Ancient DNA Research

Mitochondrial DNA haplotypes of Devensian hyaenas from Creswell Crags, England

by Danae Dodge

Dodge, D.R., Bouwman, A., Pettitt, P.B., Brown, T., Mitochondrial DNA haplotypes of Devensian hyaenas from Creswell Crags, England. Archaeological and Anthropological Sciences DOI: 10.1007/s12520-012-0096-1

Spotted hyaena (Crocuta crocuta) remains have been recovered from British Middle and Upper Pleistocene sites at... more Spotted hyaena (Crocuta crocuta) remains have been recovered from British Middle and Upper Pleistocene sites at intervals within the period 700–730 ka BP. Morphological studies have suggested that hyaenas of the Last Interglacial sensu stricto (Ipswichian: Marine Isotope Stage [MIS] 5e, 130–115 ka BP) and Last Glacial (Devensian: MIS 3, 61–24 ka BP) were two distinct populations, the Ipswichian hyaenas becoming extinct in Britain during MIS 5 and the Devensian ones arriving via a subsequent migration from continental Europe. However, the apparent presence of hyaenas in later MIS 5 deposits has led to the alternative suggestion that there was a southern relict population from which the Devensian hyaenas originated.
We obtained ancient DNA (aDNA) sequences from four Devensian hyaena specimens from Creswell Crags, Derbyshire, dated to around 45 ka 14C BP. Each of these four specimens belonged to the mitochondrial DNA (mtDNA) clade A. This clade is not thought to have been present in Europe until ~360 ka BP, after the initial arrival of hyaenas in Britain. The DNA results, therefore, suggest that there were at least two waves of hyaena dispersals into Britain. The results are consistent with the repeated dispersals into Britain of another Pleistocene social carnivore, Homo sapiens.

First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns

by Ron Pinhasi

Withering Away—25,000 Years of Genetic Decline Preceded Cave Bear Extinction

by Ron Pinhasi

Kovatsi et al: DNA repair enables sex identification in genetic material from human teeth

by Sofia Voutsaki

(2009) Kovatsi, L., Nikou, D., Triantaphyllou, S., Njau, S.N., Kouidou, S. Voutsaki, S. DNA repair enables sex identification in genetic material from human teeth. Hippokratia 13:3, 165-168.

Background: The purpose of this study was to test the effectiveness of a DNA repair protocol in improving genetic... more Background: The purpose of this study was to test the effectiveness of a DNA repair protocol in improving genetic testing
in compromised samples, frequently encountered in Forensic Medicine.
Methods: In order to stretch the experiment conditions to the limits, as far as quality of samples and DNA is concerned,
we tried the repair protocol on ten ancient human teeth obtained from an equal number of skeletons from a burial site in
Lerna, Middle Helladic Greece (2100 - 1700 BC). For these samples, sex was previously determined morphologically,
serving as a reference to compare our molecular data with. The samples were analysed using the DNA amelogenin sex
test assay prior and after DNA polymerase repair. For every individual, two molecular sex determinations were obtained
by visualising PCR products on an agarose gel.
Results: DNA repair enabled genetic testing in these samples. Successful amplification of the amelogenin gene was
obtained only from the repaired DNA in eight out of ten samples. Prior to the repair treatment, none of these samples
yielded any PCR products, thus attesting to the authenticity of the amplified sequence. The concordance between morphological
and molecular analysis was in reasonable agreement (71%).
Conclusions: These results reveal the impact of the repair process in studying single copy genes from low quality DNA.
This protocol could facilitate molecular analysis in compromised samples, encountered in forensic medicine, as well as
enable genetic studies in ancient remnants. Hippokratia 2009; 13 (3): 165-168
Key words: DNA; repair; sex; amelogenin; forensics

Palaeogentic analysis of bovine remains from Camino de las Yeseras and Humanejos

by Corina Liesau von Lettow-Vorbeck

E.-M. Geigl, S.de Guimaraes & C. Liesau. In :C. Blasco, C. Liesau, P. Ríos (Eds.) (2011): Yacimientos calcolíticos con campaniforme de la región de Madrid. Patrimonio Arqueológico/6 Universidad Autónoma de Madrid: 199-210.

Over the last few years, thousands of bovine bone remains were recovered from Camino de las Yeseras, selected and... more Over the last few years, thousands of bovine bone remains were recovered from Camino de las Yeseras, selected and cleaned. Almost a hundred aurochs (Bos primigenius, Boj.) bones were found in different contexts. Two crania found in peculiar deposits, prompted us to perform a more comprehensive study beyond traditional archaeozoological, osteomorpho-logical and metrical characterization. Close cooperation between the Department of Prehistory and Archaeology of the Universidad Autónoma de Madrid and the Palaeogenome group of the Jacques Monod Institute, enabled us to successfully carry out a palaeogenetic study of these bone remains, which along with being integrated into a larger study of the genetic diversity of aurochsen, yielded new and interesting results on a more local scale as well, i.e., on the genetic population structure of recent Holocene aurochsen of the Iberian Peninsula.

Indo-European and Asian origins for modern Chilean and Pacific archaeological chickens revealed by mtDNA

by Nic Rawlence

Correction: Indo-European and Asian origins for modern Chilean and Pacific archaeological chickens revealed by mtDNA

by Nic Rawlence

Reply to Storey et al.: More DNA and dating studies needed for ancient El-Arenal-1 chickens

by Nic Rawlence

Coprolite deposits reveal the diet and ecology of the extinct New Zealand megaherbivore moa (Aves, Dinornithiformes)

by Nic Rawlence

DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa

by Nic Rawlence

Evolutionary history of the Falklands wolf

by Nic Rawlence

Moa’s Ark or volant ghosts of Gondwana? Insights from nineteen years of ancient DNA research on the extinct moa (Aves: Dinornithiformes) of New Zealand

by Nic Rawlence

Paleoparasitological Findings in Medieval and Early Modern Archaeological Deposits from Hradební Street, Chrudim, Czech Republic

by Interdisciplinaria Archaeologica IANSA

Morphology and Molecular Analysis of Ancient Grape Seeds

by Interdisciplinaria Archaeologica IANSA

Bioarchaeological Analysis of Bronze Age Human Remains from the Podillya Region of Ukraine

by Interdisciplinaria Archaeologica IANSA

Comprehensive Site Chronology and Ancient Mitochondrial DNA Analysis from Verteba Cave – a Trypillian Culture Site of Eneolithic Ukraine

by Interdisciplinaria Archaeologica IANSA

Ancient Solomon Islands mtDNA: assessing Holocene settlement and the impact of European contact

by Tim Thomas

Ricaut, F.-X.; Thomas, T.; Mormina, M.; Cox, M.P.; Bellatti, M.; Foley, R.A. & Mirazon-Lahr, M. (2010) Ancient Solomon Islands mtDNA: assessing Holocene settlement and the impact of European contact. Journal of Archaeological Science 37: 1161-1170.

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

by Angela Graefen

Andreas Keller, Angela Graefen, Markus Ball, Mark Matzas, Valesca Boisguerin, Frank Maixner, Petra Leidinger, Christina Backes, Rabab Khairat, Michael Forster, Björn Stade, Andre Franke, Jens Mayer, Jessica Spangler, Stephen McLaughlin, Minita Shah, Clarence Lee, Timothy T. Harkins, Alexander Sartori, Andres Moreno-Estrada, Brenna Henn, Martin Sikora, Ornella Semino, Jacques Chiaroni, Siiri Rootsi, Natalie M. Myres, Vicente M. Cabrera, Peter A. Underhill, Carlos D. Bustamante, Eduard Egarter Vigl, Marco Samadelli, Giovanna Cipollini, Jan Haas, Hugo Katus, Brian D. O'Connor, Marc R.J. Carlson, Benjamin Meder, Nikolaus Blin, Eckart Meese, Carsten M. Pusch & Albert Zink

Nature Communications 3

The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the... more The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.

Bayesian estimation of substitution rates from ancient DNA sequences with low information content

by Sergios-Orestis Kolokotronis

Systematic Biology

Characterising the potential of sheep wool for ancient DNA analyses

by Margarita Gleba

With L. Ø. Brandt, L. D. Tranekjer, M. Mannering, M. Ringgaard, K. M. Frei, E. Willerslev, and M. T. P. Gilbert, 2011, Archaeological and Anthropological Sciences 3 (2), 209-221

The use of wool derived from sheep (Ovis aries) hair shafts is widespread in ancient and historic textiles. Given that... more The use of wool derived from sheep (Ovis aries) hair shafts is widespread in ancient and historic textiles. Given that hair can represent a valuable source of ancient DNA, wool may represent a valuable genetic archive for studies on the domestication of the sheep. However, both the quality and content of DNA in hair shafts are known to vary, and it is possible that common treatments of wool such as dyeing may negatively impact the DNA. Using quantitative real-time polymerase chain reaction (PCR), we demonstrate that in general, short fragments of both mitochondrial and single-copy nuclear DNA can be PCR-amplified from wool derived from a variety of breeds, regardless of the body location or natural pigmentation. Furthermore, although DNA can be PCR-amplified from wool dyed with one of four common plant dyes (tansy, woad, madder, weld), the use of mordants such as alum or iron leads to considerable DNA degradation. Lastly, we demonstrate that mtDNA at least can be PCR-amplified, cloned and sequenced from a range of archaeological and historic Danish, Flemmish and Greenlandic wool textile samples. In summary, our data suggest that wool offers a promising source for future ancient mitochondrial DNA studies.