aDNA Research Research Articles

On engagement with anthropology: A critical evaluation of skeletal and developmental abnormalities in the Atacama preterm baby and issues of forensic and bioarchaeological research ethics. Response to Bhattacharya et al. “Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia” in Genome Research, 2018, 28: 423–431. Doi: 10.1101/gr.223693.117

Here we evaluate Bhattacharya et al.’s (2018) recent paper “Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia” published in Genome Research. In this short report, we examine the hypothesis that the so-called “Atacama skeleton” has skeletal abnormalities indicative of dysplasia, critique the validity of the interpretations of disease based on genomic analyses, and comment on the ethics of research on this partially mummified human foetus. The current paper acts as a case study of the importance of using an anthropological approach for aDNA research on human remains. A critical evaluation of the ethically controversial paper by Bhattacharya et al. highlights how an understanding of skeletal biological processes, including normal and abnormal growth and development, taphonomic processes, environmental context, and close attention to ethical issues of dealing with human remains, is vital to scientific interpretations. To this end, close collaboration with palaeopathologists and local archaeologists through appropriate peer-reviewed journals will add to the rigour of scientific interpretation and circumvent misinterpretation.

Ancient DNA as a Tool for Navigating the Anthropocene

AbstractAncient DNA (aDNA) analysis has led to significant breakthroughs in our understanding of the origin of our own species as well as that of many commensal and wild species. New approaches in aDNA research promise to make it a major tool for adaptation to and mitigation of the impacts of the rapidly changing climates of the Anthropocene. This article reviews a number of these new lines of research and their current and potential future contributions to responding to climate change, particularly in two areas: the generation of deeper baseline data on ecological and environmental change, and the tracking and recovery of lost genetic diversity to strengthen the resilience of living species. The article argues that aDNA analysis is creating a powerful new pathway for archeology to engage with the challenges of the Anthropocene.

ADNA Research From aHistorical Perspective

aDNA studies are acooperative field of research with abroad range of applications including evolutionary biology, genetics, anthropology and archaeology. Scientists are using ancient molecules as source material for historical questions. Colleagues from the humanities are observing this with both interest and concern because aDNA research is affecting academic identities and both concepts of history and historiography. aDNA research developed in away that can be described as aHype Cycle (Chackie Fenn). Technological triggers such as Sanger Sequencing and the Polymerase Chain Reaction kicked off amultitude of experiments with ancient DNA during the 1980s and 1990s. Geneticists, microbiologists, anthropologists and many more euphorically joined a"molecule hunt". aDNA was promoted as atime machine. Media attention was enormous. As experiments and implementations began to fail and contamination was discovered to be atremendous problem, media interest waned and many labs lost their interest. Some turned their disillusionment into systematic research into methodology and painstakingly established lab routines. The authenticity problem was first addressed by control oriented measures but later approached from amore cognitive theoretical perspective as the pitfalls and limits of aDNA became clearer. By the end of the 2000s the field reached its current plateau of productivity. Cross-disciplinary debates, conflicts and collaborations are increasing critical reflection among all participants. Historians should consider joining the field in akind of critical friendship to both make the most of its possibilities and give an input from aconstructivist perspective.

Human evolution: a tale from ancient genomes.

The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.

Diet and Mobility in the Corded Ware of Central Europe

Isotopic investigations of two cemetery populations from the Corded Ware Culture in southern Germany reveal new information on the dating of these graves, human diet during this period, and individual mobility. Corded Ware Culture was present across much of temperate Europe ca. 2800–2200 cal. BC and is represented by distinctive artifacts and burial practices. Corded Ware was strongly influenced by the Yamnaya Culture that arose in the steppes of eastern Europe and western Eurasia after 3000 BC, as indicated by recent aDNA research. However, the development of CW on different chronological and spatial scales has to be evaluated. Examination of the CW burials from southern Germany supports an argument for substantial human mobility in this period. Several burials from gravefields and larger samples from two large cemeteries at Lauda-Königshofen "Wöllerspfad" and at Bergheinfeld “Hühnerberg” contributed the human remains for our study of bone and tooth enamel from the Corded Ware Culture. Our results suggest that Corded Ware groups in this region at least were subsisting on a mix of plant and animal foods and were highly mobile, especially the women. We interpret this as indicating a pattern of female exogamy, involving different groups with differing economic strategies.

The First Attested Extraction of Ancient DNA in Legumes (Fabaceae).

Ancient DNA (aDNA) is any DNA extracted from ancient specimens, important for diverse evolutionary researches. The major obstacles in aDNA studies are mutations, contamination and fragmentation. Its studies may be crucial for crop history if integrated with human aDNA research and historical linguistics, both general and relating to agriculture. Legumes (Fabaceae) are one of the richest end economically most important plant families, not only from Neolithic onwards, since they were used as food by Neanderthals and Paleolithic modern man. The idea of extracting and analyzing legume aDNA was considered beneficial for both basic science and applied research, with an emphasis on genetic resources and plant breeding. The first reported successful and attested extraction of the legume aDNA was done from the sample of charred seeds of pea (Pisum sativum) and bitter vetch (Vicia ervilia) from Hissar, southeast Serbia, dated to 1,350–1,000 Before Christ. A modified version of cetyltrimethylammonium bromide (CTAB) method and the commercial kit for DNA extraction QIAGEN DNAesy yielded several ng μl-1 of aDNA of both species and, after the whole genome amplification and with a fragment of nuclear ribosomal DNA gene 26S rDNA, resulted in the detection of the aDNA among the PCR products. A comparative analysis of four informative chloroplast DNA regions (trnSG, trnK, matK, and rbcL) among the modern wild and cultivated pea taxa demonstrated not only that the extracted aDNA was genuine, on the basis of mutation rate, but also that the ancient Hissar pea was most likely an early domesticated crop, related to the modern wild pea of a neighboring region. It is anticipated that this premier extraction of legume aDNA may provide taxonomists with the answers to diverse questions, such as leaf development in legumes, as well as with novel data on the single steps in domesticating legume crops worldwide.

Ancient DNA – Pitfalls and Prospects

Ancient DNA (a-DNA) studies in past three decades has been uplifted from short stretch archaeological mtDNA retrieval to reconstruction of complete mitochondrial genome sequence using next generation sequencing. Study of a-DNA acts as validating tool to test the assumed hypothesis used in origin, evolution, diversification, distribution, domestication and extinction of species; although, scientific progression in the field is frequently hindered by erroneous reports due to contamination and other technical bottlenecks. With the advent of appropriate methodologies such as 3’-C3 spacer tagged oligonucleotide blocking, shotgun sequencing, amplicon sequencing Polymerase Chain Reaction, single primer extension methodology, development of broad spectrum ancient sequence primer, slippage proof amplification methods, use of multiplexing strategy in PCR (Polymerase Chain Reaction) amplification, etc. in a-DNA research try to minimize the difficulties associated with it. Present review highlighted the pitfalls as well as prospects of a-DNA study and tries to assess the significance and acceptability of a-DNA research for its future application in understanding of evolutionary biology.

Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site.

By analysing ancient DNA (aDNA) from 74 (14)C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (rXY) in six microsatellite markers genotyped from aDNA, coupled with overlapping radiocarbon ages. The observed rXY values in the four dyads exceeded a conservative cutoff value for potential relatives obtained from simulated data. In three of the four dyads, the kinship was further supported by observing shared and rare mitochondrial haplotypes. Simulations demonstrated that the proportion of observed dyads above the cutoff value was at least 20 times higher than expected in a randomly mating population with temporal sampling, also when introducing population structure in the simulations. We conclude that the results must reflect social structure in the moa population and we discuss the implications for future aDNA research.

The current and future applications of ancient DNA in Quaternary science

ABSTRACTThe introduction of next‐generation sequencing methods has broadened the scope and utility of ancient DNA (aDNA) research, and is opening up exciting new applications in Quaternary science. Palaeogenomes – partial or complete genome sequences for extinct taxa – are now available for Neanderthals and Denisovans, various megafauna, and preserved microorganisms. The analysis of aDNA in sediments, including cores in which there are no visible macro‐ or microfossils, is helping to reconstruct past ecosystems, especially in Arctic regions where aDNA preservation is relatively good. In this review we follow the development of aDNA research over the last 30 years, showing how the problems caused by contamination of ancient samples with modern DNA have gradually been overcome, and highlighting those technical challenges that still exist. We then survey the current standing of palaeogenomics and sedimentary aDNA studies, and indicate how these fields might be developed further in coming years.

Ancient population genomics and the study of evolution.

Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.

Ancient genomics.

The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

Mycobacterium tuberculosisComplex in Remains of 18th–19th Century Slaves, Brazil

<i>Mycobacterium tuberculosis</i>Complex in Remains of 18th–19th Century Slaves, Brazil

Advances in ancient DNA research can help radiological interpretations of archaeological diseases

Evolutionary medicine explores among other things the human vulnerability towards pathogens. To increase the diagnostic level of evidence, alongside radiological investigations, molecular techniques (such as ancient DNA analyses) are often being applied. Ancient DNA (aDNA) is DNA recovered from archaeological and historical specimens. This DNA is highly degraded and fragmented by biological and environmental factors and is therefore difficult to analyse. However, sequences retrieved from ancient material are highly useful in many ways, including for medical purposes. The first aDNA experiment was conducted in 1984 to determine the biological classification of the extinct quagga, revealedtobeacloserelativeofthezebra[1].Inthe1980sand 1990s there were multiple publications in which the authors claimed to have extracted aDNA from a variety of samples. However,someofthesesequenceswerelaterdeterminedtobe the result of modern contamination. This led to the introduction of vigorous anti-contamination procedures in the field of aDNA research. At this time a greater understanding of the need for hypothesis-led research allowed for a great diversity of targets. Ancient DNA has been used extensively, for example, to clarify the domestication events of animals and plants, to understand the movements of humans, and to examine the history of modern and ancient disease.

Symbolic construction, the scene from Sahul (Greater Australia)

The Pacific region provides unique opportunities to study human evolution including through analyses of ancient DNA. While some of the earliest studies involving ancient DNA from skeletal remains focused on Pacific samples, in the following 25 years, several factors meant that little aDNA research, particularly research focused on human populations, has emerged. This paper briefly presents the genetic evidence for population origins, reviews what ancient DNA work has been undertaken to address human history and evolution in the Pacific region, and argues that the future is bright but research requires a collaborative approach between academic disciplines but also with local communities.

Improving ancient DNA read mapping against modern reference genomes

BackgroundNext-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA.ResultsIn this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%.ConclusionsWe have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material.

Nondestructive sampling of human skeletal remains yields ancient nuclear and mitochondrial DNA

Museum curators and living communities are sometimes reluctant to permit ancient DNA (aDNA) studies of human skeletal remains because the extraction of aDNA usually requires the destruction of at least some skeletal material. Whether these views stem from a desire to conserve precious materials or an objection to destroying ancestral remains, they limit the potential of aDNA research. To help address concerns about destructive analysis and to minimize damage to valuable specimens, we describe a nondestructive method for extracting DNA from ancient human remains. This method can be used with both teeth and bone, but it preserves the structural integrity of teeth much more effectively than that of bone. Using this method, we demonstrate that it is possible to extract both mitochondrial and nuclear DNA from human remains dating between 300 BC and 1600 AD. Importantly, the method does not expose the remains to hazardous chemicals, allowing them to be safely returned to curators, custodians, and/or owners of the samples. We successfully amplified mitochondrial DNA from 90% of the individuals tested, and we were able to analyze 1-9 nuclear loci in 70% of individuals. We also show that repeated nondestructive extractions from the same tooth can yield amplifiable mitochondrial and nuclear DNA. The high success rate of this method and its ability to yield DNA from samples spanning a wide geographic and temporal range without destroying the structural integrity of the sampled material may make possible the genetic study of skeletal collections that are not available for destructive analysis.

The relationship of the Mimbres to other southwestern and Mexican populations

Previous aDNA research in the Southwest provides a framework to understand the Mimbres population which maintains a unique identity in the archeology of the desert Southwest of North America. Both the mitochondrial DNA (mtDNA) haplogroups and haplotypes of a sample of 46 Mimbres individuals were identified from skeletal remains and compared to those of other ancient and modern populations in the American Southwest and Mexico. The haplogroup frequency distribution of the Mimbres resembles that of other Southwestern populations, suggesting a close relationship between the Mimbres and the neighboring populations and population continuity for a long period of time. However, their relatively low frequency of haplogroup A (11% n = 5) is consistent with a clinal distribution of haplogroup A from Mesoamerica to the Southwest. Moreover, unlike other Southwestern populations, the Mimbres share haplotypes with populations to the south, such as the Cora, Huichol, and Nahua, suggesting gene-flow from Mesoamerica. Here we discuss this data in light of the origin of the Mimbres population and their relationship to other Southwestern and Mexican populations.

Moa's Ark or volant ghosts of Gondwana? Insights from nineteen years of ancient DNA research on the extinct moa (Aves: Dinornithiformes) of New Zealand

The moa (Aves: Dinornithiformes) of New Zealand represent one of the extinct iconic taxa that define the field of ancient DNA (aDNA), and after almost two decades of genetic scrutiny of bones, feathers, coprolites, mummified tissue, eggshell, and sediments, our knowledge of these prehistoric giants has increased significantly. Thanks to molecular and morphological-based research, the insights that have been obtained into moa phylogenetics, phylogeography, and palaeobiology exceeds that of any other extinct taxon. This review documents the strengths of applying a multidisciplinary approach when studying extinct taxa but also shows that cross-disciplinary controversies still remain at the most fundamental levels, with highly conflicting interpretations derived from aDNA and morphology. Moa species diversity, for example, is still heavily debated, as well as their relationship with other ratites and the mode of radiation. In addition to increasing our knowledge on a lineage of extinct birds, further insights into these aspects can clarify some of the basal splits in avian evolution, and the evolutionary implications of the breakup of the prehistoric supercontinent Gondwana. Did a flightless moa ancestor drift away on proto New Zealand (Moa's Ark) or did a volant ancestor arrive by flight? Here we provide an overview of 19 years of aDNA research on moa, critically assess the attempts and controversies in placing the moa lineage among palaeognath birds, and discuss the factors that facilitated the extensive radiation of moa. Finally, we identify the most obvious gaps in the current knowledge to address the future potential research areas in moa genetics.

Paleoparasitological report on Ascaris aDNA from an ancient East Asian sample

In this study, Ascaris DNA was extracted and sequenced from a medieval archaeological sample in Korea. While Ascaris eggs were confirmed to be of human origin by archaeological evidence, it was not possible to pinpoint the exact species due to close genetic relationships among them. Despite this shortcoming, this is the first Ascaris ancient DNA (aDNA) report from a medieval Asian country and thus will expand the scope of Ascaris aDNA research.

Ancient DNA Studies in Physical Anthropology

▪ Abstract Nucleic acids are preserved in prehistoric samples under a wide range of depositional environments. The development of new molecular methods, especially the polymerase chain reaction, has made possible the recovery and manipulation of these molecules, and the subsequent molecular genetic characterization of the ancient samples. The analysis of ancient (a)DNA is complicated by the degraded nature of ancient nucleic acids, as well as the presence of enzymatic inhibitors in aDNA extracts. We review aspects of ancient DNA preservation, a variety of methods for the extraction and amplification of informative DNA segments from ancient samples, and the difficulties encountered in documenting the authenticity of ancient DNA template. Studies using aDNA to address questions in human population history or human evolution are reviewed and discussed. Future prospects for the field and potential directions for future aDNA research efforts in physical anthropology are identified.