Publications by authors named "Alexandra Buzhilova"

14 Publications

  • Page 1 of 1

Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes.

BMC Biol 2021 10 5;19(1):220. Epub 2021 Oct 5.

Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

Background: Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period.

Results: Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria.

Conclusions: Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12915-021-01120-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8493730PMC
October 2021

Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians.

Sci Adv 2021 Mar 26;7(13). Epub 2021 Mar 26.

Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/sciadv.abe4414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7997506PMC
March 2021

Diet and subsistence in Bronze Age pastoral communities from the southern Russian steppes and the North Caucasus.

PLoS One 2020 14;15(10):e0239861. Epub 2020 Oct 14.

Integrative Prehistory and Archaeological Science IPAS, Basel University, Basel, Switzerland.

The flanks of the Caucasus Mountains and the steppe landscape to their north offered highly productive grasslands for Bronze Age herders and their flocks of sheep, goat, and cattle. While the archaeological evidence points to a largely pastoral lifestyle, knowledge regarding the general composition of human diets and their variation across landscapes and during the different phases of the Bronze Age is still restricted. Human and animal skeletal remains from the burial mounds that dominate the archaeological landscape and their stable isotope compositions are major sources of dietary information. Here, we present stable carbon and nitrogen isotope data of bone collagen of 105 human and 50 animal individuals from the 5th millennium BC to the Sarmatian period, with a strong focus on the Bronze Age and its cultural units including Maykop, Yamnaya, Novotitorovskaya, North Caucasian, Catacomb, post-Catacomb and late Bronze Age groups. The samples comprise all inhumations with sufficient bone preservation from five burial mound sites and a flat grave cemetery as well as subsamples from three further sites. They represent the Caucasus Mountains in the south, the piedmont zone and Kuban steppe with humid steppe and forest vegetation to its north, and more arid regions in the Caspian steppe. The stable isotope compositions of the bone collagen of humans and animals varied across the study area and reflect regional diversity in environmental conditions and diets. The data agree with meat, milk, and/or dairy products from domesticated herbivores, especially from sheep and goats having contributed substantially to human diets, as it is common for a largely pastoral economy. This observation is also in correspondence with the faunal remains observed in the graves and offerings of animals in the mound shells. In addition, foodstuffs with elevated carbon and nitrogen isotope values, such as meat of unweaned animals, fish, or plants, also contributed to human diets, especially among communities living in the more arid landscapes. The regional distinction of the animal and human data with few outliers points to mobility radii that were largely concentrated within the environmental zones in which the respective sites are located. In general, dietary variation among the cultural entities as well as regarding age, sex and archaeologically indicated social status is only weakly reflected. There is, however, some indication for a dietary shift during the Early Bronze Age Maykop period.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0239861PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7556513PMC
November 2020

Population genomics of the Viking world.

Nature 2020 09 16;585(7825):390-396. Epub 2020 Sep 16.

NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway.

The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-020-2688-8DOI Listing
September 2020

Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age.

Science 2020 07;369(6502)

Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark.

Smallpox, one of the most devastating human diseases, killed between 300 million and 500 million people in the 20th century alone. We recovered viral sequences from 13 northern European individuals, including 11 dated to ~600-1050 CE, overlapping the Viking Age, and reconstructed near-complete variola virus genomes for four of them. The samples predate the earliest confirmed smallpox cases by ~1000 years, and the sequences reveal a now-extinct sister clade of the modern variola viruses that were in circulation before the eradication of smallpox. We date the most recent common ancestor of variola virus to ~1700 years ago. Distinct patterns of gene inactivation in the four near-complete sequences show that different evolutionary paths of genotypic host adaptation resulted in variola viruses that circulated widely among humans.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aaw8977DOI Listing
July 2020

Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia.

Cell 2020 06 20;181(6):1232-1245.e20. Epub 2020 May 20.

Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany. Electronic address:

Modern humans have inhabited the Lake Baikal region since the Upper Paleolithic, though the precise history of its peoples over this long time span is still largely unknown. Here, we report genome-wide data from 19 Upper Paleolithic to Early Bronze Age individuals from this Siberian region. An Upper Paleolithic genome shows a direct link with the First Americans by sharing the admixed ancestry that gave rise to all non-Arctic Native Americans. We also demonstrate the formation of Early Neolithic and Bronze Age Baikal populations as the result of prolonged admixture throughout the eighth to sixth millennium BP. Moreover, we detect genetic interactions with western Eurasian steppe populations and reconstruct Yersinia pestis genomes from two Early Bronze Age individuals without western Eurasian ancestry. Overall, our study demonstrates the most deeply divergent connection between Upper Paleolithic Siberians and the First Americans and reveals human and pathogen mobility across Eurasia during the Bronze Age.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2020.04.037DOI Listing
June 2020

Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions.

Nat Commun 2019 02 4;10(1):590. Epub 2019 Feb 4.

German Archaeological Institute, Department of Natural Sciences, Im Dol 2-6, D-14195, Berlin, Germany.

Archaeogenetic studies have described the formation of Eurasian 'steppe ancestry' as a mixture of Eastern and Caucasus hunter-gatherers. However, it remains unclear when and where this ancestry arose and whether it was related to a horizon of cultural innovations in the 4 millennium BCE that subsequently facilitated the advance of pastoral societies in Eurasia. Here we generated genome-wide SNP data from 45 prehistoric individuals along a 3000-year temporal transect in the North Caucasus. We observe a genetic separation between the groups of the Caucasus and those of the adjacent steppe. The northern Caucasus groups are genetically similar to contemporaneous populations south of it, suggesting human movement across the mountain range during the Bronze Age. The steppe groups from Yamnaya and subsequent pastoralist cultures show evidence for previously undetected farmer-related ancestry from different contact zones, while Steppe Maykop individuals harbour additional Upper Palaeolithic Siberian and Native American related ancestry.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-018-08220-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360191PMC
February 2019

Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

PLoS Genet 2013 14;9(2):e1003296. Epub 2013 Feb 14.

Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia.

North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1003296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3573127PMC
June 2013

Identification of viral DNA (Anelloviridae) in a 200-year-old dental pulp sample (Napoleon's Great Army, Kaliningrad, 1812).

Infect Genet Evol 2011 Mar 2;11(2):358-62. Epub 2010 Dec 2.

UMR CNRS 6578 Anthropologie Bioculturelle, Equipe Emergence et co-évolution virale, Etablissement Français du Sang Alpes-Méditerranée, Université de la Méditerranée, 27 Bd. Jean Moulin, 13005 Marseille, France.

Ancient human remains are potential sources of biological information including traces of past infections, since previous studies have demonstrated the effective detection of several bacterial agents or host-integrated viruses in old biological remnants like tissues or teeth. Studies of skeletal dental pulp samples are of particular interest since this location is potentially exposed to bloodborne agents during life through its vascularization, and could be considered as well preserved from environment after death of the host. DNA viruses belonging to the family Anelloviridae are highly present in human populations where they harbor an extreme genetic diversity but a yet undefined implication in hosts' health. We hypothesized that anelloviruses would be detected in ancient remains and that they may also serve as tracer viruses for the study of other viral agents. We analyzed 200-year-old dental pulp samples from remains of soldiers of Napoleon's Great Army during the Russian Retreat. Successful detection of Anelloviridae DNA by PCR was obtained for 1/21 ancient samples tested. The sequence identified showed 23% nucleotide divergence with the closest group of modern isolates (genus Gammatorquevirus), and was confirmed as phylogenetically distinct from those identified in saliva samples from the two investigators in charge of the study (genera Alphatorquevirus and Betatorquevirus). PCR directed toward the human beta globin gene was also performed. Negative controls were negative. Our results demonstrate that an ubiquitary, non-integrated, DNA virus is detectable from ancient biological material, with potential developments in terms of evolution studies or subsequent molecular investigations involving further viral agents.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.meegid.2010.11.007DOI Listing
March 2011

Brief communication: paleopathology of the Kiik-Koba 1 Neandertal.

Am J Phys Anthropol 2008 Sep;137(1):106-12

Department of Anthropology, Washington University, St. Louis, MO 63130, USA.

The Kiik-Koba 1 Neandertal partial skeleton (canine, partial hands, partial leg, and feet), of a approximately 40-year-old probable male, exhibits a suite of pathological lesions, including hypercementosis, minor fibrous ossifications, pedal phalangeal fracture, and pronounced enthesopathies on the patella and calcanei in the context of no articular degenerations. The first two sets of lesions are related to age in the context of advanced dental attrition and physical strains. The third lesion joins a series of healed minor traumatic lesions among the Neandertals. The last represents either pronounced tendinous inflammation, albeit in the context of no articular degenerations, or a case of diffuse idiopathic skeletal hyperostosis (DISH) in the Late Pleistocene. Kiik-Koba 1 therefore adds to the high incidence of pathological lesions among the Neandertals and, if a diagnosis of DISH is correct, to a high frequency of this disorder among older Neandertals.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ajpa.20833DOI Listing
September 2008

The environment and health condition of the upper palaeolithic sunghir people of Russia.

J Physiol Anthropol Appl Human Sci 2005 Jul;24(4):413-8

Laboratory of Physical Anthropology, Institute of Archaeology of Russian Academy of Sciences, Moscow, Russia.

Human bones from the Sunghir Late Palaeolithic settlement of the Northern-East part of the Eastern European Plane were observed by a gross study of possible skeletal lesions. The complex of pathological conditions we studied could mirror the features of the ancient environment. The climatic conditions of the Upper Palaeolithic, especially in its final stages, were severe. Thus environmental change and the fall of temperature is reflected in the distribution of pathological indicators. The comparative analysis of early and late Upper Palaeolithic populations demonstrates the increasing frequency of some stress markers. The analysis of physiological stress markers convincingly demonstrates that the Sunghir people had an active lifestyle without experiencing considerable negative stress. Living in the cold conditions and a humid climate, the Sunghir people had adequate reactions relative to their life conditions. Different types of physical activity were noted for both children and adult man. It could be that this is the result of the influence of gender diversity in labour.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2114/jpa.24.413DOI Listing
July 2005

Double child burial from Sunghir (Russia): pathology and inferences for upper paleolithic funerary practices.

Am J Phys Anthropol 2004 Jul;124(3):189-98

Department of Ethology, Ecology, and Evolution, University of Pisa, 56126 Pisa, Italy.

The double child burial from Sunghir (Russia) is a spectacular Mid Upper Palaeolithic funerary example dated to about 24,000 BP. A boy (Sunghir 2) and a girl (Sunghir 3), about 12-13 and 9-10 years old, respectively, were buried at the same time, head to head, covered by red ocher and ornamented with extraordinarily rich grave goods. Examination of the two skeletons reveals that the Sunghir 3 femora are short and exhibit marked antero-posterior bowing. The two femora do not show any asymmetry in the degree of shortening and bowing. Bowing affects the whole diaphysis and shows a regularly incurved profile, with the highest point at midshaft. Pathology is confined to the femora, and no other part of this well-preserved specimen shows abnormality. The isolated nature of the Sunghir 3 anomalies points to cases reported in the medical literature under the label of "congenital bowing of long bones" (CBLB). These are a group of rare conditions exhibiting localized, sometimes bilateral, bowing and shortening which are nonspecific and may result from different causes, including abnormalities of the primary cartilaginous anlage (i.e., the aggregation of cells representing the first trace of an organ). Localized ossification disturbances, possibly linked to a diabetic maternal condition, might explain the shortening and the coincidence of maximum midshaft curvature with the position of the primary ossification center, as well as the lack of involvement of other skeletal parts. This scenario, rather than other possibilities (early bilateral midshaft fracture, acute plastic bowing deformities, or faulty fetal posture), provides the most likely explanation for the Sunghir 3 femoral deformities. The intriguing combination of a pathological condition apparent since birth with a spectacular burial of unusually positioned young individuals of different sexes recalls significant aspects of the triple burial from the contemporary site of Dolní Vestonice (Moravia), evoking a patterned relationship between physical abnormality and extraordinary Upper Paleolithic funerary behavior.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ajpa.10273DOI Listing
July 2004
-->