in ochre. Additional file 9: Figure S5 Title: Correlation between IDI values and the year of birth of donors Additional file 10: Figure S6 Title: Prediction of IDI values based on donor’s year of birth and the motivation for entry into collection Description: Type I (for endangered breeds) is represented in purple and type III (for representative individuals of a breed over a period) is represented in orange.

opencc-by-4.0Jul 2023View details →

Genetic and phenotypic data of sexual cross

Genotypic and phenotypic data of offspring from a sexual cross of Aspergillus fumigatus strains AfIR974 and AfIR964. Genotypic data was obtained from Illumina whole genome sequencing off all progeny, and then filtered as described in Auxier et al. 2023. Phenotypic data consists of growth on different nitrogen sources (nitrate (NO3), nitrite (NO2), and hypoxanthine (hx)), which can be used to map the cnx and nia mutations introduced into the two parents using UV mutagenesis. Growth of each offspring was also assessed on 25, 50, and 100 µg/mL of acriflavine as binary states of either growth or no growth. Additionally, the data from Stapley et al. 2017, https://doi.org/10.1098/rstb.2016.0455, is presented in a more useful csv format, which was used in the publication of Auxier et al. 2023. Finally, data from Fernandes et al. 2018, https://doi.org/10.1073/pnas.171307811, was subsetted to include relevant species for comparison in Auxier et al. 2023. https://doi.org/10.1073/pnas.171307811

opencc-zeroMay 2023View details →

Tectona grandis: Narrow Genetic Base? A New Perspective on the Genetic Variability of Teak

Teak (Tectona grandis Linn. f.) is considered one of the most expensive hardwoods in the world. The dispersion of the species over the years has taken the teak beyond its origin centers and little is known about the genetic origin and genetic variability. This study aimed to investigate the genetic diversity and population structure existing in a teak germplasm bank collection in Brazil. DNA was extracted from young leaves and each sample were genotyped by whole genome sequencing at 8x of coverage, the sequencing were aligned using the genome at NCBI, and SNPcalls and quality control were made. To study the population structure of the genotypes, Bayesian variational inference was used via fastStructure, the phylogenetic tree was based on the modified Euclidean distance and the clustering by the UPGMA hierarchical method. Genetic diversity was analyzed based on the pairwise genetic divergence (Fst) of Weir and Cockerham. Genotyping by sequencing resulted in a database of approximately 1.4 million of variations SNPs were used for analysis. It was possible to identify four subpopulations with genetic variability between and within the subpopulations, so this study made it possible to confirm the existence of genetic variability in teak, contrary to what was expected.

Genetic architecture and polygenic risk score prediction of degenerative suspensory ligament desmitis (DSLD) in the Peruvian Horse

Introduction: Spontaneous rupture of tendons and ligaments is common in several species including humans. In horses, degenerative suspensory ligament desmitis (DSLD) is an important acquired idiopathic disease of a major energy-storing tendon-like structure. DSLD risk is increased in several breeds, including the Peruvian Horse. Affected horses have often been used for breeding before the disease is apparent. Breed predisposition suggests a substantial genetic contribution, but heritability and genetic architecture of DSLD have not been determined. Methods: To identify genomic regions associated with DSLD, we recruited a reference population of 183 Peruvian Horses, phenotyped as DSLD cases or controls, and undertook a genome-wide association study (GWAS), a regional window variance analysis using local genomic partitioning, a signatures of selection (SOS) analysis, and polygenic risk score (PRS) prediction of DSLD risk. We also estimated trait heritability from pedigrees. Results: Heritability was estimated in a population of 1,927 Peruvian horses at 0.22±0.08. After establishing a permutation-based threshold for genome-wide significance, 151 DSLD risk single nucleotide polymorphisms (SNPs) were identified by GWAS. Multiple regions of enriched local heritability were identified across the genome, with strong enrichment signals on chromosomes 1, 2, 6, 10, 13, 16, 18, 22, and the X chromosome. With SOS analysis, there were 66 genes with a selection signature in DSLD cases that was not present in the control group that included the TGFB3 gene. Pathways enriched in DSLD cases included proteoglycan metabolism, extracellular matrix homeostasis, and signal transduction pathways that included the hedgehog signaling pathway. The best PRS predictive performance was obtained when we fitted 1% of top SNPs using a Bayesian Ridge Regression model which achieved the highest mean of R2 on both the probit and logit liability scales, indicating a strong predictive performance. Discussion: We conclude that within-breed GWAS of DSLD in the Peruvian Horse has further confirmed that moderate heritability and a polygenic architecture underlies the trait and identified multiple DSLD SNP associations in novel tendinopathy candidate genes influencing disease risk. Pathways enriched with DSLD risk variants include ones that influence glycosaminoglycan metabolism, extracellular matrix homeostasis, and signal transduction pathways.

Dataset of avian samples collected and analyzed in: Genetic identification of avian samples recovered from solar energy installations

Renewable energy production and development will drastically affect how we meet global energy demands, while simultaneously reducing the impact of climate change. Although the possible effects of renewable energy production (mainly from solar- and wind-energy facilities) on wildlife have been explored, knowledge gaps still remain, and collecting data from wildlife remains (when negative interactions occur) at energy installations can act as a first step regarding the study of species and communities interacting with facilities. In the case of avian species, samples can be collected relatively easily (as compared to other sampling methods), but may only be able to be identified when morphological characteristics are diagnostic for a species. Therefore, many samples that appear as partial remains, or "feather spots" – known to be of avian origin but not readily assignable to species via morphology – may remain unidentified, reducing the efficiency of sample collection and the accuracy of patterns observed. To obtain data from these samples and ensure their identification and inclusion in subsequent analyses, we applied, for the first time, a DNA barcoding approach that uses mitochondrial genetic data to identify unknown avian samples collected at solar facilities to species. We also verified and compared identifications obtained by our genetic method to traditional morphological identifications using a blind test, and discuss discrepancies observed. Our results suggest that this genetic tool can be used to verify, correct, and supplement identifications made in the field and can produce data that allow accurate comparisons of avian interactions across facilities, locations, or technology types. We recommend implementing this genetic approach to ensure that unknown samples collected are efficiently identified and contribute to a better understanding of wildlife impacts at renewable energy projects.