Contamination controls when preparing archaeological remains for ancient DNA analysis

Yang, Dongya; Watt, Kathy

doi:10.1016/j.jas.2004.09.008

Cited by 121 publications

(104 citation statements)

References 33 publications

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“…Although we consider that our protocol is validated following this procedure, we could not totally remove the incidence of contamination, one of the most difficult aspects when working with ancient or historical samples (Hebsgaard et al 2005;Kelman & Kelman 1999;Yang & Watt 2005). The presence of four chimeric sequences in our alignment could be explained by cross-specimen contamination via organic micro-fragments and mucus through the steps of collective storage during field work and once in the collections (Wandeler et al 2007), and/or the proneness of samples with low DNA quantity and quality, such as historical samples, to exogenous DNA contamination (Pääbo et al 2004) and artifact formation (e.g.…”

Section: Discussionmentioning

confidence: 99%

Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus <i>Orestias</i> (Teleostei: Cyprinodontidae)

Garrigos

Hugueny²,

Koerner³

et al. 2013

Zootaxa

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Specimens stored in museum collections represent a crucial source of morphological and genetic information, notably for taxonomically problematic groups and extinct taxa. Although fluid-preserved specimens of groups such as teleosts may constitute an almost infinite source of DNA, few ancient DNA protocols have been applied to such material. In this study, we describe a non-invasive Guanidine-based (GuSCN) ancient DNA extraction protocol adapted to fluid-preserved specimens that we use to re-assess the systematics of the genus Orestias (Cyprinodontidae: Teleostei). The latter regroups pupfishes endemic to the inter-Andean basin that have been considered as a 'species flock', and for which the morphologybased taxonomic delimitations have been hotly debated. We extracted DNA from the type specimens of Orestias kept at the Muséum National d'Histoire Naturelle of Paris, France, including the extinct species O. cuvieri. We then built the first molecular (control region [CR] and rhodopsin [RH]) phylogeny including historical and recently collected representatives of all the Orestias complexes as recognized by Parenti (1984a): agassizii, cuvieri, gilsoni and mulleri. Our ancient DNA extraction protocol was validated after PCR amplification through an approach based on fragment-by-fragment chimera detection. After optimization, we were able to amplify < 200 bp fragments from both mitochondrial and nuclear DNA (CR and RH, respectively) from probably formalin-fixed type specimens bathed entirely in the extraction fluid. Most of the individuals exhibited few modifications of their external structures after GuSCN bath. Our approach combining type material and 'fresh' specimens allowed us to taxonomically delineate four clades recovered from the well-resolved CR tree into four redefined complexes: agassizii (sensu stricto, i.e. excluding luteus-like species), luteus, cuvieri and gilsoni. The mulleri complex is polyphyletic. Our phylogenetic analyses based on both mitochondrial and nuclear DNA revealed a main, deep dichotomy within the genus Orestias, separating the agassizii complex from a clade grouped under shallow dichotomies as (luteus, (cuvieri, gilsoni)). This 'deep and shallow' diversification pattern could fit within a scenario of ancient divergence between the agassizii complex and the rest of Orestias, followed by a recent diversification or adaptive radiation within each complex during the Pleistocene, in-and outside the Lake Titicaca. We could not recover the reciprocal monophyly of any of the 15 species or morphotypes that were considered in our analyses, possibly due to incomplete lineage sorting and/or hybridization events. As a consequence, our results starkly question the delineation of a series of diagnostic characters listed in the literature for Orestias. Although not included in our phylogenetic analysis, the syntype of O. jussiei could not be assigned to the agassizii complex as newly defined. The CR sequence of the extinct O. cuvieri was recovered within the cuvieri clade (same haplotype as on...

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Section: Discussionmentioning

confidence: 99%

Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus <i>Orestias</i> (Teleostei: Cyprinodontidae)

Garrigos

Hugueny²,

Koerner³

et al. 2013

Zootaxa

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“…Ideally, samples are taken directly at the excavation, taking care to prevent contamination from the environment (see ''Verification in plant ancient DNA research''; Yang and Watt 2005). Detailed morphological documentation is needed as DNA investigations are destructive.…”

Section: Methodsmentioning

confidence: 99%

Ancient plant DNA in archaeobotany

Schlumbaum

Tensen

Jaenicke-Després

2007

Veget Hist Archaeobot

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Plant diaspores, tissues and wood are preserved in natural and anthropogenic sediments. Also, over the past centuries, plants have been collected in herbaria. These plant remains carry macroscopic and molecular information, making them a rich source for reconstructing past plant use, agriculture, diet or vegetation-they are thus proxies for past economies, ecology, migrations or trade. This article focuses on the application of ancient DNA analyses from plants excavated at Holocene archaeological sites. A short methodological section is added to illustrate possibilities and limitations of ancient DNA research in plants.

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“…İkincisi de DNA'nın güvenirliliğini gösteren bir seri kriterin uygulanmasıdır. Bu kriterler arasında örneklerin dış kontaminantlardan temizlenmesi için uygulanması gereken dekontaminasyon süreci de yer alır (Paabo, 2004;Yang, 2005).…”

Section: Discussionunclassified

Farklı Koşullarda Bulunan Antik İskelet Örneklerinden Dekontaminasyon Süreci ile İlgili Metodolojik Yaklaşım

APAK¹,

DOĞAN²,

Yeşim³

2017

Antropoloji

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Contamination controls when preparing archaeological remains for ancient DNA analysis

Cited by 121 publications

References 33 publications

Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus <i>Orestias</i> (Teleostei: Cyprinodontidae)

Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus <i>Orestias</i> (Teleostei: Cyprinodontidae)

Ancient plant DNA in archaeobotany

Farklı Koşullarda Bulunan Antik İskelet Örneklerinden Dekontaminasyon Süreci ile İlgili Metodolojik Yaklaşım

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