Publikasjoner
NIBIOs ansatte publiserer flere hundre vitenskapelige artikler og forskningsrapporter hvert år. Her finner du referanser og lenker til publikasjoner og andre forsknings- og formidlingsaktiviteter. Samlingen oppdateres løpende med både nytt og historisk materiale. For mer informasjon om NIBIOs publikasjoner, besøk NIBIOs bibliotek.
2025
Sammendrag
Mitochondrial genomes (mitogenomes) display relatively rapid mutation rates, low sequence recombination, high copy numbers, and maternal inheritance patterns, rendering them valuable blueprints for mapping lineages, uncovering historical migration patterns, understanding intraspecific population dynamics, and investigating how environmental pressures shape traits underpinned by genetic variation. Here, we present the bioinformatic pipeline and code used to assemble and annotate the complete mitogenomes of five houndsharks (Chondrichthyes: Triakidae) and compare them to the mitogenomes of other closely related species. We demonstrate the value of a combined assembly approach for detecting deviations in mitogenome structure and describe how to select an assembly approach that best suits the sequencing data. The datasets required to run our analyses are available on the GitHub and Dryad repositories
Sammendrag
The limited standards for the rigorous and objective use of mitochondrial genomes (mitogenomes) can lead to uncertainties regarding the phylogenetic relationships of taxa under varying evolutionary constraints. The mitogenome exhibits heterogeneity in base composition, and evolutionary rates may vary across different regions, which can cause empirical data to violate assumptions of the applied evolutionary models. Consequently, the unique evolutionary signatures of the dataset must be carefully evaluated before selecting an appropriate approach for phylogenomic inference. Here, we present the bioinformatic pipeline and code used to expand the mitogenome phylogeny of the order Carcharhiniformes (groundsharks), with a focus on houndsharks (Chondrichthyes: Triakidae). We present a rigorous approach for addressing difficult-to-resolve phylogenies, incorporating multi-species coalescent modelling (MSCM) to address gene/species tree discordance. The protocol describes carefully designed approaches for preparing alignments, partitioning datasets, assigning models of evolution, inferring phylogenies based on traditional site-homogenous concatenation approaches as well as under multispecies coalescent and site heterogenous models, and generating statistical data for comparison of different topological outcomes. The datasets required to run our analyses are available on GitHub and Dryad repositories.
Sammendrag
Observations of two apparent phenotypic expressions (morphodemes) of the composite thallus of the lichen-forming ascomycete species Ricasolia amplissima (Scop.) De Not. (formerly Lobaria amplissima (Scop.) Forss.) inspired us to investigate the morphological and genetic variation of the species in Norway. The morphodemes differ in thallus shape and occurrence of apothecia and/or cephalodia, each dominating in climatically different parts of southern Norway. We investigated the morphology of herbarium collections as well as fresh samples from various areas, including localities where the two morphodemes occur together. The nrITS barcode marker was sequenced to investigate the genetic variation along the climatic gradient of the Hardangerfjord area. We also included barcode sequences of specimens from other parts of the world in order to establish if the Norwegian pattern of variation has a wider geographical significance. Results suggest that the genetic variation found in Ricasolia amplissima corresponds to morphology independently of geography/climate. The two haplotype groups cluster in two distinct sister clades, however, the within-species variation is too small to justify taxonomic recognition. Specimens with the cephalodiate morphodeme and its haplotypes are mainly found in the oceanic west, whereas specimens with apotheciate morphodemes and its haplotypes occur mainly in the drier eastern parts. The results can be interpreted as 1) immigration to Norway from different gene pools in separate glacial refugia, or, 2) natural selection for water efficient cephalodiate morphodemes in the oceanic west and apotheciate (sexually reproducing) in drier suboceanic east parts of Norway. We argue that within-species genetic variation should always be considered before conservation actions such as transplants of lichen thalli are taken.
Sammendrag
Det er ikke registrert sammendrag
Forfattere
Kristian Hansen Håvard Steinshamn Sissel Hansen Matthias Koesling Tommy Dalgaard Bjørn Gunnar HansenSammendrag
To evaluate the environmental impact across multiple dairy farms cost-effectively, the methodological frame- work for environmental assessments may be redefined. This article aims to assess the ability of various statistical tools to predict impact assessment made from a Life Cyle Assessment (LCA). The different models predicted estimates of Greenhouse Gas (GHG) emissions, Energy (E) and Nitrogen (N) intensity. The functional unit in the study was defined as 2.78 MJMM human-edible energy from milk and meat. This amount is equivalent to the edible energy in one kg of energy-corrected milk but includes energy from milk and meat. The GHG emissions (GWP100) were calculated as kg CO2-eq per number of FU delivered, E intensity as fossil and renewable energy used divided by number of FU delivered, and N intensity as kg N imported and produced divided by kg N delivered in milk or meat (kg N/kg N). These predictions were based on 24 independent variables describing farm characteristics, management, use of external inputs, and dairy herd characteristics. All models were able to moderately estimate the results from the LCA calculations. However, their precision was low. Artificial Neural Network (ANN) was best for predicting GHG emissions on the test dataset, (RMSE = 0.50, R2 = 0.86), followed by Multiple Linear Regression (MLR) (RMSE = 0.68, R2 = 0.74). For E intensity, the Supported Vector Machine (SVM) model was performing best, (RMSE = 0.68, R2 = 0.73), followed by ANN (RMSE = 0.55, R2 = 0.71,) and Gradient Boosting Machine (GBM) (RMSE = 0.55, R2 = 0.71). For N intensity predictions the Multiple Linear Regression (MLR) (RMSE = 0.36, R2 = 0.89) and Lasso regression (RMSE = 0.36, R2 = 0.88), followed by the ANN (RMSE = 0.41, R2 = 0.86,). In this study, machine learning provided some benefits in prediction of GHG emission, over simpler models like Multiple Linear Regressions with backward selection. This benefit was limited for N and E intensity. The precision of predictions improved most when including the variables “fertiliser import nitrogen” (kg N/ha) and “proportion of milking cows” (number of dairy cows/number of all cattle) for predicting GHG emission across the different models. The inclusion of “fertiliser import nitrogen” was also important across the different models and prediction of E and N intensity.
Forfattere
Chala Adugna Kufa Afework Bekele Anagaw Meshesha Atickem Desalegn Chala Diress Tsegaye Alemu Torbjørn Ergon Nils Christian Stenseth Dietmar ZinnerSammendrag
Ethiopia is home to two subspecies of Colobus guereza, C. g. guereza and C. g. gallarum. Whereas C. g. guereza is listed as Least Concern by IUCN, the conservation status of C. g. gallarum is unclear, but according to a recent assessment, it will most likely be listed as Vulnerable, because of habitat loss due to agricultural expansion. We used climate data to model the habitat suitability for both taxa in a comparative study to identify suitable habitats within and outside of protected areas that may serve as Anthropocene refugia. Our ensemble models estimated 168,731 km2 as climatically suitable habitat for C. g. guereza and 69,542 km2 for C. g. gallarum with an overlap between the two taxa of 17.2 %. Areas that qualified as refugia, i.e., areas covered by forest, were 47,101 km2 (only 27.9 % of the total suitable habitat) and 8430 km2 (12.1 % of the suitable habitat) for C. g. guereza and C. g. gallarum, respectively. Of these, 39.8 % (C. g. guereza) and 53.7 % (C. g. gallarum) are within Ethiopia’s current protected area network. Given that potential Anthropocene refugia are found only partly within protected areas, conservation management should include this information when developing conservation strategies for both taxa. As the majority of suitable habitats for the two colobus taxa exist in non-forested regions, afforestation in these areas would be highly beneficial and is strongly recommended.
Forfattere
Eystein Skjerve Erik Georg Granquist Tone Kristin Bjordal Johansen Ingrid Olsen Truls Nesbakken Amin Sayyari Kristin Opdal Seljetun Morten Tryland Åsa Maria Olofsdotter Espmark Grete H. M. Jørgensen Janicke Nordgreen Ingrid Olesen Sonal Jayesh Patel Sokratis Ptochos Marco Vindas Tor Atle MoSammendrag
Following the verification of bovine tuberculosis (bTB) after an outbreak in 2022, concerns were raised about the true epidemiological situation of bTB in Norway. Consequently, the Norwegian Food Safety Authority commissioned VKM to assess the risk of introducing Mycobacterium bovis to Norway, and the risk of its spread and establishment in Norwegian livestock and wild fauna. VKM was also tasked with assessing the risk of infection to humans and identifying risk-reducing measures and diagnostic options for detecting infection in Norway. Background: bTB is a bacterial disease affecting animals and humans, caused by M. bovis. The prevalence varies greatly across European countries. Norway has held an official free status since 1963, with only a few cases reported in the 1980s. The 2022 outbreak was identified through routine meat inspection, revealing several infected animals in a specific herd. The source of this outbreak remains unidentified, and no infected animals have been detected since early 2023. Contact network tracing linked many farms to the index (outbreak) herd through cattle trade. The identified contact herds are still monitored for infection, and the possibility of a spread to other farm animals or wildlife cannot be excluded. Norway maintains strict regulations on live animal imports and monitors the presence of bTB through mandatory reporting, meat inspections, and breeding station testing. M. bovis can infect a wide variety of domestic and wildlife species. Furthermore, there is a significant public health concern due to its zoonotic potential. bTB is a chronic disease, and the incubation period can span from months to years. The bacterium can survive for months in the environment. Diagnosing bTB in live animals is challenging and time-consuming, implying that detection and eradication of the infection is difficult. Key Findings: Norway has had a very low number of imported cattle during the past 10 years. However, some imports of small ruminants and camelids (llamas, alpacas, camels) have occurred. Import of cattle and camelids from countries with bTB in the animal population is assessed as a risk of introducing the bacterium to Norwegian cattle. This risk assessment concludes that introduction of bTB to Norway from imported cattle is unlikely based on the current situation with low number of imports. However, introduction by camelids is regarded as more likely. There is significant domestic trade and transport of beef and dairy cattle within Norway, sometimes without proper registration. If bTB is established in the country, cattle movements are likely to spread the infection between herds. Furthermore, direct and indirect transmission to other domestic species or free-ranging animals (semi-domesticated reindeer and wildlife) may occur, which may complicate the control of bTB in outbreak regions. Indirect transmission can occur via contaminated feeds, pastures, and salt licks that are shared with free-ranging animals. Many species of free-ranging animals are susceptible to M. bovis. Depending on population density and other ecological factors, these species may play the role as hosts and a source of infection for cattle, other livestock and humans. Based on experience from Europe, M. bovis is considered as extremely difficult to eradicate in a country if established in free-ranging species. Badgers, cervid species (i.e. red deer, reindeer, roe deer, and moose), and a growing population of wild boars are of special concern. A contingency plan that takes into account the risk of spread to wild fauna may thus be crucial for successful control of an outbreak with bTB. In periods of severe drought, import of roughage to Norway may be necessary. It is uncertain how well different feed materials and ensiling methods will enable survival of M. bovis. Therefore, restricting import of roughage to Norway to countries and regions certified as officially tuberculosis free (OTF), will reduce the risk of introduction to Norwegian cattle. In the event of introduction and establishment of M. bovis to Norwegian cattle, slurry may pose a risk of spread to domestic and wild animals due to survival of the bacterium in liquid manure. Survival in slurry is uncertain; however, a minimum of six months storage before spreading or alternatively disinfection of slurry will reduce the risk. Zoonotic transmission of bTB remains a relatively rare event, also in countries where the infection is present in animal populations. However, M. bovis can be transmitted by direct contact between animals and humans, through handling (farmers, veterinarians, and slaughterhouse workers) carcasses, and indirectly by consumption of unpasteurised milk and dairy products, but rarely through consumption of meat and meat products. Meat inspection is the key measure for surveillance of bTB in cattle and other domestic animals. Diagnosing bTB is challenging due to the nature of the disease and the lack of a gold standard test. Test-positive animals may not show visible lesions postmortem, and sensitive methods like cultivation and PCR depend on the presence of bacteria in sampled tissues. Any test-strategy aiming to increase the possibility to detect latent infected animals will result in a higher number of culled animals where the infection cannot be confirmed. Too extensive testing in low-risk herds can lead to false positives and must be balanced against the financial costs of restrictions and culling. Combining different tests (skin test, IFN-γ test, and boosted antibody tests) improve sensitivity, and this strategy is particularly advised for imported animals and during outbreak investigations. To achieve the best sensitivity, one should apply the tuberculin test at the same time as the IFN-γ test, followed by serology 10-30 days after the tuberculin test. Culling testpositive animals, and retest after at least 60 days of animals with an inconclusive test will reduce the risk of introducing M. bovis to Norway. While tuberculin tests are labor-intensive and costly, they are regarded as the methods of choice for surveillance in endemic regions. Serological assays like Enferplex show promise for general surveillance, however, the sensitivity is relatively low without prior skin-test. Ongoing studies are evaluating the test performance in bulk-milk screening. In culled animals with suspected lesions, real-time PCR, alongside culture, is recommended for quicker diagnosis. Whole-genome sequencing is the preferred tool for molecular surveillance and outbreak investigations.
Forfattere
Ove BergersenSammendrag
Det er ikke registrert sammendrag
Forfattere
Monica Sanden Eirill Ager-Wick Johanna Eva Bodin Nur Duale Kristian Prydz Volha Shapaval Tage ThorstensenSammendrag
The Norwegian Scientific Committee for Food and Environment (VKM) has assessed an application for approval of soy leghemoglobin produced from genetically modified Komagataella phaffii for food uses in the EU. In accordance with an assignment specified by the Norwegian Food Safety Authority (NFSA) and the Norwegian Environment Agency (NEA), VKM assesses whether genetically modified organisms (GMOs) intended for the European market can pose risks to human or animal health, or the environment in Norway. VKM assesses the scientific documentation regarding GMO applications seeking approval for use of GMOs as food and feed, processing, or cultivation. The EU Regulation 1829/2003/EC (Regulation) covers living GMOs that fall under the Norwegian Gene Technology Act, as well as processed food and feed from GMOs (dead material) that fall under the Norwegian Food Act. The regulation is currently not part of the EEA agreement or implemented in Norwegian law. Norway conducts its own assessments of GMO applications in preparation for the possible implementation of the Regulation. In accordance with the assignment by NFSA and NEA, VKM assesses GMO applications during scientific hearings initiated by the European Food Safety Authority (EFSA), as well as after EFSA has published its own risk assessment of a GMO, up until EU member countries vote for or against approval in the EU Commission. The assignment is divided into three stages. Soy leghemoglobin produced from genetically modified Komagataella phaffii This application is submitted to gain authorisation for the use of soy leghemoglobin (the liquid preparation is referred to as “LegH Prep”) produced from genetically modified Komagataella phaffii (yeast) as a flavouring (“meaty taste”) in meat analogue products that will be marketed in the European Union (EU). Soy leghemoglobin is intended for addition to meat analogue products that are for use in foods such as burgers, meatballs, and sausages. Komagataella phaffii-strain employed in the production of soy leghemoglobin contains genetic modifications which allow it to express this protein. Following fermentation, the cells are lysed, and the soy leghemoglobin is concentrated by physical means. The soy leghemoglobin is delivered in a liquid preparation (LegH Prep) that is standardised to contain up to 9% soy leghemoglobin on a wet weight basis and a soy leghemoglobin protein purity of at least 65%. The remainder of the protein fraction in the LegH Prep is accounted for by residual proteins from the Komagataella phaffii production strain. These residual proteins are all endogenous to Komagataella phaffii as the gene coding for the expression of soy leghemoglobin is the only gene from a different organism. VKM has assessed the documentation in application EFSA-GMO- NL-2019-162 and EFSA's scientific opinion for the use of soy leghemoglobin produced from genetically modified Komagataella phaffii. The scientific documentation provided in the application is adequate for risk assessment, and in accordance with the EFSA guidance on risk assessment of genetically modified microorganisms for use in food or feed. The VKM GMO Panel does not consider leghemoglobin from genetically modified Komagataella phaffii to imply potential specific health risks in Norway, compared to EU-countries. The EFSA opinion is adequate also for Norwegian considerations. Therefore, a full risk assessment was not performed by VKM. About the assignment: (...)
Forfattere
Anne Linn HykkerudSammendrag
Det er ikke registrert sammendrag