MiTiSegmenter: Software for high throughput segmentation and meshing of microCT data in microtiter plate arrays by Kendrick Connah, Buckley Michael, Charlotte Brassey

“…We foresee MiTiSegmenter as particularly useful when incorporated into workflows that ultimately require the destructive testing of specimens, including sampling for ancient DNA and proteomics. The software may also play an important role in national museums' ongoing mass digitisation efforts, facilitating the high-speed archiving of specimen 3D morphology across extensive collections with very minimal user intervention or prior training. • We present MiTiSegmenter, a software package for semi-automated image processing and segmentation of array-based batch microCT data. • Implemented in Python, MiTiSegmenter expedites cropping, meshing and exporting samples within stacked microtiter plates, facilitating the rapid digitisation of hundreds-thousands of samples per scan. • We illustrate MiTiSegmenter's capabilities when applied to bulk archiving of valuable zooarchaeological and palaeontological remains…”
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Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities by Gianluca Grasso, Valeria Bianciotto, Roland Marmeisse

“…Abstract By deciphering information encoded in degraded ancient DNA extracted from up to million‐years‐old samples, molecular paleomicrobiology enables to objectively retrace the temporal evolution of microbial species and communities. …”
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Using the irisplex system for eye color prediction on skeletal remaining from the past 30 years by Alireza Rafati, Sayed Mostafa Hosseini, Hasan Zamani Far

“…The prediction of dark and blue eye colors could be suitable from ancient DNA provided from remain skeletal samples using only IrisPlex system, based on our results, IrisPlex system is a suitable method for the prediction of dark and blue eye color. …”
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The 2005 Chios Ancient Shipwreck Survey: New Methods for Underwater Archaeology by Foley, Brendan, Dellaporta, Katerina, Sakellariou, Dimitris, Bingham, Brian S., Camilli, Richard, Eustice, Ryan M., Evagelistis, Dionysis, Ferrini, Vicki Lynn, Katsaros, Kostas, Kourkoumelis, Dimitris, Mallios, Aggelos, Micha, Paraskevi, Mindell, David A., Roman, Christopher, Singh, Hanumant, Switzer, David S., Theodoulou, Theotokis

“…Molecular biological analysis of two amphoras from the 4th-century wreck revealed ancient DNA of olive, oregano, and possibly mastic, part of a cargo outbound from Chios.…”
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Establishing the validity of domestication genes using DNA from ancient chickens by Girdland Flink, L, Allen, R, Barnett, R, Malmstrom, H, Peters, J, Eriksson, J, Andersson, L, Dobney, K, Larson, G

“…A growing body of evidence from ancient DNA studies, however, has revealed that ancient and even historic populations often bear little resemblance to their modern counterparts. …”

Searching for archaic contribution in Africa by Santander, C, Montinaro, F, Capelli, C

“…</p> <p><strong>Conclusion:</strong> 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.…”

Patagonian partnerships: the extinct Dusicyon avus and its interaction with prehistoric human communities by Abbona, CC, Lebrasseur, O, Prevosti, FJ, Peralta, E, González Venanzi, L, Frantz, L, Larson, G, Gil, AF, Neme, GA

“…In this study, we used ancient DNA analysis, morphological examination and stable isotope analysis (&delta;¹³C_col&nbsp;and &delta;¹⁵N) to re-evaluate the taxonomic assignment of a canid discovered at the Late Holocene burial site of Ca&ntilde;ada Seca. …”

Tree measures and the number of segregating sites in time-structured population samples. by Forsberg, R, Drummond, A, Hein, J

“…CONCLUSION: The methodology and results presented here is of use to the design and interpretation of ancient DNA experiments. Furthermore, the results may be useful in further development of statistical tests of e.g. population dynamics and selection, which include temporal information.…”

Mitochondrial DNA from prehistoric canids highlights relationships between dogs and South-East European wolves. by Verginelli, F, Capelli, C, Coia, V, Musiani, M, Falchetti, M, Ottini, L, Palmirotta, R, Tagliacozzo, A, De Grossi Mazzorin, I, Mariani-Costantini, R

“…The earliest fossil dogs, dated approximately 17-12,000 radiocarbon ((14)C) years ago (YA), were found in Europe and in the Middle East. Ancient DNA (a-DNA) evidence could contribute to the identification of dog-founder wolf populations. …”

Tree measures and the number of segregating sites in time-structured population samples by Forsberg, R, Drummond, A, Hein, J

“…Conclusion: The methodology and results presented here is of use to the design and interpretation of ancient DNA experiments. Furthermore, the results may be useful in further development of statistical tests of e.g. population dynamics and selection, which include temporal information.…”

Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives. by Greenwood, A, Lee, F, Capelli, C, DeSalle, R, Tikhonov, A, Marx, P, MacPhee, R

“…Conventionally, empirical studies of proviral amplification and diversification have been limited to extant species, but taxa having good Quaternary fossil records could potentially be investigated using the techniques of "ancient" DNA research. To examine evolutionary parameters of ERV-Ls across both time and taxa, we characterized this proviral class in the extinct woolly mammoth (Mammuthus primigenius) and living elephants, as well as extant members of the larger clade to which they belong (Uranotheria, a group containing proboscideans, sirenians, hyraxes, and their extinct relatives). …”

Inferring population histories for ancient genomes using genome-wide genealogies by Speidel, L, Cassidy, L, Davies, RW, Hellenthal, G, Skoglund, P, Myers, SR

“…Application to 278 present-day and 430 ancient DNA samples of >0.5x mean coverage allows us to identify dynamic population structure and directional gene flow between early farmer and European hunter-gatherer groups. …”

Mitochondrial genome sequencing in Mesolithic North East Europe Unearths a new sub-clade within the broadly distributed human haplogroup C1. by Clio Der Sarkissian, Paul Brotherton, Oleg Balanovsky, Jennifer E L Templeton, Bastien Llamas, Julien Soubrier, Vyacheslav Moiseyev, Valery Khartanovich, Alan Cooper, Wolfgang Haak, Genographic Consortium

“…The human mitochondrial haplogroup C1 has a broad global distribution but is extremely rare in Europe today. Recent ancient DNA evidence has demonstrated its presence in European Mesolithic individuals. …”
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Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals by Emrah Kırdök, Natalija Kashuba, Hege Damlien, Mikael A. Manninen, Bengt Nordqvist, Anna Kjellström, Mattias Jakobsson, A. Michael Lindberg, Jan Storå, Per Persson, Björn Andersson, Andrés Aravena, Anders Götherström

“…Abstract Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. …”
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Genetic and functional odorant receptor variation in the Homo lineage by Claire A. de March, Hiroaki Matsunami, Masashi Abe, Matthew Cobb, Kara C. Hoover

“…Summary: Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. …”
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First molecular data on the human roundworm Ascaris lumbricoides species complex from the Bronze and Iron Age in Hallstatt, Austria by Elisabeth Barsch, Kerstin Kowarik, Katharina Rodler, Christoph Hörweg, Hans Reschreiter, Helmut Sattmann, Julia Walochnik

“…The aim of this study was to recover ancient DNA of intestinal parasites from these coprolites. …”
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Weak Influence of Paleoenvironmental Conditions on the Subsurface Biosphere of Lake Ohrid over the Last 515 ka by Camille Thomas, Alexander Francke, Hendrik Vogel, Bernd Wagner, Daniel Ariztegui

“…Gammaproteobacteria were often co-occurring with cyanobacterial sequences or soil-related OTUs suggesting preservation of ancient DNA from the water column or catchment back to at least 340 ka, particularly in dry glacial intervals. …”
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Identification of microbial pathogens in Neolithic Scandinavian humans by Nora Bergfeldt, Emrah Kırdök, Nikolay Oskolkov, Claudio Mirabello, Per Unneberg, Helena Malmström, Magdalena Fraser, Federico Sanchez-Quinto, Roger Jorgensen, Birgitte Skar, Kerstin Lidén, Mattias Jakobsson, Jan Storå, Anders Götherström

“…This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. …”
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Genomic palaeoparasitology traced the occurrence of Taenia asiatica in ancient Iran (Sassanid Empire, 2th cent. CE–6th cent. CE) by Zeynab Askari, Frank Ruehli, Abigail Bouwman, Vahid Shariati, Saied Reza Naddaf, Domenico Otranto, Santiago Mas-Coma, Mostafa Rezaeian, Nicole Boenke, Thomas Stöllner, Abolfazl Aali, Iraj Mobedi, Gholamreza Mowlavi

“…Today, advances in detecting ancient DNA have cast light on dark corners that microscopy could never reach. …”
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Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia by Xixian Ma, Shuhua Xu

“…Leveraging new methods and available ancient DNA data, we further demonstrated that the beneficial haplotypes reached a high frequency at least 10,000 years ago and are maintained persistently in present-day East Asians. …”
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