Publikasjoner
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Baalsrud, Helle T; Tørresen, Ole K; Danneels, Bram; Ferrari, Giada; Tooming-Klunderud, Ave & Skage, Morten
[Vis alle 12 forfattere av denne artikkelen]
(2026).
Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758).
Journal of Heredity.
ISSN 0022-1503.
117(4),
s. 750–760.
doi:
https:/academic.oup.com/jhered/article/117/4/750/8497176.
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The phylum Bryozoa is an understudied, yet commonly occurring, globally distributed bilaterian metazoan organismal group. They have a colonial lifestyle and an evolutionary history that spans at least 480 million years but likely longer. Despite their contentious phylogenetic affinities among metazoans, disproportionately few genomic investigations have been performed thus far. Here, we describe the first chromosome-level genome assembly of an individual Flustra foliacea colony belonging to the order Cheilostomatida, collected in southern Norway. The haplotype-resolved assembly of F. foliacea contains two pseudo-haplotypes spanning 956 megabases and 880 megabases, respectively. Both assemblies are highly complete both in terms of scaffolding (>90% of sequences placed in eight autosomal chromosomal pseudomolecules), and gene content (BUSCO completeness scores >90%). We also present gene and repeat annotations of the two assemblies. A comparison of our newly sequenced F. foliacea with five previously published bryozoan genomes supports the hypothesis that the group has undergone extensive genome rearrangements. This includes multiple chromosomal fusions in F. foliacea since their split with other cheilostome bryozoans. These fusions were enriched with long terminal repeat retrotransposons, highlighting the complex interplay between genome organization and genomic repeats. Our study contributes to a deeper understanding of bryozoan genome evolution and the role of repeats in metazoan genome organization.
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Koch, Thomas Lund; Ferrari, Giada; Sumanam, Sunita B; Salcedo, Paula Flórez; Watkins, Maren & Chase, Kevin
[Vis alle 13 forfattere av denne artikkelen]
(2026).
From neuropeptides to toxins: illuminating the origins of venom complexity in cone snails.
Molecular Biology and Evolution (MBE).
ISSN 0737-4038.
43,
s. 1–20.
doi:
10.1093/molbev/msag206.
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New genes and gene functions are key drivers of evolutionary innovation. Venomous animals, such as cone snails, provide striking examples of gene innovation, yet the mechanisms by which toxins arise remain poorly understood. Using the Conus textile genome, we uncover how neuropeptide genes were recruited into the venom and neofunctionalized as doppelgänger toxins. We identify over 20 independent recruitment events that evolved dynamically across the Conus lineage. Rather than arising from ohnologs of a whole-genome duplication event ∼200 mya, these toxins evolved through diverse mechanisms, including exon shuffling, alternative splicing, and ectopic recombination, often facilitated by lineage-specific transposable elements. Our findings reveal a dynamic interplay between genome architecture and molecular innovation, offering broad insight into the evolution of complex gene repertoires in venoms and beyond.
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Tørresen, Ole K; Tooming-Klunderud, Ave; Skage, Morten; Streitlien, Anne Eline; Strand, Olav & Rolandsen, Christer Moe
[Vis alle 10 forfattere av denne artikkelen]
(2025).
Chromosome-level genome assembly of Norwegian wild alpine reindeer (Rangifer tarandus tarandus).
Journal of Heredity.
ISSN 0022-1503.
doi:
10.1093/jhered/esaf094.
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We describe a chromosome-level genome assembly from a wild alpine reindeer individual (Rangifer tarandus tarandus) from the Rondane area in Southern Norway. The assembly is resolved into two pseudo-haplotypes: hap 1 spanning 3,081 Mb and hap 2 spanning 2,633 Mb. Contig N50 and scaffold N50 lengths are in the range of 31 to 41 and 66 to 69 Mb, respectively. A large part of these two haplotypes (83.8% and 90.4%, respectively) are scaffolded into 34 autosomal chromosomal pseudomolecules, and in sex chromosomes X and Y for hap 1. The BUSCO completeness scores are 98.0% and 95.2%, respectively, and gene annotations of the assemblies identified 37,998 and 36,977 protein-coding genes. We also present an updated and improved genome assembly for Svalbard reindeer (Rangifer tarandus platyrhynchus; contig N50 46 to 48 Mb, scaffold N50 67 to 71 Mb, BUSCO 95.4% to 98.0%) and a comparison with previously published genome assemblies of reindeer.
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Eriksen, Emma Falkeid; Andrews, Adam Jon; Nielsen, Svein Vatsvåg; Persson, Per; Malca, Estrella & Onar, Vedat
[Vis alle 19 forfattere av denne artikkelen]
(2025).
Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA.
Heredity.
ISSN 0018-067X.
134,
s. 175–185.
doi:
10.1038/s41437-025-00745-1.
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Mitonuclear discordance between species is readily documented in marine fishes. Such discordance may either be the result of past natural phenomena or the result of recent introgression from previously seperated species after shifts in their spatial distributions. Using ancient DNA spanning five millennia, we here investigate the long-term presence of Pacific bluefin tuna (Thunnus orientalis) and albacore (Thunnus alalunga) -like mitochondrial (MT) genomes in Atlantic bluefin tuna (Thunnus thynnus), a species with extensive exploitation history and observed shifts in abundance and age structure. Comparing ancient (n = 130) and modern (n = 78) Atlantic bluefin MT genomes from most of its range, we detect no significant spatial or temporal population structure, which implies ongoing gene flow between populations and large effective population sizes over millennia. Moreover, we identify discordant MT haplotypes in ancient specimens up to 5000 years old and find that the frequency of these haplotypes has remained similar through time. We therefore conclude that MT discordance in the Atlantic bluefin tuna is not driven by recent introgression. Our observations provide oldest example of directly observed MT discordance in the marine environment, highlighting the utility of ancient DNA to obtain insights in the long-term persistence of such phenomena.
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Garcia, Lourdes Martinez; Cuevas, Angelica; Ferrari, Giada; Hufthammer, Anne Karin; Vedeler, Marianne & Hirons, Alex
[Vis alle 9 forfattere av denne artikkelen]
(2024).
Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA.
Proceedings of the Royal Society of London. Biological Sciences.
ISSN 0962-8452.
291(2035).
doi:
10.1098/rspb.2024.2019.
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Marine resources have been important for the survival and economic development of coastal human communities across northern Europe for millennia. Knowledge of the origin of such historic resources can provide key insights into fishing practices and the spatial extent of trade networks. Here, we combine ancient DNA and stable isotopes (δ13C, δ15N, non-exchangeable δ2H and δ34S) to investigate the geographical origin of archaeological cod remains in Oslo from the eleventh to seventeenth centuries CE. Our findings provide genetic evidence that Atlantic cod was obtained from different geographical populations, including a variety of distant-water populations like northern Norway and possibly Iceland. Evidence for such long-distance cod trade is already observed from the eleventh century, contrasting with archaeological and historical evidence from Britain and other areas of Continental Europe around the North and Baltic Seas, where such trade increased during the thirteenth to fourteenth centuries. The genomic assignments of specimens to different populations coincide with significantly different δ13C values between those same specimens, indicating that multiple Atlantic cod populations living in different environments were exploited. This research provides novel information about the exploitation timeline of specific Atlantic cod stocks and highlights the utility of combining ancient DNA (aDNA) methods and stable isotope analysis to describe the development of medieval and post-medieval marine fisheries.
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Garcia, Lourdes Martinez; Ferrari, Giada; Cuevas, Angelica; Atmore, Lane Margaret; López-Arias, Begoña & Culling, Mark
[Vis alle 18 forfattere av denne artikkelen]
(2022).
Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe.
Proceedings of the Royal Society of London. Biological Sciences.
ISSN 0962-8452.
289(1985).
doi:
10.1098/rspb.2022.1107.
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Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050–1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens were derived from distant sources. Our results further suggest that Icelandic cod was indeed exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole-genome sequencing and ancient DNA approaches to describe the globalization of marine fisheries and increase our understanding regarding the extent of the North Atlantic fish trade and long-range fisheries in medieval and early modern times.
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Garcia, Lourdes Martinez; Ferrari, Giada; Hufthammer, Anne Karin; Jakobsen, Kjetill Sigurd; Jentoft, Sissel & Barrett, James Harold
[Vis alle 7 forfattere av denne artikkelen]
(2022).
Ancient DNA reveals a southern presence of the Northeast Arctic cod during the Holocene.
Biology Letters.
ISSN 1744-9561.
18(5).
doi:
10.1098/rsbl.2022.0021.
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Climate change has been implicated in an increased number of distributional shifts of marine species during the last century. Nonetheless, it is unclear whether earlier climatic fluctuations had similar impacts. We use ancient DNA to investigate the long-term spawning distribution of the Northeast Arctic cod (skrei) which performs yearly migrations from the Barents Sea towards spawning grounds along the Norwegian coast. The distribution of these spawning grounds has shifted northwards during the last century, which is thought to be associated with food availability and warming temperatures. We genetically identify skrei specimens from Ruskeneset in west Norway, an archaeological site located south of their current spawning range. Remarkably, 14C analyses date these specimens to the late Holocene, when temperatures were warmer than present-day conditions. Our results either suggest that temperature is not the only driver influencing the spawning distribution of Atlantic cod, or could be indicative of uncertainty in palaeoclimate reconstructions in this region. Regardless, our findings highlight the utility of aDNA to reconstruct the historical distribution of economically important fish populations and reveal the complexity of long-term ecological interactions in the marine environment.
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Atmore, Lane Margaret; Ferrari, Giada; Garcia, Lourdes Martinez; Jagt, Inge van der; Blevis, Rachel & Granado, José
[Vis alle 14 forfattere av denne artikkelen]
(2022).
Ancient DNA sequence quality is independent of fish bone weight.
Journal of Archaeological Science.
ISSN 0305-4403.
149.
doi:
10.1016/j.jas.2022.105703.
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The field of ancient DNA (aDNA) typically uses between 50 and 200 mg of minimum input weight of bone material for the extraction of DNA from archaeological remains. While laboratory and analysis techniques have focused on improved efficiency of extracting useable sequence data from older and poorer quality remains, bone material input requirements have rarely been critically evaluated. Here, we present the aDNA analysis of 121 size-constrained Atlantic herring remains – weighing between <10 and 70 mg – that were individually sequenced to explore the capacity of successful aDNA retrieval from small archaeological remains. We statistically evaluate the relationship between bone weight and several response variables, including library success, endogenous DNA content, and library complexity, i.e., the number of unique molecules that are obtained. Remarkably, we find no relationship between bone weight and library success, levels of endogenous DNA, or library complexity. Our results imply that – at least in the case of fish bone – even minute bones can yield positive results and that the presumed minimum sample size required should be re-evaluated. Archaeological site, instead of bone size, is the primary driver of DNA sequence quality. Our work expands the number of specimens considered suitable for aDNA analyses, and therefore facilitates efforts to minimize the destructive impact of aDNA research and mediate some of the ethical concerns surrounding destructive analysis.
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Oosting, Tom; Garcia, Lourdes Martinez; Ferrari, Giada; Verry, Alexander J. F.; Scarsbrook, Lachie & Rawlence, Nicolas J.
[Vis alle 9 forfattere av denne artikkelen]
(2022).
Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus).
Heredity.
ISSN 0018-067X.
130,
s. 30–39.
doi:
10.1038/s41437-022-00579-1.
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Abstract Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern ( n = 350) and ancient ( n = 26) mitochondrial genomes from Australasian snapper ( Chrysophrys auratus ) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years ( p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
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Barrett, James; Khamaiko, Natalia; Ferrari, Giada; Cuevas, Angelica; Kneale, Catherine & Hufthammer, Anne Karin
[Vis alle 8 forfattere av denne artikkelen]
(2022).
Walruses on the Dnieper: new evidence for the intercontinental trade of Greenlandic ivory in the Middle Ages.
Proceedings of the Royal Society of London. Biological Sciences.
ISSN 0962-8452.
289(1972),
s. 1–9.
doi:
10.1098/rspb.2021.2773.
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Mediaeval walrus hunting in Iceland and Greenland—driven by Western European demand for ivory and walrus hide ropes—has been identified as an important pre-modern example of ecological globalization. By contrast, the main origin of walrus ivory destined for eastern European markets, and then onward trade to Asia, is assumed to have been Arctic Russia. Here, we investigate the geographical origin of nine twelfth-century CE walrus specimens discovered in Kyiv, Ukraine—combining archaeological typology (based on chaîne opératoire assessment), ancient DNA (aDNA) and stable isotope analysis. We show that five of seven specimens tested using aDNA can be genetically assigned to a western Greenland origin. Moreover, six of the Kyiv rostra had been sculpted in a way typical of Greenlandic imports to Western Europe, and seven are tentatively consistent with a Greenland origin based on stable isotope analysis. Our results suggest that demand for the products of Norse Greenland's walrus hunt stretched not only to Western Europe but included Ukraine and, by implication given linked trade routes, also Russia, Byzantium and Asia. These observations illuminate the surprising scale of mediaeval ecological globalization and help explain the pressure this process exerted on distant wildlife populations and those who harvested them.
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Garcia, Lourdes Martinez; Ferrari, Giada; Oosting, Tom; Ballantyne, Rachel; Jagt, Inge van der & Ystgaard, Ingrid
[Vis alle 20 forfattere av denne artikkelen]
(2021).
Historical demographic processes dominate genetic variation in ancient Atlantic cod mitogenomes.
Frontiers in Ecology and Evolution.
9,
s. 1–14.
doi:
10.3389/fevo.2021.671281.
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Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
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Ferrari, Giada; Cuevas, Angelica; Wyrozemska, Agata Teresa; Ballantyne, Rachel; Kersten, Oliver & Palsdottir, Albina Hulda
[Vis alle 18 forfattere av denne artikkelen]
(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.
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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.
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Ferrari, Giada; Atmore, Lane Margaret; Jentoft, Sissel; Jakobsen, Kjetill Sigurd; Makowiecki, Daniel & Barrett, James
[Vis alle 7 forfattere av denne artikkelen]
(2021).
An accurate assignment test for extremely low-coverage whole-genome sequence data.
Molecular Ecology Resources.
ISSN 1755-098X.
s. 1–15.
doi:
10.1111/1755-0998.13551.
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Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.
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Ferrari, Giada; Neukamm, Judith; Baalsrud, Helle Tessand; Breidenstein, Abagail; Ravinet, Mark & Phillips, Carina
[Vis alle 9 forfattere av denne artikkelen]
(2020).
Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox.
Philosophical Transactions of the Royal Society of London. Biological Sciences.
ISSN 0962-8436.
375(1812),
s. 1–9.
doi:
10.1098/rstb.2019.0572.
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Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Ferrari, Giada; Lischer, Heidi E L; Neukamm, Judith; Rayo, Enrique; Borel, Nicole & Pospischil, Andreas
[Vis alle 9 forfattere av denne artikkelen]
(2018).
Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf.
Genes.
9(9),
s. 1–17.
doi:
10.3390/genes9090436.
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The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies. However, as for all ancient DNA (aDNA) studies, environmental and laboratory contamination need to be specifically addressed. Here we attempted to reconstruct the tissue-specific metagenomes of a 42,000-year-old, permafrost-preserved woolly mammoth calf through shotgun high-throughput sequencing. We analyzed the taxonomic composition of all tissue samples together with environmental and non-template experimental controls and compared them to metagenomes obtained from permafrost and elephant fecal samples. Preliminary results suggested the presence of tissue-specific metagenomic signals. We identified bacterial species that were present in only one experimental sample, absent from controls, and consistent with the nature of the samples. However, we failed to further authenticate any of these signals and conclude that, even when experimental samples are distinct from environmental and laboratory controls, this does not necessarily indicate endogenous presence of ancient host-associated microbiomic signals.
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Publisert
22. mars 2023 09:43
- Sist endret
24. mars 2023 11:52
