Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics

Abstract It is important to determine the sex of elephants from their samples—faeces from the field or seized ivory—for forensic reasons or to understand population demography and genetic structure. Molecular sexing methods developed in the last two decades have often shown limited efficiency, parti...

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Autores principales:	Laetitia Aznar-Cormano, Julie Bonnald, Sabrina Krief, Nelson Guma, Régis Debruyne
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/687b8b286b4a4b7382928099b6413295
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spelling	oai:doaj.org-article:687b8b286b4a4b7382928099b64132952021-12-02T18:17:42ZMolecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics10.1038/s41598-021-86010-x2045-2322https://doaj.org/article/687b8b286b4a4b7382928099b64132952021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86010-xhttps://doaj.org/toc/2045-2322Abstract It is important to determine the sex of elephants from their samples—faeces from the field or seized ivory—for forensic reasons or to understand population demography and genetic structure. Molecular sexing methods developed in the last two decades have often shown limited efficiency, particularly in terms of sensitivity and specificity, due to the degradation of DNA in these samples. These limitations have also prevented their use with ancient DNA samples of elephants or mammoths. Here we propose a novel TaqMan-MGB qPCR assay to address these difficulties. We designed it specifically to allow the characterization of the genetic sex for highly degraded samples of all elephantine taxa (elephants and mammoths). In vitro experiments demonstrated a high level of sensitivity and low contamination risks. We applied this assay in two actual case studies where it consistently recovered the right genotype for specimens of known sex a priori. In the context of a modern conservation survey of African elephants, it allowed determining the sex for over 99% of fecal samples. In a paleogenetic analysis of woolly mammoths, it produced a robust hypothesis of the sex for over 65% of the specimens out of three PCR replicates. This simple, rapid, and cost-effective procedure makes it readily applicable to large sample sizes.Laetitia Aznar-CormanoJulie BonnaldSabrina KriefNelson GumaRégis DebruyneNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Laetitia Aznar-Cormano Julie Bonnald Sabrina Krief Nelson Guma Régis Debruyne Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics
description	Abstract It is important to determine the sex of elephants from their samples—faeces from the field or seized ivory—for forensic reasons or to understand population demography and genetic structure. Molecular sexing methods developed in the last two decades have often shown limited efficiency, particularly in terms of sensitivity and specificity, due to the degradation of DNA in these samples. These limitations have also prevented their use with ancient DNA samples of elephants or mammoths. Here we propose a novel TaqMan-MGB qPCR assay to address these difficulties. We designed it specifically to allow the characterization of the genetic sex for highly degraded samples of all elephantine taxa (elephants and mammoths). In vitro experiments demonstrated a high level of sensitivity and low contamination risks. We applied this assay in two actual case studies where it consistently recovered the right genotype for specimens of known sex a priori. In the context of a modern conservation survey of African elephants, it allowed determining the sex for over 99% of fecal samples. In a paleogenetic analysis of woolly mammoths, it produced a robust hypothesis of the sex for over 65% of the specimens out of three PCR replicates. This simple, rapid, and cost-effective procedure makes it readily applicable to large sample sizes.
format	article
author	Laetitia Aznar-Cormano Julie Bonnald Sabrina Krief Nelson Guma Régis Debruyne
author_facet	Laetitia Aznar-Cormano Julie Bonnald Sabrina Krief Nelson Guma Régis Debruyne
author_sort	Laetitia Aznar-Cormano
title	Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics
title_short	Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics
title_full	Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics
title_fullStr	Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics
title_full_unstemmed	Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics
title_sort	molecular sexing of degraded dna from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/687b8b286b4a4b7382928099b6413295
work_keys_str_mv	AT laetitiaaznarcormano molecularsexingofdegradeddnafromelephantsandmammothsagenotypingassayrelevantbothtoconservationbiologyandtopaleogenetics AT juliebonnald molecularsexingofdegradeddnafromelephantsandmammothsagenotypingassayrelevantbothtoconservationbiologyandtopaleogenetics AT sabrinakrief molecularsexingofdegradeddnafromelephantsandmammothsagenotypingassayrelevantbothtoconservationbiologyandtopaleogenetics AT nelsonguma molecularsexingofdegradeddnafromelephantsandmammothsagenotypingassayrelevantbothtoconservationbiologyandtopaleogenetics AT regisdebruyne molecularsexingofdegradeddnafromelephantsandmammothsagenotypingassayrelevantbothtoconservationbiologyandtopaleogenetics
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Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics

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