First ancient bovine DNA evidence from India: difficult but not impossible

Ancient DNA isolation from the tropical countries has been shown to be very difficult in the past. Here for the first time we have been successful in isolating ancient DNA from Indian cattle samples. We were able to obtain DNA and sequence the partial mitochondrial D-loop in 3 of the 15 bovine fossil samples ranging in age from 2000 BC to 1000 AD, and were able to further identify the most recent sample as being of Bos indicus origin. Our results on ancient DNA extraction from India will encourage other researchers in this field to carry out further studies of ancient DNA from Indian bovine samples. Our results represent the first successful extraction and amplification of bovine ancient DNA from India, and thus may pave the road for a better understanding of demographic and historical processes of cattle domestication that has taken place in this region.     

Biofilm growth in human skeletal material from ancient Mesopotamia

Investigators have long recognised the effects of microbial activity on archaeological bone. These investigators, however, have focused on single or groups of microbes rather than on complex microbial aggregates such as biofilms, a focus that has affected our understanding of archaeological bone biodeterioration. In this paper, we report on the investigation of a biofilm in archaeological human bone from the site of Tell Leilan, Syria (2900–1900 BCE). Scanning electron microscopy indicated that the biofilm is characterised by single cells and microcolonies of bacteria and fungi, as well as calcite crystals that were all embedded within extracellular polymeric substances. Using culture techniques and DNA sequencing, we isolated and identified several microbes from the biofilm including Amycolatopsis sp., Penicillium chrysogenum, Aspergillus sp., Chaetomium sp., and Cladosporium sp. Having characterised the Leilan biofilm, we are now closer to understanding the complex process of bone biodeterioration in archaeological bone collections.     

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

Archaeologists, linguists and geneticists generally agree that Near Oceania was subject to two major pulses of human dispersal: a Pleistocene occupation around 40,000 BP and a Late-Holocene migration at 3500 BP commonly associated with the Austronesian expansion out of Taiwan. The latter led to the development of the Lapita cultural complex in the Bismarck Archipelago which resulted in the settlement of Remote Oceania and there are a variety of competing models (express train, slow boat, entangled bank, etc.) used to explain this. Recent genetic studies have focused on this issue, but none of them have taken into consideration the bias possibly introduced by 19th-century historically reported population decline caused by European contact.     

Identification of animal skin of historical parchments by polymerase chain reaction (PCR)-based methods

This study deals with establishing of a PCR-based strategy with the aim to recognize the animal origin of different historical parchments. This is one of relatively rare studies on the analysis of ancient DNA from parchments. Robustness of the PCR technology is demonstrated by successful identification of the animal species using only a small amount of DNA isolated from 12 parchment samples. Ten PCR-based assays specific for the detection of different animal species (Bos taurus, Ovis aries, Capra hircus, Sus scrofa, Oryctolagus domestica, Cervus elaphus, Capreolus capreolus, Dama dama) and two PCR assays utilizing universal primers were evaluated and optimized with the aim to find a rapid parchment identification method, which would be more reliable than the classical microscopic examination. The optimized PCR methods produced satisfactory results. Out of 12 investigated parchments, 9 items were unambiguously identified, DNA from 2 samples could not be amplified with any of the species-specific PCR assays, and only one parchment produced controversial results. The species-specific PCR results were confirmed by direct sequencing and PCR cloning with consequent sequencing. Our approach, including isolation of parchment DNA by chaotropic solid-phase extraction, optimization of the PCR programs and high-stringency annealing temperatures, demonstrated to be effective, easy and reliable for the analysis of historical parchment DNA. We consider this PCR-based strategy potentially useful also for investigation of other types of animal items conserved in museums, galleries or libraries.     

A flock of sheep,goats and cattle: ancient DNA analysis reveals complexities of historical parchment manufacture

Parchments comprise one of the most common and valuable sources of archaeological and historical data. Previous studies have shown that parchment also preserves genetic data. These data could be valuable for population studies, to understand past animal husbandry, the development of breeds and varieties and to comment on the provenance of parchments. To improve our understanding of DNA contained in parchments, we analysed genetic data, including both mitochondrial and autosomal loci, from 18th to 19th century English parchments which stable isotope analysis had indicated were well-preserved. DNA results were unexpected. All but one of the parchments produced multiple sequences matching several different species. Ion beam analysis ruled out surface treatments of the parchments (including ink and animal glues) as the origin of these multiple sequences. Our results suggest that the DNA content of parchment is more complex than previous research has suggested and that multiple stages of parchment manufacture, treatment and storage are preserved in parchment DNA extracts.     

MtDNA origins of an enslaved labor force from the 18th century Schuyler Flatts Burial Ground in colonial Albany,NY: Africans,Native Americans,and Malagasy?

A burial ground located in the Town of Colonie, NY along the Hudson River revealed fourteen individuals dated from the 17th through the early 19th centuries. Bioarchaeological analysis suggested some of these individuals were of African ancestry who had worked and died on the property owned by the prominent Schuyler family. Mitochondrial DNA (mtDNA) analysis was carried out on skeletal remains of seven adults using restriction fragment length polymorphism typing and direct sequencing of the control region to infer their origins and relatedness. Results show that none of the individuals were maternally related, with four individuals identified as African haplogroup L, one identified as Native American haplogroup X, and two identified as haplogroup M and M7. Individuals of African ancestry correlate with published mtDNA data on African Americans and their geographical origins corroborate with the various exit points during the African slave trade to New York State. Individuals identified as haplogroup M7 and M resemble lineages found in Madagascar. Historical documents suggest several hundred people were imported from Madagascar through illegal trading to New York by the end of the 17th century. This study highlights the diverse origins of the enslaved labor force in colonial New York and contributes to our understanding of African American history in the northeast.     

Aspartic acid racemization variability in ancient human remains: implications in the prediction of ancient DNA recovery

The extent of racemization of aspartic acid (Asp) – expressed as d/l ratio – has been used as a marker of biomolecular degradation in ancient remains. However, Asp racemization rate is highly variable, and depends on biochemical and geochemical factors. In this paper we aim to determine to which extent the fraction analyzed and the kind of sample used may influence the d/l Asp ratios. Other factors, such as burial site and sample preservation conditions, are also considered.     

DNA AND PROTEIN RECOVERY FROM WASHED EXPERIMENTAL STONE TOOLS*

Traces of protein and DNA are preserved on stone tools used to process animals. Previous research documents the identification of protein residues from tools sonicated in 5% ammonium hydroxide, but it remains untested whether the same treatment yields useable DNA. In this study we report both DNA and protein recovery using 5% ammonium hydroxide from residues on stone tools. We extracted 13‐year‐old residues from experimentally manufactured stone tools used to butcher a single animal. We also show that surface washing procedures typically used to curate stone tools remove only a small fraction of the DNA and protein deposited during animal butchery.