Ancient DNA Research Articles

Ancient DNA: a promising tool for understanding the evolutionary history of and human pressure on the highly endangered limpet Patella ferruginea

Ancient DNA: a promising tool for understanding the evolutionary history of and human pressure on the highly endangered limpet Patella ferruginea

Leveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift.

Large ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. While recent studies have used time-stratified aDNA for selection scans, most focus on single-locus methods. We conducted a multi-locus genotype scan on 708 samples spanning 7000 years of European history. We show that the G12 statistic, originally designed for unphased diploid data, can effectively detect selection in aDNA processed to create 'pseudo-haplotypes'. In simulations and at known positive control loci (e.g., lactase persistence), G12 outperforms the allele frequency-based selection statistic, SweepFinder2, previously used on aDNA. Applying our approach, we identified 14 candidate regions of selection across four time periods, with half the signals detectable only in the earliest period. Our findings suggest that selective events in European prehistory, including from the onset of animal domestication, have been obscured by neutral processes like genetic drift and demographic shifts such as admixture.

Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations.

The tripartite ancestral structure is a recently proposed model for the genetic origin of modern Japanese, comprising indigenous Jomon hunter-gatherers and two additional continental ancestors from Northeast Asia and East Asia. To investigate the impact of the tripartite structure on genetic and phenotypic variation today, we conducted biobank-scale analyses by merging Biobank Japan (BBJ; n = 171,287) with ancient Japanese and Eurasian genomes (n = 22). We demonstrate the applicability of the tripartite model to Japanese populations throughout the archipelago, with an extremely strong correlation between Jomon ancestry and genomic variation among individuals. We also find that the genetic legacy of Jomon ancestry underlies an elevated body mass index (BMI). Genome-wide association analysis with rigorous adjustments for geographical and ancestral substructures identifies 132 variants that are informative for predicting individual Jomon ancestry. This prediction model is validated using independent Japanese cohorts (Nagahama cohort, n = 2993; the second cohort of BBJ, n = 72,695). We further confirm the phenotypic association between Jomon ancestry and BMI using East Asian individuals from UK Biobank (n = 2286). Our extensive analysis of ancient and modern genomes, involving over 250,000 participants, provides valuable insights into the genetic legacy of ancient hunter-gatherers in contemporary populations.

High definition 3D models of small legume seed: a close up application to support ancient plant genomics

Abstract. Legume seeds are essential for nutrition and play crucial roles in food security, climate change mitigation, biodiversity conservation, and sustainability. Among them, the common bean (Phaseolus vulgaris L.) is the most widely cultivated and vital to the food value chain. Originating in Mesoamerica and independently domesticated there and in the Andes about 8,000 years ago, common beans have adapted to diverse environments globally following the Columbian exchange. Ancient DNA (aDNA) sequencing offers insights into the bean’s adaptation and evolution, but traditional methods struggle with detailed 3D phenotypic analysis due to the beans’ small size and the destructive nature of aDNA extraction. Expensive high-detail optical instruments are not commonly available in genetic labs. This research proposes macro-photogrammetry as a low-cost technique for creating detailed 3D digital replicas of beans. By using samples from archaeological sites in northern Peru, this method preserves phenotypic information despite the destruction of physical samples during DNA extraction. The study details the process of capturing high-detail images with specialized equipment to build a digital phenotype library, preserving the morphological features of ancient beans for further study and future comparison with modern varieties.

Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer

Horizontal gene transfer is one of the most important drivers of bacterial evolution. Transformation by uptake of extracellular DNA is traditionally not considered to be an effective mode of gene acquisition, simply because extracellular DNA is degraded in a matter of days when it is suspended in e.g. seawater. Recently the age span of stored DNA was increased to at least 2 Ma. Here, we show that Acinetobacter baylyi can incorporate 60 bp DNA fragments adsorbed to common sedimentary minerals and that the transformation frequencies scale with mineral surface properties. Our work highlights that ancient environmental DNA can fuel the evolution of contemporary bacteria. In contrast to heritable stochastic mutations, the processes by which bacteria acquire new genomic material during times of increased stress and needs, indicate a non-random mechanism that may propel evolution in a non-stochastic manner.

Cost-effectiveness and other considerations for different research techniques applied in ancient DNA analysis.

Ancient DNA (aDNA) analysis has developed rapidly since it first emerged in the 1980s, becoming an almost indispensable tool in anthropological and archaeological sciences. Earlier aDNA study was based on the polymerase chain reaction (PCR) technique, with which, unfortunately, modern DNA contamination and other authenticity issues were often incurred. These technical hurdles were soon overcome by application of advancements in the forms of the next generation sequencing (NGS) technique and others. However, since NGS requires money, time, and, in the case of large projects, manpower as well, genetic analysis of some ancient samples considered to be insignificant is commonly delayed or, in the worst cases, neglected entirely. We acknowledge that as a diagnostic tool in aDNA analysis, PCR is less accurate than NGS and more easily affected by modern DNA contamination; but it also has advantages, such as simplicity, time-saving, and greater ease of interpretation, among others. The role of PCR in aDNA analysis, then, should be reconsidered.

Population expansion from Central Plain to northern coastal China inferred from ancient human genomes

Population expansion from Central Plain to northern coastal China inferred from ancient human genomes

Ancient DNA challenges prevailing interpretations of the Pompeii plaster casts

Ancient DNA challenges prevailing interpretations of the Pompeii plaster casts

The demic diffusion of Han culture into the Yunnan-Guizhou plateau inferred from ancient genomes

The demic diffusion of Han culture into the Yunnan-Guizhou plateau inferred from ancient genomes

The genomic natural history of the aurochs.

Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia1. Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs-European, Southwest Asian, North Asian and South Asian-each of which has dynamic trajectories that have responded to changes in climate and human influence. Similarly to Homo heidelbergensis, aurochsen first entered Europe around 650 thousand years ago2, but early populations left only trace ancestry, with both North Asian and European B. primigenius genomes coalescing during the most recent glaciation. North Asian and European populations then appear separated until mixing after the climate amelioration of the early Holocene. European aurochsen endured the more severe bottleneck during the Last Glacial Maximum, retreating to southern refugia before recolonizing from Iberia. Domestication involved the capture of a small number of individuals from the Southwest Asian aurochs population, followed by early and pervasive male-mediated admixture involving each ancestral strain of aurochs after domestic stocks dispersed beyond their cradle of origin.

Biofilms in modern CaCO3-supersaturated freshwater environments reveal viral proxies

Biofilms are mucilaginous-organic layers produced by microbial activity including viruses. Growing biofilms form microbial mats which enhance sediment stability by binding particles with extracellular polymeric substances and promoting growth through nutrient cycling and organic matter accumulation. They preferentially develop at the sediment-water interface of both marine and non-marine environments, and upon the growing surfaces of modern tufa and travertine. In this context, however, little is known about the factors, environmental or anthropogenic, which affect viral communities in freshwater spring settings. To explore this issue, geochemical and metagenomic data were subjected to multidimensional analyses (Principal Component Analysis, Classical Multidimensional Scaling, Partial Least Squares analysis and cluster analysis based on beta-diversity), and these show that viral composition is specific and dependent on environment. Indeed, waters precipitating tufa and travertine do vary in their geochemistry with their viruses showing distinct variability between sites. These differences between virus groups allow the formulation of a viral proxy, based on the Caudoviricetes/Megaviricetes ratio established on the most abundant groups of viruses. This ratio may be potentially used in analysing ancient DNA preserved in carbonate formations as an additional source of information on the microbiological community during sedimentation.

Zooarchaeological and ancient DNA identification of a non-local gopher tortoise (Gopherus polyphemus) in New Orleans, Louisiana, USA

Zooarchaeological and ancient DNA identification of a non-local gopher tortoise (Gopherus polyphemus) in New Orleans, Louisiana, USA

Restoration of the spike architectonics in ancient barley excavated at the twelfth-century settlement of Usvyaty

Background. The data are presented on the architectonics of ancient barley spikes from the 12th century, excavated in 2019 at Usvyaty Settlement. Modern molecular genetics approaches were used to study domestication genes (Btr1, Btr2, and Vrs) in ancient and contemporary barleys (germplasm accessions preserved at VIR).Materials and methods. The carbonized kernels found by archaeologists during the excavations at Usvyaty were analyzed. Primers for domestication genes were designed, and PCR was performed on contemporary and ancient barley grains. Ancient kernels were studied in accordance with the rules established for organizing a paleogenetics laboratory, which excluded any contamination with contemporary DNA. Fragments of domestication genes from contemporary and ancient barley grain samples underwent Sanger sequencing. Results. Ancient DNA was isolated and enriched. The analysis of domestication gene sequences made it possible to reconstruct the ancient barley spike’s features. Conclusion. The ancient cereal crop architectonics was restored to ascertain a brittle two-row spike of ancient barley

Heterochronous mitogenomes shed light on the Holocene history of the Scandinavian brown bear

Following glacial retreat after the last ice age, brown bears (Ursus arctos) recolonised Scandinavia. Previous research based on mitochondrial markers suggests that bears recolonised from both the north and the south, with a contact zone in central Scandinavia. More recently, the Scandinavian brown bear was subjected to a strong population decline with only ca. 130 remaining individuals, due to intense human persecution approximately 100 years ago. Here, we analyse 41 ancient, historical, and modern mitochondrial genomes, to examine the number of female lineages involved in the postglacial recolonisation event and temporal changes in the Scandinavian brown bears’ mitochondrial genetic diversity. Our results support the bi-directional recolonisation hypothesis, indicating multiple mitochondrial lineages from clade 1a possibly followed a southern route, while only a single lineage from clade 3a appears to have followed a northern route. Furthermore, we found that the recent bottleneck had a strong impact on the southern subpopulation, resulting in only one remaining haplotype in the contemporary brown bears. For the northern subpopulation, the impact was moderate, and most haplotypes were retained throughout the bottleneck. By exploring the postglacial recolonisation and recent population pressures, our study enhances understanding of how these factors have influenced the genetic diversity of Scandinavian brown bears.

Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage.

One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state-of-the-art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data.

Contextualising Edix Hill: First-Pandemic Plague and Britain

Abstract: The 2019 discovery of Yersinia pestis ancient DNA at Edix Hill in Cambridgeshire unquestionably confirms that plague was present in sixth-century Britain. Prior treatments of this evidence have decontextualised it from its British setting, considering it aside from the richly studied British archaeological and textual records, to detrimental effect. This article considers this new evidence in context, presenting a historiography of early medieval British epidemics and a summary of current scientific knowledge of the topic to contend that the discovery marks a significant shift in our understanding of early British plague and to clarify what palaeoscientific data can and cannot tell us about plague’s presence in and its impact on Britain. It then argues a new theory of the spread of plague based on recent developments in our understanding of British demographics, ecology and trade routes, contending that early first-pandemic Y. pestis was transmitted to Britain at least two distinct times via separate routes, with the first introduction potentially pre-dating the introduction of plague to Constantinople in 542 CE. The article then reflects on why British sources have been omitted from or misused in plague scholarship, arguing that this trend speaks to British history’s damaging insularity and to methodological issues within plague studies. It concludes by connecting this issue to wider geographical hierarchies within scholarship on Late Antiquity and suggests ways in which future plague scholarship can respond to these challenges.

Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation.

Previous studies suggested that the copy number of the human salivary amylase gene, AMY1, correlates with starch-rich diets. However, evolutionary analyses are hampered by the absence of accurate, sequence-resolved haplotype variation maps. We identified 30 structurally distinct haplotypes at nucleotide resolution among 98 present-day humans, revealing that the coding sequences of AMY1 copies are evolving under negative selection. Genomic analyses of these haplotypes in archaic hominins and ancient human genomes suggest that a common three-copy haplotype, dating as far back as 800 KYA, has seeded rapidly evolving rearrangements through recurrent non-allelic homologous recombination. Additionally, haplotypes with more than three AMY1 copies have significantly increased in frequency among European farmers over the past 4,000 years, potentially as an adaptive response to increased starch digestion.

Episode 41: Biolore: How ancient DNA is unlocking lost secrets of the planet

Episode 41: Biolore: How ancient DNA is unlocking lost secrets of the planet

Improved detection of methylation in ancient DNA

Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.

NOthing goes toWAste (NOWA): A protocol to optimise sampling of ancient teeth

Advancements in archaeological sciences through innovative scientific techniques applied to ancient human remains have increasingly been transforming the study of the past. Destructive analyses of bioarchaeological or palaeontological specimens such as dental histology, isotopic or elemental analysis of dental mineralised tissues, 14C dating, proteomic analysis or ancient DNA are increasingly being applied to obtain ever more refined past life histories. In tandem with spatially-resolved analyses, mineralised dental tissues, especially enamel, have proven to be ideal archives. The main concern with any of these techniques is the need for some level of destructive sampling and thus damage to specimens. In compliance with the ALARA (As Low [damage] As Reasonably Achievable) principle, we present a standardised protocol (the NOWA protocol) for the optimisation, in terms of minimising the destructive approach, of tooth sampling for histology, biomolecular and biogeochemical analyses. The NOWA protocol enables the collection of multiple datasets through optimised sampling of a single dental specimen, ensuring the preservation of most of the tooth and, to a substantial degree, its morphology. Overall, this approach balances the significant scientific insights from such investigations against the inevitable conservation requirements of valuable archaeological and palaeontological specimens, thus maximising the feasibility of future analyses of individual specimens that need to be evaluated on a case-to-case basis.