Identifying Bird Remains Using Ancient DNA Barcoding

Dalén, Love; Lagerholm, Vendela Kempe; Nylander, Johan A. A.; Barton, Nick; Bocheński, Zbigniew M.; Tomek, Teresa; Rudling, David; Ericson, Per G. P.; Irestedt, Martin; Stewart, John R.

doi:10.3390/genes8060169

Cited by 13 publications

(6 citation statements)

References 27 publications

(29 reference statements)

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“…DNA in very old samples is often severely fragmented and highly contaminated, and thus it is very difficult to successfully amplify for species identification—even for very short amplicons (e.g. <100 bp) [14,16,21,22]. In another study, 80 woolly mammoth samples were amplified using a species-specific primer pair with an amplicon size of 114 bp, and 19 samples could not be successfully sequenced.…”

Section: Discussionmentioning

confidence: 99%

“…Presently, the most frequently used methods for species identification are genetic-based PCR amplifications followed by sequencing and BLAST search (). These techniques have been continuously developed and widely used in various fields, including forensic science, paleontology, archaeology, wildlife research, and bird strike investigations [13,14,15,16,17]. DNA barcoding has become one of the most promising methods for species identification since Hebert et al [18] established the first barcoding system using a ~600 bp DNA fragment located in the mitochondrial gene cytochrome c oxidase I ( COI ).…”

Section: Introductionmentioning

confidence: 99%

“…The use of small amplicons plus multiple loci seems to be a more reasonable way to satisfy this tradeoff. Several studies have proved that this combination can successfully identify ancient birds [14], ancient fish [21], and other ancient animals [16,22]. However, although the amplicons used in these studies were smaller than 100 bp, the PCR amplification often failed to produce products necessary to identify the species of many ancient samples, which may have resulted from the highly degraded endogenous DNA.…”

Section: Introductionmentioning

confidence: 99%

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Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data

Lan

Lin

Njaramba-Ngatia

et al. 2019

Genes

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The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data

Lan

Lin

Njaramba-Ngatia

et al. 2019

Genes

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“…For example, ancient DNA has been used for establishing the biological sex [8], for providing species identification (e.g. [9,10]) and to infer familiar genetic relationships within archaeological communities [11][12][13] as well as to reconstruct past diets and environments (e.g. [14]).…”

Section: Introductionmentioning

confidence: 99%

Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories

Loog

2020

Phil. Trans. R. Soc. B

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Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records. This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.

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“…Given their abundance in museum collections and the diversity of writing supports made of plant material, such as papyrus scrolls, wood tablets, and paper, with one exception [ 12 ], plant derived manuscripts are an underexplored target for DNA analyses. In theory, DNA molecules can be obtained from any organic material such as bone [ 13 , 14 ], eggshell [ 15 ], wood [ 16 , 17 ], as well as from processed material, for example food [ 18 , 19 ], clothing [ 20 – 22 ], and parchment [ 1 – 4 , 23 ]. The survival and preservation of DNA molecules is not only influenced by the age of a sample, but to a higher degree by the organic source [ 24 – 26 ] and the environment [ 27 , 28 ], with arid conditions and low temperature fluctuations favoring long time DNA survival.…”

Section: Introductionmentioning

confidence: 99%

Not stealing from the treasure chest (or just a bit): Analyses on plant derived writing supports and non-invasive DNA sampling

Schulz¹,

Lautner

Fromm

et al. 2018

PLoS ONE

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Written communication plays a crucial role in the history of modern civilizations as manuscripts do not only exist contemporarily, but are passed on to subsequent generations. Besides a document’s content, information is stored in the materials used for its production. Analyses of the composition allow, for example, identifying the biological origins of materials, dating, and help to understand degradation patterns. A combination of microscopic and DNA approaches was applied in order to analyze various plant derived writing sheets. Given their diversity and abundance in museum collections, plant based writing supports are yet an underexplored target for DNA studies. DNA retrieval of paper is low compared to raw paper plant material, which is likely due to the loss of organic components during paper production. Optimizing DNA extraction for each respective material drastically increased DNA recovery. Finally, we present a non-invasive DNA sampling method that utilizes nylon membranes, commonly used for bacterial DNA sampling and that is applicable to delicate material. Although bacterial infestation was visible on one sample, as indicated by scanning electron microscopy, endogenous DNA was retrieved. The results presented here are promising as they extend the scope of sources for DNA analyses by demonstrating that DNA molecules can be retrieved from a variety of plant derived writing supports. In future, such analyses can help to explore the biological diversity not only of plants and of additives utilized for producing writing supports, but also of the plenty products made from paper.

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Identifying Bird Remains Using Ancient DNA Barcoding

Cited by 13 publications

References 27 publications

Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data

Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data

Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories

Not stealing from the treasure chest (or just a bit): Analyses on plant derived writing supports and non-invasive DNA sampling

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