Ancient DNA Research

This paper provides a critical review of computational paleohistory and outlines a new strategic framework for the field. It is being made available as a preprint to invite feedback, establish precedence, and foster interdisciplinary collaboration. Abstract The study of human prehistory is split between three powerful but conflicting paradigms: the abstract, backward-in-time Coalescent; the realistic but computationally costly Forward-Time Simulations; and the continuous, macro-scale Stochastic Partial Differential Equations (SPDEs)[cite: 214]. This paper provides a critical review of these theoretical pillars [cite: 214], the inferential tools used to connect them to data (from MCMC to SBI) [cite: 319], and the empirical data they seek to explain (aDNA, archaeology, climate)[cite: 470]. We use the Neanderthal extinction enigma as a case study to demonstrate that the field's goal should *not* be a single, monolithic "Unified Engine," which creates methodological monocultures[cite: 549, 577, 584]. Instead, we propose a strategic shift toward an "**interoperable ecosystem**"[cite: 592]. The true unification is not the simulation model but the **Bayesian probabilistic framework** that connects them[cite: 595, 596]. We conclude by providing a complete architectural recommendation for this meta-framework, built on Simulation-Based Inference (SBI) [cite: 627], modern PPLs (NumPyro) [cite: 630], and a JAX-based SPDE backend[cite: 608], creating a transparent and powerful workbench for comparing competing historical hypotheses.

This paper outlines a novel conceptual framework for integrating disparate data sources in the study of human evolution. It is being made available as a preprint to invite feedback, establish precedence, and foster interdisciplinary collaboration.

This comprehensive report integrates fossil records, genetic mutation epochs, ice-core climate data, catastrophic geological events, early human census records, and the first religious structures and writings. It aims to reveal patterns of Earth's cyclical resets-epochs where climate, tectonics, or celestial factors may have influenced the evolution or mutation of DNA, forcing human and pre-human species to adapt.

When, as well as who, may have brought in the new elitism and compulsory authority to the Americas. "For the Tlingit (branch of the Na-Dené language family), hereditary slavery was practiced extensively until it was outlawed by the United States. Wealth and economic power are important indicators of rank. Scientists suggest that the main ancestor of the Ainu and of the Tlingit can be traced back to Paleolithic groups in Southern Siberia."

• Dené-Yeniseian language, Old Copper Complex, and Pre-Columbian Mound Builders?

One of the major challenges of molecular biology in anthropological analysis is the identification via DNA typing of bone or teeth samples that can be collected from archaeological site in order to investigate kinship relationships. Due to the difficulties of isolating and analysing DNA from such samples, several efforts have been made to solve these problems, but less work has been conducted to identify the proper type of bone samples for the DNA analysis. Therefore, following the promising results obtained from the DNA analysis of petrous bones by different groups of researchers, for the first time, here we investigated the possibility of using petrous bones as skeletal elements useful for short tandem repeat (STR) typing via capillary electrophoresis technique in ancient bone samples. In order to compare the results from petrous bone, femur and tooth samples, a total of 39 skeletal elements were collected from 13 different individuals excavated from Italian archaeological sites, ...

This paper presents the Accidental Emergence Theory (AET), integrating insights from meditation and the sermons of sages in India with both modern and ancient scientific knowledge. The theory examines the origin of life, the emergence of intelligence, and the cycles of creation and dissolution in the universe. It recognizes that religious beliefs and the concept of an invisible God or universal power primarily serve human psychological needs, providing reassurance that individuals exist under the care of a higher force that governs cosmic cycles of destruction, reward, and renewal. AET considers past, present, and future lives as part of this universal continuity, acknowledging that all beings experience consequences and evolution across multiple lifetimes.

Ancient Y-DNA results enable researchers to objectively verify or disprove connections between ancient and prehistoric populations, or between them and contemporary populations. Based on these connections we can set up strong hypotheses about their ethnic identity and spoken language. Ancient DNA data from Iron Age Transdanubia are in line with the Celtic conquest, while the southern regions of the Great Hungarian Plain suggest the mixing of Sarmatians with populations similar to present-day peoples from the Southern Balkans. We identify three Northeast Asian tribes from the Hunnic and Avar periods, two of which survived among contemporary Székely Hungarians but the Rourouan elite became extinct. The Middle and Late Avar period shows the cohabitation of various ethnic groups with a numerical dominance of Thracian-like genes. The settlement and cemetery organizations are patriarchal. The already very diverse Magyar conquerors from multiple genetic backgrounds settled into this mix. Therefore, we might explain the elite dominance of the Hungarian language – originally only a numerical minority – with a lingua franca effect that may have been a necessity for the centralization of political power and the foundation of the unitary Kingdom of Hungary.

Az archeogenetikai Y-kromoszóma adatok alkalmasak annak feltérképezésére, hogy a történelmi és prehistorikus korokban objektíven mérhető kapcsolatot (vagy annak hiányát) tárjunk fel az egykori népességek között, illetve a ma élő népességekkel, amelyből az etnikai identitásukra és általuk beszélt nyelvekre is megalapozott feltételezésekkel élhetünk. A vaskori Dunántúl genetikai adatai megerősítik a kelta hódítást, míg az Alföld déli részén a mai Dél-Balkáni népességek szarmatákkal való keveredését feltételezhetjük. A hun és avar északkelet-ázsiai elitek három azonosított nemzetségéből kettő megtalálható a mai székelységben, azonban a zsuanzsuan elitcsoport kihalt. A középső és késő avar korszak a korábbi elemek egymás mellett élését mutatja egy számszerű trák jellegű genetikai dominancia mellett. A település-és temetőszervezet alapvetően patriarchális. Az eleve nagyon változatos, többféle genetikai eredetű honfoglaló csoportok erre a sokszínűségre telepedtek rá, így a magyar nyelv számszerű kisebbségből nemzetformálóvá válását lingua franca egységesítő hatással magyarázhatjuk, amit a politikai hatalom centralizációja és az államalapítás kívánt meg.

Over the past decade, the ability to recover whole genomes from ancient remains (aDNA) has emerged as a powerful tool for understanding the human past. From a strictly biological perspective, the sequencing of ancient genomes has resolved the dispute over our evolutionary relationship with Neanderthals, revealed the extent of gene flow within and between modern and archaic humans, shed light on genetic and health consequences, and uncovered genomic changes in recent human evolution ( 1 ). More generally, these insights have demonstrated that our population history is marked by complex, actively combining and diverging channels, replete with demographic bottlenecks and bursts ( 2 ), proving that moving and mating have been more the rule than the exception. For all this, aDNA research has rightly been described as revolutionary, even a 'celebrity science' ( 3 ).

Московский государственный областной университет 105005, г. Москва, ул. Радио, д. 10А, Российская Федерация Аннотация. В настоящее время по проблеме происхождения праславян и локализации их прародины существуют несколько концепций. Согласно одной из них, праславяне как этническая и языковая общность выделились из среды поздних индоевропейцев Подунавья и инкорпорировались в древнеевропейскую общность на севере Центральной Европы в виде лужицкой культуры, смешавшись там с постшнуровыми культурами комаровского тшинецкого культурного круга, и вытеснив тшинецкую на территорию Среднего Поднепровья в XII-XI вв. до н. э. Вторая волна переселения праславян в союзе с готами шла с Вислы в Поднепровье во II в. до н.э. Использована методика соотнесения данных археологии и лингвистики. Вывод статьи заключается в том, что согласно новым исследованиям прародина славян локализуется на Среднем Днепре.

The article tells the story of the remains of the last Russian Tsar Nicholas II and his family, who were killed in Ekaterinburg in 1918, discovered in 1979, found again in 1991, solemnly buried in 1998, and canonized as saints by the Russian Orthodox Church in 2000. Thoroughly researched in the cause of official criminal investigation and identified with genetic tests in several labs in Russia and abroad, the royal remains have not been recognized by the Church. The failure to reach a consensus on the veracity of the remains of the Romanovs occurred in parallel with the inability to decide what to do with the mummified body of Soviet founder Vladimir Lenin, a contemporary of Nicholas II who has been kept in a mausoleum in the Red Square since the 1920s. Though, after 1991, voices have been raised for removing his body from this symbolic center of the country, no consensus has been reached so far as to where to move it and why. Revisiting Verdery's famous work, the present article argues that such a movement necessitates a political commitment to voicing new notions of belonging and citizenship. The liminal status of these two bodies proves that the contemporary state in Russia is a continuation of both the Soviet and imperial state programs, not a new political structure like other post-socialist countries. Based on the works by Kantorowicz and Cherniavsky, this research develops the concept of popular theopolitics and aims to examine how people's political and religious ontologies make use of the Tsar's image.

This paper provides a critical analysis of the attribution of ancient DNA (aDNA) samples published in studies on the genetics of Anatolia and the Hittite Kingdom (Lazaridis et al., Skourtanioti et al., Damgaard et al.). We show that almost all genetic samples labeled as "Hittite" actually originate from pre-Hittite (Hattian) or non-Indo-European (Hurrian) cultural contexts. Genetic studies rely on pit or stone burials that do not correspond to Hittite funerary practices. Hittite culture was characterized predominantly by cremation of the elite and burials in pithoi (clay jars) for commoners and children. Such pithoi occur in 10-20% of Hittite cemeteries and represent a rare source of potentially preserved DNA, yet they are not included in modern genetic samples. This methodological discrepancy leads to systematic errors in attribution. The analyzed pit burials (Alacahöyük, İkiztepe, Titrish Höyük, Ovaören, Hattusa) belong to Hattian or Hurrian layers preceding the formation of the Hittite state (17th-12th centuries BCE). As a result, conclusions about a "minimal steppe component" or "Caucasian origin" of the Hittites are unreliable, since the samples do not represent the Hittites themselves but earlier populations of Anatolia. Accurate reconstruction of the Hittite genetic profile requires re-evaluation of archaeological contexts and targeted analysis of pithos burials, which could reflect the composition of the Hittite Kingdom population, including possible Indo-European patrilines of the elite.

Dog domestication was multifaceted Dogs were the first domesticated animal, likely originating from human-associated wolves, but their origin remains unclear. Bergstrom et al. sequenced 27 ancient dog genomes from multiple locations near to and corresponding in time to comparable human ancient DNA sites (see the Perspective by Pavlidis and Somel). By analyzing these genomes, along with other ancient and modern dog genomes, the authors found that dogs likely arose once from a now-extinct wolf population. They also found that at least five different dog populations ∼10,000 years before the present show replacement in Europe at later dates. Furthermore, some dog population genetics are similar to those of humans, whereas others differ, inferring a complex ancestral history for humanity's best friend. Science , this issue p. 557 ; see also p. 522

Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focused on the maternal genetic makeup of the Neolithic (∼ 5500-3000 BCE), Chalcolithic (∼ 3000-2200 BCE) and Early Bronze Age (∼ 2200-1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we...

The northern and southern peripheries of ancient Mesoamerica are poorly understood. There has been speculation over whether borderland cultures such as Greater Nicoya and Casas Grandes represent Mesoamerican outposts in the Isthmo-Colombian area and the Greater Southwest, respectively. Poor ancient DNA preservation in these regions challenged previous attempts to resolve these questions using conventional genetic techniques. We apply advanced in-solution mitogenome capture and high-throughput sequencing to fourteen dental samples obtained from the Greater Nicoya sites of Jícaro and La Cascabel in northwest Costa Rica (n = 9; A.D. 800-1250) and the Casas Grandes sites of Paquimé and Convento in northwest Mexico (n = 5; A.D. 1200-1450). Full mitogenome reconstruction was successful for three individuals from Jícaro and five individuals from Paquimé and Convento. The three Jícaro individuals belong to haplogroup B2d, a haplogroup found today only among Central American Chibchan-speaker...

UPDATED VERSION (30 October 2025) 
As you board this time machine...buckle your seatbelt!  You’ll be starting your journey when life on Earth began and then rocket through the eons into modern times.  You’ll be seeing the sights on this trip through the lens of one specific Y-chromosome genetic lineage.  For that line’s descendants, the entire thrilling adventure is their story.  But anyone with Jewish heritage—or any Middle-Eastern origin—will find much of this trip relevant.

The genetic lineage in focus is marked by the J2a-FGC4992 Y-chromosome DNA mutation, found in over 400 testers worldwide.  Although a handful of these men are adoptees, converts or descend from paternal “bulls who jumped the fence,” all the rest are men of known Jewish paternal heritage.  More than that, in over 95% of the cases, the tester or his recent ancestors were fully aware of their direct paternal lineage having a cohanim tradition, i.e. of descent from an ancient Israelite priest. 

The core historical narrative here is based on science—albeit with humorous nods to Jewish culture.  Underpinning the story are the time periods and locations suggested by genetic results, genealogies, established historic events and known population movements.

Highlights d Two now-extinct horse lineages lived in Iberia and Siberia some 5,000 years ago d Iberian and Siberian horses contributed limited ancestry to modern domesticates d Oriental horses have had a strong genetic influence within the last millennium d Modern breeding practices were accompanied by a significant drop in genetic diversity Authors

This rebuttal examines and refutes the methodological and interpretive claims advanced in "Evaluating Population Genetics and Ancient DNA Interpretation in Africa." The author of that paper, Andrew Adeitun-King, asserts that ascertainment bias, limited African sampling, and Western institutional influence have systematically distorted interpretations of African and North African population history in favor of Eurasian origins. This analysis finds that while concerns over under-sampling and media misrepresentation are valid, the paper commits fundamental errors in genetics, population modeling, and historical inference. The rebuttal employs a forensic framework parallel to prior analytic standards in population genetics and ancient DNA studies. It demonstrates that alleged Eurocentric distortions are unsupported, that cited studies such as Schuenemann et al. (2017), Llorente et al. (2015), Fregel et al. (2018), and Morez et al. (2025) maintain methodological rigor and internal consistency, and that the empirical record overwhelmingly confirms North African population continuity with partial Near Eastern admixture, not replacement or ideological fabrication.

Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000-3,000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed in the historical period onward (3,000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia, France). We found that most regions show remarkable inter-individual heterogeneity. Around 8% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring the geographic map. We ...

Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focused on the maternal genetic makeup of the Neolithic (∼ 5500-3000 BCE), Chalcolithic (∼ 3000-2200 BCE) and Early Bronze Age (∼ 2200-1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we...

This article explores alternative ways of conceptualizing kinship in prehistoric contexts beyond the confines of genetic reductionism. While ancient DNA research has revitalized interest in the archaeology of kinship, it often privileges patrilineal or matrilineal models and risks obscuring forms of relatedness not grounded in biological ties. Drawing on comparative anthropological models and archaeological case studies, the paper highlights the complexity of kinship as manifested in practices of adoption, fosterage, commensality, co-residence, and non-biological affiliation within (non)nuclear households. By integrating socio-cultural, economic, and material dimensions, it demonstrates the diverse methodological and theoretical approaches necessary to move beyond descent-centered reconstructions. The discussion advocates for an interdisciplinary framework that challenges reductionist assumptions and opens new avenues for understanding relatedness in the deep past. Finally, the article emphasizes the village as a unit of analysis within a multi-scalar approach. It presents future directions and archaeological correlates of adoption, child circulation, and fosterage derived from archaeological, genetic, and ethnographic evidence.

This paper evaluates the landmark population-genomic study “Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India” (Bose et al., 2021) and its implications for the Indigenous Aryan (Out-of-India) perspective. Using a novel computational framework (COGG), the study quantitatively demonstrates that linguistic affiliation and social endogamy—not geography—are the primary drivers of genetic differentiation in the Indian subcontinent. Analysis of 891 individuals from 90 ethnolinguistic groups reveals deep demographic continuity across regions, with no evidence for large-scale Bronze Age population replacements expected under the Aryan Migration Theory. Instead, the genomic record indicates millennia of internal admixture and cultural synthesis, particularly between Indo-European and Dravidian speakers, consistent with an indigenous civilizational evolution from Harappan to Vedic contexts. Bidirectional genetic drift patterns extending toward Central Asia and East Asia further suggest outward diffusion rather than unilateral influx. These findings reinforce archaeological continuities and linguistic convergences, supporting a model in which South Asia functions as a civilizational core, generating diversity internally while influencing neighboring regions. Bose et al. therefore provide a rigorous, data-driven foundation for re-evaluating colonial migration narratives and affirm the long-term biocultural continuity of the subcontinent.

Background: The evolutionary relationships of Felidae during their Early-Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths. Methods: Here, we sequenced a draft nuclear genome of Smilodon populator, dated to 13,182 ± 90 cal BP, making this the oldest palaeogenome from South America to date, a region known to be problematic for ancient DNA preservation. We analysed this genome, together with genomes from other extinct and extant cats to investigate their phylogenetic relationships. Results: We confirm a deep divergence (~20.65 Ma) within sabretoothed cats. Through the analysis of both simulated and empirical data, we show a lack of gene flow between Smilodon and contemporary Felidae.

The purpose of this study was to test the effectiveness of a DNA repair protocol in improving genetic testing in compromised samples, frequently encountered in Forensic Medicine. In order to stretch the experiment conditions to the limits, as far as quality of samples and DNA is concerned, we tried the repair protocol on ten ancient human teeth obtained from an equal number of skeletons from a burial site in Lerna, Middle Helladic Greece (2100-1700 BC). For these samples, sex was previously determined morphologically, serving as a reference to compare our molecular data with. The samples were analysed using the DNA amelogenin sex test assay prior and after DNA polymerase repair. For every individual, two molecular sex determinations were obtained by visualising PCR products on an agarose gel. DNA repair enabled genetic testing in these samples. Successful amplification of the amelogenin gene was obtained only from the repaired DNA in eight out of ten samples. Prior to the repair tre...

The paper represents an introductory section and two chapters with 6 proofing figures of Voynich Codex decryption done in these book fragments for the first time. I have used the Peruvian ethnographer Daniel Ruzzo`s principle of the solar light tangency and the watcher`s position intuited previously by the Romanian historian Nicolae Densushianu, in 1899. By this principle, the Romanian historian Ion Gheorghe has decoded the Proto-Latin language. I have extracted megalithic ideograms and charades from the 27 th page bottom-left section. By reading the charades from right to left and from left to right, mathematic model used by Ion Gheorghe, I have obtained megalithic Proto-European kings and queens with their associated customs and laws converging to the God Orpheus and to his brother, the poet Mousaios. The obtained information has resulted in a gnostic adamic poem.

Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ 2 =1022.00, p<<0.0005), and CSNB, testing 43 horses (χ 2 =43, p<<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.

This paper explores the current narratives of migration for the start and spread of the Neolithic with a particular focus on the role that the new ancient DNA data have provided. While the genetic data are important and instructive, here it is argued that archaeologists should also consider other strands of evidence. More nuanced appreciations of migration as a long-term process can be created by exploring modern mobility studies alongside considerations of continued mobility throughout the Neolithic in Europe. We can also re-interpret the material evidence itself in the light of these approaches to help trace multiple possible links and migrations from multiple different origin points. This involves the investigation of complex, but connected, practices, such as monument construction and deposition across wider areas of northern Europe than are currently normally investigated. Such an approach will enable us to address long-term processes of movement, migration and interaction and ...

All derived equations and simulations are openly reproducible using parameters listed in the appendices. Acknowledgment: The author acknowledges the guidance of the Unified Resonant Field and the structural inspiration derived from empirical resonance phenomena observed in nature and cognition.

Between 2001 and 2023, Michael Nicoll Yahgulanaas recovered many of the traditions of the Haida nation in the North-Western Pacific coast, creating hybrid narratives halfway between the textual and the pictorial. Yahgulanaas used different adaptations of the ancestral figure of the shaman to express the journey his people have gone through. Yahgulanaas’s shamans are usually elements of confrontation between the static world of the Haidas and the external world, being the last barrier of defense against the destruction of the natural and social context in which the stories are held and told. The objective of this article is to focus on Yahgulanaas’s so-called “Haida mangas” in order to explore how his shamans (his transcendent characters) can heal society and history through a deep connection with the spiritual world of the Haidas and through a deep understanding of how the supernatural is connected to them.

Reindeer herding emerged among the indigenous Sámi of Northern Fennoscandia between ca. 800 and 1500 CE. While the details of the reindeer domestication process are still actively debated, it has been hypothesized that the transition to reindeer herding affected Sámi ritual practice, especially animal offerings given at various sacred sites. To explore this hypothesis, we analyzed DNA from reindeer bone samples dating to ca. 1200-1700 CE from Sámi offering sites located in present-day Northern Finland as well as from samples originating from ancient dwelling site in Southern Finland and Kola Peninsula, Russia. The results show that haplotypes related to wild Finnish forest reindeer (Rangifer tarandus fennicus) began to be replaced by haplotypes common in modern domesticated reindeer in the faunal assemblages from offering sites starting between 1400 and 1600 CE. The results suggest that, although the role of reindeer herding in the economy of the Sámi communities varied greatly, the transition to reindeer herding may have affected ritual practices, testifying to a shared way of reciprocating with the land and animals.

Near Eastern Neolithic farmers introduced several species of domestic plants and animals as they dispersed into Europe. Dogs were the only domestic species present in both Europe and the Near East prior to the Neolithic. Here, we assessed whether early Near Eastern dogs possessed a unique mitochondrial lineage that differentiated them from Mesolithic European populations. We then analysed mitochondrial DNA sequences from 99 ancient European and Near Eastern dogs spanning the Upper Palaeolithic to the Bronze Age to assess if incoming farmers brought Near Eastern dogs with them, or instead primarily adopted indigenous European dogs after they arrived. Our results show that European pre-Neolithic dogs all possessed the mitochondrial haplogroup C, and that the Neolithic and Post-Neolithic dogs associated with farmers from Southeastern Europe mainly possessed haplogroup D. Thus, the appearance of haplogroup D most probably resulted from the dissemination of dogs from the Near East into E...

The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from survivi...

Dog domestication was multifaceted Dogs were the first domesticated animal, likely originating from human-associated wolves, but their origin remains unclear. Bergstrom et al. sequenced 27 ancient dog genomes from multiple locations near to and corresponding in time to comparable human ancient DNA sites (see the Perspective by Pavlidis and Somel). By analyzing these genomes, along with other ancient and modern dog genomes, the authors found that dogs likely arose once from a now-extinct wolf population. They also found that at least five different dog populations ∼10,000 years before the present show replacement in Europe at later dates. Furthermore, some dog population genetics are similar to those of humans, whereas others differ, inferring a complex ancestral history for humanity&#39;s best friend. Science , this issue p. 557 ; see also p. 522

Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom’s northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.

The Casas Grandes region in northwest Chihuahua, Mexico, is ideally situated to explore the notion of contact between the US  Southwest/Northwest Mexico and Mesoamerica, as it lies geographically in a region where cultural traditions were combined in unique aways. In order to explain these dynamics, past researchers have suggested that the primary catalyst for the flourishing Casas Grandes population in the thirteenth century A.D. was caused by migrants from Mesoamerica or from larger populations to the north. We analyzed mitochondrial genetic data from individuals interred at sites that date to earlier (A.D. 700–1200) and later (A.D. 1200–1450) time periods, which allowed us to examine changes in gene pools over time and to test these migration hypotheses.
Comparing the full mitogenomes from 114 individuals, we show that low levels of migration occurred diachronically, although they still may have contributed to hybridized cultural practices. These data counter the long-standing assumption that widescale population replacement was the cause for the rise of Paquimé, the center of the Casas Grandes world in the thirteenth-century A.D.

Haplogroup H dominates present-day Western European mitochondrial DNA variability (440%), yet was less common (B19%) among Early Neolithic farmers (B5450 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 (B5450 BC) and Bronze Age (B2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (B4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (B2800 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 estimates for human mitochondria.

Les langues australo-pacifiques comme les langues papoues pourraient être la branche la plus précoce de la phase finale de la langue originelle Proto-Sapiens du fait des migrations précoces de l'Homo sapiens dans ces parties reculées du Monde, couvrant l'Australie et la Papouasie Nouvelle Guinée modernes, dont les langues eurasiennes, dont le Gaulois, pourraient être issues.

Les langues australo-pacifiques comme les langues papoues pourraient être la branche la plus précoce de la phase finale de la langue originelle Proto-Sapiens du fait des migrations précoces de l'Homo sapiens dans ces parties reculées du Monde, couvrant l'Australie et la Papouasie Nouvelle Guinée modernes, dont les langues eurasiennes, dont le Gaulois, pourraient être issues.

Les langues australo-pacifiques comme les langues papoues pourraient être la branche la plus précoce de la phase finale de la langue originelle Proto-Sapiens du fait des migrations précoces de l'Homo sapiens dans ces parties reculées du Monde, couvrant l'Australie et la Papouasie Nouvelle Guinée modernes, dont les langues eurasiennes, dont le Gaulois, pourraient être issues.

Les langues australo-pacifiques comme les langues papoues pourraient être la branche la plus précoce de la phase finale de la langue originelle Proto-Sapiens du fait des migrations précoces de l'Homo sapiens dans ces parties reculées du Monde, couvrant l'Australie et la Papouasie Nouvelle Guinée modernes, dont les langues eurasiennes, dont le Gaulois, pourraient être issues.

Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200–1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900–1200 BCE. British Neolithic farmers were...

To understand the impact of human practices on Mid-Holocene vegetation in northwestern France, more pollen records and multi-proxy studies with accurate chronologies located near excavated archaeological sites are needed. In northwestern Normandy, the Caen Plain is particularly suitable for gaining further insight into the impact of early human activity on the landscape, due to the high density of recognized and excavated archaeological sites dating back to Neolithic times. Therefore, in this area, we developed a high temporal resolution approach using multiple palaeobiological proxies (pollen, non-pollen palynomorphs (NPPs), charcoal analysis, and sedimentary ancient DNA (sedaDNA)), along with sedimentological proxies to analyze a new sequence from the Vey valley, located close to the excavated Neolithic site of Cairon, and which could be compared to the archaeobotanical and archaeozoological data from archaeological excavations. Our specific objective was to propose a reconstruction of the landscape changes under human influence at a local scale, in order to gain a precise understanding of the processes of anthropization in the Caen Plain at the end of the Mesolithic and during the Neolithic. The impact of human activity during the Mesolithic and Early Neolithic appears to have been limited. Nevertheless, the end of the Late Mesolithic (5900-5200 BCE; 7850-7150 cal. BP) showed the first increase in local fire frequency. These fires were responsible for temporary clearings of the forest along the wetland, and sedaDNA indicated that wild boar were present in the wetland. Most notably, the Cairon site offered the first opportunity to precisely determine the impact of changing land use in an area that had been inhabited since the Middle Neolithic (4400-3475 BCE; 6350-5425 cal. BP). The combined use of sedaDNA, NPPs, and charcoal analysis demonstrated the importance of pastoral practices and fires in opening up environments and transforming alluvial wetlands during this period.

Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom’s northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.

We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain ca. 4000 BCE, a millennium after they appear in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remains unclear. We assembled genome-wide data from six Mesolithic and 67 Neolithic individuals found in Britain, dating from 8500-2500 BCE. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically-structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by ca. 6000 BCE.

Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focused on the maternal genetic makeup of the Neolithic (∼ 5500-3000 BCE), Chalcolithic (∼ 3000-2200 BCE) and Early Bronze Age (∼ 2200-1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we...

Late Antiquity Dalmatia was a time and place of political unrest in the Roman Empire that influenced the lives of the people living in that region. The Late Antique burial site of Hvar -Radošević, spanning the 3 rd to 5 th centuries, is located on the Croatian Dalmatian island of Hvar. Given the time frame and its location on a busy marine trade route, study of this burial site offers us a glimpse into the lives of the Late Antique population living on this island. It comprises 33 individuals, with 17 buried within a confined grave tomb, and the remaining individuals buried in separate locations in the tomb's proximity. Our objective was to provide new perspectives on the lives of people on the island during those times by studying ancestry, population structure, possible differences within the buried population, dietary habits, and general health. Analysis of the ancestral origins of the individuals buried at Hvar -Radošević revealed a diverse population reflective of the era's genetic variability. The identification of genetic outliers suggests affiliations with distinct regions of the Roman Empire, possibly linked to trade routes associated with the Late Antique port in ancient Hvar. Stable isotope ratio analysis (δ¹³C and δ¹⁵N) indicated a diet mainly consisting of C3 plants, with minimal consumption of marine foods. High childhood mortality rates, physiological stress markers, and dental diseases suggest a low quality of life in the population. Assessment of kinship and dietary patterns revealed no discernible distinctions between individuals buried within the tomb and those buried outside, indicative of an absence of differential burial practices based on social status and familial ties.