Bence Viola

The Teshik-Tash 1 child whose remains were found in Uzbekistan represents the southeastern-most extent of the known Neandertal range, providing an important link with the better studied Caucasus and Altai Mountain ranges. However, due to poor DNA preservation, studying the genetics of Teshik Tash 1 has remained elusive. Here we present analyses of the nuclear DNA from the Teshik-Tash 1, from extracts that are highly contaminated with present-day human DNA. To achieve this, we developed a new computational method, admixslug , that jointly models contamination and population relationships, in order to infer the relationship of a target individual from which only low-quality nuclear DNA is available, to high-quality archaic human genomes. After validating admixslug , we show that Teshik-Tash 1 is genetically more similar to later Neandertals from Western Eurasia than to older Neandertals from the Altai Mountains. We estimate that Teshik-Tash 1 split from the Western Eurasian lineage between 80,000 and 100,000 years ago. Despite the geographical proximity of Teshik-Tash 1 to the Denisovan range, we find no evidence for Denisovan ancestry in his genome. Our results demonstrate that admixslug enables the study of archaic human specimens in cases where DNA preservation was previously considered too poor for population genetic analyses.

The foot has undergone significant morphological change throughout the hominin lineage as our extinct relatives evolved to walk upright. The midfoot displays key adaptations for terrestrial bipedal locomotion, and is therefore considered a target of natural selection. Prior work suggests that early selection for bipedalism targeted the lateral elements of the foot, but that later, among australopiths, these elements were less morphologically diverse, and less influenced by directional selection than medial elements. Here, we apply methods from quantitative genetics to test which evolutionary processes (directional vs. stabilizing selection) shaped hominin midfoot diversification under a null hypothesis of genetic drift. Results demonstrate that the lateral midfoot may have been the primary target of selection for bipedalism in Ardipithecus ramidus, but that later in the hominin lineage, there is no consistent evidence that the lateral elements were less influenced by directional selection. Instead, we find a complex interaction of evolutionary processes shaping midfoot diversification, characterized by genetic drift, directional selection, and indirect responses to selection based on correlation between different elements. In sum, we emphasize that narratives of the evolution of bipedalism should consider the role of genetic drift and correlation among skeletal elements, as both have been historically underestimated.

The Grub-Kranawetberg site cluster is embedded in the rich Upper Palaeolithic landscape of the Middle Danube region. Here we present an updated list of the sites around the villages of Grub and Stillfried, summarise the setting of the Grub-Kranawetberg site cluster in the landscape and provide a detailed overview of the research history for the sites of Grub-Kranawetberg including an updated overview of the different excavation areas. This is followed by an overview of our new fieldwork activities since 2021 in the area including a surface survey on the Kranawetberg/Hönigsberg ridge and new fieldwork at both Grub-Kranawetberg I and Grub-Kranawetberg II. We summarise the findings of the surface survey and implications for understanding the extent and preservation of the archaeological deposits on the Kranawetberg/Hönigsberg ridge. The excavation at Grub-Kranawetberg I in 2021 produced a small assemblage of lithic artefacts and faunal remains, which is presented here for the first time. Overall, the lithic typology, the use of raw material and the faunal spectrum correspond well to previous excavations at the site. We also present our fieldwork and some preliminary results at the new site of Grub-Kranawetberg II, east of Grub-Kranawetberg I, which has been under excavation since 2022. We also discuss our new findings since 2021 in light of previous fieldwork at the site complex, compare them to the other sites in the region and discuss the Grub-Kranawetberg sites in the broader Middle Danube region context.

Modern humans and archaic hominins, namely Denisovans and Neanderthals, have a long history of admixture. Some of these admixture events have allowed modern humans to adapt to new environments outside of Africa. Little research has been done on the impact of archaic introgression on genes associated with reproduction. In this study we report evidence of adaptive introgression of 118 genes within modern humans that have been previously associated with reproduction in mice or modern humans. We identified 11 archaic core haplotypes, three that have been positively selected, with 327 archaic alleles being genome-wide significant for a variety of traits. Over 300 of these variants were discovered to be eQTLs regulating 176 genes with 81% of the archaic eQTLs overlapping a core haplotype region regulating genes expressed in reproductive tissues. Several of the adaptively introgressed genes in our results are enriched in developmental and cancer pathways, while some have been associated with embryo development and reproductive-inhibiting phenotypes like endometriosis and preeclampsia. Lastly, we find that archaic alleles overlapping an introgressed segment on chromosome 2 are protective against prostate cancer. Our results highlight that archaic alleles show connections with important developmental pathways throughout the lifespan and may help regulate these critical processes.

Modern humans and archaic hominins, namely Denisovans and Neanderthals, have been demonstrated to have a long history of admixture. Specifically, some of these admixture events have been adaptive and allowed modern humans to adapt to their new environments outside of Africa. Little research has been done on the impact of archaic introgression on genes associated with reproduction. In this study we report evidence of putative adaptive introgression of 118 genes within modern humans that have been previously associated with reproduction in mice or modern humans. From these genes we identified 11 archaic core haplotypes, three that have been positively selected. Additionally, we found that 327 archaic alleles have genome-wide significance for a variety of traits and 308 of these variants were discovered to be eQTLs regulating 176 genes. We highlight that 81% of the archaic eQTLs overlapping a core haplotype region regulate genes expressed in ovaries, prostate, testes, and vagina compared to other tissues. We also found that several of the putatively adaptively introgressed genes in our results are enriched in developmental and cancer pathways. Further, some of these genes have been associated with embryo development and reproductive-inhibiting phenotypes like preeclampsia. Lastly, we found that archaic alleles overlapping an introgressed segment on chromosome 2 are protective against prostate cancer. Taken together, our results describe how archaic haplotypes, when introduced into a modern human background, may be important in regulating development across the lifespan of an individual.

The Middle Danube region is a key area for understanding Upper Palaeolithic hunter-gatherer behaviours in a climatic context due to its long loess–palaeosol sequences and rich archaeological record spanning from the onset of the Upper Palaeolithic to the Last Glacial Maximum and beyond. Recently, new approaches focusing on high-resolution studies of the stratigraphy, geoarchaeological studies at microscopic scale and investigations of organic matter at molecular scale (biomarker analyses) have shown great new insights in human behaviour. Many sites in the Middle Danube region have been excavated a long time ago without opportunity to apply such approaches. The aim of this paper is to introduce Ollersdorf-Heidenberg, a loess open-air site. The site is located ~ 26 km northeast of Vienna close to the Morava River valley and preserves several Upper Palaeolithic archaeological horizons. The site has been known since a pipeline construction in 1998. Here, we report the first results of new research at the site including new excavations in two trenches. We describe and analyse the stratigraphy, present a first radiocarbon date, describe and analyse lithic and faunal collections, and assess potential in situ combustion activity and the preservation of organic matter. Research at the site is ongoing, but our preliminary results let us suggest good preservation of organic matter and, hence, Ollersdorf-Heidenberg has a remarkable potential for providing valuable insights in past hunter-gatherer behaviours at the climatic downturn towards the Last Glacial Maximum.

Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans^1–8, but the social organization of Neanderthal communities remains poorly understood. Here, we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave^9,10 and two from Okladnikov Cave¹¹ - making this the largest genetic study of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father-daughter pair and a pair of second degree relatives, indicating that at least some of the individuals lived at the same time. Up to a third of these individuals’ genomes occur in long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range.

Введение. В данной статье рассматриваются результаты изучения пепловых слоев из голоценовых отложений пещеры Сельунгур. Цель исследования заключается в апробации применения метода определения копромаркеров в археологических отложениях. Полевое изучение голоценовых отложений объекта проводилось в полевые сезоны 2018 и 2021 гг., здесь выявлено 7 голоценовых слоев, представляющих собой стратифицированные слои сгоревшего помета травоядных животных. Последовательность содержит свидетельства о землетрясениях, которые нарушали осадочный слой, вызывая образование водовыпускных структур, пластических деформаций и разломов. Тем не менее стратиграфия остается легко читаемой. К сожалению, археологические и палеофаунистические материалы здесь не обнаружены, но серия пеплосодержащих прослоев позволяет предположить, что пещера неоднократно посещалась древними людьми. Материалы и методы. Всего было отобрано 7 образцов, по одному из каждого слоя для проведения анализа на содержание макроуглей, а после газ-хромато-спектрометрического анализа. В пепловых отложениях методом анализа макроуглей были выявлены участки концентрации сгоревшего дерева, которое использовались для разведения костров. По всему разрезу голоценовых отложений были отобраны серии проб для анализа методом газовой масс-спектрометрии. Также был проведен анализ современного навоза травоядных животных, обитающих на данной территории: коров, овец, коз, лошадей и ослов, полученные данные были использованы в качестве сравнительной коллекции. Результаты и выводы. К сожалению, в слое 7 пещеры Сельунгур плохо сохранились продукты горения, богатые данные мы получили из слоев 6–1. Полученные результаты позволяют идентифицировать копростерины и установить, что в слоях 6–2 в качестве топлива использовался конский навоз, а в первом слое — козий. Наиболее широкое распространение лошадей в этом регионе происходило в период существования государства Давань (Паркан), в III в. до н. э. и позднее — в средние века. Скорее всего, в эти периоды горный коридор, в котором находится Сельунгур, мог использоваться как один из перевалов Великого шелкового пути, соединявший Ферганскую и Алайскую долины. Накопление верхнего слоя, на наш взгляд, связано с современным периодом.

Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans^1–8, but the social organization of Neanderthal communities remains poorly understood. Here we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave^9,10 and 2 from Okladnikov Cave¹¹—making this one of the largest genetic studies of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father–daughter pair and a pair of second-degree relatives, indicating that at least some of the individuals lived at the same time. Up to one-third of these individuals’ genomes had long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range.