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Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany.

https://arctichealth.org/en/permalink/ahliterature292108
Source
Proc Natl Acad Sci U S A. 2017 08 22; 114(34):9152-9157
Publication Type
Historical Article
Journal Article
Research Support, Non-U.S. Gov't
Date
08-22-2017
Author
Bastiaan Star
Sanne Boessenkool
Agata T Gondek
Elena A Nikulina
Anne Karin Hufthammer
Christophe Pampoulie
Halvor Knutsen
Carl André
Heidi M Nistelberger
Jan Dierking
Christoph Petereit
Dirk Heinrich
Kjetill S Jakobsen
Nils Chr Stenseth
Sissel Jentoft
James H Barrett
Author Affiliation
Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindern, NO-0316 Oslo, Norway; n.c.stenseth@ibv.uio.no bastiaan.star@ibv.uio.no.
Source
Proc Natl Acad Sci U S A. 2017 08 22; 114(34):9152-9157
Date
08-22-2017
Language
English
Publication Type
Historical Article
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
Arctic Regions
Atlantic Ocean
Bone and Bones - metabolism
DNA, Ancient - analysis - isolation & purification
Ecosystem
Fisheries - history
Fossils
Gadus morhua - genetics
Geography
Germany
History, Medieval
Norway
United Kingdom
Abstract
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.
Notes
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PubMed ID
28784790 View in PubMed
Less detail

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany.

https://arctichealth.org/en/permalink/ahliterature284838
Source
Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):9152-9157
Publication Type
Article
Date
Aug-22-2017
Author
Bastiaan Star
Sanne Boessenkool
Agata T Gondek
Elena A Nikulina
Anne Karin Hufthammer
Christophe Pampoulie
Halvor Knutsen
Carl André
Heidi M Nistelberger
Jan Dierking
Christoph Petereit
Dirk Heinrich
Kjetill S Jakobsen
Nils Chr Stenseth
Sissel Jentoft
James H Barrett
Source
Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):9152-9157
Date
Aug-22-2017
Language
English
Publication Type
Article
Abstract
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.
Notes
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PubMed ID
28784790 View in PubMed
Less detail

De novo gene evolution of antifreeze glycoproteins in codfishes revealed by whole genome sequence data.

https://arctichealth.org/en/permalink/ahliterature287449
Source
Mol Biol Evol. 2017 Dec 05;
Publication Type
Article
Date
Dec-05-2017
Author
Helle Tessand Baalsrud
Ole Kristian Tørresen
Monica Hongrø Solbakken
Walter Salzburger
Reinhold Hanel
Kjetill S Jakobsen
Sissel Jentoft
Source
Mol Biol Evol. 2017 Dec 05;
Date
Dec-05-2017
Language
English
Publication Type
Article
Abstract
New genes can arise through duplication of a pre-existing gene or de novo from non-coding DNA, providing raw material for evolution of new functions in response to a changing environment. A prime example is the independent evolution of antifreeze glycoprotein genes (afgps) in the Arctic codfishes and Antarctic notothenioids to prevent freezing. However, the highly repetitive nature of these genes complicates studies of their organization. In notothenioids, afgps evolved from an extant gene, yet the evolutionary origin of afgps in codfishes is unknown. Here, we demonstrate that afgps in codfishes have evolved de novo from non-coding DNA 13-18?Ma, coinciding with the cooling of the Northern Hemisphere. Using whole-genome sequence data from several codfishes and notothenioids, we find higher copy number of afgp in species exposed to more severe freezing suggesting a gene dosage effect. Notably, antifreeze function is lost in one lineage of codfishes analogous to the afgp losses in non-Antarctic notothenioids. This indicates that selection can eliminate the antifreeze function when freezing is no longer imminent. Additionally, we show that evolution of afgp-assisting antifreeze potentiating protein genes (afpps) in notothenioids coincides with origin and lineage-specific losses of afgp. The origin of afgps in codfishes is one of the first examples of an essential gene born from non-coding DNA in a non-model species. Our study underlines the power of comparative genomics to uncover past molecular signatures of genome evolution, and further highlights the impact of de novo gene origin in response to a changing selection regime.
PubMed ID
29216381 View in PubMed
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Proton-pumping rhodopsins are abundantly expressed by microbial eukaryotes in a high-Arctic fjord.

https://arctichealth.org/en/permalink/ahliterature300090
Source
Environ Microbiol. 2018 02; 20(2):890-902
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
02-2018
Author
Anna Vader
Haywood D Laughinghouse
Colin Griffiths
Kjetill S Jakobsen
Tove M Gabrielsen
Author Affiliation
University Centre in Svalbard, Longyearbyen, Norway.
Source
Environ Microbiol. 2018 02; 20(2):890-902
Date
02-2018
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Arctic Regions
Cryptophyta - genetics - metabolism
Dinoflagellida - genetics - metabolism
Estuaries
Haptophyta - genetics - metabolism
Ion Transport - genetics
Oceans and Seas
Photosynthesis - genetics
Phylogeny
Proton Pumps - genetics - metabolism
RNA, Ribosomal, 18S - genetics
Rhodopsin - biosynthesis - genetics
Stramenopiles - genetics - metabolism
Svalbard
Transcriptome - genetics
Abstract
Proton-pumping rhodopsins provide an alternative pathway to photosynthesis by which solar energy can enter the marine food web. Rhodopsin genes are widely found in marine bacteria, also in the Arctic, and were recently reported from several eukaryotic lineages. So far, little is known about rhodopsin expression in Arctic eukaryotes. In this study, we used metatranscriptomics and 18S rDNA tag sequencing to examine the mid-summer function and composition of marine protists (size 0.45-10 µm) in the high-Arctic Billefjorden (Spitsbergen), especially focussing on the expression of microbial proton-pumping rhodopsins. Rhodopsin transcripts were highly abundant, at a level similar to that of genes involved in photosynthesis. Phylogenetic analyses placed the environmental rhodopsins within disparate eukaryotic lineages, including dinoflagellates, stramenopiles, haptophytes and cryptophytes. Sequence comparison indicated the presence of several functional types, including xanthorhodopsins and a eukaryotic clade of proteorhodopsin. Transcripts belonging to the proteorhodopsin clade were also abundant in published metatranscriptomes from other oceanic regions, suggesting a global distribution. The diversity and abundance of rhodopsins show that these light-driven proton pumps play an important role in Arctic microbial eukaryotes. Understanding this role is imperative to predicting the future of the Arctic marine ecosystem faced by a changing light climate due to diminishing sea-ice.
PubMed ID
29266690 View in PubMed
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Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod.

https://arctichealth.org/en/permalink/ahliterature270917
Source
Sci Rep. 2016;6:23246
Publication Type
Article
Date
2016
Author
Paul R Berg
Bastiaan Star
Christophe Pampoulie
Marte Sodeland
Julia M I Barth
Halvor Knutsen
Kjetill S Jakobsen
Sissel Jentoft
Source
Sci Rep. 2016;6:23246
Date
2016
Language
English
Publication Type
Article
Abstract
Identification of genome-wide patterns of divergence provides insight on how genomes are influenced by selection and can reveal the potential for local adaptation in spatially structured populations. In Atlantic cod - historically a major marine resource - Northeast-Arctic- and Norwegian coastal cod are recognized by fundamental differences in migratory and non-migratory behavior, respectively. However, the genomic architecture underlying such behavioral ecotypes is unclear. Here, we have analyzed more than 8.000 polymorphic SNPs distributed throughout all 23 linkage groups and show that loci putatively under selection are localized within three distinct genomic regions, each of several megabases long, covering approximately 4% of the Atlantic cod genome. These regions likely represent genomic inversions. The frequency of these distinct regions differ markedly between the ecotypes, spawning in the vicinity of each other, which contrasts with the low level of divergence in the rest of the genome. The observed patterns strongly suggest that these chromosomal rearrangements are instrumental in local adaptation and separation of Atlantic cod populations, leaving footprints of large genomic regions under selection. Our findings demonstrate the power of using genomic information in further understanding the population dynamics and defining management units in one of the world's most economically important marine resources.
Notes
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PubMed ID
26983361 View in PubMed
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