Archaeogenetics

This paper provides a broad overview of the current state of archaeogenetic research in Arabia. We summarise recent studies of mitochondrial DNA and lactase persistence allele -13915*G in order to reconstruct the population histories of modern Arabs. These data, in turn, enable us to assess different scenarios for the peopling of the Pen- insula over the course of the Late Pleistocene and Early Holocene. The evidence sup- ports the posited existence of Arabian refugia, although it is inconclusive which (e.g. Persian Gulf basin, Yemeni highlands and/or Red Sea basin) was/were responsible for housing ancestral populations during the Last Glacial Maximum. Synthesising genetic and archaeological data sets, we conclude that a substantial portion of the present South Arabian gene pool derives from a deeply rooted population that underwent sig- nificant internal growth within Arabia some 12,000 years ago. At the same time, we interpret the disappearance of Nejd Leptolithic archaeological sites in southern Arabia around 8000 years ago to represent the termination of a significant component of the Pleistocene gene pool.

E x p l o r i n g C e l t i c O r i g i n s is the fruit of collaborative work by
researchers in archaeology, historical linguistics, and archaeogenetics
over the past ten years. T his team works towards the goal of a better
understanding of the background in the Bronze Age and Beaker P eriod
of the people who emerge as Celts and speakers of Celtic languages
documented in the I ron Age and later times. L ed by S ir Barry Cunliffe
and John Koch, the contributors present multidisciplinary chapters
in a lively user-friendly style, aimed at accessibility for workers in
the other fields, as well as general readers. T he collection stands as
a pause to reflect on ways forward at the moment of intellectual
history when the genome-wide sequencing of ancient DNA (a.k.a.
‘the archaeogenetic revolution’) has suddenly changed everything in
the study of later European prehistory. How do we deal with what
appears to be an irreversible breach in the barrier between science
and the humanities? Exploring Celtic O rigins includes colour maps
and illustrations and annotated Further R eading for all chapters.

An international conference bringing together geneticists, historians and archaeologists for an open exchange about the possibilities, limitations and risks of the emerging new discipline "Genetic History" (the use of DNA as a historical source). Convened by Joerg Feuchter and Stefanie Samida (Archaeology/Public History, Potsdam) and funded by Fritz Thyssen Foundation. For more information please click on the link to the program or go to the conference website (www.genetic-history.com)

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much ...

H. Meller/K. W. Alt (Hrsg.), Anthropologie, Isotopie und DNA – biografische Annäherung an namenlose vorgeschichtliche Skelette? 2. Mitteldeutscher Archäologentag vom 08. bis 10. Oktober 2009 in Halle (Saale). Tagungen Landesmus. Vorgesch. Halle 3 (Halle [Saale] 2010).

This paper describes archaeogenetic data mining results based on a novel mitochondrial and y-chromosome haplogroup distance metric. The analysis shows that the Minoan genes are composed of two originally distinct groups. One group was the descendant of Mesolithic European hunter-gatherers, while the other group was from Neolithic farmer populations from Anatolia. These groups intermingled in the Danube Basin and the western Black Sea littoral area for thousands of years as indicated by the presence of mutations that appear first in those areas. A group from that population migrated southward to Crete to form the Minoan culture.

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 ten 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. Update of 23 January 2021: Since the original publication of this paper, a multi-branch descending tree connecting Aharon the Priest to modern-day descendants has been re-constructed. A summary of these new findings entitled 'AharonSupplementalData_23Jan2021" is attached to the original paper. The earlier phylogeography of J1-Z18271 is covered in the companion paper: https://www.academia.edu/44710820/ (NB: Footnote 18 to 'Tracing the yDNA Lineage of Aharon..." was updated with new findings on 08 November  2021)

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this 'real-time' genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current

2 new individuals in Khvalynsk II:
1 Male MtDNA H2a1/ YDNA M R1b-L754; Khvalynsk II (Grave 13; I6403 / skel. SVP35)
1 Male MtDNA H2a1/ YDNA M R1b-L754; Khvalynsk II (Grave 29; I6402) from David W. Anthony, A. A. Khokhlov, S. A. Agapov, D. S. Agapov, R. Schulting. I. Olalde,
D. Reich (2022) The Eneolithic cemetery at Khvalynsk on the Volga
River, Praehistorische Zeitschrift 2022; aop. De Gruyter. https://doi.org/10.1515/pz-2022-2023

According to recent researches bearers of H2a1 MtDNA suddenly appeared between Araxes, Don and Volga Rivers during Chalcolithic and spread in Eurasia until Late Bronze Age during what is commonly called Indo-European Migrations. We demonstrate in this paper that this sudden and fast expansion is in fact the last step of a prior and longer ethnogenesis's process for the H2a MtDNA bearers rooted to Levantine Pastoralism for Milk that expanded before and after Late Glacial Maximum (LGM). It also demonstrates that women were a key element in the Neolithic Revolution and proposes the theory according to which their strong political position was linked to a solid oral transmission of knowledge that has been weakened by the new 'way of like' that shortened their life's expectancy due to the convergence of an increased birth rate and the apparition of new diseases (Yersinia Pestis/ Tuberculosis). Then the H2a MtDNA weak demic diffusion of Agriculture/ Pastoralism was accompanied by a strong cultural diffusion that also blurred cultural epicentres. However, this balance reversed in Lesser Caucasus during Chalcolithic, particularly in Hal (Vorotan River, Lesser Caucasus) where favourable political and geoclimatic conditions promoted this 'women's caste' specialized in domestication and dairying products (Cheese) to became major building block of the Neolithic and Chalcolithic expansions in Europe. In the aftermath of a first migration towards Balkans/ Calabria, a second expansion of H2a1 MtDNA towards the Eurasian steppe (Bronze Age) was the result of a successful political adaptation to rapid and radical political changes in Transcaucasia due to the emergence of a nomadic military/ merchant's caste specialized in equitation and warfare. In other words, both Neolithic and Chalcolithic expansions diffused the scarce H2a MtDNA and the omnipresent H2a1 MtDNA lineages who enriched a single common cultural background that reveals the whole history of populations since the Pre-Pottery Neolithic to Eneolithic.

Queste pagine nascono per provare a dare delle risposte sia a chi le ha scritte sia a chi si accinge a leggerle. Il titolo è solo un punto di partenza: provare a parlare di Lupatia, cioè di un antico luogo, oggi probabilmente corrispondente a Santeramo in Colle (Bari), del quale è riportato, in testi antichi, solo il nome e nulla più, non può essere se non la chiave per aprire, attraverso mezzi diversi da quelli tradizionali, i veli della storia.
Qui non troverete né verità assolute né certezze, ma solo domande e moltissimi dubbi, perché questi devono essere connaturati a chi esegue indagini con l’onestà d’intelletto e l’umiltà dello spirito necessarie a rivoltare quelle zolle che hanno ormai, da migliaia di anni, ricoperto i residui ricordi e reso omogenei i paesaggi in una melassa indistinta
di luoghi comuni astorici e antistorici.
Scienza quindi, non credenze o miti-storia, ma cifre, datazioni, fatti derivanti non da antichi testi ma da indagini scientifiche. Come quelle che definiscono le cronologie assolute o come quelle che ricostruiscono la demoscopia e l’economia antica in base alle condizioni paleoclimatiche, ai ritrovamenti paleobiologici o archeometallurgici.
Nel presente e maggiormente nel futuro, quello che è realmente accaduto in antico si allontana dai polverosi testi e si avvicina a quanto si viene a scoprire nei diversi e più moderni laboratori, svelando verità inattese sul nostro passato.

The start time of Homo sapiens is still controversial between 150 thousand and 2 million years ago. A new paradigm is requisite. If modern humans first emerged in Africa, why is the origin of anatomically modern humans statistically (design matrix) in the Levant? If modern behavior originated in Africa, why are the oldest known shell beads and the earliest known intentional burials in the Levant? Also, if Neandertals evolved from pre-Neandertals at least 250 ka (thousand years) ago, why is the most recent common mtDNA ancestor between 84.6 and 138.5 ka ago? Similarly, why is the DNA sequence divergence between the Vindija and Mezmaiskaya Neandertals about 140 ka ago? The anatomical, genetic, archaeological, bioanthropological data are best compatible with the new paradigm that pre-150 ka Homo was in reality a distinct genus, not “true human”, they went extinct and H. sapiens macroevolutionary appeared in the Levant circa 150 ka ago with new characteristics such as a dual-opposite genetic potential (both modern and archaic), early weaning, adolescent growth spurt, and also the genetic potentials of complex syntactic language, behavioral modernity and true chin.

Keywords: anatomically modern humans, Neandertals, Denisovans, Homo floresiensis, complex language, behavioral modernity

CELTIC FROM THE WEST 3. The Celtic languages and groups called
Keltoi (i.e. ‘Celts’) emerge into our written records at the pre-Roman Iron Age. The impetus for this book is to explore from the perspectives of three disciplines—archaeology, genetics, and linguistics—the background in later European prehistory to these developments. There is a traditional scenario, according to which, Celtic speech and the associated group identity came in to being during the Early Iron Age in the north Alpine zone and then rapidly spread across central and western Europe. This idea of ‘Celtogenesis’ remains deeply entrenched in scholarly and
popular thought. But it has become increasingly difficult to reconcile with recent discoveries pointing towards origins in the deeper past. It should no longer be taken for granted that Atlantic Europe during the 2nd and 3rd millennia BC were pre-Celtic or even pre-Indo-European. The explorations in Celtic from the West 3 are drawn together in this spirit, continuing two earlier volumes in the influential series.

NB: Paper updated 21 May 2021 This paper looks closely at the ancient genetics of one small lineage within a sub-branch of a people sometimes known as Semitic, with implications for Near Eastern history. Applying a combination of tools: yDNA haplogrouping, ancientDNA, Primary Component Analysis, biblical genealogies, and archaeological finds, the result is a reconstruction of the lineage from the Epipaleolithic to the Early Iron Age. Some of the questions addressed include: 1) what is the deep genetic ancestry of the ‘antediluvian’ Near Eastern people, 2) where did the events reported in the Great Flood story occur, 3) where did Noah’s grandson Arphaxad live, 4) where did Abraham live before being instructed by G-d to migrate to Canaan, 5) what socio-political conditions surrounded Abraham’s migration, and 6) is there genetic evidence for the historicity of biblical genealogies involving Shem, Arphaxad, Abraham, Ishmael, and Aharon? Aharonic (Cohanim Modal Haplotype) aspects and implications of this yDNA lineage are the subject of a companion paper:https://www.academia.edu/43340967/

Formation of the Indo-European branches in the light of the Archaeogenetic Revolution
John T. Koch
University of Wales Centre for Advanced Welsh and Celtic Studies
Draft of paper read at the conference ‘Genes, Isotopes and Artefacts. How should we interpret the movement of people throughout Bronze Age Europe?’ Austrian Academy of Sciences, Vienna, 13–14 December 2018.

Introduction
Using the historical-comparative method, linguists can recover many details of prehistoric languages. With enough of the right kind of data, it is possible to reconstruct detailed lexicons and grammatical descriptions of unattested languages. Even so, it can be difficult to determine an absolute date, geographical location, or cultural context for some of the most fully reconstructed prehistoric languages. The common ancestor of the attested Indo-European languages is such a case, and the question of its homeland has been disputed since the 19th century, through the 20th, and into the 21st. In recent years, with the availability of ancient DNA data, the situation has suddenly improved, now adding to the evidence base genetic relationships between populations in the historical period speaking attested languages and prehistoric groups. 
This essay works from recently published archaeogenetic evidence, drawing attention to what it might imply for some longstanding issues in historical linguistics. Seven working hypotheses are presented concerning prehistoric languages in western Eurasia. These hypotheses aim to situate speech communities in time and space, and to identify archaeological cultures and genetic populations associated with them. Hypotheses 1–6 deal with particular nodes and splits on the tree model of the Indo-European macro-family, the seventh with the prehistoric ancestor of the non-Indo-European language Basque.

The Kushites lived in Africa and Eurasia. Kushites originated in Africa. Researchers have observed that many of the Caucasus hunter-gatherers (CHG) and early European farmers (EF) populations carried R1a and R1b clades, and cultivated millet, which was not cultivated in Central Asia and the Middle East until 1000s of years after it was cultivated at Nabta Playa in Africa, and in the Ukraine by CHG and EF populations. Interestingly, the CHG carried the R1b1, and R1b1a lineages. Some researchers claim that these clades are " distant relatives " of V88, and that V88 is the result of a back migration from Eurasia to Central Africa. The archaeological evidence, on the other hand, lacks any corroboration of a back migration from Eurasia. Instead, the archaeogenetic evidence indicates that Niger-Congo speaking Africans from North Africa and the Saharo-Sahel, called Kushites in the historical literature early settled Crete, Iberia and Anatolia, and that these Africans introduced R1b, the Bell Beaker and the agro-pastoral cultural traditions into Eurasia during the Neolithic.

Der Übergang von der aneignenden zur produzierenden Wirtschaft, oder vielleicht deutlicher vom Sammeln und Jagen zum Bodenbau, ist weltweit eine der bedeutendsten Umbruchsperioden in der Menschheitsgeschichte. Es ist ein wirtschaftlicher und gesellschaftlicher Quantensprung: in den meisten Fällen ist mit dem Anbau von Nahrungspflanzen und der Zucht von Haustieren auch Sesshaftigkeit verbunden. Dies, wie auch die nun stetiger und verlässlicher vorhandenen Nahrungsgrundlagen, führen oftmals zu rascher Bevölkerungszunahme. Jene macht wiederum neue politische Organisationsformen und soziale Strukturen notwendig, Hierarchien und Eliten bilden sich heraus: Die Gesellschaften teilen sich auf in mächtige und wohlhabende und eben weniger erfolgreiche Individuen bzw. Gruppen. [...]

Las pruebas genéticas recién publicadas en la Revista Sciencie confirman la hipótesis del equipo de la 'Revista Argárica' de que entre los fundadores del Argar, además de los ya más que esperados esteparios, hubo gente procedente de las antiguas tierras de Canaán, concretamente gente con linaje paterno típico de ancestrías afroasiático-semíticas.

Synopsis
This book is a study of the inherited vocabulary shared uniquely by Celtic, Germanic, and the other Indo-European languages of North and West Europe. The focus is on contact and common developments in the prehistoric period. Words showing the earmarks of loanwords datable to Roman times or the Middle Ages are excluded. Most of the remaining collection predates Grimm’s Law. This and further linguistic criteria are consistent with contexts before ~500 BC. The evidence and analysis here lead to the following explanatory hypothesis. Metal-poor Scandinavia’s sustained demand for resources led to a prolonged symbiosis with the Atlantic façade and Central Europe during the Bronze Age. Complementary advantages of the Pre-Germanic North included Baltic amber and societies favourably situated and organized to build seagoing vessels and recruit crews for long-distance maritime expeditions. An integral dimension of this long-term network was intense contact between the Indo-European dialects that became Celtic and those that became Germanic. The Celto-Germanic vocabulary—like the motifs shared by Iberian stelae and Scandinavian rock art—illuminates this interaction, opening a window onto the European Bronze Age. Much of the word stock can be analyzed as shared across still mutually intelligible dialects rather than borrowed between separate languages. In this respect, what is revealed resembles more the last gasp of Proto-Indo-European than a forerunner of the Celtic–Germanic confrontations of the post-Roman Migration Period and Viking Age.
 This 2020 edition puts into the public domain some first fruits of a cross-disciplinary research project that will continue until 2023.

https://www.wales.ac.uk/Resources/Documents/Centre/2020/Celto-Germanic2020.pdf

The field of Genetic Biblical Historicity is in its infancy, premised on a simple hypothesis holding that parts of the Bible may contain kernels of scientifically verifiable genealogy, but limited by the extensive sample size required to probe any body of big data. Recent work confirming the Cohanic yDNA lineage of J1-Z18271  has opened up the possibility of identifying other Levitic lines stemming from the same J1-Z18271, but there is today much confounding evidence of Levitic and Cohanic lines traditions stemming from  yDNA lineages which could not be related to that same founder. In this study I attempt to reconcile the divergent evidence into two working hypotheses.

This project examines methods for learning about prehistoric languages that have left no written records. It focuses on the origins and expansion of the Indo-European language family (the world’s largest by total speaking population, today including most languages between Iceland and India) and its associated speakers, who likely emerged from someplace in eastern Europe or western Asia during the Neolithic . There are two competing hypotheses regarding the origins of these languages and the so-called Indo-Europeans themselves: 1) that they arose via the expansion of agriculture out of Anatolia and into Europe, c. 5000 BC; and 2) that the languages spread through migrations of highly mobile pastoralists outward from the Black Sea steppes at the end of the Neolithic, c. 3000 BC. The latter is now generally favored. This project will explore the developing interface between archaeology, genetics, and linguistics in prehistoric resarch by taking the Proto-Indo-Europeans as a case study. It covers three main areas: (1) the background and historical context of Indo-European studies; (2) methodological interaction among archaeology, linguistics, and genetics; and (3) recent archaeological, genetic, and linguistic data as they pertain to the understanding the origins of the Indo-Europeans.

Wolfgang Haak , Iosif Lazaridis , Nick Patterson , Nadin Rohland , Swapan Mallick , Bastien Llamas , Guido Brandt , Susanne Nordenfelt , Eadaoin Harney , Kristin Stewardson , Qiaomei Fu , Alissa Mittnik , Eszter Bánffy , Christos Economou , Michael Francken , Susanne Friederich , Rafael Garrido Pena , Fredrik Hallgren , Valery Khartanovich , Aleksandr Khokhlov , Michael Kunst , Pavel Kuznetsov , Harald Meller , Oleg Mochalov , Vayacheslav Moiseyev , Nicole Nicklisch , Sandra L. Pichler , Roberto Risch , Manuel A. Rojo Guerra , Christina Roth , Anna Szécsényi-Nagy , Joachim Wahl , Matthias Meyer , Johannes Krause , Dorcas Brown , David Anthony , Alan Cooper , Kurt Werner Alt , David Reich

The Indo-European debate has been going on for a century and a half. Initially confined to linguistics, race-based anthropology and comparative mythology, it soon extended to archaeology, especially with the discovery of the Harappan civilization, and peripheral disciplines such as agriculture, archaeometallurgy or archaeoastronomy. The latest entrant in the field, archaeogenetics, is currently all but claiming that it has finally laid to rest the whole issue of a hypothetical migration of Indo-Aryan speakers to the Indian subcontinent in the second millennium BCE. This paper questions the finality of this claim by pointing to inherent limitations, methodological issues and occasional biases in current studies as well as in the interpretation of archaeological evidence.

John T. Koch*

Formation of the Indo-European Branches in the light of the Archaeogenetic Revolution

Philology and archaeology evolved in tandem for over a century in a general awareness that reconstructed proto-languages (such as Proto-Indo-European, Proto-Germanic, Proto-Celtic) and later prehistoric cultures inhabited the same world. In effect, the two disciplines were studying the same thing. However, mapping reconstructed linguistic evidence onto text-free archaeology presented a near insurmountable challenge. The widespread astonishment that greeted the decipherment of Linear B as Late Bronze Age Greek illustrates the unreliability of carefully argued circumstantial inferences, even at the protohistoric horizon. David Anthony’s The Horse, the Wheel, and Language (2007) impressed many readers, but I know of no prior adherents of the Anatolian hypothesis of Indo-European origins who changed views upon reading it.
By then, we knew that ancient DNA evidence was coming. What we had not expected is that it would reveal, not incremental changes of population, but changes so dramatic that they very probably came with a change of language. In particular, this was the case with massive gene flow from the Pontic–Caspian steppe in the 3rd millennium BC, which transformed the Siberian Altai and central, northern, and western Europe. In other words, this new data seemed to confirm, for at least some key elements, the steppe hypothesis that had been constructed and won adherents on the basis of completely non-genetic evidence, rather linguistic and archaeological.
There were also less dramatic negative discoveries. For example, Cassidy et al. 2016 shows that three Early Bronze Age men from Rathlin Island were very different genetically from Neolithic woman from near Giant’s Ring outside Belfast. But the men were much closer to the modern Irish. In other words, the shift at the Neolithic–Bronze Age Transition was much greater, and relatively little had happened since. The authors accordingly suggested that the Rathlin men spoke the Indo-European language that then evolved into Gaelic in situ.
We can anticipate that genome-wide samples of ancient Europeans will soon number many 10,000s, filling gaps in most parts between the expansion from the steppe and historical populations speaking attested pre-Roman languages. We shall soon see whether this new evidence (archaeogenetic and isotopic) provides a conclusive advance for mapping nodes of the Indo-European family tree onto prehistoric populations and archaeological cultures. The paper will attempt a snapshot, reviewing results of some recent archaeogenetic studies and what they might imply about languages in later prehistoric Europe. What gaps and uncertainties remain? And where might answers come from?       

*University of Wales, Centre for Advanced Welsh and Celtic Studies

The first historically documented pandemic caused by Yersinia pestis started as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although palaeogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 20 sites in Austria, Britain, Germany, France and Spain for Y. pestis DNA and reconstructed six new genomes. We present a novel methodological approach assessing SNPs in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis reveals the existence of previously undocumented Y. pestis diversity during the 6th-7th centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. ...

Thanks to a pluri-disciplinary approach using archaeogenetics, archaeology and linguistics, this paper proposes the Ishkhanasar Mountain and Aghitu to be the place of the mythic flood at the origin of the Noah’s history. It also proposes the hypothesis according to which the flood was followed by a Yersinia Pestis outbreak leading to the development of a new cultural entity focused on medicine.