Sex determination of baleen whale artefacts:Implications for ancient DNA use in zooarchaeology
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...
Published in: | Journal of Archaeological Science: Reports |
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Format: | Article in Journal/Newspaper |
Language: | English |
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2016
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Online Access: | https://hdl.handle.net/11370/d1059212-1ff8-4cec-92e2-9e83fff0e4a7 https://research.rug.nl/en/publications/d1059212-1ff8-4cec-92e2-9e83fff0e4a7 https://doi.org/10.1016/j.jasrep.2016.11.001 https://pure.rug.nl/ws/files/40658570/1_s2.0_S2352409X16306915_main.pdf http://www.scopus.com/inward/record.url?scp=84994681063&partnerID=8YFLogxK |
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ftunigroningenpu:oai:pure.rug.nl:publications/d1059212-1ff8-4cec-92e2-9e83fff0e4a7 2024-06-23T07:51:34+00:00 Sex determination of baleen whale artefacts:Implications for ancient DNA use in zooarchaeology Sinding, Mikkel Holger S 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 D. 2016-12-01 application/pdf https://hdl.handle.net/11370/d1059212-1ff8-4cec-92e2-9e83fff0e4a7 https://research.rug.nl/en/publications/d1059212-1ff8-4cec-92e2-9e83fff0e4a7 https://doi.org/10.1016/j.jasrep.2016.11.001 https://pure.rug.nl/ws/files/40658570/1_s2.0_S2352409X16306915_main.pdf http://www.scopus.com/inward/record.url?scp=84994681063&partnerID=8YFLogxK eng eng https://research.rug.nl/en/publications/d1059212-1ff8-4cec-92e2-9e83fff0e4a7 info:eu-repo/semantics/openAccess 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 Sex determination Zooarchaeology article 2016 ftunigroningenpu https://doi.org/10.1016/j.jasrep.2016.11.001 2024-06-10T16:25:50Z 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 DNA. Article in Journal/Newspaper baleen whale bowhead whale University of Groningen research database 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 Groningen research database |
op_collection_id |
ftunigroningenpu |
language |
English |
topic |
Ancient DNA Sex determination Zooarchaeology |
spellingShingle |
Ancient DNA Sex determination Zooarchaeology Sinding, Mikkel Holger S 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 D. Sex determination of baleen whale artefacts:Implications for ancient DNA use in zooarchaeology |
topic_facet |
Ancient DNA Sex determination Zooarchaeology |
description |
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 DNA. |
format |
Article in Journal/Newspaper |
author |
Sinding, Mikkel Holger S 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 D. |
author_facet |
Sinding, Mikkel Holger S 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 D. |
author_sort |
Sinding, Mikkel Holger S |
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://hdl.handle.net/11370/d1059212-1ff8-4cec-92e2-9e83fff0e4a7 https://research.rug.nl/en/publications/d1059212-1ff8-4cec-92e2-9e83fff0e4a7 https://doi.org/10.1016/j.jasrep.2016.11.001 https://pure.rug.nl/ws/files/40658570/1_s2.0_S2352409X16306915_main.pdf http://www.scopus.com/inward/record.url?scp=84994681063&partnerID=8YFLogxK |
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_relation |
https://research.rug.nl/en/publications/d1059212-1ff8-4cec-92e2-9e83fff0e4a7 |
op_rights |
info:eu-repo/semantics/openAccess |
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 |
_version_ |
1802642685821976576 |