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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

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Abstract

Since 2005, the population of the trans-border brown bear (Ursus arctos) in Trilateral Park Pasvik-Inari (Norway-Finland-Russia) has been monitored by using genetic analyses of hair and faeces collected randomly in the field. A more systematic method using hair traps every fourth year was initiated in 2007 to collect brown bear hairs for genetic analysis. The method consisted of 56 hair traps in Norway, Finland and Russia in a 5 x 5 km2 grid cell system (ca 1400 km2). The project was repeated in 2011, 2015, 2019 and now in 2023. This season’s sampling was carried out in Pasvik (Norway) - Inari (Finland) area (43 squares, 1075 km2), using the same methodology as in the previous studies. A total of 97 samples were collected, where 45 samples came from Finland and 52 samples from Norway. In the bear specific analysis, 71 (73 %) of the 97 hair samples were positive. A complete DNA profile could be determined for 63 of the positive samples. In total, 22 different bear individuals were detected (10 females and 12 males). Of these 22 bears, 12 bears were detected in previous years, while 10 were previously unknown bears. In total, 13 bears were detected in Finland and 11 bears in Norway. This year’s sampling has the 2nd highest success rate in number of individuals detected per grid square, with 0,51 individual per grid square compared to 0,81 individuals in 2019 (highest success rate), 0,49 in 2015, 0,35 in 2011 and 0,42 in 2009. Our results showed that even with a smaller study area, the hair trap project every 4th year provides valuable information on the brown bear individuals in addition to a random sampling in the field (The National Monitoring Program for brown bears in Norway).

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Abstract

Aim Effective management of non-indigenous species requires knowledge of their dispersal factors and founder events. We aim to identify the main environmental drivers favouring dispersal events along the invasion gradient and to characterize the spatial patterns of genetic diversity in feral populations of the non-native pink salmon within its epicentre of invasion in Norway. Location Mainland Norway and North Atlantic Basin. Methods We first conducted SDM using four modelling techniques with varying levels of complexity, which encompassed both regression-based and tree-based machine-learning algorithms, using climatic data from the present to 2050. Then, we used the triple-enzyme restriction-site associated DNA sequencing (3RADseq) approach to genotype over 30,000 high-quality single-nucleotide polymorphisms to elucidate the patterns of genetic diversity and gene flow within the pink salmon putative invasion hotspot. Results We discovered temperature- and precipitation-related variables drove pink salmon distributional shifts across its non-native ranges and that climate-induced favourable areas will remain stable for the next 30 years. In addition, all SDMs identified north-eastern Norway as the epicentre of the pink salmon invasion, and genomic data revealed that there was minimal variation in genetic diversity across the sampled populations at a genome-wide level in this region. While utilizing a specific group of ‘diagnostic’ SNPs, we observed a significant degree of genetic differentiation, ranging from moderate to substantial, and detected four hierarchical genetic clusters concordant with geography. Main Conclusions Our findings suggest that fluctuations in climate extreme events associated with ongoing climate change will likely maintain environmental favourability for the pink salmon outside its ‘native’/introduced ranges. Locally invaded rivers are themselves potential source populations of invaders in the ongoing secondary spread of pink salmon in Northern Norway. Our study shows that SDMs and genomic data can reveal species distribution determinants and provide indicators to aid in post-control measures and potentially inferences about their success.

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Abstract

Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene–environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype–environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.

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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.

Abstract

Background The order Lepidoptera has an abundance of species, including both agriculturally beneficial and detrimental insects. Molecular data has been used to investigate the phylogenetic relationships of major subdivisions in Lepidoptera, which has enhanced our understanding of the evolutionary relationships at the family and superfamily levels. However, the phylogenetic placement of many superfamilies and/or families in this order is still unknown. In this study, we determine the systematic status of the family Argyresthiidae within Lepidoptera and explore its phylogenetic affinities and implications for the evolution of the order. We describe the first mitochondrial (mt) genome from a member of Argyresthiidae, the apple fruit moth Argyresthia conjugella. The insect is an important pest on apples in Fennoscandia, as it switches hosts when the main host fails to produce crops. Results The mt genome of A. conjugella contains 16,044 bp and encodes all 37 genes commonly found in insect mt genomes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and a large control region (1101 bp). The nucleotide composition was extremely AT-rich (82%). All detected PCGs (13) began with an ATN codon and terminated with a TAA stop codon, except the start codon in cox1 is ATT. All 22 tRNAs had cloverleaf secondary structures, except trnS1, where one of the dihydrouridine (DHU) arms is missing, reflecting potential differences in gene expression. When compared to the mt genomes of 507 other Lepidoptera representing 18 superfamilies and 42 families, phylogenomic analyses found that A. conjugella had the closest relationship with the Plutellidae family (Yponomeutoidea-super family). We also detected a sister relationship between Yponomeutoidea and the superfamily Tineidae. Conclusions Our results underline the potential importance of mt genomes in comparative genomic analyses of Lepidoptera species and provide valuable evolutionary insight across the tree of Lepidoptera species.

2023

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Abstract

Studies on host–parasite systems that have experienced distributional shifts, range fragmentation, and population declines in the past can provide information regarding how parasite community richness and genetic diversity will change as a result of anthropogenic environmental changes in the future. Here, we studied how sequential postglacial colonization, shifts in habitat, and reduced host population sizes have influenced species richness and genetic diversity of Corynosoma (Acanthocephala: Polymorphidae) parasites in northern European marine, brackish, and freshwater seal populations. We collected Corynosoma population samples from Arctic, Baltic, Ladoga, and Saimaa ringed seal subspecies and Baltic gray seals, and then applied COI barcoding and triple-enzyme restriction-site associated DNA (3RAD) sequencing to delimit species, clarify their distributions and community structures, and elucidate patterns of intraspecific gene flow and genetic diversity. Our results showed that Corynosoma species diversity reflected host colonization histories and population sizes, with four species being present in the Arctic, three in the Baltic Sea, two in Lake Ladoga, and only one in Lake Saimaa. We found statistically significant population-genetic differentiation within all three Corynosoma species that occur in more than one seal (sub)species. Genetic diversity tended to be high in Corynosoma populations originating from Arctic ringed seals and low in the landlocked populations. Our results indicate that acanthocephalan communities in landlocked seal populations are impoverished with respect to both species and intraspecific genetic diversity. Interestingly, the loss of genetic diversity within Corynosoma species seems to have been less drastic than in their seal hosts, possibly due to their large local effective population sizes resulting from high infection intensities and effective intra-host population mixing. Our study highlights the utility of genomic methods in investigations of community composition and genetic diversity of understudied parasites.

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Abstract

Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for “cleaner fish” to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype–environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our ‘global’ sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway.