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opencc-zeroApr 2022View details →

Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq

Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RADADOR, to mitigate the ADO in outgroups by recovering missing loci from previously published transcriptomes in our study of a gymnosperm genus Torreya. Using the supplemented RAD-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and test hypotheses on diversity anomaly in eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya. Using the fossilized-birth-death model and divergence-extinction-cladogenesis method we resolved detailed biogeographic history of Torreya that suggested a Jurassic origin in the Laurasia and differential speciation and extinction among continents accounting for the modern diversity anomaly biased toward Eastern Asia (EA). The history also supported a vicariance origin of the modern Torreya from a widespread ancestor in EA and NA in the mid-Eocene, cross-Beringia exchange in the early Paleogene before the vicariant isolation, in contrast to the "Out of NA" pattern common to gymnosperms and in contrast to the "Out of EA" hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies on T. jackii, suggesting differential lineage sorting of plastid genomes among Torreya species or plastid genome capture in T. jackii.

opencc-zeroSep 2022View details →

Raw RADseq data for: Population genomics analysis with RAD, reprised: Stacks 2

Restriction enzymes have been one of the primary tools in the population genetics toolkit for 50 years, being coupled with each new generation of technology to provide a more detailed view into the genetics of natural populations. Restriction site-Associated DNA protocols, which joined enzymes with short-read sequencing technology, have democratized the field of population genomics, providing a means to assay the underlying alleles in scores of populations. More than 10 years on, the technique has been widely applied across the tree of life and served as the basis for many different analysis techniques. Here, we provide a detailed protocol to conduct a RAD analysis from experimental design to de novo analysis—including parameter optimization—as well as reference-based analysis, all in Stacks version 2, which is designed to work with paired-end reads to assemble RAD loci up to 1000 nucleotides in length. The protocol focuses on major points of friction in the molecular approaches and downstream analysis, with special attention given to validating experimental analyses. Finally, the protocol provides several points of departure for further analysis.

zenodo40/100

RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" in Journal of Evolutionary Biology

This a data set from the paper RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" to be published in Journal of Evolutionary Biology

opencc-by-4.0Mar 2018View details →

zenodo40/100

VCF File containing genotype calls for 136 Populus alba x Populus tremula hybrids obtained through both RAD-seq and GBS

VCF file used to compare genotype calls obtained through RAD-seq and GBS for 126 common garden seedlings of Populus tremula and Populus alba hybrids. See Bresadola et al. (2019) for more details.

opencc-by-4.0Mar 2019View details →

publicApr 2022View details →

Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq

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publicSep 2022View details →

Raw RADseq data for: Population genomics analysis with RAD, reprised: Stacks 2

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opencc-zeroAug 2020View details →

Data from: Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

Background The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Results Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7,542 high-quality SNPs were retained. From these, 4,236 high-quality genome-wide loci were selected for bates-probe development and 4,194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. Conclusion Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.

opencc-zeroApr 2020View details →

Sex-linked markers by genome-wide RAD sequencing to identify XX/XY Sex Chromosomes in the spiny frog (Quasipaa boulengeri)

We use genotyping by sequencing as an approach to identify sex-linked markers in the spiny frog Quasipaa boulengeri with 43 wild-collected adults from a single site. The GBS methodology identified 2 loci on sex differences in allele frequencies, 50 loci on sex differences in heterozygosity, and 523 loci on male-limited occurrence, altogether associated with males heterogamety, indicating an XX-XY system. The sex specificity of five markers was further validated by PCR amplification with a large number of additional individuals from 26 various populations in this species. A total of 27 sex linkage markers were matched to Dmrt1 gene, a ubiquitous role in sex determination and differentiation from flies and nematodes to mammals. Chromosome 1, that harboring Dmrt1, has further been assigned to a highly potential candidate sex chromosome in anurans. Five sex-linked SNP makers explored 3 sex reversals out of 133 individuals here, sparsely showing sex reversal detected in wild amphibian populations.

opencc-zeroDec 2017View details →

Data from: Finding stories in noise: mitochondrial portraits from RAD data

Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years, however, recent trends focus on genome-wide analyses. One method proposed for calibrating inferences from noisy Next-Generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequences. Most researchers using this approach appear to be unaware that many Single Nucleotide Polymorphisms (SNPs) identified from genome-wide sequence data are themselves mitochondrial, or assume that these are too few to bias analyses. Here we demonstrate two methods for mining mitochondrial markers using RAD sequence data from three South African species of yellowfish, Labeobarbus. First, we use a rigorous SNP discovery pipeline using the program STACKS, to identify variant sites in mtDNA, which we then combine into haplotypes. Secondly, we directly map sequence reads against a mitochondrial genome reference. This method allowed us to reconstruct up to 98% of the Labeobarbus mitogenome. We validated these mitogenome reconstructions through BLAST database searches and by comparisons with cytochrome b gene sequences obtained through Sanger sequencing. Finally, we investigate the organismal consequences of these data including ancient genetic exchange and a recent translocation among populations of L. natalensis, as well as interspecific hybridisation between L. aeneus and L. kimberleyensis.

opencc-zeroDec 2017View details →

Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics

Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies, and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (i) the efficacy of bleach decontamination, (ii) the effect of decontamination on RAD genotypes, and (iii) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and non-spawning (uncontaminated) herring. Samples were soaked for 10 minutes in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction-site associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes, and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes, and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data, and can impact downstream analyses.

opencc-zeroNov 2023View details →

Genetic diversity, genetic differentiation and demographic history of Cryptomeria (Cupressaceae), a Tertiary relict plant in East Asia based on RAD sequencing

Genetic structure and distribution patterns of modern floras are strongly affected by climatic change and geographical isolation. In the present study, we applied restriction-site-associated DNA sequencing (RAD-seq) to analyze the genetic structure and to simulate the demographic history of two extant Cryptomeria species in Japan (C. japonica) and Southeastern China (C. japonica var. sinensis). Thirteen natural populations representing the entire species distributed in East Asia were collected from Japan and China. At the species level, the genetic diversity of Cryptomeria was moderate (Ho = 0.217, He = 0.203) with a significant genetic differentiation among populations (85.30%, P < 0.001), especially between Japan and China lineages (FST = 0.147). Except for the Lushan (LS) population in China, all populations were clustered into two lineages (Japanese and Chinese), which was consistent with their geographical distribution. Approximate Bayesian computations (ABC) model indicated that the current two geographical lineages diverged from a common ancestral lineage and that their divergence time was about 0.417 ~ 0.139 million years ago (Mya). Geographical isolation, climate change in the Quaternary, and human disturbance played important roles in genetic variation and distribution patterns of Cryptomeria in East Asia. Our results shed light on the speciation processes of Cryptomeria and provide a reference for the conservation of this species.

opencc-by-4.0Dec 2024View details →

IT-RAD weather radar data collected on 5 September 2015 during an exceptionally intense hailstorm in the Gulf of Naples

On 5 September 2015 a violent hailstorm hit the Gulf and the city of Naples in Italy. The storm originated over the Tyrrhenian Sea dropping 7–10 cm diameter hailstones along its path. The event was observed by a dual-polarization Doppler C-band, namely the Monte il Monte radar operated by the Italian Department of Civil Protection, being part of the Italian radar network (IT-RAD).  The dataset is composed by high-resolution polar volumes of the following radar parameters: Uncorrected reflectivity Z (UZ), Corrected reflectivity Z (CZ), differential reflectivity (ZDR), uncorrected differential phase shift (PHIDP), co-polar correlation coefficient (RHOHV), Doppler Velocity (V), Doppler Width (W). The scan strategy is based on inverse elevation mode (from the highest to the lowest elevation angle) with variable PRF. The different phases of the event were well captured by the weather radar of “Monte il Monte” (lat = 41.9394 °, lon = 14.6208 °, altitude = 710 m) which, at the time of the event, was affected by a differential bias (on ZDR) of about 0.8 dB to be algebraically subtracted from the measured quantities. The user should be informed about some spot regions of missing data that might be present in the radar variables, especially on the V and differential phase. This is caused by the thresholding approach applied at RSP level on the signal quality index (SQI) to compensate for W-LAN interferences. The dataset, consisting of 44 raw radar data volumes with 5 minutes sampling rate, is provided in a proprietary format (“Datamet”) that is manageable by using the python code named read_datamet.py that is available at <a href="https://zenodo.org/record/4897245">https://zenodo.org/record/4897245</a>.

opencc-zeroApr 2022View details →

IIb-RAD-seq coupled with random forest classification indicates regional population structuring and sex-specific differentiation in salmon lice (Lepeophtheirus salmonis)

The aquaculture industry has been dealing with salmon lice problems forming serious threats to salmonid farming. Several treatment approaches have been used to control the parasite. Treatment effectiveness must be optimized, and the systematic genetic differences between sub-populations must be studied to monitor louse species and enhance targeted control measures. We have used IIb-RAD sequencing in tandem with a random forest classification algorithm to detect the regional genetic structure of the Norwegian salmon lice and identify important markers for sex differentiation of this species. We identified 19428 single nucleotide polymorphisms (SNPs) from 95 individuals of salmon lice. These SNPs, however, were not able to distinguish differential structure of lice populations. Using the random forest algorithm, we selected 91 SNPs important for geographical classification and 14 SNPs important for sex classification. The geographically important SNP data substantially improved the genetic understanding of the population structure and classified regional demographic clusters along the Norwegian coast. We also uncovered SNP markers that could help determine the sex of the salmon louse. A large portion of the SNPs identified to be under directional selection were also ranked highly important by random forest. According to our findings, there is a regional population structure of salmon lice associated with the geographical location along the Norwegian coastline.

opencc-byFeb 2021View details →

Diplomski rad

One of five heads located on "Hill of Roses" in park Sremska Kamenica, Serbia Source: Objaverse 1.0 / Sketchfab

opencc-by-4.0Jul 2018View details →

correction_sol_rad_2018_v.1.0

Addtition Data for Correction of Solar Radiation on Patscherkofel. A Project by students of ACINN, University of Innsbruck, 2018. For more Information see: https://transparency-lecture.github.io/docs/home/

opencc-by-4.0Mar 2019View details →

VCF File containg replicate RAD-seq genotype calls for four Populs alba x Populus tremula hybrids.

VCF file used to estimate RAD-seq genotyping errors in Bresadola et al. (2019).

opencc-by-4.0Sep 2024View details →

RAD-seq generated single nucleotide polymorphisms resolve patterns of genetic diversity and structure of the freshwater mussel Ptychobranchus fasciolaris in glaciated and unglaciated regions of North America

Included are the initial unfiltered SNP output from the STACKS pipeline, and the final filtered SNP dataset in VCF format used to do analysis in the manuscript titled "RAD-seq generated single nucleotide polymorphisms resolve patterns of genetic diversity and structure of the freshwater mussel Ptychobranchus fasciolaris in glaciated and unglaciated regions of North America" which was submitted to Hydrobiologia in September 2024.