Publications
NIBIOs employees contribute to several hundred scientific articles and research reports every year. You can browse or search in our collection which contains references and links to these publications as well as other research and dissemination activities. The collection is continously updated with new and historical material.
2024
Abstract
“rswap” is an R package under development for SWAP 4.2 with the goal of simplifying, automating, and improving user interaction with the model. The package functions by detecting and translating SWAP input files into R-compatible dataframes, allowing for easy and automated modifications to parameters. Modified model inputs can then be re-written to files and run in SWAP from the R console using "rswap". SWAP model output can be automatically imported into the R environment and visualized using a variety of (interactive) graphing functions. If observational data is provided by the user, then the package can adjust output settings to match (variables and depth). Modelled and observed data can then be graphically compared in-line and “goodness-of-fit” statistics can be generated and plotted. Additionally, model runs can be saved and interactively compared with each other, functions are thoroughly documented with runnable examples, and a baseline runnable model setup can be automatically initialized. Further planned developments to the package include support for parallel running of model runs, enabling rapid automated sensitivity analysis, scenario analysis, as well as automated “hard calibration” routines and parameter estimation. Through this functionality, “rswap” can connect the SWAP model to an integrated development environment (IDE), such as “RStudio”, allowing users to efficiently perform all their work (setup, calibration, execution, analysis) in a single environment. Importantly, the packages allows for direct use of SWAP with the vast array of research software on the R platform. “rswap” is an open-source project originally developed for use in OPTAIN (optain.eu) and has been applied in multiple case studies and thesis projects.
2023
Authors
Milica Fotiric-Aksic U Gasic T Tosti Jasminka Milivojevic Z Tesic Mekjell MelandAbstract
No abstract has been registered
Authors
Milica Fotiric-Aksic U Gasic T Tosti Jasminka Milivojevic Z Tesic Mekjell MelandAbstract
No abstract has been registered
Authors
Claire CoutrisAbstract
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Authors
Marit JørgensenAbstract
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Authors
Tomás Brůna Rishi Aryal Olga Dudchenko Daniel James Sargent Daniel Mead Matteo Buti Andrea Cavallini Timo Hytönen Javier Andrés Melanie Pham David Weisz Flavia Mascagni Gabriele Usai Lucia Natali Nahla Bassil Gina E. Fernandez Alexandre Lomsadze Mitchell Armour Bode Olukolu Thomas Poorten Caitlin Britton Jahn Davik Hamid Ashrafi Erez Lieberman Aiden Mark Borodovsky Margaret WorthingtonAbstract
Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosomelength assembly and annotation of the diploid blackberry germplasm accession “Hillquist” (R. argutus). “Hillquist” is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The “Hillquist” assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298Mb, of which 270Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the “Hillquist” genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.
Abstract
No abstract has been registered
Abstract
Parametric modeling of downwelling longwave irradiance under all-sky conditions (LW↓) typically involves “correcting” a clear- (or non-overcast) sky model estimate using solar-irradiance-based proxies of cloud cover in lieu of actual cloud cover given uncertainties and measurement challenges of the latter. While such approaches are deemed sound, their application in time and space is inherently limited. We report on a correction model free of solar irradiance-derived cloud proxies that is applicable at the true daily (24 hr) and global scales. The new “cloud-free” correction model demonstrates superior performance in a range of environments relative to existing cloud-free modeling approaches and to corrections based on solar-derived cloudiness proxies. Literature-based performance benchmarking indicates a performance that is often comparable to—and in some cases superior to—performances yielded by conventional parametric modeling approaches employing locally or regionally calibrated parameters, as well as to performances of satellite-based algorithms.
Abstract
No abstract has been registered
Abstract
The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.