Novel high-resolution characterization of ancient DNA reveals C &gt; U-type base modification events as the sole cause of post mortem miscoding lesions

Brotherton, Paul; Endicott, Phillip; Sánchez, Juan José Martínez; Beaumont, Mark A.; Barnett, Ross; Austin, Jeremy J.; Cooper, Alan

doi:10.1093/nar/gkm588

Cited by 233 publications

(223 citation statements)

References 51 publications

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“…It is notable that of the 6,569 bp duplicated at ACAD (from 64 amplicons), comparison with the final consensus sequences revealed only minor discrepancies (67 differences; average number of differences per base per fragment ϭ 0.884%). As expected, a large majority of the variants (74.6%) consisted of GC3AT substitutions and are likely to derive from postmortem cytosine deamination characteristic of ancient templates (27,28). The base recovered from the majority of independent amplicons was accepted as authentic, in agreement with standard recommendations (27,29), and importantly, the extent of damage-induced errors was well below the intraspecific levels of genetic diversity among equids (Table S3).…”

Section: Resultssupporting

confidence: 78%

Revising the recent evolutionary history of equids using ancient DNA

Orlando

Metcalf

Alberdi

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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143

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The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.DNA taxonomy ͉ equid evolution ͉ macroevolution ͉ phylogeny ͉ ancient DNA T he original sequence of horse fossils found in the 1870s by paleontologist Othaniel Charles Marsh, and popularized by Thomas Huxley (1), has been enriched by a large fossil record over the years and has now become one of the most widely known examples of macroevolutionary change (2). The original linear model of gradual modification of fox-sized animals (Hyracothere horses) to the modern forms has been replaced by a more complex tree, showing periods of explosive diversification and branch extinctions over 55 MY (3). The end of the Early Miocene (15-20 MYA) marks a particularly important transition, separating an initial phase of small leafy browsers from a second phase of more diverse animals, exhibiting tremendous body-size plasticity and modifications in tooth morphology (4). This explosive diversification has been accompanied by several stages of geographic extension from North America to the rest of the New and Old Worlds, so that by the end of the Miocene (5 MYA) more than a dozen distinct genera are represented in the fossil record (4) (Astrohippus,

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Section: Resultssupporting

confidence: 78%

Revising the recent evolutionary history of equids using ancient DNA

Orlando

Metcalf

Alberdi

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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143

125

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“…The predominant C to T substitutions found at the 5′ ends and G to A substitutions at the 3′ ends are typical of ancient DNA (15,26,27). This pattern is not seen in the fragments mapping to the vector region of the pPCP1 plasmid, lending additional support to the notion that the majority of these fragments are indeed derived from contaminating expression vectors of the supplied reagents (Fig.…”

Section: Resultsmentioning

confidence: 99%

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid ofYersinia pestisfrom victims of the Black Death

Schuenemann

Bos

DeWitte

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

244

209

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Although investigations of medieval plague victims have identified Yersinia pestis as the putative etiologic agent of the pandemic, methodological limitations have prevented large-scale genomic investigations to evaluate changes in the pathogen's virulence over time. We screened over 100 skeletal remains from Black Death victims of the East Smithfield mass burial site (1348-1350, London, England). Recent methods of DNA enrichment coupled with high-throughput DNA sequencing subsequently permitted reconstruction of ten full human mitochondrial genomes (16 kb each) and the full pPCP1 (9.6 kb) virulence-associated plasmid at high coverage. Comparisons of molecular damage profiles between endogenous human and Y. pestis DNA confirmed its authenticity as an ancient pathogen, thus representing the longest contiguous genomic sequence for an ancient pathogen to date. Comparison of our reconstructed plasmid against modern Y. pestis shows identity with several isolates matching the Medievalis biovar; however, our chromosomal sequences indicate the victims were infected with a Y. pestis variant that has not been previously reported. Our data reveal that the Black Death in medieval Europe was caused by a variant of Y. pestis that may no longer exist, and genetic data carried on its pPCP1 plasmid were not responsible for the purported epidemiological differences between ancient and modern forms of Y. pestis infections.ancient DNA | paleopathology

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“…The PCR duplicates were removed with FilterUniqueSAMCons.py (Kircher, 2012). Obtained DNA fragments were then checked for presence of 3′ and 5′ degradation patterns characteristic of ancient DNA (Briggs et al, 2007, Brotherton et al, 2007, Sawyer, Krause, Guschanski, Savolainen, & Pääbo, 2012) using PMDtools (Skoglund et al, 2014). Molecular sex assignment was estimated based on the ratio of sequences aligning to the two sex chromosomes, X and Y (Skoglund, Storå, Götherström, & Jakobsson, 2013) (Figure 3, S4).…”

Section: Methodsmentioning

confidence: 99%

A female Viking warrior confirmed by genomics

Hedenstierna-Jonson

Kjellström

Zachrisson

et al. 2017

American J Phys Anthropol

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ObjectivesThe objective of this study has been to confirm the sex and the affinity of an individual buried in a well‐furnished warrior grave (Bj 581) in the Viking Age town of Birka, Sweden. Previously, based on the material and historical records, the male sex has been associated with the gender of the warrior and such was the case with Bj 581. An earlier osteological classification of the individual as female was considered controversial in a historical and archaeological context. A genomic confirmation of the biological sex of the individual was considered necessary to solve the issue.Materials and methodsGenome‐wide sequence data was generated in order to confirm the biological sex, to support skeletal integrity, and to investigate the genetic relationship of the individual to ancient individuals as well as modern‐day groups. Additionally, a strontium isotope analysis was conducted to highlight the mobility of the individual.ResultsThe genomic results revealed the lack of a Y‐chromosome and thus a female biological sex, and the mtDNA analyses support a single‐individual origin of sampled elements. The genetic affinity is close to present‐day North Europeans, and within Sweden to the southern and south‐central region. Nevertheless, the Sr values are not conclusive as to whether she was of local or nonlocal origin.DiscussionThe identification of a female Viking warrior provides a unique insight into the Viking society, social constructions, and exceptions to the norm in the Viking time‐period. The results call for caution against generalizations regarding social orders in past societies.

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Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions

Cited by 233 publications

References 51 publications

Revising the recent evolutionary history of equids using ancient DNA

Revising the recent evolutionary history of equids using ancient DNA

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid ofYersinia pestisfrom victims of the Black Death

A female Viking warrior confirmed by genomics

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