Systematic relationships of five newly sequenced cervid species by Nicola S. Heckeberg, Dirk Erpenbeck, Gert Wörheide, Gertrud E. Rössner

“…Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences for Mazama bricenii, Mazama chunyi, Muntiacus atherodes, Pudu mephistophiles, and Rusa marianna, including three holotypes. …”
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Usefulness of Microbiome for Forensic Geolocation: A Review by Christian Haarkötter, María Saiz, Xiomara Gálvez, María Isabel Medina-Lozano, Juan Carlos Álvarez, José Antonio Lorente

“…The aim of this review is to highlight the main findings in this field, including the current sample storage, DNA extraction, sequencing and data analysis techniques that are being used, and its potential applications in human trafficking and ancient DNA studies. Second, the challenges and limitations of forensic microbiomics and geolocation are emphasised, providing recommendations for the establishment of this tool in the forensic science community.…”
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Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data by Vaidehi Pusadkar, Rajeev K. Azad

“…Our results revealed that, compared to deamination and fragmentation, human and environmental contamination of ancient DNA (with modern DNA) has the most pronounced effect on the performance of each profiler. …”
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Host Diversity and Origin of Zoonoses: The Ancient and the New by Judith Recht, Verena J. Schuenemann, Marcelo R. Sánchez-Villagra

“…Paleopathology studies of ancient human bone lesions, in combination with ancient DNA analysis of the causative pathogen, have contributed to our understanding of the origin of zoonotic diseases, including brucellosis and mycobacterial zoonoses. …”
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Genotyping Yersinia pestis in Historical Plague: Evidence for Long-Term Persistence of Y. pestis in Europe from the 14th to the 17th Century. by Lisa Seifert, Ingrid Wiechmann, Michaela Harbeck, Astrid Thomas, Gisela Grupe, Michaela Projahn, Holger C Scholz, Julia M Riehm

“…Ancient DNA (aDNA) recovered from plague victims of the second plague pandemic (14th to 17th century), excavated from two different burial sites in Germany, and spanning a time period of more than 300 years, was characterized using single nucleotide polymorphism (SNP) analysis. …”
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Mediterranean Y-chromosome 2.0—why the Y in the Mediterranean is still relevant in the postgenomic era by Maarten H. D. Larmuseau, Claudio Ottoni

“…Conclusions: There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. …”
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Detection of chromosomal aneuploidy in ancient genomes by Anastasiadou, K, Silva, M, Booth, T, Speidel, L, Audsley, T, Barrington, C, Buckberry, J, Fernandes, D, Ford, B, Gibson, M, Gilardet, A, Glocke, I, Keefe, K, Kelly, M, Masters, M, McCabe, J, McIntyre, L, Ponce, P, Rowland, S, Ruiz Ventura, J, Swali, P, Tait, F, Walker, D, Webb, H, Williams, M, Witkin, A, Holst, M, Loe, L, Armit, I, Schulting, R, Skoglund, P

“…Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. …”

Ancient genomes indicate population replacement in Early Neolithic Britain by Brace, S, Diekmann, Y, Booth, TJ, Van Dorp, L, Faltyskova, Z, Rohland, N, Mallick, S, Olalde, I, Ferry, M, Michel, M, Oppenheimer, J, Broomandkhoshbacht, N, Stewardson, K, Martiniano, R, Walsh, S, Kayser, M, Charlton, S, Hellenthal, G, Armit, I, Schulting, R, Craig, OE, Sheridan, A, Pearson, M, Stringer, C, Reich, D, Thomas, MG, Barnes, I

“…The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. …”

Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene. by Meng Yue Wu, Giovanni Forcina, Gabriel Weijie Low, Keren R Sadanandan, Chyi Yin Gwee, Hein van Grouw, Shaoyuan Wu, Scott V Edwards, Maude W Baldwin, Frank E Rheindt

“…When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20-50%. …”
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Sex Determination and Isotopic Analysis of the Nivåfjord Mesolithic Burials, Zealand, Denmark by Kurt J. Gron, Harry Robson, Nicolas A. Stewart, Peter Rowley-Conwy, Ole Lass Jensen, Janet Montgomery

“…Unfortunately, the micro-region is characterised by poor organic preservation, restricting the successful application of biomolecular techniques to human remains, including large-scale radiocarbon dating programmes as well as both stable isotope and ancient DNA analyses. Here, we apply an alternative technique, an acid etch peptide-based method, to determine the sex of eight individuals from Nivå 10 as well as the Nivågård child. …”
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Searching for archaic contribution in Africa by Cindy Santander, Francesco Montinaro, Cristian Capelli

“…Conclusion: In light of the caveats with implementing current archaic introgression detection methods in Africa, we recommend future studies to concentrate on unravelling the complicated demographic history of Africa through means of ancient DNA where possible and through more focused efforts to sequence modern DNA from more representative populations across the African continent.…”
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Identifying Complex DNA Contamination in Pig-Footed Bandicoots Helps to Clarify an Anomalous Ecological Transition by Matthew J. Phillips, Manuela Cascini, Mélina Celik

“…The sources of non-target DNA that were identified range from other bandicoot species to a bird—emphasizing the importance of sequence authentication for historical museum specimens, as has become standard for ancient DNA studies. Upon excluding the putatively contaminated fragments, <i>Chaeropus</i> was resolved as the sister to all other bandicoots (Peramelidae), to the exclusion of bilbies (<i>Macrotis</i>). …”
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Inferring language dispersal patterns with velocity field estimation by Sizhe Yang, Xiaoru Sun, Li Jin, Menghan Zhang

“…Our results show that the dispersal trajectories of these languages are primarily compatible with population movement routes inferred from ancient DNA and archaeological materials, and their dispersal centres are geographically proximate to ancient homelands of agricultural or Neolithic cultures. …”
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Paleomicrobiology: revealing fecal microbiomes of ancient indigenous cultures. by Raul J Cano, Jessica Rivera-Perez, Gary A Toranzos, Tasha M Santiago-Rodriguez, Yvonne M Narganes-Storde, Luis Chanlatte-Baik, Erileen García-Roldán, Lucy Bunkley-Williams, Steven E Massey

“…The present study shows that ancient DNA is not entirely degraded in humid, tropical environments, and that dietary and/or host genetic differences in ancient populations may be reflected in the composition of their gut microbiome. …”
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The past, present and future of ancient bacterial DNA by Arning, N, Wilson, DJ

“…Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. …”

Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions by Larson, G, Boivin, N, Zeder, M, Fuller, D, Alison, C, Erlandson, J, Tim, D, Petraglia, M

“…We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. …”

Improving the extraction of ancient Yersinia pestis genomes from the dental pulp by Pierre Clavel, Lexane Louis, Clio Der Sarkissian, Catherine Thèves, Claudia Gillet, Lorelei Chauvey, Gaétan Tressières, Stéphanie Schiavinato, Laure Calvière-Tonasso, Norbert Telmon, Benoît Clavel, Richard Jonvel, Stéfan Tzortzis, Laetitia Bouniol, Jean-Marc Fémolant, Jennifer Klunk, Hendrik Poinar, Michel Signoli, Caroline Costedoat, Maria A. Spyrou, Andaine Seguin-Orlando, Ludovic Orlando

“…Summary: Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. …”
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A fresh perspective on infrared spectroscopy as a prescreening method for molecular and stable isotopes analyses on ancient human bones by Cinzia Scaggion, Maurizio Marinato, Gregorio Dal Sasso, Luca Nodari, Tina Saupe, Serena Aneli, Luca Pagani, Christiana L. Scheib, Manuel Rigo, Gilberto Artioli

“…The predictive model based on Infrared parameters is effective in determining the occurrence of ancient DNA (aDNA); however, the quality/quantity of aDNA cannot be determined because of the influence of environmental and local factors experienced by the examined bones during the burial period.…”
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Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases [version 2; peer review: 2 approved] by Abigail S Gancz, Laura S Weyrich

“…In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. …”
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Genotyping Single Nucleotide Polymorphisms Using Different Molecular Beacon Multiplexed within a Suspended Core Optical Fiber by Linh Viet Nguyen, Sara Giannetti, Stephen Warren-Smith, Alan Cooper, Stefano Selleri, Annamaria Cucinotta, Tanya Monro

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