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1.	Bergström, Anders, et al. (author) Grey wolf genomic history reveals a dual ancestry of dogs 2022 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 607:7918, s. 313-320 Journal article (peer-reviewed)abstract The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
2.	Pečnerová, Patrícia, et al. (author) Population genomics of the muskox' resilience in the near absence of genetic variation 2024 In: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 33:2 Journal article (peer-reviewed)abstract Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.
3.	Seersholm, Frederik Valeur, et al. (author) Repeated plague infections across six generations of Neolithic Farmers 2024 In: Nature. - 0028-0836 .- 1476-4687. ; 632:8023, s. 114-121 Journal article (peer-reviewed)abstract In the period between 5,300 and 4,900 calibratedyears before present (cal. bp), populations across large parts of Europe underwent a period of demographic decline1,2. However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline3, others for the spread of an early form of plague4. Here we use population-scale ancient genomics to infer ancestry, social structure and pathogen infection in 108 Scandinavian Neolithic individuals from eight megalithic graves and a stone cist. We find that the Neolithic plague was widespread, detected in at least 17% of the sampled population and across large geographical distances. We demonstrate that the disease spread within the Neolithic community in three distinct infection events within a period of around 120 years. Variant graph-based pan-genomics shows that the Neolithic plague genomes retained ancestral genomic variation present in Yersinia pseudotuberculosis, including virulence factors associated with disease outcomes. In addition, we reconstruct four multigeneration pedigrees, the largest of which consists of 38 individuals spanning six generations, showing a patrilineal social organization. Lastly, we document direct genomic evidence for Neolithic female exogamy in a woman buried in a different megalithic tomb than her brothers. Taken together, our findings provide a detailed reconstruction of plague spread within a large patrilineal kinship group and identify multiple plague infections in a population dated to the beginning of the Neolithic decline.
4.	Altınışık, N. Ezgi, et al. (author) A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition 2022 In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:44 Journal article (peer-reviewed)abstract Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting Çayönü’s cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia’s cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.
5.	Atag, Gözde, et al. (author) Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages 2024 In: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 16:5 Journal article (peer-reviewed)abstract Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (N-e). Meanwhile, N-e and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term N-e, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.
6.	Bergfeldt, Nora, et al. (author) Identification of microbial pathogens in Neolithic Scandinavian humans 2024 In: Scientific Reports. - : NATURE PORTFOLIO. - 2045-2322. ; 14 Journal article (peer-reviewed)abstract With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.
7.	Blaschikoff, Ludmilla, et al. (author) A multidisciplinary study of Iberian Chalcolithic dogs 2022 In: Journal of Archaeological Science. - : Elsevier BV. - 2352-409X .- 2352-4103. ; 42 Journal article (peer-reviewed)abstract Domesticated dogs have been present in the Iberian Peninsula long before other domesticated species, back to the late Palaeolithic period. Their origin is still uncertain, but dogs were already well established during the Chalcolithic period (ca. 5000-4000 BP). This study employed a multidisciplinary approach comprising osteometric, radiographic and palaeogenomic analyses to characterize Chalcolithic Iberian Canis remains. Two Chalcolithic archaeological sites - Leceia, Oeiras, in Portugal, and El Caset ' on de la Era, Villalba de los Alcores, Valladolid, in Spain - were the main focus of this study. Osteometric and odontometric data from eleven other sites in Iberia were also included. Osteometric results show signs of phenotypic variability, likely the result of human-driven selective pressure. Dental radiographic and dental wear analyses allowed age at death estimation for four individuals (two juvenile and two adults). Three Chalcolithic Iberian dogs had their mitogenomes resequenced and the mitochondrial DNA analysis allowed to assign each individual to two of the major known haplogroups - A and C. Molecular sex infered by the chromosomeX/chromosome1 coverage ratio allowed to identify one female and two males. This study unveils some aspects of the Iberian Chalcolithic dogs: these dogs already exhibited various morphotypes whose profiles might be associated to the performance of certain tasks, as well as mitogenomes of two distinct lineages that help tracking the evolutionary paths of Iberian dogs.
8.	Chylenski, Maciej, et al. (author) Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age 2023 In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14 Journal article (peer-reviewed)abstract The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups. By analysing 91 Bronze Age genomes from East-Central Europe, the authors discovered that Middle Bronze Age populations were formed by an admixture event involving hunter-gatherers and that the social structure of resulting population was primarily patrilocal.
9.	Ericson, Per G P, 1956-, et al. (author) A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture 2022 In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 5:1 Journal article (peer-reviewed)abstract The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution.
10.	Götherström, Anders, 1969- (author) Acquired or inherited prestige? : molecular studies of family structures and local horses in Central Svealand during the Early Medieval period 2001 Doctoral thesis (other academic/artistic)abstract This is a study of the role of inheritance among the élite in Early Medieval central Svealand and the possibility to study it by molecular genetic methods. The study is a part of the research project Svealand in the Vendel and Viking periods (SIV). The study rests on classical as well as a new type of source material.Hypotheses are built on the results from a research tradition resting on more than a century of data gathering and analysis. The boat cemeteries in central Svealand hold a central position in this work. Several models have been constructed over the years to explain the appearance of these special and often rich remains. In this work they are discussed in terms of inherited or acquired status, the status that gave the individual the right to such burial. Since these sites have often been discussed in terms of control of northern trade routs, a discussion on ethnicity is inevitable. A distinction between genetic and cultural belonging is made.To test the models, built upon classic archaeological research, molecular genetics is applied to the material. A variety of such molecular systems exist for studies on modern material. Some of them have been selected and heavily modified to be applicable to archaeological material. Systems based on maternally as well as paternally and Mendelian inheritances are used. One of the goals in the methodological work has been to establish which of the methods that may reveal relevant information if applied to archaeological material.Bone material from humans as well as from horses was used to test the models. The human material was mainly gathered from excavations of boat cemeteries in central Svealand, but also from an early Christian site in southern Norrland. The horse material was from a wider geographical area, including central Svealand as well as the Baltic islands Öland and Gotland, and sites in Estonia. The material was mainly from contexts of a high social status, but also, to a much lesser extent, from more common society levels. The results reveal an archaeological potential in the genetic studies of ancient bones. Genetic relations were identified on several cemeteries (Badelunda, Alsike and Björned), but also individuals with no genetic relation to the others were identified (Alsike and Björned). Horses of different sexes and with different maternal origin were also identified.The results indicate that the kin was an important feature in the upper class during the Early Medieval period in central Svealand. The kin probably had a higher importance than gender belonging. The studied horses reveal a similar situation where features other than the sex seems to have been important. However, the family seems to have been an open unit where it was possible for outsiders to enter and become a part. Thus, inheritance was important, but it was possible for an individual with deviating background to reach a desired position in other ways. There was no absolute connection between social status and genetics. As for one of the main status object, the horse, a dynamic and continuous distribution is suggested, either based on trade or on a gift system.
11.	Kirdok, Emrah, et al. (author) Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals 2024 In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13:1 Journal article (peer-reviewed)abstract Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.
12.	Koptekin, Dilek, et al. (author) Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean 2023 In: Current Biology. - : Cell Press. - 0960-9822 .- 1879-0445. ; 33:1, s. 41-57 Journal article (peer-reviewed)abstract We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of com-plex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holo-cene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holo-cene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model."Interestingly, this increase in in-ter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.
13.	Krzewińska, Maja, 1978-, et al. (author) Related in Death? Further Insights on the Curious Case of Bishop Peder Winstrup and His Grandchild's Burial 2024 In: Heritage. - 2571-9408. ; 7:2, s. 576-584 Journal article (peer-reviewed)abstract In 2021, we published the results of genomic analyses carried out on the famous bishop of Lund, Peder Winstrup, and the mummified remains of a 5–6-month-old fetus discovered in the same burial. We concluded that the two individuals were second-degree relatives and explored the genealogy of Peder Winstrup to further understand the possible relation between them. Through this analysis, we found that the boy was most probably Winstrup’s grandson and that the two were equally likely related either through Winstrup’s son, Peder, or his daughter, Anna Maria von Böhnen. To further resolve the specific kinship relation, we generated more genomic data from both Winstrup and the boy and implemented more recently published analytical tools in detailed Y chromosome- and X chromosome-based kinship analyses to distinguish between the competing hypotheses regarding maternal and paternal relatedness. We found that the individuals’ Y chromosome lineages belonged to different sub-lineages and that the X-chromosomal kinship coefficient calculated between the two individuals were elevated, suggesting a grandparent–grandchild relation through a female, i.e., Anna Maria von Böhnen. Finally, we also performed metagenomic analyses, which did not identify any pathogens that could be unambiguously associated with the fatalities.
14.	Maróti, Zoltán, et al. (author) The genetic origin of Huns, Avars, and conquering Hungarians 2022 In: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 32:13, s. 2858-2870, 2858–2870.e1–e7 Journal article (peer-reviewed)abstract Huns, Avars, and conquering Hungarians were migration-period nomadic tribal confederations that arrived in three successive waves in the Carpathian Basin between the 5th and 9th centuries. Based on the historical data, each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations have been debated. Recently, hundreds of ancient genomes were analyzed from Central Asia, Mongolia, and China, from which we aimed to identify putative source populations for the above-mentioned groups. In this study, we have sequenced 9 Hun, 143 Avar, and 113 Hungarian conquest period samples and identified three core populations, representing immigrants from each period with no recent European ancestry. Our results reveal that this “immigrant core” of both Huns and Avars likely originated in present day Mongolia, and their origin can be traced back to Xiongnus (Asian Huns), as suggested by several historians. On the other hand, the “immigrant core” of the conquering Hungarians derived from an earlier admixture of Mansis, early Sarmatians, and descendants of late Xiongnus. We have also shown that a common “proto-Ugric” gene pool appeared in the Bronze Age from the admixture of Mezhovskaya and Nganasan people, supporting genetic and linguistic data. In addition, we detected shared Hun-related ancestry in numerous Avar and Hungarian conquest period genetic outliers, indicating a genetic link between these successive nomadic groups. Aside from the immigrant core groups, we identified that the majority of the individuals from each period were local residents harboring “native European” ancestry.
15.	Mattila, Tiina M., et al. (author) Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe 2023 In: Communications Biology. - : Springer Nature. - 2399-3642. ; 6:1 Journal article (peer-reviewed)abstract The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River. Genome-wide sequencing of 56 ancient hunter-gatherer and early farmer individuals from Stone Age Central and Eastern Europe reveals striking population continuity in the east in contrast to central Europe that displays extensive admixture.
16.	Morez, Adeline, et al. (author) Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK 2023 In: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 19:4 Journal article (peer-reviewed)abstract There are longstanding questions about the origins and ancestry of the Picts of early medieval Scotland (ca. 300–900 CE), prompted in part by exotic medieval origin myths, their enigmatic symbols and inscriptions, and the meagre textual evidence. The Picts, first mentioned in the late 3rd century CE resisted the Romans and went on to form a powerful kingdom that ruled over a large territory in northern Britain. In the 9th and 10th centuries Gaelic language, culture and identity became dominant, transforming the Pictish realm into Alba, the precursor to the medieval kingdom of Scotland. To date, no comprehensive analysis of Pictish genomes has been published, and questions about their biological relationships to other cultural groups living in Britain remain unanswered. Here we present two high-quality Pictish genomes (2.4 and 16.5X coverage) from central and northern Scotland dated from the 5th-7th century which we impute and co-analyse with >8,300 previously published ancient and modern genomes. Using allele frequency and haplotype-based approaches, we can firmly place the genomes within the Iron Age gene pool in Britain and demonstrate regional biological affinity. We also demonstrate the presence of population structure within Pictish groups, with Orcadian Picts being genetically distinct from their mainland contemporaries. When investigating Identity-By-Descent (IBD) with present-day genomes, we observe broad affinities between the mainland Pictish genomes and the present-day people living in western Scotland, Wales, Northern Ireland and Northumbria, but less with the rest of England, the Orkney islands and eastern Scotland—where the political centres of Pictland were located. The pre-Viking Age Orcadian Picts evidence a high degree of IBD sharing across modern Scotland, Wales, Northern Ireland, and the Orkney islands, demonstrating substantial genetic continuity in Orkney for the last ~2,000 years. Analysis of mitochondrial DNA diversity at the Pictish cemetery of Lundin Links (n = 7) reveals absence of direct common female ancestors, with implications for broader social organisation. Overall, our study provides novel insights into the genetic affinities and population structure of the Picts and direct relationships between ancient and present-day groups of the UK.
17.	Naumann, Elise, et al. (author) Slaves as burial gifts in Viking Age Norway? : Evidence from stable isotope and Ancient DNA analyses 2013 In: Journal of Archaeological Science. - : Elsevier BV. - 0305-4403 .- 1095-9238. ; 41, s. 533-540 Journal article (peer-reviewed)abstract Ten Viking Age individuals from the northern Norwegian site at Flakstad were analysed for δ13C, δ15N and ancient mitochondrial DNA fragments. The material derives from both single and multiple burials with individuals treated in different ways. The genetic analyses show that the individuals buried together were unlikely to be maternally related, and stable isotope analyses suggest different strata of society. It is, therefore, suggested that slaves may have been offered as grave gifts at Flakstad. A comparison with the remaining population from single graves shows that the presumed slaves had a diet similar to that of the common population, whereas the high status individuals in multiple graves had a diet different from both slaves and the common population. The results provide an insight into the subsistence of different social groups in a Viking Age society, exposing unexpected patterns of living conditions and food distribution.
18.	Niebylski, Jakub M., et al. (author) Unveiling Hunnic legacy : Decoding elite presence in Poland through a unique child’s burial with modified cranium 2024 In: Journal of Archaeological Science. - 2352-409X .- 2352-4103. ; 56 Journal article (peer-reviewed)abstract This article presents a double burial from Czulice indicating elements of the Hunnic culture. Individual I, aged 7–9, and Individual II, aged 8–9 with a skull deformation, were both genetically identified as boys. Individual II, who exhibited genetic affinity to present day Asian populations, was equipped with gold and silver items. In contrast, Individual I displayed European ancestry. The application of strontium isotope analysis shed light on the origins of the individuals. Individual I was non-local, while Individual II was identified as a local, but also falling within the range commonly associated with the Pannonian Plain. Stable isotope analysis suggested a diet consisting of inland resources. Through radiocarbon dating, this burial was determined to date back to the years 395–418 CE, making it the earliest grave of its kind discovered in Poland. The analyses have provided new insights into the nature of the relationship between the Huns and the local inhabitants.
19.	Oleszczak, L., et al. (author) The food culture of the Iron Age nomadic elite from the 'Valley of the Kings' in Tuva : radiocarbon dating, stable carbon and nitrogen analysis of the Chinge Tey barrows (Turan-Uyuk Basin, Russia) 2023 In: Journal of Archaeological Science. - 2352-409X .- 2352-4103. ; 51 Journal article (peer-reviewed)abstract Subsistence strategies of Eurasian pastoral populations have been broadly studied in the archaeological literature. The 'Valley of the Kings' in Tuva, Russia, has captivated archaeologists with its remarkable collection of large burial mounds, containing lavishly equipped tombs of nomadic kings, warlords, and aristocracy. These barrows bear witness to the ancestral connections between the deceased leaders, highlighting the alliances among prehistoric nomads in Central Asia. In this research, we present comprehensive radiocarbon dating and 813C/815N isotopic data from the Chinge Tey barrows, which represent the burial sites of 12 high-ranking individuals. The chronological alignment of both Chinge Tey monuments with the Arzhan 1 and Arzhan 2 reference frames sheds light on their historical context. This study delves into intricate aspects of ecological adaptability, pastoral food practices, social hierarchies, and nomadic mortuary rituals. Analysis of carbon and nitrogen stable isotopes indicates potential connections between the barrows in the 'Valley of the Kings' and diverse nomadic cultures, suggesting that dietary habits among neighboring populations may have exhibited significant variation.
20.	Pečnerová, Patrícia, 1990-, et al. (author) Mammuthus sp. (Early and Middle Pleistocene Mammoths) 2021 In: Trends in Genetics. - : Cell Press. - 0168-9525 .- 1362-4555. ; 37:7, s. 682-683 Journal article (other academic/artistic)
21.	Pérez-Ramallo, Patxi, et al. (author) Multi-isotopic study of the earliest mediaeval inhabitants of Santiago de Compostela (Galicia, Spain) 2022 In: Archaeological and Anthropological Sciences. - : Springer Science and Business Media LLC. - 1866-9557 .- 1866-9565. ; 14:11 Journal article (peer-reviewed)abstract Santiago de Compostela is, together with Rome and Jerusalem, one of the three main pilgrimage and religious centres for Catholicism. The belief that the remains of St James the Great, one of the twelve apostles of Jesus Christ, is buried there has stimulated, since their reported discovery in the 9th century AD, a significant flow of people from across the European continent and beyond. Little is known about the practical experiences of people living within the city during its rise to prominence, however. Here, for the first time, we combine multi-isotope analysis (δ13C, δ15N, δ18Oap, δ13Cap and 87Sr/86Sr) and radiocarbon dating (14C) of human remains discovered at the crypt of the Cathedral of Santiago to directly study changes in diet and mobility during the first three centuries of Santiago’s emergence as an urban centre (9th–12th centuries AD). Together with assessment of the existing archaeological data, our radiocarbon chronology broadly confirms historical tradition regarding the first occupation of the site. Isotopic analyses reveal that the foundation of the religious site attracted migrants from the wider region of the northwest corner of the Iberian Peninsula, and possibly from further afield. Stable isotope analysis of collagen, together with information on tomb typology and location, indicates that the inhabitants of the city experienced increasing socioeconomic diversity as it became wealthier as the hub of a wide network of pilgrimage. Our research represents the potential of multidisciplinary analyses to reveal insights into the origins and impacts of the emergence of early pilgrimage centres on the diets and status of communities within Christian mediaeval Europe and beyond.
22.	Pérez-Ramallo, Patxi, et al. (author) To the field of stars : Stable isotope analysis of medieval pilgrims and populations along the Camino de Santiago in Navarre and Aragon, Spain 2023 In: Journal of Archaeological Science. - : Elsevier BV. - 2352-409X .- 2352-4103. ; 48 Journal article (peer-reviewed)abstract The Camino de Santiago emerged in the first half of the 9th century CE following the reported discovery of the remains of the Apostle St James by the bishop of Iria-Flavia, Teodomiro. Since then, hundreds of thousands of pilgrims have walked from different parts of the Iberian Peninsula, Europe, and further afield to Santiago de Compostela's Cathedral. This route was particularly important to the populations of Navarre and Aragon, two kingdoms in northern Spain that rose to prominence with the resurgence of Christianity from the 11th century onwards. Here, we present multidisciplinary analysis of medieval individuals buried in Navarre and Aragon at a time when the Camino de Santiago was reaching its peak of popularity (11th-15th centuries CE). We use stable isotope analysis (δ15N, δ13C, δ18O, and δ13Cap) and radiocarbon dating to investigate a total of 82 human individuals together with 42 fauna samples from 8 different archaeological sites located in the northeast of the Iberian Peninsula. Twenty of these individuals were buried with a scallop shell, a symbol of a pilgrim who had completed the Camino de Santiago. Our data corroborate the use of the pilgrim's shell since at least the 11th century CE. Moreover, our results suggest that the pilgrimage was mainly an urban phenomenon for populations from the northern Iberian Peninsula, conducted equally by women and men, although with indications that female pilgrims may have had greater access to animal protein than their male counterparts. Our results represent the largest isotopic dataset of medieval individuals linked to the Camino de Santiago, allowing us to further investigate the origins and diets of potential pilgrims and, more generally, other sampled portions of northeastern Iberian society.
23.	Pochon, Zoé, et al. (author) aMeta : an accurate and memory-efficient ancient metagenomic profiling workflow 2023 In: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24 Journal article (peer-reviewed)abstract Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.
24.	Rissech, Carme, et al. (author) Skeletal remains of human perinatal individuals from the fortified Iberian Period settlement of Ca n’Oliver (6th century to 50 years BCE) 2023 In: Archaeological and Anthropological Sciences. - 1866-9557 .- 1866-9565. ; 15:10 Journal article (peer-reviewed)abstract Burial customs in the Iberian Period (Iron Age II) included cremation. Only perinatal and newborn infants were buried directly beneath floor settlement. These infants represent the very few unburned human remains recovered from Iberian sites. The interpretation of these infant burials is in debate, focusing on whether they are unnatural or natural deaths. Our aim is to infer mortality patterns and developmental conditions of these individuals, in order to respond if infanticide was present in these assemblages. A large perinatal human skeletal sample from the Ca n’Oliver site (sixth century to 50 years BCE) from the Iberian Period of the northeast of the Iberian Peninsula was analysed, combining osteological methods together with tooth histology and aDNA analysis. Combining osteological and odontological estimates indicated ages between 22 and 42 weeks of gestation for 47 out of a total of 48 individuals. The remaining individual died at about 6 months after birth. Tooth height and enamel histology indicated in 9 out of a subgroup of 13 individuals a low probability of live birth. The remaining 4 individuals possibly survived birth for less than 2 months. According to morphological and molecular results, the sex ratio of this sample is approximately 1:1 male to female. The mortality distribution is consistent with natural mortality. These perinatal deaths were probably spontaneous abortions and neonatal deaths, reflecting an endogenous mortality profile due to genetic and maternal influences. The present study will serve to broaden our knowledge on perinatal individuals of the Iberian Period.
25.	Rodríguez-Varela, Ricardo, et al. (author) The genetic history of Scandinavia from the Roman Iron Age to the present 2023 In: Cell. - : Elsevier. - 0092-8674 .- 1097-4172. ; 186:1, s. 32-46 Journal article (peer-reviewed)abstract We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.
26.	Sarmento, Cindy, et al. (author) A Study on Burrows-Wheeler Aligner’s Performance Optimization for Ancient DNA Mapping 2022 In: Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021). - Cham : Springer. - 9783030862572 - 9783030862589 ; , s. 105-114 Book chapter (peer-reviewed)abstract The high levels of degradation characteristic of ancient DNA molecules severely hinder the recovery of endogenous DNA fragments and the discovery of genetic variation, limiting downstream population analyses. Optimization of read mapping strategies for ancient DNA is therefore essential to maximize the information we are able to recover from archaeological specimens. In this paper we assess Burrows-Wheeler Aligner (BWA) effectiveness for mapping of ancient DNA sequence data, comparing different sets of parameters and their effect on the number of endogenous sequences mapped and variants called. We also consider different filtering options for SNP calling, which include minimum values for depth of coverage and base quality in addition to mapping quality. Considering our results, as well as those of previous studies, we conclude that BWA-MEM is a good alternative to the current standard BWA-backtrack strategy for ancient DNA studies, especially when the computational resources are limited and time is a constraint.
27.	Yaka, Reyhan, 1988-, et al. (author) Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples 2024 In: BioTechniques. - 0736-6205 .- 1940-9818. ; 76:5, s. 221-228 Journal article (peer-reviewed)abstract Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.

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