Jarl Andreas Anmarkrud

• Mauvisseau, Quentin; Ewers, Isabelle; Blumeris, Isabella; Bongo, Sandra Irén; Oliveira, Luiz Filipe Brito de & Gouvea, Bruno [Show all 45 contributors for this article] (2026). On-site metabarcoding analysis of environmental DNA samples. Hydrobiologia. ISSN 0018-8158. doi: 10.1007/s10750-026-06433-3. Full text in Research Archive Show summary

  Abstract Environmental DNA metabarcoding is a powerful monitoring tool for assessing aquatic biodiversity, as well as the sustainability and impacts of fisheries and aquaculture. However, conventional laboratory workflows remain time-consuming and dependent on dedicated infrastructures. Here, we present a field trial of a fully portable, off-site eDNA metabarcoding pipeline that enables end-to-end analysis within a few days using compact equipment, including a BentoLab workstation and an Oxford Nanopore Technologies (ONT) MinION sequencer. The workflow was implemented during two international training courses in Norway and Brazil, where students and early career researchers collected environmental samples, extracted and amplified DNA, prepared DNA libraries, and sequenced on-site before performing bioinformatics and statistical analyses. In the case study detailed here, seven eDNA samples collected and analysed on-site in the Oslofjord allowed detection of 16 fish and elasmobranch species. Although overall diversity was lower than in earlier studies using Illumina-based sequencing, our protocol reliably detected key species and demonstrates that portable eDNA metabarcoding is feasible for rapid ecological assessment, surveillance of high-risk regions and/or deployment in remote or resource-limited settings.

• Cei, Aisha Carolina; Silva, Dalila Costa; Rodrigues, Alan Erik Souza; Sviggum, Silvana Melo; Rosa, Fabricio dos Anjos Santa & Martins, Rasna Figueiredo [Show all 13 contributors for this article] (2025). Invasive giant river prawns as opportunistic, generalist predators in the Amazon Delta: Insights from metabarcoding. Ecosphere. 16(11). doi: 10.1002/ecs2.70439. Full text in Research Archive Show summary

  Invasive species alter habitats and biological communities. The giant river prawn Macrobrachium rosenbergii (de Man 1879) was introduced to Brazil for aquaculture, and invasive populations have established in the Amazon Delta region where they are believed to pose a risk to the native aquatic fauna. To assess potential impacts, we performed dietary metabarcoding using generalist COI primers on 105 stomach contents collected from prawns from the southern Amazon Delta. Overall, M. rosenbergii presents an opportunistic and generalist diet that reflects the dominant aquatic and terrestrial fauna of the region, including the orders Diptera, Characiformes, and Lepidoptera as dominant dietary items in terms of both frequency of occurrence and richness. One unidentified congeneric species was identified in the diet, indicating the potential for negative effects on the native prawn fauna. Additionally, while there is a general overlap in the diet for all categories of sex and reproductive phase, smaller immature individuals and molted females showed reduced diversity in their diet, suggesting limitations in prey handling or access. We conclude that dietary metabarcoding of opportunistic generalists and/or detritivores appears to be a potentially useful tool for monitoring biodiversity as well as understanding their role in the food web.

• Anmarkrud, Jarl Andreas; Rosa, Fabricio dos Anjos Santa; Thorbek, Birgitte Lisbeth Graae; Schrøder-Nielsen, Audun; Sviggum, Silvana Melo & Ready, Jonathan Stuart [Show all 8 contributors for this article] (2025). eDNA Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across Habitats. Environmental DNA. 7(3). doi: 10.1002/edn3.70095. Full text in Research Archive Show summary

  Environmental DNA-based monitoring has been increasingly used in the last decade to monitor biodiversity in aquatic and terrestrial systems. Molecular-based surveys now allow quick and reliable production of baseline knowledge of species community composition on a large scale, allowing a better understanding of ecosystem function and mitigation of stressors linked to anthropogenic activities. Despite this, technical hurdles often remain, and the impact of replicates, PCR polymerases, and amplicon size on the recovered species richness is still poorly understood. Here, we conducted a large controlled experiment, with bulk samples collected from terrestrial, marine, and freshwater environments to assess the impact of natural and technical replicates, PCR polymerases with different degrees of fidelity or proofreading activity, as well as amplicon size on species richness recovery across habitats. In this study, we consistently found variations in sample species richness depending on PCR polymerase choice. We further demonstrate the dissimilar impacts between natural and technical replicates on species richness recovery and the necessity of increasing natural replications in eDNA-based surveys. We highlight the benefits and limitations of replication strategies, polymerase choice, and amplicon size across terrestrial, marine, and freshwater habitats, and provide recommendations to increase the reliability of future eDNA-based metabarcoding studies.

• Anmarkrud, Jarl Andreas; Rosa, Fabricio dos Anjos Santa; Thorbek, Birgitte Lisbeth Graae; Schrøder-Nielsen, Audun; Melo, Silvana & Ready, Jonathan Stuart [Show all 8 contributors for this article] (2024). eDNA replicates, polymerase and amplicon size impact inference of richness across habitats. BioRxiv. ISSN 0362-4331. doi: 10.1101/2024.11.19.624235. Full text in Research Archive
• Lifjeld, Jan Terje; Hernando, Miguel de Gabriel; Marcos, Benito Fuertes; Grønstøl, Gaute; Anmarkrud, Jarl Andreas & Matschiner, Michael [Show all 7 contributors for this article] (2023). Rapid sperm length divergence in a polygynandrous passerine: a mechanism of cryptic speciation? Evolution. ISSN 0014-3820. 77(11), p. 2352–2364. doi: 10.1093/evolut/qpad146. Full text in Research Archive
• Montserrat, Torres-Oliva; Anmarkrud, Jarl Andreas; Arnesen, Paal; Arnesen, Øyvind Kongstun; Arnold, Philipp & Blaj, Iulia [Show all 27 contributors for this article] (2023). Whole-genome sequencing of reindeer (Rangifer tarandus) populations reveals independent origins of dwarf ecotypes and potential molecular mechanisms underpinning cold adaptation. Research Square. ISSN 2693-5015. doi: 10.21203/rs.3.rs-3619721/v1. Full text in Research Archive
• Rekdal, Silje Larsen; Anmarkrud, Jarl Andreas; Lifjeld, Jan Terje & Johnsen, Arild (2023). Do female bluethroats without extra-pair offspring have more MHC-compatible social mates? Behavioral Ecology and Sociobiology. ISSN 0340-5443. 77(3). doi: 10.1007/s00265-023-03311-z. Full text in Research Archive Show summary

  Abstract Genes of the major histocompatibility complex (MHC) are crucial for adaptive immunity in jawed vertebrates, and theory predicts that there should be mate choice for optimizing MHC constitution in the offspring. In a previous study, we demonstrated a non-random female choice of extra-pair males in the bluethroat ( Luscinia svecica ), yielding offspring that was closer to an intermediate MHC class II (MHCII) allele count than their within-pair halfsiblings. The present study tests whether social pairs with only within-pair young (WPY) in their brood, in the same study population, had a combined MHC-constitution closer to a presumed intermediate optimum, than social pairs with extra-pair young (EPY), with a corresponding pattern in their offspring. As expected, we found that WPY from pure WPY-broods were more MHC-optimal than WPY from mixed broods, but only in broods of young (second year) males. Correspondingly, there was a tendency for social pairs with only WPY in their brood to be more MHC-compatible than social pairs with EPY in their brood, when the male was young. Older bluethroat males have considerably larger testes than young males, and their higher sperm competitiveness could help them secure paternity in their own brood, also when they are not MHC-compatible. In other words, in the sexual conflict over paternity, females may be more likely to realise their preference for a MHC-compatible mate when paired to a young male. As a possible fitness indicator, immune responsiveness to an injected antigen (PHA) was elevated for offspring closer to “the golden mean” in MHCII allele count. Significance statement This study contributes to our understanding of MHC-based mate choice in extra-pair mating systems, by showing that female bluethroats ( Luscinia svecica ) with an MHCII-compatible social mate tend to have no extra-pair young in their brood, but only when the social male is young. This elucidates a possible sexual conflict, in which older social males are able to override female preferences and prevent other males from gaining paternity in their brood through higher sperm production. Studying systems in which extra-pair paternity occurs offers an insight into the genetic benefits of mate choice, as extra-pair males, in contrast to social males, generally contribute only sperm. Further, the strict and thorough genotyping scheme applied in this study enabled us to demonstrate a preference for “the golden mean” in MHC-diversity in a species with one of the highest MHC class II-diversity known to date.

• Ribas, Talita; Sales, João Bráullio de Luna; Boer, Hugo de; Anmarkrud, Jarl Andreas; Oliveira, Renato Renison Moreira & Laux, Marcele [Show all 11 contributors for this article] (2021). Unexpected diversity in the diet of Doryteuthis sanpaulensis (Brakoniecki, 1984) (Mollusca: Cephalopoda) from the southern Brazilian sardine fishery identified by metabarcoding. Fisheries Research. ISSN 0165-7836. doi: 10.1016/j.fishres.2021.105936. Full text in Research Archive
• Rekdal, Silje Larsen; Anmarkrud, Jarl Andreas; Lifjeld, Jan Terje & Johnsen, Arild (2021). Elevated phytohaemagglutinin‐induced skin‐swelling response at an intermediate number of MHC class II alleles in bluethroat nestlings. Journal of Avian Biology. ISSN 0908-8857. doi: 10.1111/jav.02734. Full text in Research Archive Show summary

  Genes of the major histocompatibility complex (MHC) are crucial for adaptive immunity, and theory predicts that the optimal number of alleles is intermediate rather than maximal. Support for such an intermediate optimum in MHC allele count has mainly been demonstrated in studies on parasite load and reproductive traits. In this study we tested if an intermediate number of MHC class II (MHCII) alleles based on positively selected sites was correlated with an increased skin-swelling response to two consecutive injections of phytohaemagglutinin (PHA) in bluethroat Luscinia svecica nestlings. We found that nestlings that were closer to the population mean in their number of alleles had a higher response to the first injection, supporting an intermediate, optimal number of alleles. After the second PHA injection, we found that the skin swelling was associated with MHCII allele count only at the among-brood level, and with paternity (extra-pair offspring had a larger swelling than within-pair offspring). We therefore conclude that the PHA response is partly correlated with MHCII allele count, but that additional factors must be involved in both the PHA response and in female extra-pair mate choice in this species.

• Raclariu-Manolică, Ancuţa Cristina; Anmarkrud, Jarl Andreas; Kierczak, Marcin; Rafati, Nima; Thorbek, Birgitte Lisbeth Graae & Schrøder-Nielsen, Audun [Show all 7 contributors for this article] (2021). DNA Metabarcoding for Quality Control of Basil, Oregano, and Paprika. Frontiers in Plant Science. doi: 10.3389/fpls.2021.665618. Full text in Research Archive Show summary

  Herbs and spices are some of the most vulnerable products in terms of fraud and adulteration in the food sector. Although standard analytical methods are accurate for quality control of specific lead or marker compounds, they cannot accurately assess the entire species composition of many marketed products. Complementary analytical approaches are thus often used for comprehensive screening of herbs and spices. In this study we evaluate DNA metabarcoding for the identification and authentication of 62 products, containing basil, oregano, and paprika collected from different retailers and importers in Norway. Our results show varying degrees of discrepancy between the constituent species and those listed on the product labels, despite high product authenticity. We suggest the false positives result from the sensitivity of DNA metabarcoding and filtering thresholds should be integrated into protocols to reduce false positives. Our results highlight how integrating DNA metabarcoding into the toolbox of analytical methods for quality control of fresh and/or processed plant-based food can improve product quality.

• Saroja, Seethapathy Gopalakrishnan; Raclariu, Ancuta Cristina; Anmarkrud, Jarl Andreas; Wangensteen, Helle & Boer, Hugo de (2019). DNA Metabarcoding Authentication of Ayurvedic Herbal Products on the European Market Raises Concerns of Quality and Fidelity. Frontiers in Plant Science. 10, p. 1–11. doi: 10.3389/fpls.2019.00068. Full text in Research Archive
• Rekdal, Silje Larsen; Anmarkrud, Jarl Andreas; Lifjeld, Jan Terje & Johnsen, Arild (2019). Extra‐pair mating in a passerine bird with highly duplicated major histocompatibility complex class II: Preference for the golden mean. Molecular Ecology. ISSN 0962-1083. doi: 10.1111/mec.15273. Full text in Research Archive Show summary

  Genes of the major histocompatibility complex (MHC) are essential in vertebrate adaptive immunity, and they are highly diverse and duplicated in many lineages. While it is widely established that pathogen‐mediated selection maintains MHC diversity through balancing selection, the role of mate choice in shaping MHC diversity is debated. Here, we investigate female mating preferences for MHC class II (MHCII) in the bluethroat (Luscinia svecica), a passerine bird with high levels of extra‐pair paternity and extremely duplicated MHCII. We genotyped family samples with mixed brood paternity and categorized their MHCII alleles according to their functional properties in peptide binding. Our results strongly indicate that females select extra‐pair males in a nonrandom, self‐matching manner that provides offspring with an allelic repertoire size closer to the population mean, as compared to offspring sired by the social male. This is consistent with a compatible genes model for extra‐pair mate choice where the optimal allelic diversity is intermediate, not maximal. This golden mean presumably reflects a trade‐off between maximizing pathogen recognition benefits and minimizing autoimmunity costs. Our study exemplifies how mate choice can reduce the population variance in individual MHC diversity and exert strong stabilizing selection on the trait. It also supports the hypothesis that extra‐pair mating is adaptive through altered genetic constitution in offspring.

• Rekdal, Silje Larsen; Anmarkrud, Jarl Andreas; Johnsen, Arild & Lifjeld, Jan Terje (2018). Genotyping strategy matters when analyzing hypervariable major histocompatibility complex-Experience from a passerine bird. Ecology and Evolution. 8(3), p. 1680–1692. doi: 10.1002/ece3.3757. Full text in Research Archive
• Anmarkrud, Jarl Andreas & Lifjeld, Jan Terje (2017). Complete mitochondrial genomes of eleven extinct or possibly extinct bird species. Molecular Ecology Resources. ISSN 1755-098X. 17(2), p. 334–341. doi: 10.1111/1755-0998.12600. Full text in Research Archive Show summary

  Natural history museum collections represent a vast source of ancient and historical DNA samples from extinct taxa that can be utilized by high-throughput sequencing tools to reveal novel genetic and phylogenetic information about them. Here, we report on the successful sequencing of complete mitochondrial genome sequences (mitogenomes) from eleven extinct bird species, using de novo assembly of short sequences derived from toepad samples of degraded DNA from museum specimens. For two species (the Passenger Pigeon Ectopistes migratorius and the South Island Piopio Turnagra capensis), whole mitogenomes were already available from recent studies, whereas for five others (the Great Auk Pinguinis impennis, the Imperial Woodpecker Campehilus imperialis, the Huia Heteralocha acutirostris, the Kauai Oo Moho braccathus and the South Island Kokako Callaeas cinereus), there were partial mitochondrial sequences available for comparison. For all seven species, we found sequence similarities of >98%. For the remaining four species (the Kamao Myadestes myadestinus, the Paradise Parrot Psephotellus pulcherrimus, the Ou Psittirostra psittacea and the Lesser Akialoa Akialoa obscura), there was no sequence information available for comparison, so we conducted blast searches and phylogenetic analyses to determine their phylogenetic positions and identify their closest extant relatives. These mitogenomes will be valuable for future analyses of avian phylogenetics and illustrate the importance of museum collections as repositories for genomics resources. The final version of this research has been published in Molecular Ecology Resources. © 2017 Wiley

• Tronstad, Rune Rose; Kummen, Martin; Holm, Kristian; Volkmann, Hilde Løland Von; Anmarkrud, Jarl Andreas & Høivik, Marte Lie [Show all 13 contributors for this article] (2017). Guanylate cyclase C activation shapes the intestinal microbiota in patients with familial diarrhea and increased susceptibility for Crohn's disease. Inflammatory Bowel Diseases. ISSN 1078-0998. 23(10), p. 1752–1761. doi: 10.1097/MIB.0000000000001264. Full text in Research Archive
• Johnsen, Arild; Kearns, Anna Marika; Omland, Kevin E. & Anmarkrud, Jarl Andreas (2017). Sequencing of the complete mitochondrial genome of the common raven Corvus corax (Aves: Corvidae) confirms mitogenome-wide deep lineages and a paraphyletic relationship with the Chihuahuan raven C. cryptoleucus. PLOS ONE. 12(10). doi: 10.1371/journal.pone.0187316. Full text in Research Archive Show summary

  Previous studies based on single mitochondrial markers have shown that the common raven (Corvus corax) consists of two highly diverged lineages that are hypothesised to have undergone speciation reversal upon secondary contact. Furthermore, common ravens are paraphyletic with respect to the Chihuahuan raven (C. cryptoleucus) based on mitochondrial DNA (mtDNA). Here we explore the causes of mtDNA paraphyly by sequencing whole mitochondrial genomes of 12 common ravens from across the Northern Hemisphere, in addition to three Chihuahuan ravens and one closely related brown-necked raven (C. ruficollis) using a long-range PCR protocol. Our raven mitogenomes ranged between 16925–16928 bp in length. GC content varied from 43.3% to 43.8% and the 13 protein coding genes, two rRNAs and 22 tRNAs followed a standard avian mitochondrial arrangement. The overall divergence between the two common raven clades was 3% (range 0.3–5.8% in 16 regions including the protein coding genes, rRNAs and the control region). Phylogenies constructed from whole mitogenomes recovered the previously found mitochondrial sister relationship between the common raven California clade and the Chihuahuan raven (overall divergence 1.1%), which strengthens the hypothesis that mtDNA paraphyly in the common raven results from speciation reversal of previously distinct Holarctic and California lineages.

• Schrumpf, Elisabeth; Jiang, Xiaojun; Zeissig, Sebastian; Pollheimer, Marion J.; Anmarkrud, Jarl Andreas & Tan, Corey [Show all 10 contributors for this article] (2017). The role of natural killer T cells in a mouse model with spontaneous bile duct inflammation. Physiological Reports. 5:e13117(4), p. 1–12. doi: 10.14814/phy2.13117. Full text in Research Archive
• Jørgensen, Silje Fjellgård; Trøseid, Marius; Kummen, Martin; Anmarkrud, Jarl Andreas; Michelsen, Annika & Osnes, Liv T. N. [Show all 21 contributors for this article] (2016). Altered gut microbiota profile in common variable immunodeficiency associates with levels of lipopolysaccharide and markers of systemic immune activation. Mucosal Immunology. ISSN 1933-0219. doi: 10.1038/mi.2016.18. Full text in Research Archive
• Lifjeld, Jan Terje; Anmarkrud, Jarl Andreas; Calabuig, Pascual; Cooper, Joseph E.J.; Johannessen, Lars Erik & Johnsen, Arild [Show all 12 contributors for this article] (2016). Species-level divergences in multiple functional traits between the two endemic subspecies of Blue Chaffinches Fringilla teydea in Canary Islands. BMC Zoology. doi: 10.1186/s40850-016-0008-4. Full text in Research Archive Show summary

  Background One of the biggest challenges in avian taxonomy is the delimitation of allopatric species because their reproductive incompatibility cannot be directly studied in the wild. Instead, reproductive incompatibility has to be inferred from multiple, divergent character sets that indicate a low likelihood of allopatric populations amalgamating upon secondary contact. A set of quantitative criteria for species delimitation has been developed for avian taxonomy. Results Here, we report a broad multi-trait comparison of the two insular subspecies of the Blue Chaffinch Fringilla teydea, endemic to the pine forests of Tenerife (ssp. teydea) and Gran Canaria (ssp. polatzeki) in the Canary Islands. We found that the two taxa were reciprocally monophyletic in their whole mitogenomes and two Z chromosome introns. The genetic distance in mitogenomes indicates around 1 Mya of allopatric evolution. There were diagnostic differences in body morphometrics, song and plumage reflectance spectra, whose combined divergence score (=11) exceeds the threshold level (=7) set for species delimitation by Tobias et al. (Ibis 152:724–746, 2010). Moreover, we found a marked divergence in sperm lengths with little range overlap. Relatively long sperm with low intra- and intermale CV compared to other passerines suggest a mating system with high levels of sperm competition (extrapair paternity) in these taxa. Conclusion The large and diagnostic divergences in multiple functional traits qualify for species rank, i.e., Tenerife Blue Chaffinch (Fringilla teydea) and Gran Canaria Blue Chaffinch (Fringilla polatzeki). We encourage a wider use of sperm traits in avian taxonomy because sperm divergences might signal reproductive incompatibility at the postcopulatory prezygotic stage, especially in species with sperm competition.

• Kummen, Martin; Holm, Kristian; Anmarkrud, Jarl Andreas; Nygård, Ståle; Vesterhus, Mette & Høivik, Marte [Show all 14 contributors for this article] (2016). The gut microbial profile in patients with primary sclerosing cholangitis is distinct from patients with ulcerative colitis without biliary disease and healthy controls. Gut. ISSN 0017-5749. 66(4), p. 611–619. doi: 10.1136/gutjnl-2015-310500. Full text in Research Archive Show summary

  Objective: Gut microbiota could influence gut, as well as hepatic and biliary immune responses. We therefore thoroughly characterised the gut microbiota in primary sclerosing cholangitis (PSC) compared with healthy controls (HC) and patients with ulcerative colitis without liver disease. Design: We prospectively collected 543 stool samples. After a stringent exclusion process, bacterial DNA was submitted for 16S rRNA gene sequencing. PSC and HC were randomised to an exploration panel or a validation panel, and only significant results (p<0.05, QFDR<0.20) in both panels were reported, followed by a combined comparison of all samples against UC. Results: Patients with PSC (N=85) had markedly reduced bacterial diversity compared with HC (N=263, p<0.0001), and a different global microbial composition compared with both HC (p<0.001) and UC (N=36, p<0.01). The microbiota of patients with PSC with and without IBD was similar. Twelve genera separated PSC and HC, out of which 11 were reduced in PSC. However, the Veillonella genus showed a marked increase in PSC compared with both HC (p<0.0001) and UC (p<0.02). Using receiver operating characteristic analysis, Veillonella abundance yielded an area under the curve (AUC) of 0.64 to discriminate PSC from HC, while a combination of PSC- associated genera yielded an AUC of 0.78. Conclusions: Patients with PSC exhibited a gut microbial signature distinct from both HC and UC without liver disease, but similar in PSC with and without IBD. The Veillonella genus, which is also associated with other chronic inflammatory and fibrotic conditions, was enriched in PSC.

• Wittig, Michael; Anmarkrud, Jarl Andreas; Kässens, Jan C.; Koch, Simon; Forster, Michael & Ellinghaus, Eva [Show all 14 contributors for this article] (2015). Development of a high-resolution NGS-based HLA-typing and analysis pipeline. Nucleic Acids Research (NAR). ISSN 0305-1048. 43:e70(11). doi: 10.1093/nar/gkv184. Full text in Research Archive
• Hov, Johannes Espolin Roksund; Zhong, Huanzi; Qin, Bincai; Anmarkrud, Jarl Andreas; Holm, Kristian & Franke, Andre [Show all 8 contributors for this article] (2015). The influence of the autoimmunity-associated ancestral HLA haplotype AH8.1 on the human gut microbiota: A cross-sectional study. PLOS ONE. 10:e0133804(7). doi: 10.1371/journal.pone.0133804. Full text in Research Archive
• Næss, Sigrid; Björnsson, Einar; Anmarkrud, Jarl Andreas; Mamari, Said Al; Juran, Brian D. & Lazaridis, Konstantinos N. [Show all 15 contributors for this article] (2014). Small duct primary sclerosing cholangitis without inflammatory bowel disease is genetically different from large duct disease. Liver international (Print). ISSN 1478-3223. 34(10), p. 1488–1495. doi: 10.1111/liv.12492. Full text in Research Archive
• Johnsen, Arild; Brabrand, Åge; Anmarkrud, Jarl Andreas; Bjørnstad, Gro; Pavels, Henning & Saltveit, Svein Jakob (2014). Impact of human-induced environmental changes on genetic structure and variability in Atlantic salmon, Salmo salar. Fisheries Management and Ecology. ISSN 0969-997X. 21(1), p. 32–41. doi: 10.1111/fme.12049. Full text in Research Archive
• Shi, Jihua; Liu, Shuzheng; Wierød, Lene; Scholz, Hanne Bjørnson; Anmarkrud, Jarl Andreas & Huitfeldt, Henrik [Show all 8 contributors for this article] (2013). RAF-targeted therapy for hepatocellular carcinoma in the regenerating liver. Journal of Surgical Oncology. ISSN 0022-4790. 107(4), p. 393–401. doi: 10.1002/jso.23224. Full text in Research Archive
• Wannhoff, A; Hov, Johannes Espolin Roksund; Folseraas, Trine; Rupp, C; Friedrich, K & Anmarkrud, Jarl Andreas [Show all 13 contributors for this article] (2013). FUT2 and FUT3 genotype determines CA19-9 cut-off values for detection of cholangiocarcinoma in patients with primary sclerosing cholangitis. Journal of Hepatology. ISSN 0168-8278. 59(6), p. 1278–1284. doi: 10.1016/j.jhep.2013.08.005. Full text in Research Archive
• Gohli, Jostein; Anmarkrud, Jarl Andreas; Johnsen, Arild; Kleven, Oddmund; Borge, Thomas & Lifjeld, Jan Terje (2013). Female promicuity is positively associated with neutral and selected genetic diversity in passerine birds. Evolution. ISSN 0014-3820. 67(5), p. 1406–1419. doi: 10.1111/evo.12045. Full text in Research Archive
• Anmarkrud, Jarl Andreas; Kleven, Oddmund; Jakob, Augustin; Bentz, Kristofer H; Blomqvist, Donald & Fernie, Kim J [Show all 14 contributors for this article] (2011). Factors affecting germline mutations in a hypervariable microsatellite: a comparative analysis of six species of swallows (Aves: Hirundinidae). Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. ISSN 0027-5107. 708(1-2), p. 37–43. doi: 10.1016/j.mrfmmm.2011.01.006. Full text in Research Archive
• Anmarkrud, Jarl Andreas; Johnsen, Arild; Bachmann, Lutz & Lifjeld, Jan Terje (2010). Ancestral polymorphism in exon 2 of bluethroat (Luscinia svecica) MHC class II B genes. Journal of Evolutionary Biology. ISSN 1010-061X. 23(6), p. 1206–1217. doi: 10.1111/j.1420-9101.2010.01999.x. Full text in Research Archive
• Canal, David; Alcaide, Miguel; Anmarkrud, Jarl Andreas & Potti, Jaime (2010). Towards the simplification of MHC typing protocols: targeting classical MHC class II genes in a passerine, the pied flycatcher Ficedula hypoleuca. BMC Research Notes. 3(236). Full text in Research Archive
• Anmarkrud, Jarl Andreas; Kleven, Oddmund; Bachmann, Lutz & Lifjeld, Jan Terje (2008). Microsatellite evolution: Mutations, sequence variation, and homoplasy in the hypervariable avian microsatellite locus HrU10. BMC Evolutionary Biology. 8(138). doi: 10.1186/1471-2148-8-138. Full text in Research Archive Show summary

  BACKGROUND Microsatellites are frequently used genetic markers in a wide range of applications, primarily due to their high length polymorphism levels that can easily be genotyped by fragment length analysis. However, the mode of microsatellite evolution is yet not fully understood, and the role of interrupting motifs for the stability of microsatellites remains to be explored in more detail. Here we present a sequence analysis of mutation events and a description of the structure of repeated regions in the hypervariable, pentanucleotide microsatellite locus HrU10 in barn swallows (Hirundo rustica) and tree swallows (Tachycineta bicolor). RESULTS In a large-scale parentage analysis in barn swallows and tree swallows, broods were screened for mutations at the HrU10 locus. In 41 cases in the barn swallows and 15 cases in the tree swallows, mutations corresponding to the loss or gain of one or two repeat units were detected. The parent and mutant offspring alleles were sequenced for 33 of these instances (26 in barn swallows and 7 in tree swallows). Replication slippage was considered the most likely mutational process. We tested the hypothesis that HrU10, a microsatellite with a wide allele size range, has an increased probability of introductions of interruptive motifs (IMs) with increasing length of the repeated region. Indeed, the number and length of the IMs was strongly positively correlated with the total length of the microsatellite. However, there was no significant correlation with the length of the longest stretch of perfectly repeated units, indicating a threshold level for the maximum length of perfectly repeated pentanucleotide motifs in stable HrU10 alleles. The combination of sequence and pedigree data revealed that 15 barn swallow mutations (58%) produced alleles that were size homoplasic to other alleles in the data set. CONCLUSIONS Our results give further insights into the mode of microsatellite evolution, and support the assumption of increased slippage rate with increased microsatellite length and a stabilizing effect of interrupting motifs for microsatellite regions consisting of perfect repeats. In addition, the observed extent of size homoplasy may impose a general caution against using hypervariable microsatellites in genetic diversity measures when alleles are identified by fragment length analysis only.

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• Cruz, Marcelo Merten; Rodrigues, Alan Erik Souza; Carvalho, Cintia Oliveira; Rosa, Fabricio dos Anjos Santa; Anmarkrud, Jarl Andreas & Melo, Silvana [Show all 10 contributors for this article] (2024). Bony fish diversity identified from environmental DNA identifies regional biogeographic breaks. Full text in Research Archive
• Rodrigues, Alan Erik Souza; Brito, Rafaela Maria Serra de; Nunes, Jorge Luiz Silva; Anmarkrud, Jarl Andreas; Melo, Silvana & Boer, Hugo de [Show all 10 contributors for this article] (2024). INSIGHTS ON THE DIET OF THREE THREATENED ELASMOBRANCHS OBTAINED USING A MOLECULAR APPROACH OF STOMACH CONTENTS. Full text in Research Archive
• Rodrigues, Alan Erik Souza; Carvalho, Cintia Oliveira; Rosa, Fabricio dos Anjos Santa; Charvet, Patricia; Faria, Vicente & Anmarkrud, Jarl Andreas [Show all 10 contributors for this article] (2024). Environmental DNA identifies sharks and rays across their biodiversity hotspot along the northern coast of Brazil. Full text in Research Archive
• Amaral, Aisha Carolina Cei; Rodrigues, Alan Erik Souza; Silva, Dalila Costa; Anmarkrud, Jarl Andreas; Melo, Silvana & Sales, João Bráullio de Luna [Show all 10 contributors for this article] (2024). MOLECULAR ANALYSIS OF THE DIETARY HABITS OF THE INVASIVE PRAWN MACROBRACHIUM ROSENBERGII (DE MAN, 1789): A GENERALIST PREDATOR IN AMAZON DELTA. Full text in Research Archive
• Amaral, Aisha Carolina Cei; Rodrigues, Alan Erik Souza; Silva, Dalila Costa; Anmarkrud, Jarl Andreas; Melo, Silvana & Sales, João Bráullio de Luna [Show all 10 contributors for this article] (2024). Molecular analysis shows that the invasive shrimp Macrobrachium rosenbergii is a generalist and opportunistic predator in the Amazon delta. Full text in Research Archive
• Paiva, Bianca Lima; Rodrigues, Alan Erik Souza; Carvalho, Cintia Oliveira; Anmarkrud, Jarl Andreas; Melo, Silvana & Charvet, Patricia [Show all 11 contributors for this article] (2024). Endangered species for sale. Full text in Research Archive
• Rekdal, Silje Larsen; Anmarkrud, Jarl Andreas; Lifjeld, Jan Terje & Johnsen, Arild (2022). MHC-based mate choice in bluethroats. Full text in Research Archive
• Kummen, Martin; Holm, Kristian; Anmarkrud, Jarl Andreas; Vesterhus, Mette; Høivik, Marte & Trøseid, Marius [Show all 12 contributors for this article] (2015). O082 : THE GUT MICROBIOTA IN PRIMARY SCLEROSING CHOLANGITIS DIFFERS FROM THAT OF HEALTHY CONTROLS AND ULCERATIVE COLITIS PATIENTS WITHOUT BILIARY DISEASE. Full text in Research Archive
• Wittig, Michael; Anmarkrud, Jarl Andreas; Forster, Michael; Ellinghaus, Eva; Holm, Kristian & Wienbrandt, L [Show all 12 contributors for this article] (2013). In solution HLA capture and high-resolution NGS-based typing method and an automated, integrated analysis framework. Full text in Research Archive
• Naess, Sigrid; Anmarkrud, Jarl Andreas; Björnsson, Einar; Mamari, Said Al; Juran, Brian D. & Lazaridis, Konstantios N [Show all 13 contributors for this article] (2012). HLA associations in small-duct compared with large-duct primary sclerosing cholangitis. Hepatology. ISSN 0270-9139. 56, p. 1134A–1134A. Full text in Research Archive
• Anmarkrud, Jarl Andreas; Johnsen, Arild; Bachmann, Lutz & Lifjeld, Jan Terje (2009). Evolution of MHC Class II exon 2 in the bluethroat (Luscinia svecica). Full text in Research Archive
• Anmarkrud, Jarl Andreas; Kleven, Oddmund; Bachmann, Lutz & Lifjeld, Jan Terje (2007). The mode of microsatellite evolution revealed through pedigree analysis in barn swallow (Hirundo rustica). Full text in Research Archive
• Anmarkrud, Jarl Andreas (2011). Evolution of genetic diversity at two hypervariable markers: a microsatellite and the MHC. Universitetet i Oslo. Full text in Research Archive Show summary

  Genetic variation is a prerequisite for evolution. The present thesis examines how genetic diversity arises and is maintained. The thesis can be divided into two subprojects, addressing neutral and functional genetic variation, respectively. In the first subproject, germline mutation patterns on the presumably non-functional microsatellite locus HrU10 were investigated. By sequencing observed mutations uncovered by microsatellite length typing, a significant association between microsatellite length and number of interrupting motifs (sequence motifs deviating from the repeated core unit) was found. Moreover, a majority of the mutations revealed homoplasic alleles. This result may imply a general caution in population genetic studies where genotypes are based on allele sizes only. In a comparative analysis of HrU10 mutations in six species of swallows, the following sex specific patterns in HrU10 mutability were found: (i) Mutations in long alleles were typically attributed to male germlines and mutations in short alleles were most pronounced in female germlines. (ii) Mutations in the male germlines were significantly biased for expansions while no such effects were uncovered in female germlines. These results indicate fundamental dimorphism in male and female gametogenesis with respect to slippage mutations. The aim of the second subproject was to study the polymorphism at genes of the Major Histocompatibility Complex (MHC). The gene products of the MHC are important for immune response and subsequently individual fitness. First, the polymorphism at exon 2 in bluethroat (Luscinia svecica) MHC class II genes was assessed. The results revealed at least eleven different loci, and the amino acids involved with antigen recognition were subjected to significant diversifying selection. MHC class IIB (MHCIIB) exon 2 sequences from the thrush nightingale (L. luscinia) were also analyzed for comparison. Phylogenetic analyses indicate an ancestral origin of some of the polymorphism uncovered at the MHCIIB exon 2. Secondly, a standardized multispecies genotyping strategy was developed to estimate MHC diversity at eight closely related passerine species with known levels of promiscuity. Interestingly, an association between MHCIIB exon 2 diversity and promiscuity levels was identified. This result may indicate that promiscuity in passerine birds is a mechanism creating MHC diversity, and consequently promoting offspring immunological quality.

• Anmarkrud, Jarl Andreas (2006). Analyser av et system for regulert genuttrykk i melkesyrebakterier. Universitet for Miljø og Biovitenskap. Full text in Research Archive

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