Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull

Bro-Jørgensen, Maiken Hemme; Carøe, Christian; Vieira, Filipe Garrett; Nestor, Sofia; Hallström, Ann; Gregersen, Kristian Murphy; Etting, Vivian; Gilbert, M. Thomas P.; Sinding, Mikkel‐Holger S.

doi:10.1016/j.jas.2018.09.001

Cited by 14 publications

(17 citation statements)

References 41 publications

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“…Ancient DNA data can also be used to track hybrid species, including camelid hybrids (for example, tulu) and equine hybrids (such as mules and hinnies 131 ), which often possessed desirable characteristics that include enhanced immunity and stamina compared with the parental species. Insights such as these can be particularly useful when investigating the military and trade logistics of past societies, and can be supplemented by genetic information extracted from parchment 132 , textiles 133 and artefacts 134 , to advance our knowledge of past economies.…”

Section: [H1] Perspectivesmentioning

confidence: 99%

Animal domestication in the era of ancient genomics

et al. 2020

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The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have made possible the sequencing of whole ancient genomes and helped researchers to reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in the light of recent contributions from ancient genomics.

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Section: [H1] Perspectivesmentioning

confidence: 99%

Animal domestication in the era of ancient genomics

et al. 2020

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“…3 Whenever the loss of anatomical features or heavy processing of biological tissues make morphological classification impossible, a decision needs to be made between two types of biochemical species identification: Targeted approaches like amplification-based polymerase chain reaction (PCR) 4 and immunoassays 3 can cope with enormous sample sets but can only detect one or a few species at a time. Global approaches, such as next-generation DNA sequencing (NGS) 5 or proteomics, 6 are theoretically able to identify any species, but the low throughput and high costs prohibit large studies, even with the latest nanopore sequencing technology. 7 One method aimed at achieving both high throughput and global species identification is peptide-mass fingerprinting (PMF).…”

Section: Introductionmentioning

confidence: 99%

SPIN - Species by Proteome INvestigation

Ruether

Husic

Bangsgaard

et al. 2021

Preprint

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Genetic species determination has become an indispensable tool in forensics, archaeology, ecology, and food authentication. The available methods are either suited for detecting a single taxon across many samples or for screening a wide range of species across a few samples. Here, we introduce "Species by Proteome INvestigation" (SPIN), a proteomics workflow capable of querying over 150 mammalian species in 7.2 minutes of mass spectrometry (MS) analysis. Streamlined and automated sample preparation by protein aggregation capture, high-speed chromatography and data-independent acquisition, and a confident species inference algorithm facilitate processing hundreds of samples per day. We demonstrate the correct classification of known references, reproducible species identification in degraded Iron-Age material from Scandinavia, and test the limits of our methods with Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable with other biological tissues and taxa.

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“…More recently, the advent of high-throughput sequencing methods allow for genetic sexing approaches beyond targeting a short specific DNA region. These methods are ideal for studies that focus on getting a broader genetic insight as sex identification can be obtained alongside of multiple other types of analyses on the same data set (Bro-Jørgensen et al, 2018). High-throughput shotgun sequencing generates a raw data set, which do not target any specific regions of the genome and therefore roughly represents the genome components of the sampled individuals.…”

Section: Introductionmentioning

confidence: 99%

“…For both males and females, the autosomal chromosomes are represented by two copies in the genome and are therefore roughly represented by reads in proportion to their chromosome size. For simplicity, as well as visual reasons, a ratio of the read representation is usually calculated based on the X chromosome and one autosomal chromosome of similar size (see for example Pečnerová et al, 2017;Bro-Jørgensen et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Sex identification of ancient pinnipeds using the dog genome

Bro-Jørgensen

Keighley

Ahlgren

et al. 2019

Preprint

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Determining the male and female representation in zooarchaeological material from hunted animal species is essential, to fully investigate the effects and means of prehistoric hunting practices, and may further provide valuable biological information on past animal life-history, behaviour and demography. However, the fragmented nature of the zooarchaeological record and a lack of clear diagnostic skeletal markers, often prevents such inference. Here, we test the usability of the dog nuclear genome (CanFam3.1) for sex identification of pinnipeds. First, a contemporary sample set (n=72) of ringed seals (Pusa hispida), with known sex was used to test the genetic sex identification method. By quantifying the proportion of X chromosome reads, as the chrX/chr1 ratio, the ratios clustered in two clearly distinguishable sex groups. Of the 72 individuals, 69 were identified to the accurate sex, which proves a high reliability of the genetic method. Second, random down sampling of a subset of the ringed seal samples to different read number, suggests at least 5000 DNA sequence reads mapped to the reference genome as the lower limit for which this method is applicable. Finally, applying this standard, sex identification was successfully carried out on a broad set of ancient pinniped samples, including walruses (Odobenus rosmarus), grey seals (Halichoerus grypus) and harp seals (Pagophilus groenlandicus), which all showed clearly distinct male and female chrX/chr1 ratio groups.

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Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull

Cited by 14 publications

References 41 publications

Animal domestication in the era of ancient genomics

Animal domestication in the era of ancient genomics

SPIN - Species by Proteome INvestigation

Sex identification of ancient pinnipeds using the dog genome

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