Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population by Risa L. Iwasaki, Koji Ishiya, Hideaki Kanzawa-Kiriyama, Yosuke Kawai, Jun Gojobori, Yoko Satta

“…Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese.…”
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AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data by Nathan K. Schaefer, Beth Shapiro, Richard E. Green

“…This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA. Results We demonstrate the utility of AD-LIBS with synthetic data. …”
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HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data by Dimopoulos, EA, Carmagnini, A, Velsko, IM, Warinner, C, Larson, G, Frantz, LAF, Irving-Pease, EK

“…We tested the performance and accuracy of HAYSTAC using simulated Illumina libraries, both with and without ancient DNA damage, and compared the results to other currently available methods (i.e., Kraken2/Bracken, KrakenUniq, MALT/HOPS, and Sigma). …”

Novel approaches to assess the prevalence of palaeoparasites in European archaeological sites by Ryan, H

“…Currently most studies utilise ancient DNA analysis in palaeoparasitology to confirm species identification so, the second goal was to develop genetic methods to produce data that could be used to study population dynamics and dispersal of helminths. …”

The dental calculus metabolome in modern and historic samples by Velsko, I, Overmyer, K, Speller, C, Klaus, L, Collins, M, Loe, L, Frantz, L, Sankaranarayanan, K, Lewis, C, Rodriguez Martinez, J, Chaves, E, Coon, J, Larson, G, Warinner, C

“…Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens.…”

Using the Theory of Planned Behavior and Past Behavior to Explain the Intention to Receive a Seasonal Influenza Vaccine among Family Caregivers of People with Dementia by Francesco Bruno, Paolo Abondio, Valentina Laganà, Rosanna Colao, Sabrina M. Curcio, Francesca Frangipane, Gianfranco Puccio, Raffaele Di Lorenzo, Amalia C. Bruni, Raffaele Maletta

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Biodeteriogens Characterization and Molecular Analyses of Diverse Funeral Accessories from XVII Century by Zuzana Kisová, Matej Planý, Jelena Pavlović, Mária Bučková, Andrea Puškárová, Lucia Kraková, Magdaléna Kapustová, Domenico Pangallo, Katarína Šoltys

“…Different PCR assays and consequent sequencing of amplicons were employed to recognize the animal origin of bodice reinforcements and the type of plant used to embellish the young girl. The analysis of ancient DNA (aDNA from animal and plant) was also completed by the application of high-throughput sequencing through Illumina platform. …”
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Stable isotopes unveil one millennium of domestic cat paleoecology in Europe by Magdalena Krajcarz, Wim Van Neer, Maciej T. Krajcarz, Danijela Popović, Mateusz Baca, Bea De Cupere, Quentin Goffette, Hans Christian Küchelmann, Anna Gręzak, Urszula Iwaszczuk, Claudio Ottoni, Katrien Van de Vijver, Jarosław Wilczyński, Anna Mulczyk, Jan Wiejacki, Daniel Makowiecki, Hervé Bocherens

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Environmental DNA as an innovative technique to identify the origins of falsified antimalarial tablets—a pilot study of the pharmabiome by Jennifer M. Young, Craig Liddicoat, Kor-jent van Dijk, Patricia Tabernero, Celine Caillet, Nicholas J. White, Adrian Linacre, Jeremy J. Austin, Paul N. Newton

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Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing by Laura E. MacConaill, Robert T. Burns, Anwesha Nag, Haley A. Coleman, Michael K. Slevin, Kristina Giorda, Madelyn Light, Kevin Lai, Mirna Jarosz, Matthew S. McNeill, Matthew D. Ducar, Matthew Meyerson, Aaron R. Thorner

“…Abstract Background Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigations, microbial detection in human samples, or circulating cell-free tumor DNA (ctDNA) variant detection. …”
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Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia by Stephen M. Richards, Leiting Li, James Breen, Nelli Hovhannisyan, Oscar Estrada, Boris Gasparyan, Matthew Gilliham, Alexia Smith, Alan Cooper, Heng Zhang

“…To investigate the demographic and evolutionary history of the Areni-1 millet, we used ancient DNA extraction, hybridization capture enrichment, and high throughput sequencing to assemble three chloroplast genomes from the medieval grains and then compared these sequences to 50 modern P. miliaceum chloroplast genomes. …”
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The genetic structure of the British populations and their surnames by Bodmer, W, Winney, B

“…<p> Until large-scale ancient DNA studies of archaeological samples become practical, genetic studies of current human populations, with a few caveats, are a productive way to investigate past movements of peoples (Røyrvik 2010). …”

Using commensals as proxies for historical inference in the Indian ocean: genetic and zooarchaeological perspectives by Eager, H, Heidi Eager

“…Closer to the origins of the three species (the Indian subcontinent in all cases), range expansions in Eurasia and nearby islands relate to early to mid Holocene human populations, but also with signals of later secondary colonisations. Through ancient DNA studies I found genetic continuity between temporally separated populations of black rats suggesting population persistence, and high levels of diversity in Songo Mnara, a Swahili stonetown in Tanzania. …”

Island biogeography revisited: museomics reveals affinities of shelf island birds determined by bathymetry and paleo-rivers, not by distance to mainland by Kritika M. Garg, Balaji Chattopadhyay, Emilie Cros, Suzanne Tomassi, Suzan Benedick, David P. Edwards, Frank E. Rheindt

“…A key question is whether these predictions follow at a population-genomic level. Using rigorous ancient-DNA protocols, we retrieved approximately 1,000 genomic markers from approximately 100 historic specimens of two Southeast Asian songbird complexes from across the Sunda Shelf archipelago collected 1893–1957. …”
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DNA Markers Reveal Genetic Associations among 11,000-Year-Old Scots Pine (<i>Pinus sylvestris</i> L.) Found in the Baltic Sea with the Present-Day Gene Pools in Lithuania by Darius Danusevičius, Jurata Buchovska, Vladas Žulkus, Linas Daugnora, Algirdas Girininkas

“…Our study shows that salty sea water efficiently preserves ancient DNA in wood at the quality levels suitable for genetic testing of trees dated back as far as 11,000 years before present.…”
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euka: Robust tetrapodic and arthropodic taxa detection from modern and ancient environmental DNA using pangenomic reference graphs by Nicola Alexandra Vogel, Joshua Daniel Rubin, Mikkel Swartz, Juliette Vlieghe, Peter Wad Sackett, Anders Gorm Pedersen, Mikkel Winther Pedersen, Gabriel Renaud

“…However, the computational analysis of aeDNA involves the inherited challenges of ancient DNA (aDNA) and the typical difficulties of eDNA samples, such as taxonomic identification and abundance estimation of identified taxonomic groups. …”
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<i>C5</i> and <i>SRGAP3</i> Polymorphisms Are Linked to Paediatric Allergic Asthma in the Italian Population by Daria Messelodi, Cristina Giuliani, Francesca Cipriani, Silvia Armuzzi, Emanuela di Palmo, Paolo Garagnani, Luca Bertelli, Annalisa Astolfi, Donata Luiselli, Giampaolo Ricci, Andrea Pession

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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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Ancient genomics in India: Clarifying the maternal origins of 160-year-old human remains by Esha Bandyopadhyay, J.S Sehrawat, Niraj Rai, Maanasa Raghavan

“…Sequencing DNA from archaeological remains has opened up new possibilities for furthering our understanding of the origins and evolutionary history of modern humans [1]. However, most ancient DNA (aDNA) studies, thus far, have focused on ancient samples obtained from permafrozen and temperate regions, where preservation conditions are better suited for long-term DNA survival. …”
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Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions by Nikolas Hallberg Thuesen, Nikolas Hallberg Thuesen, Michael Schantz Klausen, Shyam Gopalakrishnan, Thomas Trolle, Gabriel Renaud

“…HLA typing is also used in studies of ancient DNA (aDNA), which is often based on sequencing data with lower quality and DOC. …”
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