Showing papers by "Matthias Meyer published in 2022"
TL;DR: This paper used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences of 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia.
Abstract: Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans1-8, 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 Cave9,10 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.
18 citations
TL;DR: This study identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework, and utilizing single-stranded rather than double-Stranded library preparation resulted in increased attainment of reportable mtDNA profiles.
Abstract: The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS methods. In parallel, the ancient DNA field has developed workflows specifically for degraded DNA, resulting in the successful recovery of nuclear DNA and mtDNA from skeletal remains as well as sediment over 100,000 years old. In this study we use a set of disinterred skeletal remains from the Korean War and World War II to test if ancient DNA extraction and library preparation methods improve forensic DNA profiling. We identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework. In addition, utilizing single-stranded rather than double-stranded library preparation resulted in increased attainment of reportable mtDNA profiles. This study emphasizes that the combination of ancient DNA extraction and library preparation methods evaluated here increases the success rate of DNA profiling, and likelihood of identifying historical remains.
12 citations
TL;DR: This paper investigated the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600-250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara.
Abstract: Previous research indicates that human genetic diversity in Wallacea-islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves-has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Yet, inferences based on present-day groups proved insufficient to disentangle this region's demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600-250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.
10 citations
TL;DR: This paper demonstrates that this strategy is feasible, at least for small genomic targets such as mitochondrial DNA, if the annealing temperature is increased and PCR cycles are limited in post‐capture amplification to avoid index swapping by jumping PCR, and provides a simple computational method for quantifying cross‐contamination due to index swapping in double‐indexed libraries.
Abstract: The use of hybridization capture has enabled a massive upscaling in sample sizes for ancient DNA studies, allowing the analysis of hundreds of skeletal remains or sediments in single studies. Nevertheless, demands in throughput continue to grow, and hybridization capture has become a limiting step in sample preparation due to the large consumption of reagents, consumables and time. Here, we explored the possibility of improving the economics of sample preparation via multiplex capture, that is, the hybridization capture of pools of double‐indexed ancient DNA libraries. We demonstrate that this strategy is feasible, at least for small genomic targets such as mitochondrial DNA, if the annealing temperature is increased and PCR cycles are limited in post‐capture amplification to avoid index swapping by jumping PCR, which manifests as cross‐contamination in resulting sequence data. We also show that the reamplification of double‐indexed libraries to PCR plateau before or after hybridization capture can sporadically lead to small, but detectable cross‐contamination even if libraries are amplified in separate reactions. We provide protocols for both manual capture and automated capture in 384‐well format that are compatible with single‐ and multiplex capture and effectively suppress cross‐contamination and artefact formation. Last, we provide a simple computational method for quantifying cross‐contamination due to index swapping in double‐indexed libraries, which we recommend using for routine quality checks in studies that are sensitive to cross‐contamination.
3 citations
TL;DR: In this article , the authors analyzed 33 sediment samples from different sedimentological contexts in the Paleolithic layers of Sefunim Cave (Israel) and found traces of ancient Cervidae and Hyaenidae mitochondrial DNA.
Abstract: Paleogenomic research can elucidate the evolutionary history of human and faunal populations. Although the Levant is a key land-bridge between Africa and Eurasia, thus far, relatively little ancient DNA data has been generated from this region, since DNA degrades faster in warm climates. As sediments can be a source of ancient DNA, we analyzed 33 sediment samples from different sedimentological contexts in the Paleolithic layers of Sefunim Cave (Israel). Four contained traces of ancient Cervidae and Hyaenidae mitochondrial DNA. Dating by optical luminescence and radiocarbon indicates that the DNA comes from layers between 30,000 and 70,000 years old, surpassing theoretical expectations regarding the longevity of DNA deposited in such a warm environment. Both identified taxa are present in the zooarchaeological record of the site but have since gone extinct from the region, and a geoarchaeological study suggests little movement of the sediments after their deposition, lending further support to our findings. We provide details on the local conditions in the cave, which we hypothesize were particularly conducive to the long-term preservation of DNA-information that will be pertinent for future endeavors aimed at recovering ancient DNA from the Levant and other similarly challenging contexts.
3 citations
TL;DR: Inpatient procedure volumes in Switzerland decreased considerably in the beginning of the pandemic but recovered quickly after the first wave, yet there was a net deficit in procedures at the end of the year, and health system leaders must work to ensure that adequate access to non-COVID-19 related care is maintained during future pandemic phases.
Abstract: Background: The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) pandemic forced hospitals to redistribute resources for the treatment of patients with coronavirus disease 2019 (COVID-19), yet the impact on elective and emergency inpatient procedure volumes is unclear. Methods: We analyzed anonymized data on 234 921 hospitalizations in 2017-2020 (55.9% elective) from a big Swiss health insurer. We used linear regression models to predict, based on pre-pandemic data, the expected weekly numbers of procedures in 2020 in the absence of a pandemic and compared these to the observed numbers in 2020. Compensation effects were investigated by discretely integrating the difference between the two numbers over time. Results: During the first COVID-19 wave in spring 2020, elective procedure numbers decreased by 52.9% (95% confidence interval -64.5% to -42.5%), with cardiovascular and orthopedic elective procedure numbers specifically decreasing by 45.5% and 72.4%. Elective procedure numbers normalized during summer with some compensation of postponed procedures, leaving a deficit of -9.9% (-15.8% to -4.5%) for the whole year 2020. Emergency procedure numbers also decreased by 17.1% (-23.7% to -9.8%) during the first wave, but over the whole year 2020, net emergency procedure volumes were similar to control years. Conclusion: Inpatient procedure volumes in Switzerland decreased considerably in the beginning of the pandemic but recovered quickly after the first wave. Still, there was a net deficit in procedures at the end of the year. Health system leaders must work to ensure that adequate access to non-COVID-19 related care is maintained during future pandemic phases in order to prevent negative health consequences.
2 citations
TL;DR: This article performed a range-wide analysis of complete mitogenomes of sable antelope (Hippotragus niger) to explore how these different factors may have contributed as drivers of evolution in southcentral Africa.
Abstract: The evolutionary history of African ungulates has been explained largely in the light of Pleistocene climatic oscillations and the way these influenced the distribution of vegetation types, leading to range expansions and/or isolation in refugia. In contrast, comparatively fewer studies have addressed the continent’s environmental heterogeneity and the role played by its geomorphological barriers. In this study, we performed a range‐wide analysis of complete mitogenomes of sable antelope (Hippotragus niger) to explore how these different factors may have contributed as drivers of evolution in southcentral Africa. Our results supported two sympatric and deeply divergent mitochondrial lineages in west Tanzanian sables, which can be explained as the result of introgressive hybridization of a mitochondrial ghost lineage from an archaic, as‐yet‐undefined, congener. Phylogeographical subdivisions into three main lineages suggest that sable diversification may not have been driven solely by climatic events affecting populations differently across a continental scale. Often in interplay with climate, geomorphological features have also clearly shaped the species’ patterns of vicariance, where the East Africa Rift System and the Eastern Arc Mountains acted as geological barriers. Subsequent splits among southern populations may be linked to rearrangements in the Zambezi system, possibly framing the most recent time when the river attained its current drainage profile. This work underlines how the use of comprehensive mitogenomic data sets on a model species with a wide geographical distribution can contribute to a much‐enhanced understanding of environmental, geomorphological and evolutionary patterns in Africa throughout the Quaternary.
2 citations
TL;DR: In this article , the Einsatz von RTLS with einer Microsoft Excel-basierten Anwendung zur Prozessoptimierung in einem manuellen Produktionsumfeld and die damit verbundenen Vorteile is discussed.
Abstract: Abstract Auf Basis von Real-Time Location Systemen (RTLS) können in Echtzeit Produktionsdaten digitalisiert, analysiert und dargestellt werden. Diese Daten und Informationen können dann im Rahmen von Lean Management Methoden verwendet werden, um Optimierungspotenziale von Produktionsprozessen aufzudecken und zu realisieren. Dieser Beitrag zeigt den Einsatz von RTLS mit einer Microsoft Excel-basierten Anwendung zur Prozessoptimierung in einem manuellen Produktionsumfeld und die damit verbundenen Vorteile.
TL;DR: Diagnosing the cause of a non-ST-segment elevation myocardial infarction (NSTEMI) delayed-enhancement resonance and its role in clinical practice.
Abstract: Diagnosing the cause of a non-ST-segment elevation myocardial infarction (NSTEMI) delayed-enhancement resonance