Sex determination of baleen whale artefacts:implications for ancient DNA use in zooarchaeology
Abstract Methods to determine the sex from tissue samples of mammals include the amplification of Y chromosome specific regions, which should only amplify from males, or amplification of homologous regions of the X and Y chromosome containing XY specific SNPs. A disadvantage of the first approach is...
Published in: | Journal of Archaeological Science: Reports |
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2016
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Online Access: | https://curis.ku.dk/portal/da/publications/sex-determination-of-baleen-whale-artefacts(61b25b5c-6939-4cec-a33d-33579a6feefd).html https://doi.org/10.1016/j.jasrep.2016.11.001 |
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ftcopenhagenunip:oai:pure.atira.dk:publications/61b25b5c-6939-4cec-a33d-33579a6feefd 2023-07-23T04:18:30+02:00 Sex determination of baleen whale artefacts:implications for ancient DNA use in zooarchaeology Sinding, Mikkel Holger Strander Tervo, Outi M. Grønnow, Bjarne Gulløv, Hans Christian Toft, Peter A. Bachmann, Lutz Fietz, Katharina Rekdal, Silje L. Christoffersen, Mads F. Heide-Jørgensen, Mads Peter Olsen, Morten Tange Foote, Andrew David 2016-12 https://curis.ku.dk/portal/da/publications/sex-determination-of-baleen-whale-artefacts(61b25b5c-6939-4cec-a33d-33579a6feefd).html https://doi.org/10.1016/j.jasrep.2016.11.001 eng eng info:eu-repo/semantics/closedAccess Sinding , M H S , Tervo , O M , Grønnow , B , Gulløv , H C , Toft , P A , Bachmann , L , Fietz , K , Rekdal , S L , Christoffersen , M F , Heide-Jørgensen , M P , Olsen , M T & Foote , A D 2016 , ' Sex determination of baleen whale artefacts : implications for ancient DNA use in zooarchaeology ' , Journal of Archaeological Science: Reports , vol. 10 , pp. 345-349 . https://doi.org/10.1016/j.jasrep.2016.11.001 Ancient DNA Zooarchaeology Sex determination article 2016 ftcopenhagenunip https://doi.org/10.1016/j.jasrep.2016.11.001 2023-07-05T23:01:06Z Abstract Methods to determine the sex from tissue samples of mammals include the amplification of Y chromosome specific regions, which should only amplify from males, or amplification of homologous regions of the X and Y chromosome containing XY specific SNPs. A disadvantage of the first approach is that PCR failure can be misinterpreted as the identification of a female. The latter approach is proposed to identify PCR failure through non-amplification of the X homologue, which should be present in both sexes. This method is therefore potentially more suitable for molecular sexing of degraded DNA with a high probability of PCR failure, such as for example, ancient DNA samples. Here, we investigate the validity of this assumption regarding the use of XY homologue PCR assays for molecular sexing of ancient DNA. We tested a primer set targeting the ZFX/ZFY alleles using ancient DNA extracts from 100 to 4500 years old bowhead whale samples, and for comparison on dilution series from modern bowhead whales of known sex. DNA sequencing of PCR products obtained from the ancient material confirmed a higher proportion of successful PCR amplifications of the X homologue over the Y homologue. This potentially biased sex determination was further assessed by testing highly diluted DNA extracts of modern samples, for which a consistently higher success rate of PCR amplification and lower PCR cycle threshold was found for the X homologue from females than either homologue from males. This is most likely due to the higher copy number of the X homologue in females, although other yet unknown attributes of the protocol may also cause the observed bias. The current case study provides a valuable example of a potential pitfall in molecular sex determination of ancient mammal DNA in zooarchaeology. High-throughput sequencing methods, in which sufficiently large numbers of reads can be unambiguously mapped to X and Y regions, should overcome such biases and be the most robust approach for molecular sex determination using degraded ... Article in Journal/Newspaper baleen whale bowhead whale University of Copenhagen: Research The ''Y'' ENVELOPE(-112.453,-112.453,57.591,57.591) Journal of Archaeological Science: Reports 10 345 349 |
institution |
Open Polar |
collection |
University of Copenhagen: Research |
op_collection_id |
ftcopenhagenunip |
language |
English |
topic |
Ancient DNA Zooarchaeology Sex determination |
spellingShingle |
Ancient DNA Zooarchaeology Sex determination Sinding, Mikkel Holger Strander Tervo, Outi M. Grønnow, Bjarne Gulløv, Hans Christian Toft, Peter A. Bachmann, Lutz Fietz, Katharina Rekdal, Silje L. Christoffersen, Mads F. Heide-Jørgensen, Mads Peter Olsen, Morten Tange Foote, Andrew David Sex determination of baleen whale artefacts:implications for ancient DNA use in zooarchaeology |
topic_facet |
Ancient DNA Zooarchaeology Sex determination |
description |
Abstract Methods to determine the sex from tissue samples of mammals include the amplification of Y chromosome specific regions, which should only amplify from males, or amplification of homologous regions of the X and Y chromosome containing XY specific SNPs. A disadvantage of the first approach is that PCR failure can be misinterpreted as the identification of a female. The latter approach is proposed to identify PCR failure through non-amplification of the X homologue, which should be present in both sexes. This method is therefore potentially more suitable for molecular sexing of degraded DNA with a high probability of PCR failure, such as for example, ancient DNA samples. Here, we investigate the validity of this assumption regarding the use of XY homologue PCR assays for molecular sexing of ancient DNA. We tested a primer set targeting the ZFX/ZFY alleles using ancient DNA extracts from 100 to 4500 years old bowhead whale samples, and for comparison on dilution series from modern bowhead whales of known sex. DNA sequencing of PCR products obtained from the ancient material confirmed a higher proportion of successful PCR amplifications of the X homologue over the Y homologue. This potentially biased sex determination was further assessed by testing highly diluted DNA extracts of modern samples, for which a consistently higher success rate of PCR amplification and lower PCR cycle threshold was found for the X homologue from females than either homologue from males. This is most likely due to the higher copy number of the X homologue in females, although other yet unknown attributes of the protocol may also cause the observed bias. The current case study provides a valuable example of a potential pitfall in molecular sex determination of ancient mammal DNA in zooarchaeology. High-throughput sequencing methods, in which sufficiently large numbers of reads can be unambiguously mapped to X and Y regions, should overcome such biases and be the most robust approach for molecular sex determination using degraded ... |
format |
Article in Journal/Newspaper |
author |
Sinding, Mikkel Holger Strander Tervo, Outi M. Grønnow, Bjarne Gulløv, Hans Christian Toft, Peter A. Bachmann, Lutz Fietz, Katharina Rekdal, Silje L. Christoffersen, Mads F. Heide-Jørgensen, Mads Peter Olsen, Morten Tange Foote, Andrew David |
author_facet |
Sinding, Mikkel Holger Strander Tervo, Outi M. Grønnow, Bjarne Gulløv, Hans Christian Toft, Peter A. Bachmann, Lutz Fietz, Katharina Rekdal, Silje L. Christoffersen, Mads F. Heide-Jørgensen, Mads Peter Olsen, Morten Tange Foote, Andrew David |
author_sort |
Sinding, Mikkel Holger Strander |
title |
Sex determination of baleen whale artefacts:implications for ancient DNA use in zooarchaeology |
title_short |
Sex determination of baleen whale artefacts:implications for ancient DNA use in zooarchaeology |
title_full |
Sex determination of baleen whale artefacts:implications for ancient DNA use in zooarchaeology |
title_fullStr |
Sex determination of baleen whale artefacts:implications for ancient DNA use in zooarchaeology |
title_full_unstemmed |
Sex determination of baleen whale artefacts:implications for ancient DNA use in zooarchaeology |
title_sort |
sex determination of baleen whale artefacts:implications for ancient dna use in zooarchaeology |
publishDate |
2016 |
url |
https://curis.ku.dk/portal/da/publications/sex-determination-of-baleen-whale-artefacts(61b25b5c-6939-4cec-a33d-33579a6feefd).html https://doi.org/10.1016/j.jasrep.2016.11.001 |
long_lat |
ENVELOPE(-112.453,-112.453,57.591,57.591) |
geographic |
The ''Y'' |
geographic_facet |
The ''Y'' |
genre |
baleen whale bowhead whale |
genre_facet |
baleen whale bowhead whale |
op_source |
Sinding , M H S , Tervo , O M , Grønnow , B , Gulløv , H C , Toft , P A , Bachmann , L , Fietz , K , Rekdal , S L , Christoffersen , M F , Heide-Jørgensen , M P , Olsen , M T & Foote , A D 2016 , ' Sex determination of baleen whale artefacts : implications for ancient DNA use in zooarchaeology ' , Journal of Archaeological Science: Reports , vol. 10 , pp. 345-349 . https://doi.org/10.1016/j.jasrep.2016.11.001 |
op_rights |
info:eu-repo/semantics/closedAccess |
op_doi |
https://doi.org/10.1016/j.jasrep.2016.11.001 |
container_title |
Journal of Archaeological Science: Reports |
container_volume |
10 |
container_start_page |
345 |
op_container_end_page |
349 |
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1772180851670384640 |