Special Issue "Ancient DNA"

A special issue of Diversity (ISSN 1424-2818).

Deadline for manuscript submissions: closed (30 July 2017)

Special Issue Editors

Guest Editor
Prof. Anna Linderholm

Director of The BIG lab (Bioarchaeology and Genomics Laboratory), Department of Anthropology, Texas A and M University, College Station, United States
Website | E-Mail
Interests: Ancient DNA; migration; domestication; climate change; evolution; conservation; adaptation; extinction
Guest Editor
Prof. Ben Krause-Kyora

Institut für Klinische Molekularbiologie,Christian-Albrechts Universität zu Kiel,Schittenhelmstr. 12, 24105 Kiel, Germany
Website | E-Mail
Interests: host-pathogen co-evolution; evolutionary medicine; immunogenetics; domestication; archaeology

Special Issue Information

Dear Colleagues,

Since its beginnings, the field of ancient DNA (aDNA) has made it possible to actually study what happened in prehistory and when it happened. With the advent of Next Generation Sequencing (NGS), the field of aDNA has exploded. The possibilities before us are almost endless; we can look at more detailed issues, such as causes of diseases, hair/skin color, as well as look at larger population relationships and movements. This advance has finally made it possible to investigate biodiversity on all levels. The new techniques have allowed us to investigate the microbiomes in past populations using dental calculus as a source. We are understanding what makes us human and the diversity within us using aDNA in combination with modern DNA. The extinct populations of both flora and fauna can be placed in both history and phylogenies with the specialized library and capture methods developed for aDNA.

The focus of this forthcoming Special Issue will be to explore and showcase how these cutting edge genetic techniques of NGS has made it possible to advance our understanding and knowledge of our prehistory.

Prof. Anna Linderholm
Prof. Ben Krause-Kyora
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 850 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • human diversity in prehistory
  • animal diversity in prehistory
  • plant diversity in prehistory
  • bacteria diversity in prehistory
  • disease diversity
  • diversity conservation
  • diversity threats
  • evolutionary diversity

Published Papers (7 papers)

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Research

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Open AccessArticle
The Evolution and Population Diversity of Bison in Pleistocene and Holocene Eurasia: Sex Matters
Diversity 2018, 10(3), 65; https://doi.org/10.3390/d10030065
Received: 26 March 2018 / Revised: 21 June 2018 / Accepted: 11 July 2018 / Published: 18 July 2018
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Abstract
Knowledge about the origin and evolutionary history of the bison has been improved recently owing to several genomic and paleogenomic studies published in the last two years, which elucidated large parts of the evolution of bison populations during the Upper Pleistocene and Holocene [...] Read more.
Knowledge about the origin and evolutionary history of the bison has been improved recently owing to several genomic and paleogenomic studies published in the last two years, which elucidated large parts of the evolution of bison populations during the Upper Pleistocene and Holocene in Eurasia. The produced data, however, were interpreted in contradicting manners. Here, we have gathered, reanalyzed and compared previously published or unpublished morphometric and genetic data that have not yet been integrated and that we synthesize in a unified framework. In particular, we re-estimate dates of divergence of mitogenome lineages based on an extended dataset comprising 81 complete ancient bison mitogenomes and we revisit putative gene flow between the Bos and Bison genera based on comparative analyses of ancient and modern bison genomes, thereby questioning published conclusions. Morphometric analyses taking into account sexual dimorphism invalidate a previous claim that Bison schoetensacki was present in France during the Late Pleistocene. Both morphometric and genome analyses reveal that Eurasian bison belonging to different Bison priscus and Bison bonasus lineages maintained parallel evolutionary paths with gene flow during a long period of incomplete speciation that ceased only upon the migration of B. priscus to the American continent establishing the American bison lineage. Our nuclear genome analysis of the evolutionary history of B. bonasus allows us to reject the previous hypothesis that it is a hybrid of B. priscus and Bos primigenius. Based on present-day behavioral studies of European and American bison, we propose that apparently conflicting lines of evidence can be reconciled by positing that female bison drove the specialization of bison populations to different ecological niches while male bison drove regular homogenizing genetic exchanges between populations. Full article
(This article belongs to the Special Issue Ancient DNA)
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Open AccessArticle
Centuries-Old DNA from an Extinct Population of Aesculapian Snake (Zamenis longissimus) Offers New Phylogeographic Insight
Diversity 2018, 10(1), 14; https://doi.org/10.3390/d10010014
Received: 9 February 2018 / Revised: 5 March 2018 / Accepted: 7 March 2018 / Published: 10 March 2018
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Abstract
The Aesculapian snake (Zamenis longissimus) is distributed in Central and Southern Europe, the Balkans, Anatolia, and Iran, but had a wider mid-Holocene distribution into Northern Europe. To investigate the genetic affinity of a Danish population that went extinct in historical times, [...] Read more.
The Aesculapian snake (Zamenis longissimus) is distributed in Central and Southern Europe, the Balkans, Anatolia, and Iran, but had a wider mid-Holocene distribution into Northern Europe. To investigate the genetic affinity of a Danish population that went extinct in historical times, we analysed three ethanol-preserved individuals dating back to 1810 using a silica-in-solution ancient DNA extraction method, combined with next-generation sequencing. Bioinformatic mapping of the reads against the published genome of a related colubrid snake revealed that two of the three specimens contained endogenous snake DNA (up to 8.6% of the reads), and this was evident for tooth, bone, and soft tissue samples. The DNA was highly degraded, observed by very short average sequence lengths (<50 bp) and 11–15% C to T deamination damage at the first 5′ position. This is an effect of specimen age, combined with suboptimal, and possibly damaging, molecular preservation conditions. Phylogeographic analyses of a 1638 bp mtDNA sequence securely placed the two Danish Aesculapian snakes in the Eastern (Balkan glacial refugium) clade within this species, and revealed one previously-undescribed haplotype. These results provide new information on the past distribution and postglacial re-colonization patterns of this species. Full article
(This article belongs to the Special Issue Ancient DNA)
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Open AccessCommunication
Duplex Alu Screening for Degraded DNA of Skeletal Human Remains
Diversity 2017, 9(4), 48; https://doi.org/10.3390/d9040048
Received: 31 July 2017 / Revised: 18 October 2017 / Accepted: 20 October 2017 / Published: 25 October 2017
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Abstract
The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal [...] Read more.
The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400–500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach. Full article
(This article belongs to the Special Issue Ancient DNA)
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Open AccessArticle
Staphylococcus aureus Sequences from Osteomyelitic Specimens of a Pathological Bone Collection from Pre-Antibiotic Times
Diversity 2017, 9(4), 43; https://doi.org/10.3390/d9040043
Received: 27 July 2017 / Revised: 15 September 2017 / Accepted: 28 September 2017 / Published: 1 October 2017
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Abstract
Staphylococcus aureus is a major pathogen causing osteomyelitis, amongst other diseases, and its methicillin-resistant form (MRSA) in particular poses a huge threat to public health. To increase our knowledge of the origin and evolution of S. aureus, genetic studies of historical microorganisms [...] Read more.
Staphylococcus aureus is a major pathogen causing osteomyelitis, amongst other diseases, and its methicillin-resistant form (MRSA) in particular poses a huge threat to public health. To increase our knowledge of the origin and evolution of S. aureus, genetic studies of historical microorganisms may be beneficial. Thus, the aim of this study was to investigate whether osteomyelitic skeletal material (autopsy specimens collected from the mid 19th century until the 1920s) is suitable for detecting historical S. aureus DNA sequences. We established a PCR-based analysis system targeting two specific genes of S. aureus (nuc and fib). We successfully amplified the historical S. aureus nuc and fib sequences for six and seven pre-antibiotic, osteomyelitic bone specimens, respectively. These results encourage further investigations of historical S. aureus genomes that may increase our understanding of pathogen evolution in relation to anthropogenically introduced antibiotics. Full article
(This article belongs to the Special Issue Ancient DNA)
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Open AccessArticle
Millennia-Long Co-Existence of Two Major European Whitefish (Coregonus spp.) Lineages in Switzerland Inferred from Ancient Mitochondrial DNA
Diversity 2017, 9(3), 34; https://doi.org/10.3390/d9030034
Received: 13 July 2017 / Revised: 15 August 2017 / Accepted: 20 August 2017 / Published: 23 August 2017
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Abstract
Archaeological fish remains are an important source for reconstructing past aquatic ecosystems and ancient fishing strategies using aDNA techniques. Here, we focus on archaeological samples of European whitefish (Coregonus spp.) from Switzerland covering different time periods. Coregonus bones and scales are commonly [...] Read more.
Archaeological fish remains are an important source for reconstructing past aquatic ecosystems and ancient fishing strategies using aDNA techniques. Here, we focus on archaeological samples of European whitefish (Coregonus spp.) from Switzerland covering different time periods. Coregonus bones and scales are commonly found in archaeological assemblages, but these elements lack species specific features and thus inhibit morphological species identification. Even today, fish taxonomy is confusing and numerous species and ecotypes are recognized, and even more probably existed in the past. By targeting short fragments of the mitochondrial d-loop in 48 morphologically identified Coregonus scales and vertebrae from 10 archaeological sites in Switzerland, endogenous d-loop sequences were found in 24 samples from one Neolithic, two Roman, and four Medieval sites. Two major mtDNA clades, C and N, known from contemporary European whitefish populations were detected, suggesting co-occurrence for at least 5000 years. In the future, NGS technologies may be used to explore Coregonus or other fish species and ecotype diversity in the past to elucidate the human impact on lacustrine/limnic environments. Full article
(This article belongs to the Special Issue Ancient DNA)
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Review

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Open AccessReview
Positive Diagnosis of Ancient Leprosy and Tuberculosis Using Ancient DNA and Lipid Biomarkers
Diversity 2017, 9(4), 46; https://doi.org/10.3390/d9040046
Received: 25 August 2017 / Revised: 8 October 2017 / Accepted: 9 October 2017 / Published: 15 October 2017
Cited by 3 | PDF Full-text (3834 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Diagnosis of leprosy and tuberculosis in archaeological material is most informative when based upon entire genomes. Ancient DNA (aDNA) is often degraded but amplification of specific fragments also provides reliable diagnoses. Cell wall lipid biomarkers can distinguish ancient leprosy from tuberculosis and DNA [...] Read more.
Diagnosis of leprosy and tuberculosis in archaeological material is most informative when based upon entire genomes. Ancient DNA (aDNA) is often degraded but amplification of specific fragments also provides reliable diagnoses. Cell wall lipid biomarkers can distinguish ancient leprosy from tuberculosis and DNA extraction residues can be utilized. The diagnostic power of combined aDNA and lipid biomarkers is illustrated by key cases of ancient leprosy and/or tuberculosis. Human tuberculosis was demonstrated in a woman and child from Atlit-Yam (~9 ka) in the Eastern Mediterranean and in the 600 BCE Egyptian “Granville” mummy. Both aDNA and lipids confirmed Pleistocene tuberculosis in a ~17 ka bison from Natural Trap Cave, Wyoming. Leprosy is exemplified by cases from Winchester (10th–12th centuries CE) and Great Chesterford (5th–6th centuries CE). A mixed infection from Kiskundorozsma, Hungary (7th century CE) allowed lipid biomarkers to assess the relative load of leprosy and tuberculosis. Essential protocols for aDNA amplification and analysis of mycolic, mycolipenic, mycocerosic acid, and phthiocerol lipid biomarkers are summarized. Diagnoses of ancient mycobacterial disease can be extended beyond the reach of whole genomics by combinations of aDNA amplification and lipid biomarkers, with sole use of the latter having the potential to recognize even older cases. Full article
(This article belongs to the Special Issue Ancient DNA)
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Open AccessReview
Dispersal, Isolation, and Interaction in the Islands of Polynesia: A Critical Review of Archaeological and Genetic Evidence
Diversity 2017, 9(3), 37; https://doi.org/10.3390/d9030037
Received: 11 August 2017 / Revised: 2 September 2017 / Accepted: 11 September 2017 / Published: 14 September 2017
Cited by 1 | PDF Full-text (1653 KB) | HTML Full-text | XML Full-text
Abstract
Integration of archaeology, modern genetics, and ancient DNA holds promise for the reconstruction of the human past. We examine the advances in research on the indigenous peoples of Polynesia to determine: (1) what do archaeological and genetic data (ancient and modern DNA) tell [...] Read more.
Integration of archaeology, modern genetics, and ancient DNA holds promise for the reconstruction of the human past. We examine the advances in research on the indigenous peoples of Polynesia to determine: (1) what do archaeological and genetic data (ancient and modern DNA) tell us about the origins of Polynesians; and, (2) what evidence is there for long-distance travel and contacts between Polynesians and indigenous populations of the Americas? We note that the general dispersal pattern of founding human populations in the remote islands of the Pacific and long-distance interaction spheres continue to reflect well-established models. New research suggests that the formation of an Ancestral Polynesia Culture in Western Polynesia may have involved differential patterns of dispersal followed by significant later migrations. It has also been suggested that the pause between the settlement of Western and Eastern Polynesia was centuries longer than currently thought, followed by a remarkably rapid pulse of island colonization. Long-distance travel between islands of the Pacific is currently best documented through the sourcing of artifacts, while the discovery of admixture of Native American DNA within the genome of the people from Easter Island (Rapa Nui) is strong new evidence for sustained contacts between Polynesia and the Americas. Full article
(This article belongs to the Special Issue Ancient DNA)
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