Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains.

Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate aDNA fr...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Nathan Wales, Kenneth Andersen, Enrico Cappellini, María C Avila-Arcos, M Thomas P Gilbert
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ffcd07bb2f1c416495710dd98c18977a
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:ffcd07bb2f1c416495710dd98c18977a
record_format	dspace
spelling	oai:doaj.org-article:ffcd07bb2f1c416495710dd98c18977a2021-11-18T08:35:38ZOptimization of DNA recovery and amplification from non-carbonized archaeobotanical remains.1932-620310.1371/journal.pone.0086827https://doaj.org/article/ffcd07bb2f1c416495710dd98c18977a2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24475182/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate aDNA from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated decisions as to which one to use for a given task. The experimental findings should prove useful to the aDNA and archaeological communities by guiding future research methodologies and ensuring precious archaeobotanical remains are studied in optimal ways, and may thereby yield important new perspectives on the interactions between humans and past plant communities.Nathan WalesKenneth AndersenEnrico CappelliniMaría C Avila-ArcosM Thomas P GilbertPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e86827 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nathan Wales Kenneth Andersen Enrico Cappellini María C Avila-Arcos M Thomas P Gilbert Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains.
description	Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate aDNA from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated decisions as to which one to use for a given task. The experimental findings should prove useful to the aDNA and archaeological communities by guiding future research methodologies and ensuring precious archaeobotanical remains are studied in optimal ways, and may thereby yield important new perspectives on the interactions between humans and past plant communities.
format	article
author	Nathan Wales Kenneth Andersen Enrico Cappellini María C Avila-Arcos M Thomas P Gilbert
author_facet	Nathan Wales Kenneth Andersen Enrico Cappellini María C Avila-Arcos M Thomas P Gilbert
author_sort	Nathan Wales
title	Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains.
title_short	Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains.
title_full	Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains.
title_fullStr	Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains.
title_full_unstemmed	Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains.
title_sort	optimization of dna recovery and amplification from non-carbonized archaeobotanical remains.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/ffcd07bb2f1c416495710dd98c18977a
work_keys_str_mv	AT nathanwales optimizationofdnarecoveryandamplificationfromnoncarbonizedarchaeobotanicalremains AT kennethandersen optimizationofdnarecoveryandamplificationfromnoncarbonizedarchaeobotanicalremains AT enricocappellini optimizationofdnarecoveryandamplificationfromnoncarbonizedarchaeobotanicalremains AT mariacavilaarcos optimizationofdnarecoveryandamplificationfromnoncarbonizedarchaeobotanicalremains AT mthomaspgilbert optimizationofdnarecoveryandamplificationfromnoncarbonizedarchaeobotanicalremains
_version_	1718421600383008768

Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains.

Ejemplares similares