agatag

• Wyrozemska, Agata Teresa; Kianian, Atefeh & Edholm, Eva-Stina Isabella (2025). Comparative analysis of salmonid non-classical MHC class I L lineage genes. Developmental and Comparative Immunology. ISSN 0145-305X. 170. doi: 10.1016/j.dci.2025.105422. Full text in Research Archive
• Pinsky, Malin L.; Eikeset, Anne Maria; Helmerson, Cecilia Jenny Margareta Thomas; Bradbury, Ian R.; Bentzen, Paul & Morris, Corey [Show all 17 contributors for this article] (2021). Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 118(15). doi: 10.1073/pnas.2025453118. Full text in Research Archive Show summary

  The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.

• Ferrari, Giada; Cuevas, Angelica; Wyrozemska, Agata Teresa; Ballantyne, Rachel; Kersten, Oliver & Palsdottir, Albina Hulda [Show all 18 contributors for this article] (2021). The preservation of ancient DNA in archaeological fish bone. Journal of Archaeological Science. ISSN 0305-4403. 126(105317). doi: 10.1016/j.jas.2020.105317. Full text in Research Archive Show summary

  The field of ancient DNA is dominated by studies focusing on terrestrial vertebrates. This taxonomic bias limits our understanding of endogenous DNA preservation for species with different bone physiology, such as teleost fish. Teleost bone is typically brittle, porous, lightweight, and is characterized by a lack of bone remodeling during growth. All of these factors potentially affect DNA preservation. Using high-throughput shotgun sequencing, we here investigate the preservation of DNA in a range of different bone elements from over 200 archaeological Atlantic cod (Gadus morhua) specimens from 38 sites in northern Europe, dating up to 8000 years before present. We observe that the majority of archaeological sites (79%) yield endogenous DNA, with 40% of sites providing samples containing high levels (>20%). Library preparation success and levels of endogenous DNA depend mainly on excavation site and pre-extraction laboratory treatment. The use of pre-extraction treatments lowers the rate of libraries that can be sequenced, although — if successful — the fraction of endogenous DNA can be improved by several orders of magnitude. This trade-off between library preparation success and levels of endogenous DNA allows for alternative extraction strategies depending on the requirements of down-stream analyses and research questions. Finally, we do not find particular bone elements to yield higher levels of endogenous DNA, as is the case for denser bones in mammals. Our results highlight the potential of archaeological fish bone as a source for ancient DNA and suggest a possible role of bone remodeling in the preservation of endogenous DNA.

• Nistelberger, Heidi Maria; Palsdottir, Albina Hulda; Star, Bastiaan; Leifsson, Rúnar; Gondek, Agata Teresa & Orlando, Ludovic [Show all 9 contributors for this article] (2019). Sexing Viking Age horses from burial and non-burial sites in Iceland using ancient DNA. Journal of Archaeological Science. ISSN 0305-4403. 101, p. 115–122. doi: 10.1016/j.jas.2018.11.007. Full text in Research Archive Show summary

  Horses are the most common grave goods found in Icelandic Viking Age graves. Horse skeletons have previously been sexed based on pelvis shape and the presence of canine teeth in male horses over 4–5 years of age. Morphological data has shown that all horses from Icelandic burials that were amenable to sexing were male. Yet the use of morphological methods to determine sex is problematic since they rely on finding a well-preserved pelvis and/or robust canine teeth. Furthermore, quantitative data underlying the features of the horse pelvis used for sexing is lacking and canine teeth have been reported to occur in mares. In this study we build upon and extend recently developed methodologies to make use of shotgun sequencing of ancient DNA (aDNA) for molecular sexing of Viking Age horse remains. With minimal sequencing effort we identified the sex of the largest collection (n = 22) of Viking Age Icelandic horses studied to date, sourced from both burial (n = 19) and non-burial (n = 3) sites. Our results revealed a male to female sex bias ratio of 18:1 in burial sites, versus 0:3 in non-burial sites. These findings support the significant over-representation of male horses in Viking Age graves in Iceland, yet show that –albeit rare– mares could also be selected for ritual burial in Viking Age Iceland. This cost-effective method provides statistical confidence to allow for sexing of highly fragmented archaeological specimens with low endogenous DNA content.

• Svenning, Steingrim; Wyrozemska, Agata Teresa; Wal, Yorick Andreas van der; Robertsen, Børre; Jensen, Ingvill & Jørgensen, Jorunn B [Show all 7 contributors for this article] (2019). Microbial danger signals control transcriptional induction of distinct MHC class I L lineage genes in Atlantic salmon. Frontiers in Immunology. 10. doi: 10.3389/fimmu.2019.02425. Full text in Research Archive Show summary

  Antigen processing and presentation by major histocompatibility complex (MHC) molecules is a cornerstone in vertebrate immunity. Like mammals, teleosts possess both classical MHC class I and multiple families of divergent MHC class I genes. However, while certain mammalian MHC class I-like molecules have proven to be integral in immune regulation against a broad array of pathogens, the biological relevance of the different MHC class I lineages in fish remains elusive. This work focuses on MHC class I L lineage genes and reveals unique regulatory patterns of six genes (<i>Sasa-lia, Sasa-lda, Sasa-lca, Sasa-lga, Sasa-lha</i>, and <i>Sasa-lfa</i>) in antimicrobial immunity of Atlantic salmon (<i>Salmo salar L.</i>). Using two separate <i>in vivo</i> challenge models with different kinetics and immune pathologies combined with <i>in vitro</i> stimulation using viral and bacterial TLR ligands, we show that <i>de novo</i> synthesis of different L lineage genes is distinctly regulated in response to various microbial stimuli. Prior to the onset of classical MHC class I gene expression, <i>lia</i> was rapidly and systemically induced <i>in vivo</i> by the single-stranded (ss) RNA virus salmonid alpha virus 3 (SAV3) but not in response to the intracellular bacterium <i>Piscirickettsia salmonis</i>. In contrast, <i>lga</i> expression was upregulated in response to both viral and bacterial stimuli. A role for distinct MHC class I L-lineage genes in anti-microbial immunity in salmon was further substantiated by a marked upregulation of <i>lia</i> and <i>lga</i> gene expression in response to type I IFNa stimulation <i>in vitro</i>. Comparably, <i>lha</i> showed no transcriptional induction in response to IFNa stimulation but was strongly induced in response to a variety of viral and bacterial TLR ligands. In sharp contrast, <i>lda</i> showed no response to viral or bacterial challenge. Similarly, induction of <i>lca</i>, which is predominantly expressed in primary and secondary lymphoid tissues, was marginal with the exception of a strong and transient upregulation in pancreas following SAV₃ challenge Together, these findings suggest that certain Atlantic salmon MHC class I L lineage genes play important and divergent roles in early anti-microbial response and that their regulation, in response to different activation signals, represents a system for selectively promoting the expression of distinct non-classical MHC class I genes in response to different types of immune challenges.

• Star, Bastiaan; Barrett, James H.; Gondek, Agata Teresa & Boessenkool, Sanne (2018). Ancient DNA reveals the chronology of walrus ivory trade from Norse Greenland. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. 285(1884), p. 1–9. doi: 10.1098/rspb.2018.0978. Full text in Research Archive Show summary

  The importance of the Atlantic walrus ivory trade for the colonization, peak, and collapse of the medieval Norse colonies on Greenland has been extensively debated. Nevertheless, no studies have directly traced medieval European ivory back to distinct Arctic populations of walrus. Analysing the entire mitogenomes of 37 archaeological specimens from Europe, Svalbard, and Greenland, we here discover that Atlantic walrus comprises two monophyletic mitochondrial (MT) clades, which diverged between 23 400 and 251 120 years ago. Our improved genomic resolution allows us to reinterpret the geographical distribution of partial MT data from 306 modern and nineteenth-century specimens, finding that one of these clades was exclusively accessible to Greenlanders. With this discovery, we ascertain the biological origin of 23 archaeological specimens from Europe (most dated between 900 and 1400 CE). These results reveal a significant shift in trade from an early, predominantly eastern source towards a near exclusive representation of Greenland ivory. Our study provides empirical evidence for how this remote Arctic resource was progressively integrated into a medieval pan-European trade network, contributing to both the resilience and vulnerability of Norse Greenland society.

• Gondek, Agata Teresa; Boessenkool, Sanne & Star, Bastiaan (2018). A stainless-steel mortar, pestle and sleeve design for the efficient fragmentation of ancient bone. BioTechniques. ISSN 0736-6205. 64(6), p. 266–269. doi: 10.2144/btn-2018-0008. Full text in Research Archive Show summary

  Different types of milling equipment – such as oscillating ball mills, freezer mills, mortar and pestle – can be used to fragment ancient bone prior to DNA extraction. However, each of these tools is associated with practical drawbacks. Here, we present the design for a stainless-steel mortar and pestle, with a removable sleeve to contain bone material. The tool is easy to clean, practical and its simplicity allows university workshops equipped with a lathe, boring tools and a milling machine to make these components at local expense. This design allows for the efficient fragmentation of ancient bone and improves sample throughput. This design is recommended as a useful, economical addition to existing laboratory equipment for the handling of ancient bone.

• Boessenkool, Sanne; Hanghøj, Kristian; Nistelberger, Heidi Maria; Sarkissian, Clio Der; Gondek, Agata Teresa & Orlando, Ludovic [Show all 8 contributors for this article] (2017). Combining bleach and mild pre-digestion improves ancient DNA recovery from bones. Molecular Ecology Resources. ISSN 1755-098X. 17(4), p. 742–751. doi: 10.1111/1755-0998.12623. Full text in Research Archive Show summary

  The feasibility of genome‐scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre‐extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750–1350 cal. years before present. Using high‐throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre‐extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole‐genome sequencing. The final version of this research has been published in Molecular Ecology Resources. © 2016 Wiley

• Star, Bastiaan; Boessenkool, Sanne; Gondek, Agata Teresa; Nikulina, Elena A.; Hufthammer, Anne Karin & Pampoulie, Christophe [Show all 16 contributors for this article] (2017). Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 114(34), p. 9152–9157. doi: 10.1073/pnas.1710186114. Full text in Research Archive Show summary

  Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15–46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800–1066 CE) and subsequent medieval (1066–1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.

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• Palsdottir, Albina Hulda; Barrett, James H.; Boessenkool, Sanne; Hallsson, Jón Hallsteinn; Leifsson, Rúnar & Nistelberger, Heidi Maria [Show all 9 contributors for this article] (2019). POWERFUL MALE VIKINGS WERE BURIED WITH THEIR POWERFUL MALE HORSES. [Internet]. Newsweek.com. Full text in Research Archive
• Palsdottir, Albina Hulda; Nistelberger, Heidi Maria; Leifsson, Rúnar; Orlando, Ludovic; Barrett, James H. & Star, Bastiaan [Show all 9 contributors for this article] (2019). Fornleifarannsóknir: Hryssur ekki valdar í kuml. [Journal]. Austurglugginn. Full text in Research Archive
• Palsdottir, Albina Hulda; Nistelberger, Heidi Maria; Star, Bastiaan; Leifsson, Rúnar; Wyrozemska, Agata Teresa & Orlando, Ludovic [Show all 9 contributors for this article] (2019). Kyngreining á hrossum úr kumlum með forn-DNA Hestar lagðir í kuml á Íslandi á víkingaöld. Full text in Research Archive
• Palsdottir, Albina Hulda; Barrett, James H.; Boessenkool, Sanne; Hallsson, Jón Hallsteinn; Leifsson, Rúnar & Nistelberger, Heidi Maria [Show all 9 contributors for this article] (2019). Lítið um hryssur í kumlum víkinga. [Journal]. Morgunblaðið. Full text in Research Archive
• Palsdottir, Albina Hulda; Nistelberger, Heidi Maria; Star, Bastiaan; Leifsson, Rúnar; Wyrozemska, Agata Teresa & Orlando, Ludovic [Show all 9 contributors for this article] (2019). Kyngreining á hrossum úr kumlum með fornDNA. Full text in Research Archive Show summary

  Hestar voru algengasta haugfé sem lagt var í kuml á Íslandi á víkingaöld. Beinagrindur hrossa er hægt að kyngreina á formi mjaðmagrindar og því hvort vígtennur eru til staðar. Vígtennur koma upp við 4-5 ára aldur í karldýrum en þó hafa rannsóknir sýnt að allt að þriðjungur hryssa getur haft vígtennur þó þær séu yfirleitt mun minni en í karldýrunum. Beinagreining hefur sýnt að öll hross sem hægt er að kyngreina úr íslenskum kumlum er úr karlkyns hestum en þar sem stór hluti þessara kumla fannst fyrir mörgum áratugum síðan við framkvæmdir eru beinagrindurnar oft of illa varðveittar til þess að hægt sé að kyngreina þær með vissu. Í þessari rannsókn notum við forn-DNA-greiningu til að kyngreina 22 hross frá víkingaöld. 19 hross voru úr kumlum en þrjú bein úr hellum og býlum voru einnig greind. Rannsóknir okkar leiddu í ljós að af 19 hrossum úr kumlum sem greind voru reyndist aðeins vera ein hryssa en öll sýnin sem komu úr helli og býli reyndust vera hryssur. Í greininni er einnig sýnt fram á að hægt er að kyngreina dýr jafnvel þó afar lítið sé varðveitt af DNA í hverju sýni og því má nota aðferðafræðina í greininni til að kyngreina fornleifafræðileg bein á mun stærri skala og fyrir minna fé en áður var talið. Fjallað verður um niðurstöður í nýútkominni grein Heidi M. Nistelberger, Albínu Huldu Pálsdóttur, Bastiaan Star, Rúnars Leifssonar, Agötu T. Gondek, Ludovic Orlando, James H. Barrett, Jóns Hallsteins Hallssonar og Sanne Boessenkool “Sexing Viking Age horses from burial and non-burial sites in Iceland using ancient DNA,” Journal of Archaeological Science 101 (2019), 115–122. https://doi.org/10.1016/j.jas.2018.11.007. Albína Hulda Pálsdóttir er dýrabeinafornleifafræðingur og starfar við Landbúnaðarháskóla Íslands. Hún er doktorsnemi við Óslóarháskóla en doktorsverkefni hennar heitir „Hestar og sauðfé víkinganna: Fornerfðafræði húsdýra í Norður-Atlantshafi“. Hún hefur greint dýrabeinasöfn frá Íslandi, Írlandi, Grænlandi og Færeyjum. Leiðbeinendur Albínu eru dr. Sanne Boessenkool við Óslóarháskóla, dr. Jón Hallsteinn Hallsson við Landbúnaðarháskóla Íslands og dr. Juha Kantanen hjá LUKE í Finnlandi. Verkefnið er styrkt af rannsóknasjóði Rannís á styrk nr. 162783051

• Palsdottir, Albina Hulda; Barrett, James H.; Boessenkool, Sanne; Hallsson, Jón Hallsteinn; Leifsson, Rúnar & Nistelberger, Heidi Maria [Show all 9 contributors for this article] (2019). Ancient DNA from Viking Graves Proves the Fierce Fighters Rode Male Horses. [Internet]. https://www.livescience.com/64432-vikings-buried-with-stalli. Full text in Research Archive
• Palsdottir, Albina Hulda; Barrett, James H.; Boessenkool, Sanne; Hallsson, Jón Hallsteinn; Leifsson, Rúnar & Nistelberger, Heidi Maria [Show all 9 contributors for this article] (2019). Powerful Icelandic Vikings were buried with stallions. [Internet]. phys.org. Full text in Research Archive
• Palsdottir, Albina Hulda; Barrett, James H.; Boessenkool, Sanne; Hallsson, Jón Hallsteinn; Leifsson, Rúnar & Nistelberger, Heidi Maria [Show all 9 contributors for this article] (2019). Lítið um hryss­ur í kuml­um vík­inga. [Internet]. mbl.is. Full text in Research Archive
• Palsdottir, Albina Hulda; Barrett, James H.; Boessenkool, Sanne; Hallsson, Jón Hallsteinn; Leifsson, Rúnar & Nistelberger, Heidi Maria [Show all 9 contributors for this article] (2019). Burials Suggest Icelandic Vikings Had a Thing for Stallions. [Internet]. www.smithsonianmag.com. Full text in Research Archive
• Leifsson, Rúnar; Palsdottir, Albina Hulda; Barrett, James H.; Boessenkool, Sanne; Hallsson, Jón Hallsteinn & Nistelberger, Heidi Maria [Show all 9 contributors for this article] (2019). Horses buried with Icelandic Viking nobles were male, ancient DNA shows. [Internet]. CBC news. Full text in Research Archive
• Palsdottir, Albina Hulda; Barrett, James H.; Boessenkool, Sanne; Hallsson, Jón Hallsteinn; Leifsson, Rúnar & Nistelberger, Heidi Maria [Show all 9 contributors for this article] (2019). Powerful Icelandic Vikings were buried with stallions. [Internet]. Heritage daily. Full text in Research Archive
• Palsdottir, Albina Hulda; Nistelberger, Heidi Maria; Star, Bastiaan; Leifsson, Rúnar; Gondek, Agata Teresa & Orlando, Ludovic [Show all 8 contributors for this article] (2019). Which horse should we sacrifice? Sex as a determining factor for the selection of horses in Viking Age burials in Iceland. Full text in Research Archive
• Gondek, Agata Teresa; Boessenkool, Sanne & Star, Bastiaan (2018). A stainless-steel mortar, pestle and sleeve design for the efficient fragmentation of ancient bone. Full text in Research Archive
• Palsdottir, Albina Hulda; Barrett, James H.; Boessenkool, Sanne; Hallsson, Jón Hallsteinn; Leifsson, Rúnar & Nistelberger, Heidi Maria [Show all 9 contributors for this article] (2018). Folum fórnað. [Internet]. Bændablaðið online. Full text in Research Archive
• Palsdottir, Albina Hulda; Boessenkool, Sanne; Barrett, James H.; Hallsson, Jón Hallsteinn; Leifsson, Rúnar & Nistelberger, Heidi Maria [Show all 9 contributors for this article] (2018). Mektige islandske vikinger fikk hingster med seg i graven. [Internet]. Titan.no. Full text in Research Archive
• Palsdottir, Albina Hulda; Boessenkool, Sanne; Barrett, James H.; Leifsson, Rúnar; Nistelberger, Heidi Maria & Orlando, Ludovic [Show all 9 contributors for this article] (2018). Powerful Icelandic Vikings were buried with stallions. [Internet]. Titan.no. Full text in Research Archive
• Nistelberger, Heidi Maria; Palsdottir, Albina Hulda; Star, Bastiaan; Leifsson, Rúnar; Gondek, Agata Teresa & Orlando, Ludovic [Show all 9 contributors for this article] (2018). Sexing Viking Age horses from burial and non-burial sites in Iceland using ancient DNA. Full text in Research Archive
• Barrett, James H; Star, Bastiaan; Kneale, Catherine; O'Connell, Tamsin C; Gondek, Agata Teresa & Boessenkool, Sanne (2018). Walrus Ivory in Medieval Europe: Artefactual, ancient DNA and stable isotope evidence for Ecological Globalization. Full text in Research Archive
• Boessenkool, Sanne; Hanghøj, Kristian; Nistelberger, Heidi Maria; Sarkissian, Clio Der; Gondek, Agata Teresa & Orlando, Ludovic [Show all 8 contributors for this article] (2016). Combining bleach and mild pre-digestion improves ancient DNA recovery from bones. Full text in Research Archive
• Star, Bastiaan; Boessenkool, Sanne; Gondek, Agata Teresa; Nikulina, Elena A & Barrett, James H (2016). Viking Age trade of Atlantic cod. Full text in Research Archive

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