A DNA test for sex identification in cattle confirms osteometric results

It is of vital importance to be able to sex identify cattle remains to understand the strategies and importance of cattle husbandry in an ancient society. This is usually done from osteoarchaeological assemblages and often relies on measurements of metapodials. The breadth measurement of the distal trochlea is considered an easy way to identify the sex. Bones from males appears to be easily distinguishable from female counterparts, although it has been complicated to find an external control for the morphological results. Here we investigate the reliability of these particular morphometrics for sex identifying cattle bones with molecular genetics. We use a sex discriminating single nucleotide polymorphism in the ZFXY gene and we apply it to DNA from the bones. To keep the fragment size short and suitable for ancient DNA we base the test on a SNP. The test confirms the osteological sex identification in all cases were DNA could be retrieved. This molecular method can also be used when no fragments suitable for osteological sex identification can be found or when the measurements are non-conclusive.     

Wild or domesticated: DNA analysis of ancient water buffalo remains from north China

Recent zooarchaeological studies on water buffalo (Bubalus sp.) remains from China and south Asia question the traditional view that water buffalo were first domesticated in Neolithic China over 7000 years ago. The results from several recent population genetic studies of modern domesticated buffalo (Bubalus bubalis) are not consistent with each other, placing the original center of buffalo's domestication in south Asia, southeast Asia, or China. This paper reports a study using an ancient DNA approach to analyze water buffalo remains from Neolithic sites in north China to investigate their affinities with modern domesticated water buffalo, and to shed light on the origin of modern domesticated water buffalo in China.A 169 bp fragment of D-loop mitochondrial DNA was successfully amplified and verified for 13 of 24 bone samples obtained from seven archaeological sites along the Wei River valley in Shaanxi Province, China. The bone samples which yielded positive DNA can be dated to 8000–3600 cal. BP. The phylogenetic analysis of the obtained DNA sequences along with modern water buffalo sequences indicated that the ancient water buffalos were not the direct ancestor of modern domesticated water buffalo. However, the phylogenetic analysis, along with BLAST searches of these ancient DNA sequences, did demonstrate their relatedness to water buffalo more so than to any other bovid species, confirming the existence of indigenous wild (but now extinct) water buffalo species (B. mephistopheles) in ancient China.The DNA analysis of these ancient remains failed to establish direct links between modern domesticated water buffalo (B. bubalis) and indigenous water buffalo (B. mephistopheles) from ancient China. If further DNA studies of more ancient remains from other regions of China confirm the observation of solely indigenous water buffalo species in ancient China, it would suggest modern water buffalo might not have been first domesticated in China.     

Ancient DNA in human bones from Neolithic and Bronze Age sites in Greece and Crete

Attempts were made to detect ancient DNA (aDNA) in samples of 88 human skeletons from eight Neolithic and Bronze Age sites in Greece and Crete. Ancient DNA was absent in specimens from Nea Nikomedia, Lerna, Karaviádena (Zakro), Antron Grave Circle A and Mycenae Grave Circle A. For each of three skeletons from Antron Grave Circle B that were sampled, polymerase chain reactions (PCRs) gave products for nuclear but not mitochondrial DNA, but amplicon yield was low and inconsistent with replicate PCRs failing to give reproducible results. With specimens from Mycenae Grave Circle B, evidence for mitochondrial aDNA was obtained for four of the 22 skeletons that were studied, and at Kouphovouno evidence for mitochondrial and/or nuclear aDNA was obtained with eight of the 20 skeletons that were examined. We conclude that, although aDNA might be present in some Eastern Mediterranean skeletons from later centuries of the Bronze Age, it is not commonly found in material from this period and is likely to be absent from older material.     

Cats of the Pharaohs: Genetic Comparison of Egyptian Cat Mummies to their Feline Contemporaries

The ancient Egyptians mummified an abundance of cats during the Late Period (664 - 332 BC). The overlapping morphology and sizes of developing wildcats and domestic cats confounds the identity of mummified cat species. Genetic analyses should support mummy identification and was conducted on two long bones and a mandible of three cats that were mummified by the ancient Egyptians. The mummy DNA was extracted in a dedicated ancient DNA laboratory at the University of California - Davis, then directly sequencing between 246 and 402 bp of the mtDNA control region from each bone. When compared to a dataset of wildcats (Felis silvestris silvestris, F. s. tristrami, and F. chaus) as well as a previously published worldwide dataset of modern domestic cat samples, including Egypt, the DNA evidence suggests the three mummies represent common contemporary domestic cat mitotypes prevalent in modern Egypt and the Middle East. Divergence estimates date the origin of the mummies' mitotypes to between two and 7.5 thousand years prior to their mummification, likely prior to or during Egyptian Predyanstic and Early Dynastic Periods. These data are the first genetic evidence supporting that the ancient Egyptians used domesticated cats, F. s. catus, for votive mummies, and likely implies cats were domesticated prior to extensive mummification of cats.     

Determination of a kinship system using ancient DNA,mortuary practice,and historic records in an upper Canadian pioneer cemetery

Recovered and amplified ancient DNA (aDNA), from a historically documented 19th century Upper Canadian pioneer cemetery produced genotypes that were used to infer a past societal kinship system. While the results from multiplex short tandem repeat (STR) amplifications showed an unreliable polymerase chain reaction (PCR) product, a single locus HUMTH01 analysis yielded reproducible data and an allelic frequency pattern not statistically different from modern populations. Mitochondrial (mt) DNA HVR II data showed that a combined cemetery database exhibited reduced haplotype diversity indicators, as well as clusters of probable maternally related burials. The chronological persistence and replacement of mtDNA clusters approximately every two generations suggests a patrilineal/patrilocal kinship structure from a virilocal burial program for the Harmony Road cemetery. Through the integration of the aDNA analysis with archaeological material culture, historic records, and other ethnohistoric sources of information, this conclusion is supported. In this study persisting patrilineally inherited surnames act as a surrogate for aDNA Y‐chromosome haplotype analysis. These results suggest that aDNA applications on aggregate skeletal collections where sparse, or no ethnological or historical documentation exists, may result in incorrect population history inferences if the presence of a kinship interment bias is not considered. Copyright © 2003 John Wiley & Sons, Ltd.     

Mitochondrial DNA from 3000-year old chickens at the Teouma site,Vanuatu

Chickens were part of the Lapita cultural complex, transported into and through the Pacific by prehistoric colonists; as such they can be used as a proxy for tracking prehistoric migration and interaction. The Lapita site of Teouma in Vanuatu is well known for the recovery of complete dentate stamped pots and a cemetery containing the largest collection of Lapita period skeletons ever found. Chicken bones recovered from these excavations provide the first ancient DNA sequences from any commensal organism directly associated with a Lapita context. The ancient mtDNA sequences obtained from two Teouma chicken bones are compared with previously published archaeologically derived ancient DNA sequences to extend our understanding of the spread of chickens in Pacific prehistory. The results also show that the haplogroup E signature was present in very early populations of chickens transported into Remote Oceania. This study also adds to the suite of available data relating to isotopic signatures for commensal animals during the early settlement of Vanuatu and may reveal a different diet for Teouma chickens than those from other early prehistoric assemblages in the Pacific.     

Genetic characterization of an archaeological sheep assemblage from South Africa’s Western Cape

The Neolithic Revolution, constituting a shift from food acquisition to food production, came to Africa as it did to most of the rest of the world: through processes of transmission rather than through de novo innovation. In contrast with other regions the pastoral management of cattle, sheep and goats was widespread in Africa thousands of years before settled agricultural communities or the use of domesticated plants were in evidence ( 46, 35 and 10). We report here the discovery of haplogroup B in the first genetic analysis of an African archaeological sheep assemblage.     

Ancient DNA,a Neolithic legging from the Swiss Alps and the early history of goat

Ancient DNA from a Neolithic legging (1st half of the 3rd millennium BC) found at Lenk, Schnidejoch (2750 m a.sl.) in the Swiss Alps has demonstrated, that modern distribution of genetic variation does not reflect past spatio-temporal signatures. The legging was made from the skin of a domestic goat (Capra hircus), belonging to the caprine haplogroup B1, which is marginal in Europe today, but represents a third highly diverse goat haplogroup entering Europe already in the Neolithic. Population expansion of lineage B therefore happened more than 4500 years ago, but their members were at some point almost completely replaced by goats of today's common A and C haplogroups.     

Ancient DNA (aDNA) studies of man and microbes: general similarities,specific differences

The study of ancient DNA (aDNA) using molecular methods is an increasingly valuable tactic in bioarchaeology. While this method must be carefully undertaken to ensure that the molecules detected are representative of the ancient sample and not modern contaminates, there is a danger that a ‘one size fits all’ approach to validation will lead to misinterpretation and/or missed opportunities of valuable findings. When comparing human and pathogen aDNA, there are many shared technical means that can ensure best practice. However, there are a number of assumptions that should not be used for both scenarios. We discuss these aspects in reference to a recent article published by this journal and highlight some of the latest advances in molecular detection of ancient pathogen DNA that can further improve this endeavour. Copyright © 2009 John Wiley & Sons, Ltd.     

Recovery of DNA from archaeological insect remains: first results,problems and potential

We report the recovery of short fragments of PCR amplifiable ancient DNA from exoskeletal fragments of the grain weevil Sitophilus granarius (L.) extracted from Roman and medieval deposits in Northern England. If DNA preservation in archaeological insect remains is widespread then many applications in the spheres of evolutionary studies and archaeology can be conceived, some of which are outlined.