Search

It is the dream of all researchers working with ancient DNA to identify prior to DNA extraction from bone the specimens or specific zones within them that contain the highest proportion of endogenous DNA. As it impacts the sacrifice of precious ancient specimens and the financial support needed for the analyses, the question is of high importance to the scientific field of palaeogenomics. The "Holy Grail" of palaeogenomics was reached when Cristina Gamba et al. () discovered that it was in the petrosal part of the temporal bone, the densest part of the mammalian skeleton, where DNA is exceptionally well preserved. As a consequence, osteological collections experienced a rush from palaeogenomicists to "harvest" these precious bone parts. In this issue of Molecular Ecology Resources, Alberti et al. () describe the discovery of another promising source of relatively well‐preserved endogenous DNA, that they had identified through computed tomography (CT scans), the outermost layer of cortical bone. These bones being larger and more abundant than petrous bones, this discovery increases markedly the source material for high‐quality palaeogenomic studies and releases the pressure on osteological collections. [ABSTRACT FROM AUTHOR]

Abstract: Recently, palaeogenetics encountered enormous success when parts of the nuclear genomes of mammoth and Neanderthal man were analysed. Their bones, however, had been preserved in environments favourable to DNA preservation, i.e., permafrost regions and caves in temperate regions. Few studies have tackled archaeological bones from hot, arid regions, although they bear great significance for the study of evolution of humans and the precursors of modern societies. According to archaeological evidence, a key event in neolithisation, the domestication of cattle, took place around 10,000 years ago in Southwest Asia. Genetic data from prehistoric bovine bones preserved in this region might shed light on this process, but the palaeogenetic approach has been hampered by poor DNA preservation. Here, I discuss various aspects of DNA preservation in fossils and the production of reliable palaeogenetic data and present methodological improvements that have enabled us to shed light on the process of cattle domestication in Southwest Asia and its spread into western Europe. [Copyright &y& Elsevier]

Molecular analysis of DNA preserved in archaeological bone allows bypassing of certain palaeontological biases. Studies of DNA in fossils are based on the PCR amplification of the small number of molecules that have not been destroyed over time by diagenetic processes. The sensitivity of the method, the presence of polymerase inhibitors in the fossil extracts, the small number of authentic ancient DNA molecules, and their numerous chemical modifications render this powerful approach unreliable and have led to many controversies. Here we show that real-time PCR is the method of choice to assess the initial number of genuine ancient DNA molecules in the extracts, the effect of inhibitors and the presence of low concentrations of contaminating modern target molecules. We suggest that this methodology will help to identify contaminations, to better interpret PCR results and to render ancient DNA studies more reliable. [Copyright &y& Elsevier]

We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6–6.4×. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass, secular name 'hydruntine'. Further, the Anatolian wild ass whole genome profiles fell outside the genomic diversity of other extant and past Asiatic wild ass (E. hemionus) lineages. These observations suggest that the three Anatolian wild asses represent hydruntines, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Our mitogenomic and genomic analyses indicate that E. h. hydruntinus was a clade belonging to ancient and present‐day E. hemionus lineages that radiated possibly between 0.6 and 0.8 Mya. We also find evidence consistent with recent gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome‐wide heterozygosity and runs of homozygosity suggest that the Anatolian wild ass population may have lost genetic diversity by the mid‐first millennium BCE, a possible sign of its eventual demise. [ABSTRACT FROM AUTHOR]

The third millennium BCE was a pivotal period of profound cultural and genomic transformations in Europe associated with migrations from the Pontic-Caspian steppe, which shaped the ancestry patterns in the present-day European genome. We performed a high-resolution whole-genome analysis including haplotype phasing of seven individuals of a collective burial from ~2500 cal BCE and of a Bell Beaker individual from ~2300 cal BCE in the Paris Basin in France. The collective burial revealed the arrival in real time of steppe ancestry in France. We reconstructed the genome of an unsampled individual through its relatives' genomes, enabling us to shed light on the early-stage admixture patterns, dynamics, and propagation of steppe ancestry in Late Neolithic Europe. We identified two major Neolithic/steppe-related ancestry admixture pulses around 3000/2900 BCE and 2600 BCE. These pulses suggest different population expansion dynamics with striking links to the Corded Ware and Bell Beaker cultural complexes. [ABSTRACT FROM AUTHOR]

The article focuses on the Anatolia, a region with an extended history of horse exploitation that has been considered a candidate for the origins of domestic horses but has never been subject to detailed investigation. It mentions that paleogenetic study of pre-and protohistoric horses in Anatolia and the Caucasus encompasses the presumed transition from wild to domestic horses. It also mentions that horses have played important role in human history.

Domestic cats were derived from the Near Eastern wildcat (Felis lybica), after which they dispersed with people into Europe. As they did so, it is possible that they interbred with the indigenous population of European wildcats (Felis silvestris). Gene flow between incoming domestic animals and closely related indigenous wild species has been previously demonstrated in other taxa, including pigs, sheep, goats, bees, chickens, and cattle. In the case of cats, a lack of nuclear, genome-wide data, particularly from Near Eastern wildcats, has made it difficult to either detect or quantify this possibility. To address these issues, we generated 75 ancient mitochondrial genomes, 14 ancient nuclear genomes, and 31 modern nuclear genomes from European and Near Eastern wildcats. Our results demonstrate that despite cohabitating for at least 2,000 years on the European mainland and in Britain, most modern domestic cats possessed less than 10% of their ancestry from European wildcats, and ancient European wildcats possessed little to no ancestry from domestic cats. The antiquity and strength of this reproductive isolation between introduced domestic cats and local wildcats was likely the result of behavioral and ecological differences. Intriguingly, this long-lasting reproductive isolation is currently being eroded in parts of the species' distribution as a result of anthropogenic activities. • Domestic cats and wildcats cohabitated in Europe for at least 2,000 years • During this period, interbreeding between domestic cats and wildcats was extremely limited • This reproductive isolation likely stems from behavioral and ecological differences • Today this reproductive isolation is being eroded due to anthropogenic activities Jamieson, Carmagnini, et al. generate ancient genomes from European domestic cats and wildcats. Their results show that interbreeding between domestic and wildcats was limited (less than 10%) despite cohabitating for over 2,000 years. They argue that this reproductive isolation was likely the result of behavioral and ecological differences. [ABSTRACT FROM AUTHOR]

Background: Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe's megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamics during the Pleistocene. Results: Through ancient DNA analysis we show that the emblematic European bison has experienced several waves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic diversity during the Holocene. Fifty-seven complete and partial ancient mitogenomes from throughout Europe, the Caucasus, and Siberia reveal that three populations of wisent (Bison bonasus) and steppe bison (B. priscus) alternately occupied Western Europe, correlating with climate-induced environmental changes. The Late Pleistocene European steppe bison originated from northern Eurasia, whereas the modern wisent population emerged from a refuge in the southern Caucasus after the last glacial maximum. A population overlap during a transition period is reflected in ca. 36,000-year-old paintings in the French Chauvet cave. Bayesian analyses of these complete ancient mitogenomes yielded new dates of the various branching events during the evolution of Bison and its radiation with Bos, which lead us to propose that the genetic affiliation between the wisent and cattle mitogenomes result from incomplete lineage sorting rather than post-speciation gene flow. Conclusion: The paleogenetic analysis of bison remains from the last 50,000 years reveals the influence of climate changes on the dynamics of the various bison populations in Europe, only one of which survived into the Holocene, where it experienced severe reductions in its genetic diversity. The time depth and geographical scope of this study enables us to propose temperate Western Europe as a suitable biotope for the wisent compatible with its reintroduction. [ABSTRACT FROM AUTHOR]

Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies. [ABSTRACT FROM AUTHOR]

Background: PCR amplification of minute quantities of degraded DNA for ancient DNA research, forensic analyses, wildlife studies and ultrasensitive diagnostics is often hampered by contamination problems. The extent of these problems is inversely related to DNA concentration and target fragment size and concern (i) sample contamination, (ii) laboratory surface contamination, (iii) carry-over contamination, and (iv) contamination of reagents. Methodology/Principal Findings: Here we performed a quantitative evaluation of current decontamination methods for these last three sources of contamination, and developed a new procedure to eliminate contaminating DNA contained in PCR reagents. We observed that most current decontamination methods are either not efficient enough to degrade short contaminating DNA molecules, rendered inefficient by the reagents themselves, or interfere with the PCR when used at doses high enough to eliminate these molecules. We also show that efficient reagent decontamination can be achieved by using a combination of treatments adapted to different reagent categories. Our procedure involves γ- and UV-irradiation and treatment with a mutant recombinant heat-labile double-strand specific DNase from the Antarctic shrimp Pandalus borealis. Optimal performance of these treatments is achieved in narrow experimental conditions that have been precisely analyzed and defined herein. Conclusions/Significance: There is not a single decontamination method valid for all possible contamination sources occurring in PCR reagents and in the molecular biology laboratory and most common decontamination methods are not efficient enough to decontaminate short DNA fragments of low concentration. We developed a versatile multistrategy decontamination procedure for PCR reagents. We demonstrate that this procedure allows efficient reagent decontamination while preserving the efficiency of PCR amplification of minute quantities of DNA. [ABSTRACT FROM AUTHOR]

Abstract: Early diagenesis, spanning the time a few years after death, is crucial to later fossilization, because the former may determine the success of the latter. The external environment in which bones (and fossils) have been altered is critical to early diagenesis and fossilization processes. Alteration of bones by the former may determine the successful fossilization of animal bones and their eventual preservation as part of a fossil assemblage. A long term actualistic experiment took place in Neuadd (Wales, UK) from 1976 to 2006 with the monitoring of approximately 100 animal carcasses. The Neuadd bone collection is derived from natural deaths of domestic and wild animals, the carcasses of which were left in situ and exposed under natural conditions in a series of upland environments in central Wales. Here, we report on a sample of this extensive collection, investigating possible associations between environmental or post-depositional situations and physico-chemical traits at early stages of diagenesis. One of the main agents of bone structure alteration and chemical diagenesis is bacteria, while another may be non-vascular plants. Results obtained so far suggest correlations between surface and histological modifications that are present in temperate environments, but geochemical and collagen contents need a more careful study. Modifications of the surface and histology of the bone are treated in detail and we conclude that some assumptions traditionally considered of relevance (such as soil acidity, decay conditions and bacterial activity) are less important or inadequately defined. The significance of this for diagenesis studies is discussed and correlations with indices of preservation of collagen, DNA, crystallinity, chemical composition and stable isotope signals of these specimens of the Neuadd collection are outlined, but more detailed descriptions will be presented in forthcoming papers. [Copyright &y& Elsevier]

Abstract: Palaeogenetic data obtained from fossilizing or fossil bones and teeth are of great importance to studies of vertebrate evolution, human biological and cultural evolution, plant and animal domestication and reconstructions of palaeoenvironment and palaeoecology. These studies are based on the retrieval of DNA preserved in fossilizing bones and teeth. DNA is present in fossils, if at all, in only very small amounts, which makes its amplification with PCR necessary for detailed sequence analysis. Erroneous nucleotides can be incorporated during in vitro amplification either because of post-mortem base damage of the original DNA template or simply because the fidelity of DNA polymerases is not absolute and can be decreased by suboptimal buffer conditions or possibly by compounds in the fossil extracts. These erroneously introduced nucleotides can be mistaken for authentic mutations of the ancient sequence compared to the closest extant sequence. Moreover, contamination by modern DNA, which is not chemically modified and therefore a better substrate for the Taq polymerase, can also lead to erroneous results. Here, we will present the procedures that we have developed in order to (i) ensure negligible mutagenicity of the PCR reaction, (ii) eliminate contamination by DNA molecules originating from previous PCR reactions and cloning procedures, (iii) prevent contamination with modern DNA of fossil bones and teeth during and after their excavation, and (iv) prevent degradation of ancient DNA after excavation. Finally, we will discuss our results on DNA preservation as a function of the taphonomy of the skeletal part that is analyzed and of the depositional context of preservation. [Copyright &y& Elsevier]

Despite the enormous potential of analyses of ancient DNA for phylogeographic studies of past populations, the impact these analyses, most of which are performed with fossil samples from natural history museum collections, has been limited to some extent by the inefficient recovery of ancient genetic material. Here we show that the standard storage conditions and/or treatments of fossil bones in these collections can be detrimental to DNA survival. Using a quantitative paleogenetic analysis of 247 herbivore fossil bones up to 50,000 years old and originating from 60 different archeological and paleontological contexts, we demonstrate that freshly excavated and nontreated unwashed bones contain six times more DNA and yield twice as many authentic DNA sequences as bones treated with standard procedures. This effect was even more pronounced with bones from one Neolithic site, where only freshly excavated bones yielded results. Finally, we compared the DNA content in the fossil bones of one animal, a ≈3,200-year-old aurochs, excavated in two separate seasons 57 years apart. Whereas the washed museum-stored fossil bones did not permit any DNA amplification, all recently excavated bones yielded authentic aurochs sequences. We established that during the 57 years when the aurochs bones were stored in a collection, at least as much amplifiable DNA was lost as during the previous 3,200 years of burial. This result calls for a revision of the postexcavation treatment of fossil bones to better preserve the genetic heritage of past life forms. [ABSTRACT FROM AUTHOR]

Northwestern Africa is today characterized by high geographical, climatic and ecological diversity; it is recognized as a hotspot of biodiversity and a major area for both human and faunal evolution. Studies of North African fossil microvertebrates have increased considerably in recent years, but they no longer just provide palaeontological descriptions of the species found in the assemblages. They also aim at better understanding the evolution of faunal communities in relation to Quaternary climate changes and at reconstructing the palaeoenvironmental background of prehistoric human occupations, in well-established taphonomic and chronological contexts. These studies are also increasingly adopting an integrative approach by combining archaeology, palaeontology, (palaeo)genetics, taphonomy, palaeoecology and systematics, and using new methods such as geometric morphometrics and isotopic analyses on both fossil and modern specimens. This paper aims to present a history of the studies on Quaternary terrestrial microvertebrates from northwestern Africa, and show how recent multidisciplinary studies have provided new perspectives and evidence on the respective influences of climate change and increasing human pressure on their evolution. • This paper brings an updated state-of-the-art on Quaternary North African microvertebrate studies. • We highlight the interest of combining data from different disciplines (integrative approach). • We especially explore the role of environmental and anthropogenic changes on the microvertebrate biodiversity in Morocco. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]