Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau

A late Middle Pleistocene mandible from Baishiya Karst Cave (BKC) on the Tibetan Plateau has been inferred to be from a Denisovan, an Asian hominin related to Neanderthals, on the basis of an amino acid substitution in its collagen. Here we describe the stratigraphy, chronology, and mitochondrial DNA extracted from the sediments in BKC. We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand years ago (ka) and possibly as recently as ~45 ka. The long-term occupation of BKC by Denisovans suggests that they may have adapted to life at high altitudes and may have contributed such adaptations to modern humans on the Tibetan Plateau

Integrated multidisciplinary ecological analysis from the Uluzzian settlement at the Uluzzo C Rock Shelter, south-eastern Italy

open20siThe Middle to Upper Palaeolithic transition, between 50 000 and 40 000 years ago, is a period of important ecological and cultural changes. In this framework, the Rock Shelter of Uluzzo C (Apulia, southern Italy) represents an important site due to Late Mousterian and Uluzzian evidence preserved in its stratigraphic sequence. Here, we present the results of a multidisciplinary analysis performed on the materials collected between 2016 and 2018 from the Uluzzian stratigraphic units (SUs) 3, 15 and 17. The analysis involved lithic technology, use-wear, zooarchaeology, ancient DNA of sediments and palaeoproteomics, completed by quartz single-grain optically stimulated luminescence dating of the cave sediments. The lithic assemblage is characterized by a volumetric production and a debitage with no or little management of the convexities (by using the bipolar technique), with the objective to produce bladelets and flakelets. The zooarchaeological study found evidence of butchery activity and of the possible exploitation of marine resources, while drawing a picture of a patchy landscape, composed of open forests and dry open environments surrounding the shelter. Ancient mitochondrial DNA from two mammalian taxa were recovered from the sediments. Preliminary zooarchaeology by mass spectrometry results are consistent with ancient DNA and zooarchaeological taxonomic information, while further palaeoproteomics investigations are ongoing. Our new data from the re-discovery of the Uluzzo C Rock Shelter represent an important contribution to better understand the meaning of the Uluzzian in the context of the Middle/Upper Palaeolithic transition in south-eastern Italy.First published: 13 July 2021openSARA SILVESTRINI, MATTEO ROMANDINI, GIULIA MARCIANI, SIMONA ARRIGHI, LISA CARRERA, ANDREA FIORINI, JUAN MANUEL LÓPEZ-GARCÍA, FEDERICO LUGLI, FILOMENA RANALDO, VIVIANE SLON, LAURA TASSONI, OWEN ALEXANDER HIGGINS, EUGENIO BORTOLINI, ANTONIO CURCI, MATTHIAS MEYER, MICHAEL CHRISTIAN MEYER, GREGORIO OXILIA, ANDREA ZERBONI, STEFANO BENAZZI, SPINAPOLICE ENZA ELENASARA SILVESTRINI, MATTEO ROMANDINI, GIULIA MARCIANI, SIMONA ARRIGHI, LISA CARRERA, ANDREA FIORINI, JUAN MANUEL LÓPEZ-GARCÍA, FEDERICO LUGLI, FILOMENA RANALDO, VIVIANE SLON, LAURA TASSONI, OWEN ALEXANDER HIGGINS, EUGENIO BORTOLINI, ANTONIO CURCI, MATTHIAS MEYER, MICHAEL CHRISTIAN MEYER, GREGORIO OXILIA, ANDREA ZERBONI, STEFANO BENAZZI, SPINAPOLICE ENZA ELEN

Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations

Background: Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results: In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions: The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies

Multiple sequence alignment files

This submission contains multiple sequence alignment files used for phylogenetic reconstructions. Sequences reconstructed from sediments are denominated by the site and layer of origin. The comparative data (identical in all files) is identified by the name of the individual and the accession code of its mtDNA sequence

The plastered skulls from the Pre-Pottery Neolithic B site of Yiftahel (Israel)--a computed tomography-based analysis.

Three plastered skulls, dating to the Pre-Pottery Neolithic B, were found at the site of Yiftahel, in the Lower Galilee (Israel). The skulls underwent refitting and restoration processes, details of which are described herein. All three belong to adults, of which two appear to be males and one appears to be a female. Virtual cross-sections were studied and a density analysis of the plaster was performed using computed tomography scans. These were utilized to yield information regarding the modeling process. Similarities and differences between the Yiftahel and other plastered skulls from the Levant are examined. The possible role of skull plastering within a society undergoing a shift from a hunting-gathering way of life to a food producing strategy is discussed

Methodological advances in Neanderthal identification, phylogeny, chronology, mobility, climate, and diet

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In the quest for degenerative lumbar spinal stenosis etiology: the Schmorl’s nodes model

Abstract Background Degenerative lumbar spinal stenosis (DLSS) is a common health problem in the elderly and usually associated with three-joint complex degeneration. Schmorl’s nodes (SNs) are described as vertical herniation of the disc into the vertebral body through a weakened part of the end plate that can lead to disc degeneration. Since SNs can harm the spine unit stability, the association between DLSS and SNs is expected. The aim of this study is to shed light on the relationship between degenerative lumbar spinal stenosis and SNs. Methods Two groups of individuals were studied: the first included 165 individuals with DLSS (age range: 40–88, sex ratio: 80 M/85 F) and the second 180 individuals without spinal stenosis related symptoms (age range: 40–99, sex ratio: 90 M/90 F). The presence or absence of SNs on the cranial and caudal end plate surfaces at the lumbosacral region (from L1 to S1 vertebra) was recorded, using CT images (Brilliance 64 Philips Medical System, Cleveland Ohio, thickness of the sections was 1–3 mm and MAS, 80–250). Chi-Square test was taken to compare the prevalence of SNs between the study groups (control and stenosis) by lumbar disc level, for each gender separately. Multivariable logistic regression analysis was also used to determine the association between DLSS and SNs. Results The prevalence rate of SNs was significantly greater in the stenosis males (L1-2 to L5-S1) and females (L4-5 and L4-S1) compared to their counterparts in the control (P < 0.001). In addition, the presence of SNs in both males and females was found to increase the likelihood for DLSS. Conclusions Our results indicate that SNs prevalence is significantly greater in the DLSS group compared to the control. Furthermore, SNs are strongly associated with DLSS

Mammalian mitochondrial capture, a tool for rapid screening of DNA preservation in faunal and undiagnostic remains, and its application to Middle Pleistocene specimens from Qesem Cave (Israel)

Faunal skeletal remains from prehistoric sites are often too fragmentary to enable identification at the species level based on morphology, complicating attempts to recover ancient DNA sequences from these remains. We designed a novel approach that enables large-scale screening of undiagnostic remains for the preservation of ancient mitochondrial DNA. Following DNA extraction and DNA library preparations, libraries are enriched for mitochondrial DNA using a set of probes, which cover the entire mitochondrial genomes of 242 mammalian species. We show that the efficiency of mitochondrial enrichment using mammalian capture probes is not substantially lower compared to enrichment using species-specific probes. Excavations at Qesem Cave (Israel), dated to 420–200 ka, have yielded a large assemblage of skeletal and dental remains, including a small number of hominin teeth. As recent developments in ancient DNA extraction and library preparation methods have enabled the generation of sequencing data from Middle Pleistocene samples, we aimed to investigate the feasibility of recovering ancient DNA molecules from specimens originating in Qesem Cave. The current research was carried out using forty-two faunal remains from six different areas of the cave, as a preliminary study which could then be used to select hominin remains for further genetic analysis. Unfortunately, DNA libraries from Qesem Cave samples yielded few sequences which could be mapped to a mammalian mitochondrial genome. These sequences do not exhibit the patterns of ancient DNA damage expected from endogenous sequences of that age. Thus, we could not detect the presence of ancient endogenous DNA molecules in the faunal remains from Qesem Cave

Additional file 1 of Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA

Supplementary material. (PDF 2232 kb