Age estimation of single nucleotide polymorphisms associated with autoinflammatory diseases in anatolia: insights from ancient and modern DNA.

Studies of modern and ancient DNA (aDNA) have substantially improved our understanding of the early history of human populations. Despite advances in whole-genome sequencing technologies, present studies of aDNA are largely based on a panel of preselected genomic variants; thus, valuable genetic information in aDNA should be further explored. This study analyzed genotype data from 19 ancient and 16 modern high-coverage shotgun human genomes. We used modern populations from the 1000 Genomes Project and the Human Genome Diversity Project as reference populations and selected single-nucleotide polymorphisms (SNPs) that were polymorphic in one reference population and monomorphic in the others. Ancestral spectrum analyses based on the population-specific SNPs were conducted on the 19 aDNA and 16 modern DNA samples to determine their coancestries with modern reference populations. These analyses effectively revealed the genetic affinity between aDNA and modern populations, which is also true for modern DNA. The results for the 11 aDNA samples with expected transition-to-transversion ratios agree with previous analyses; the 8 aDNA samples with excessive transition-to-transversion ratios revealed ancestral spectra indicative of a high level of DNA damage that cannot be fully explained by postmortem cytosine deamination. Additional biochemistry or bioinformatics treatments seem necessary for the meaningful study of such aDNA.

abstract: Studies of modern and ancient DNA (aDNA) have substantially improved our understanding of the early history of human populations. Despite advances in whole-genome sequencing technologies, present studies of aDNA are largely based on a panel of preselected genomic variants; thus, valuable genetic information in aDNA should be further explored. This study analyzed genotype data from 19 ancient and 16 modern high-coverage shotgun human genomes. We used modern populations from the 1000 Genomes Project and the Human Genome Diversity Project as reference populations and selected single-nucleotide polymorphisms (SNPs) that were polymorphic in one reference population and monomorphic in the others. Ancestral spectrum analyses based on the population-specific SNPs were conducted on the 19 aDNA and 16 modern DNA samples to determine their coancestries with modern reference populations. These analyses effectively revealed the genetic affinity between aDNA and modern populations, which is also true for modern DNA. The results for the 11 aDNA samples with expected transition-to-transversion ratios agree with previous analyses; the 8 aDNA samples with excessive transition-to-transversion ratios revealed ancestral spectra indicative of a high level of DNA damage that cannot be fully explained by postmortem cytosine deamination. Additional biochemistry or bioinformatics treatments seem necessary for the meaningful study of such aDNA.

The appearance of agriculture is one of the most striking features of Holocene human history, a feature that has long been studied in an interdisciplinary fashion, bringing archaeology together with plant and animal genetics. This paper reviews new developments in that study, consequent upon recent advances in DNA science. Among these advances is the possibility of complementing modern DNA data with fragmentary evidence of ancient DNA. Following a short account of the historical foundations of this research, studies of plant and animal domesticates based upon variations in protein, modern DNA and ancient DNA are reviewed in turn. The results of these studies are considered against a background of two contrasting models of how agriculture originated and spread, characterized by Blumler (1992) as ‘stimulus-diffusion’ and ‘independent invention’. We argue that existing evidence from DNA supports neither model in its extreme form, favouring instead an intermediate model.

DNA, or deoxyribonucleic acid, carries the entirety of genetic information of any living organism. The study of the bacterial DNA extracted from human bones excavated from archaeological and anthropological sites aims to analyse the evolution of microorganisms inhabiting the human body and to contribute to new insight related to the health, diet and even migration of our ancestors. This paper aims to offer a solution for the discrimination between ancient and modern bacterial DNA in dental calculus. We propose three internal representations for the considered DNA sequences in order to analyse which captures the most information and is more informative for classification models. Two of these are text-based, while the third one takes advantage of several physical and chemical properties of nucleotides in the DNA. We use a data set containing both ancient and modern dental calculus bacterial DNA and apply two supervised models, namely artificial neural networks and support vector machines to distinguish between the two types of sequences. The two main conclusions indicated by the obtained results are: the representation based on physical and chemical properties seems to best capture relevant information for the task at hand; for the considered data set and DNA encoding proposals, support vector machines outperform artificial neural networks, although results obtained by both models are promising.

The analysis of targeted genetic loci from ancient, forensic and clinical samples is usually built upon polymerase chain reaction (PCR)-generated sequence data. However, many studies have shown that PCR amplification from poor-quality DNA templates can create sequence artefacts at significant levels. With hominin (human and other hominid) samples, the pervasive presence of highly PCR-amplifiable human DNA contaminants in the vast majority of samples can lead to the creation of recombinant hybrids and other non-authentic artefacts. The resulting PCR-generated sequences can then be difficult, if not impossible, to authenticate. In contrast, single primer extension (SPEX)-based approaches can genotype single nucleotide polymorphisms from ancient fragments of DNA as accurately as modern DNA. A single SPEX-type assay can amplify just one of the duplex DNA strands at target loci and generate a multi-fold depth-of-coverage, with non-authentic recombinant hybrids reduced to undetectable levels. Crucially, SPEX-type approaches can preferentially access genetic information from damaged and degraded endogenous ancient DNA templates over modern human DNA contaminants. The development of SPEX-type assays offers the potential for highly accurate, quantitative genotyping from ancient hominin samples.

Contamination with exogenous DNA is a constant hazard to ancient DNA studies, since their validity greatly depend on the ancient origin of the retrieved sequences. Since contamination occurs sporadically, it is fundamental to show positive evidence for the authenticity of ancient DNA sequences even when preventive measures to avoid contamination are implemented. Recently the presence of wheat in the United Kingdom 8000 years before the present has been reported based on an analysis of sedimentary ancient DNA (Smith et al. 2015). Smith et al. did not present any positive evidence for the authenticity of their results due to the small number of sequencing reads that were confidently assigned to wheat. We developed a computational method that compares postmortem damage patterns of a test dataset with bona fide ancient and modern DNA. We applied this test to the putative wheat DNA and find that these reads are most likely not of ancient origin.

Contamination with exogenous DNA is a constant hazard to ancient DNA studies, since their validity greatly depend on the ancient origin of the retrieved sequences. Since contamination occurs sporadically, it is fundamental to show positive evidence for the authenticity of ancient DNA sequences even when preventive measures to avoid contamination are implemented. Recently the presence of wheat in the United Kingdom 8000 years before the present has been reported based on an analysis of sedimentary ancient DNA (Smith et al. 2015). Smith et al. did not present any positive evidence for the authenticity of their results due to the small number of sequencing reads that were confidently assigned to wheat. We developed a computational method that compares postmortem damage patterns of a test dataset with bona fide ancient and modern DNA. We applied this test to the putative wheat DNA and find that these reads are most likely not of ancient origin.DOI:http://dx.doi.org/10.7554/eLife.10005.001

Entering into the world of ancient DNA research is nontrivial. Because the DNA in most ancient specimens is degraded to some extent, the potential for contamination of ancient samples and DNA extracts with modern DNA is considerable. To minimize the risk associated with working with ancient DNA, experimental protocols specific to handling ancient specimens have been introduced. Here, I outline the challenges associated with working with ancient DNA and describe guidelines for setting up a new ancient DNA laboratory. I also discuss steps that can be taken at the sample collection and preparation stage to minimize the potential for contamination with exogenous sources of DNA.

Molecular biology techniques are increasingly being used in sex identification of skeletal remains when traditional anthropometric analyzes are not successful in identifying sex of remains that are incomplete, fragmented and /or of immature individuals. In the present work, we investigated the possibility of determining sex by using the qPCR-duplex method for both ancient and modern DNA samples. This method involves the co-amplification of two genes in a single reaction system and the subsequent analysis of the fusion curves; the gene sequences used for the construction of suitable primers are those of steroid sulfatase (STS) and testis specific protein Y-linked 1 (TSPY) genes which turned out to be two sensitive markers as they have a detection limit of 60 pg and 20 pg respectively on modern DNA. The validity of the method was verified on modern DNA in which gender was identified in all the samples with 100% accuracy; thus, allowing for the same results as the classic method with amelogenin, but in a faster and more immediate way, as it allows for sex determination solely by analyzing the denaturation curves without having to perform an electrophoretic run. The proposed molecular technique proves to be sensitive and precise even on degraded DNA, in fact on 9 archaeological finds dating from the VII-XII century in which sex had been identified through anthropometric analysis, it confirmed the sex of 8 out of 9 finds correctly.

The analysis of ancient DNA in a population genetic or phylogeographical framework is an emerging field, as traditional analytical tools were largely developed for the purpose of analysing data sampled from a single time point. Markov chain Monte Carlo approaches have been successfully developed for the analysis of heterochronous sequence data from closed panmictic populations. However, attributing genetic differences between temporal samples to mutational events between time points requires the consideration of other factors that may also result in genetic differentiation. Geographical effects are an obvious factor for species exhibiting geographical structuring of genetic variation. The departure from a closed panmictic model require researchers to either exploit software developed for the analysis of isochronous data, take advantage of simulation approaches using algorithms developed for heterochronous data, or explore approximate Bayesian computation. Here, we review statistical approaches employed and available software for the joint analysis of ancient and modern DNA, and where appropriate we suggest how these may be further developed.

Ancient DNA has revolutionized the way in which evolutionary biologists research both extinct and extant taxa, from the inference of evolutionary history to the resolution of taxonomy. Here, we present, to our knowledge, the first study to report the rediscovery of an 'extinct' avian taxon, the Tasman booby (Sula tasmani), using classical palaeontological data combined with ancient and modern DNA data. Contrary to earlier work, we show an overlap in size between fossil and modern birds in the North Tasman Sea (classified currently as S. tasmani and Sula dactylatra fullagari, respectively). In addition, we show that Holocene fossil birds have mitochondrial control region sequences that are identical to those found in modern birds. These results indicate that the Tasman booby is not an extinct taxon: S. dactylatra fullagari O'Brien & Davies, 1990 is therefore a junior synonym of Sula tasmani van Tets, Meredith, Fullagar & Davidson, 1988 and all North Tasman Sea boobies should be known as S. d. tasmani. In addition to reporting the rediscovery of an extinct avian taxon, our study highlights the need for researchers to be cognizant of multidisciplinary approaches to understanding taxonomy and past biodiversity.

Deficiencies and challenges in the study of ancient tuberculosis DNA

The Genetic Basis for Periodic Fever

High-throughput sequencing technologies frequently necessitate the use of PCR for sequencing library amplification. PCR is a sometimes enigmatic process and is known to introduce biases. Here we perform a simple amplification-sequencing assay using 10 commercially available polymerase-buffer systems to amplify libraries prepared from both modern and ancient DNA. We compare the performance of the polymerases with respect to a previously uncharacterized template length bias, as well as GC-content bias, and find that simply avoiding certain polymerase can dramatically decrease the occurrence of both. For amplification of ancient DNA, we found that some commonly used polymerases strongly bias against amplification of endogenous DNA in favor of GC-rich microbial contamination, in our case reducing the fraction of endogenous sequences to almost half.

DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets.