Ancient DNA

Abstract : this study, which first aim was to demonstrate correspondences between Gaulish and Slavic languages, between which I found 500 common words, allowed me also to establish, on the basis of genetical, archaeological and religious data, that those correspondences were linked with ancient migrations which spread the Dravidian civilisation of the Indus Valley to Iran, Mesopotamia, Anatolia, the Caucasus, the North of the Black Sea, Danubian and Balkan Europe, Gaul and Iberia, where Neolithic farmers brought about 30% of the French genetic profile and contributed to the development of the megalithic civilisation which began in 5.000 BC. This also explains the linguistic correspondences I established between Gaulish and Dravidian languages – 250 common words from the 500 words I studied, as well as similarities I found in the organisation of the Society and the religion, which lead various researchers to suggest, on the basis of the diffusion of the very ancient gene H2-P96 from India to Western Europe, that the first Europeans and the proto-Dravidians had a common origin.
Extrait : cette étude, dont l’objectif initial était de démontrer les correspondances entre le gaulois et les langues slaves, entre lesquelles j’ai trouvé 500 mots communs, m’a en outre permis de démontrer, sur la base de données génétiques, archéologiques et religieuses, que ces correspondances étaient liées à des migrations anciennes qui ont apporté environ 30% du profil génétique français et  diffusé la civilisation dravidienne de la vallée de l’Indus vers l’Iran, la Mésopotamie, l’Anatolie, le Caucase, le Nord de la Mer Noire, l’Europe danubienne et balkanique, la Gaule et l’Ibérie, où les agriculteurs néolithiques ont contribué à former la civilisation mégalithique qui s’est développée à partir de -5.000. Cela explique aussi les correspondances linguistiques que j’ai établies entre le gaulois et les langues dravidiennes - 250 mots communs sur les 500 mots étudiés, et les similitudes que j’ai constatées dans l’organisation de la société et la religion, qui amènent certains chercheurs à suggérer, sur la base de la diffusion du gène très ancien H2-P96 de l’Inde à l’Europe de l’Ouest, que les premiers Européens et les proto-Dravidiens avaient une origine commune.

Pigs (Sus scrofa) have played an important cultural role in Hawaii since Polynesians first introduced them in approximately AD 1200. Additional varieties of pigs were introduced following Captain Cook's arrival in Hawaii in 1778 and it has been suggested that the current pig population may descend primarily, or even exclusively, from European pigs. Although populations of feral pigs today are an important source of recreational hunting on all of the major islands, they also negatively impact native plants and animals. As a result, understanding the origins of these feral pig populations has significant ramifications for discussions concerning conservation management, identity and cultural continuity on the islands. Here, we analysed a neutral mitochondrial marker and a functional nuclear coat colour marker in 57 feral Hawaiian pigs. Through the identification of a new mutation in the MC1R gene that results in black coloration, we demonstrate that Hawaiian feral pigs are mostly t...

This study, which first aim was to demonstrate correspondences between Gaulish and Slavic languages, between which I found 500 common words, allowed me also to establish, on the basis of genetical, archaeological and religious data, that those correspondences were linked with ancient migrations which spread the Dravidian civilisation of the Indus Valley to Iran, Mesopotamia, Anatolia, the Caucasus, the North of the Black Sea, Danuban and Balkan Europe, Gaul and Iberia, where Neolithic farmers contributed to the development of the megalithic civilisation which began in 5.000 BC. This also explains the linguistic correspondences I established between Gaulish and Dravidian languages – 250 common words from the 500 words I studied, as well as similarities I found in the organisation of the Society and the religion, which lead various researchers to suggest, on the basis of the diffusion of the very ancient gene H2-P96 from India to Western Europe, that the first Europeans and the proto-Dravidians had a common origin.

Cette étude, dont l’objectif initial était de démontrer les correspondances entre le gaulois et les langues slaves, entre lesquelles j’ai trouvé 500 mots communs, m’a en outre permis de démontrer, sur la base de données génétiques, archéologiques et religieuses, que ces correspondances étaient liées à des migrations anciennes qui ont diffusé la civilisation dravidienne de la vallée de l’Indus vers l’Iran, la Mésopotamie, l’Anatolie, le Caucase, le Nord de la Mer Noire, l’Europe danubienne et balkanique, la Gaule et l’Ibérie, où les agriculteurs néolithiques ont contribué à former la civilisation mégalithique qui s’est développée à partir de -5.000. Cela explique aussi les correspondances linguistiques que j’ai établies entre le gaulois et les langues dravidiennes - 250 mots communs sur les 500 mots étudiés, et les similitudes que j’ai constatées dans l’organisation de la société et la religion, qui amènent certains chercheurs à suggérer, sur la base de la diffusion du gène très ancien H2-P96 de l’Inde à l’Europe de l’Ouest, que les premiers Européens et les proto-Dravidiens avaient une origine commune.

Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.

Despite toxoplasmosis being a common infection among human and other warm-blooded animals worldwide, there are no findings about Toxoplasma gondii evolutionary forms in ancient populations. The molecular techniques used for amplification of genetic material have allowed recovery of ancient DNA (aDNA) from parasites contained in mummified tissues. The application of polymerase chain reaction (PCR) to paleoparasitological toxoplasmosis research becomes a promising option, since it might allow diagnosis, acquisition of paleoepidemiological data, access to toxoplasmosis information related origin, evolution, and distribution among the ancient populations. Furthermore, it makes possible the analysis of parasite aDNA aiming at phylogenetic studies. To standardize and evaluate PCR applicability to toxoplasmosis paleodiagnostic, an experimental mummification protocol was tested using desiccated tissues from mice infected with the ME49 strain cysts, the chronic infection group (CIG), or infe...

Статья посвящена проблеме локализации прародины индоевропейцев. Это одна из самых сложных проблем археологии и лингвистики, которые в последние годы были дополнены палеогенетическими исследованиями. Начиная с неолита и до конца эпохи бронзы основные культурные импульсы, формировавшие археологические культуры Евразии,  распространялись с Ближнего Востока. Данные о миграциях с севера в регионы, где фиксируются южные индоевропейские языки (анатолийские и индоиранские), очень ограничены или отсутствуют. Реконструируемые на основе археологических данных миграции в целом соответствуют направлениям распространения генов с Ближнего Востока в Европу, в евразийскую степь и на восток, в Иран и Индию. При этом наблюдаются повторные миграции в регионы, где уже ранее появились индоевропейцы, возвратные миграции, ареалы вторичных контактов, что осложняет процедуру лингвистических реконструкций. Судя по этим данным, прародина индоевропейцев находилась на Армянском нагорье, но в дальнейшем могли формироваться ареалы вторичных прародин, где осуществлялось развитие или сближение отдельных индоевропейских диалектов.

Describes and comments on the results of a very important new Irish aDNA study into 2 Mesolithic and 42 Neolithic individuals in Ireland, whose results include the discovery that one individual buried in the enormous passage tomb at Newgrange resulted from an incestuous relationship.

The history of human populations in Africa is complex and includes various demographic events that influenced patterns of genetic variation across the continent. Through genetic studies of modern-day, and most recently, ancient African genetic variation, it became evident that deep African history is captured by the relationships among hunter-gatherers. Furthermore, it was shown that agriculture had a large influence on the distribution of current-day Africans. These later population movements changed the demographic face of the continent and descendants of farming groups today form the majority populations across Africa. Ancient DNA methods are continually evolving, and we see evidence of this in how research has advanced in the last decade. With the increased availability of full genomic data from diverse sets of modern-day and prehistoric Africans we now have more power to infer human demography. Future ancient DNA research promises to reveal more detailed stories of human prehistory in Africa.

The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

In a 2009 article published in the journal Human Genetics entitled: “Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish Priesthood” the authors found J1-P58 to be the most prevalent haplogroup among both Ashkenazic and Sephardic Cohanim. The question for our time of advanced yDNA testing is which sub-branch of J1-P58 would most accurately define the Aharonic yDNA haplogroup.Current evidence indicates that J1-Z18271 was the Cohanic haplogroup at Aharon's time. There are eight known sub-branches of Z18271, not all of which necessarily descend from  Aharon. From the current evidence, persons who discover they are within the J1-S17446 sub-branch, or descend from an ancestor within the J1-S17446 sub-tree, are themselves direct descendants of Aharon the Priest, and presumably distant nephews and nieces of Moses the Lawgiver and Miryam the Prophet.

TheAldaietacemetery(6th–7thcenturyAD,BasqueCountry) provides an excellent opportunity for analysing the relationships between biology and culture. Culturally it presents material features whose origins lie in the Northern Pyrenean Frankish kingdom, while genetically it reveals greater affinity to the present-day populations of the northern Iberian Peninsula. This raises the question of the degree of influence exerted by the large European kingdoms that emerged after the fall of the Roman Empire over the populations located on the fringes of their expansion. An analysis of the genetic constitution, both patrilineal (Y-chromosome) and matrilineal (mitochondrial DNA), of the individuals buried in the cemetery,togetherwithdemographicandculturaldata,points to a stratified or hierarchical society in which certain lineages were linked to family groupsof highersocialand/oreconomic status. This higher status, which seems to have been transmitted through family members, may have been attained by individuals who were involved in military activities with the Frankish army. It may be suggested that the major European kingdoms of Late Antiquity had not only a cultural influence but also some influence on the biosocial behaviour of the populations located on their peripheries.

Zandra Fagernäs, Maite I. García  Collado, Jessica Hendy, Courtney A. Hofman, Camilla Speller, Irina Velsko, Christina Warinner. 2020. A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus. Journal of Archaeological Science 118: 105135 (https://doi.org/10.1016/j.jas.2020.105135)

Archaeological materials are a finite resource, and efforts should be made to minimize destructive analyses. This can be achieved by using protocols combining extraction of several types of biomolecules or microparticles, which decreases the material needed for analyses while maximizing the information yield. Archaeological dental calculus is a source of several different types of biomolecules, as well as microfossils, and can tell us about the human host, microbiome, diet, and even occupational activities. Here, we present a unified protocol allowing for simultaneous extraction of DNA and proteins from a single sample of archaeological dental calculus. We evaluate the protocol on dental calculus from six individuals from a range of time periods and estimated preservation states, and compare it against previously published DNA-only and protein-only protocols. We find that most aspects of downstream analyses are unaltered by the unified protocol, although minor shifts in the recovered proteome can be detected, such as a slight loss of hydrophilic proteins. Total protein recovery depends on both the amount of starting material and choice of extraction protocol, whereas total DNA recovery is significantly reduced using the unified protocol (mean 43%). Nevertheless, total DNA recovery from dental calculus is generally very high, and we found no differences in DNA fragment characteristics or taxonomic profile between the protocols. In conclusion, the unified protocol allows for simultaneous extraction of two complementary lines of biomolecular evidence from archaeological dental calculus without compromising downstream results, thereby minimizing the need for destructive analysis of this finite resource.

Objective We assessed DNA conservation using a range of archaeological skeletal samples from Sudan (Missiminia in Upper Nubia, 350 B.C.E to 1400 C.E) from the unfavorable conditions of the Saharan milieu and humidity of the Nile valley by tracking maternal lineage on the ‘X-Group’ (Ballaneans).

Method We were able to extract, amplify, and sequence mt-DNA HVS-I (Sanger sequencing method) from 11 petrous bone samples, eight for the X-Group set and three for the reference set (one Christian, one Late Meroitic, and one Meroitic).

Results It was possible to find the haplogroups (L1b, L2, L3, H2, N, T1a, X and W) and to carry out comparative data analysis in relation to haplogroup data cited in the literature. This investigation into the maternal lineage of X-Group (350 to 500 C.E.) origins allowed us to validate the efficiency of petrous bone sampling from ancient human remains from the Nile-Saharan milieu and established that the Ballaneans experienced an in-situ development with more admixture from the Levant region and North Africa.

Conclusions Our study used mt-DNA (HVS-I) to look for the biological origins of the X-Group from Upper-Nubia and demonstrated the feasibility of ancient DNA research on skeletons from the Nile-Saharan environment. The use of Next Sequencing Generation (NGS) should optimize and improve the detection of shorter DNA strands and their sequencing in complete genomes from ancient skeletal remains (petrous bones) from hot and humid environments.

Objective: To evaluate, via a multidisciplinary approach, a distinctive paleopathological condition, believed to be fibrous dysplasia, found on a 19th/20th century skeleton from Certosa Monumental Cemetery, Bologna, Italy.
Materials: A skeletonized cranium and mandible recovered from an ossuary in 2014.
Methods: Pathological alterations were analysed by radiological examination, dental macrowear, histopathological and genetic analyses.
Result: The skeleton is believed to be an adult male. Differential diagnoses include Paget's disease, McCune-Albright syndrome, osteochondroma and osteosarcoma. The radiographic findings, along with the solitary nature of the lesions, are strong evidence for the diagnosis of fibrous dysplasia (FD). Genetic analysis further revealed a frequency of ˜1% of mutant alleles with the R201C substitution, one of the post-zygotic activating mutation frequently associated with FD.
Conclusions: The multi-analytical method employed suggests a diagnosis of monostotic form of FD. The diagnostic design incorporates multiple lines of evidence, including macroscopic, histopathological, and genetic analyses.
Significance: Through the use of a multi-analytic approach, robust diagnoses can be offered. This case serves as one of the oldest examples of FD from an historical context. The genetic mutation detected, associated with FD, has not been previously reported in historical/ancient samples.