Reconstructing Migration Trajectories using ancient DNA by Larson, G

“…Here, I focus on the use of ancient DNA to delve beneath the migration palimpsests. …”

Formal methods for evolutionary inference using ancient DNA by Loog, L

“…<p>Ancient DNA has revolutionised our ability to study past evolutionary processes by enabling direct observation of genetic variation in past populations. …”

Taming the past: Ancient DNA and the study of animal domestication by MacHugh, D, Larson, G, Orlando, L

“…During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. …”

Ancient DNA perspectives on pathogen evolution in domestic animals by Dimopoulos, EA

Early cave art and ancient DNA record the origin of European bison by Soubrier, J, Gower, G, Chen, K, Chivall, D, Douka, K, Higham, T, Larson, G

Interpreting patterns in transcriptomes and ancient DNA from Next Generation Sequencing data by Lin, AT

Subjects:

Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia by Loog, L, Thalmann, O, Sinding, M-HS, Schuenemann, VJ, Perri, A, Germonpré, M, Bocherens, H, Witt, KE, Castruita, JA, Velasco, MS, Lundstrøm, IKC, Wales, N, Sonet, G, Frantz, L, Schroeder, H, Budd, J, Jimenez, E-L, Fedorov, S, Gasparyan, B, Kandel, AW, Lázničková‐Galetová, M, Napierala, H, Uerpmann, H, Nikolskiy, PA, Pavlova, EY, Pitulko, VV, Herzig, K, Malhi, RS, Willerslev, E, Hansen, AJ, Dobney, K, Gilbert, MTP, Krause, J, Larson, G, Eriksson, A, Manica, A

Inferring allele frequency trajectories from ancient DNA indicates that selection on a chicken gene coincided with changes in medieval husbandry practices. by Loog, L, Thomas, M, Barnett, R, Allen, R, Sykes, N, Paxinos, P, Lebrasseur, O, Dobney, K, Peters, J, Manica, A, Larson, G, Eriksson, A

“…Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. …”

Human influences on animals from an ancient DNA perspective: case studies on Chinese domestic cats (felis catus), Chinese leopard cats (prionailurus bengalensis), fallow deer (dama dama), and Chinese domestic pigs (sus scrofa) by Han, Y

“…With the advance of ancient DNA techniques, the availability of genomic data from ancient samples has profoundly increased, and now with great possibilities we are able to investigate the past and gain knowledge of the phased genetic changes in history. …”

Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research by Larson, G, Velsko, I, Frantz, L, Herbig, A, Warinner, C

“…Using a set of in silico-generated metagenomic data sets, we investigated how the addition of ancient DNA (aDNA) damage patterns influences microbial taxonomic assignment by five widely used profilers: QIIME/UCLUST, MetaPhlAn2, MIDAS, CLARK-S, and MALT. …”

A composite window into human history by Johannsen, N, Larson, G, Meltzer, D, Vander Linden, M

“…The possible benefits of ancient DNA (aDNA) research for archaeology are enormous. …”

Animal domestication in the era of ancient genomics by Frantz, LAF, Bradley, DG, Larson, G, Orlando, L

“…Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. …”

Ancient shipwrecks and archaeological science: characterising cargo items through stable isotope, organic residue, and DNA analysis by Briggs, EH

“…</p> <p>The third method by which this research attempts to characterise ancient shipwreck cargo items is through ancient DNA analysis. There is tremendous potential for DNA studies to resolve long-standing questions in both terrestrial and underwater archaeology. …”

Correlating Bayesian date estimates with climatic events and domestication using a bovine case study. by Ho, S, Larson, G, Edwards, C, Heupink, T, Lakin, K, Holland, P, Shapiro, B

“…We present a Bayesian phylogenetic analysis of 481 mitochondrial D-loop sequences, including 228 radiocarbon-dated ancient DNA sequences, using a multi-demographic coalescent model. …”

Ancient chicken remains reveal the origins of virulence in Marek’s disease virus by Fiddaman, SR, Dimopoulos, EA, Lebrasseur, O, du Plessis, L, Vrancken, B, Charlton, S, Haruda, AF, Tabbada, K, Flammer, PG, Dascalu, S, Marković, N, Li, H, Franklin, G, Symmons, R, Baron, H, Daróczi-Szabó, L, Shaymuratova, DN, Askeyev, IV, Putelat, O, Sana, M, Davoudi, H, Fathi, H, Mucheshi, AS, Vahdati, AA, Zhang, L, Foster, A, Sykes, N, Baumberg, GC, Bulatović, J, Askeyev, AO, Askeyev, OV, Mashkour, M, Pybus, OG, Nair, V, Larson, G, Smith, AL, Frantz, LAF

“…Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.…”

Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos by Sinding, M-HS, Ciucani, MM, Ramos-Madrigal, J, Carmagnini, A, Rasmussen, JA, Feng, S, Chen, G, Vieira, FG, Mattiangeli, V, Ganjoo, RK, Larson, G, Sicheritz-Pontén, T, Petersen, B, Frantz, L, Gilbert, MTP, Bradley, DG

“…Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so.…”

Dog domestication and the dual dispersal of people and dogs into the Americas by Perri, AR, Feuerborn, TR, Frantz, LAF, Larson, G, Malhi, RS, Meltzer, DJ, Witt, KE

“…Advances in the isolation and sequencing of ancient DNA have begun to reveal the population histories of both people and dogs. …”

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. …”

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. …”

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. …”