Malin Holst

Genotype of a historic strain of Mycobacterium tuberculosis

The use of ancient DNA in paleopathological studies of tuberculosis has largely been restricted to confirmation of disease identifications made by skeletal analysis; few attempts at obtaining genotype data from archaeological samples have been made because of the need to perform different PCRs for each genetic locus being studied in an ancient DNA extract. We used a next generation sequencing approach involving hybridization capture directed at specific polymorphic regions of the Mycobacterium tuberculosis genome to identify a detailed genotype for a historic strain of M. tuberculosis from an individual buried in the 19th century St. George’s Crypt, Leeds, West Yorkshire, England. We obtained 664,500 sequencing by oligonucleotide ligation and detection (SOLiD) reads that mapped to the targeted regions of the M. tuberculosis genome; the coverage included 218 of 247 SNPs, 10 of 11 insertion/deletion regions, and the repeat elements IS1081 and IS6110. The accuracy of the SOLiD data was checked by conventional PCRs directed at 11 SNPs and two insertion/deletions. The data placed the historic strain of M. tuberculosis in a group that is uncommon today, but it is known to have been present in North America in the early 20th century. Our results show the use of hybridization capture followed by next generation sequencing as a means of obtaining detailed genotypes of ancient varieties of M. tuberculosis, potentially enabling meaningful comparisons between strains from different geographic locations and different periods in the past.

Genomic signals of migration and continuity in Britain before the Anglo-Saxons

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (∼1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.

Preservation of the metaproteome: variability of protein preservation in ancient dental calculus

ABSTRACT Proteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus.

Proteomic evidence of dietary sources in ancient dental calculus

Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein β-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (eighth century BC to nineteenth century AD) in England, as well as 14 dental calculus samples from contemporary dental patients and recently deceased individuals, to characterize the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detect proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches and authentication strategies in the identification of dietary proteins from archaeological dental calculus. This study demonstrates that proteomic approaches can robustly identify foodstuffs in the archaeological record that are typically under-represented due to their poor macroscopic preservation.

Recent radiocarbon dating and skeletal analysis of two log coffin burials from Yorkshire: Willie Howe and Towthorpe 139

Abstract This paper presents the results of the re-analysis and dating of skeletal material from two Early Bronze Age barrows in the east of Yorkshire, which contained log coffin burials. Towthorpe 139, which was investigated in the nineteenth century by the antiquarian JR Mortimer and Willie Howe, Cowlam which was excavated by TCM Brewster in the 1960s. Analysis of the human remains from Towthorpe revealed that the inhumed body was that of an adult male and the cremated remains, which were found in the mound above the log coffin burial were of a young person. Those from Willie Howe were of an adult male who had suffered a blow to the head. Not enough of the Towthorpe burials survived to obtain radiocarbon dates; however, two determinations were obtained on the skeleton from Willie Howe. These dates have revealed that the human remains date to the period ca. 2200–2000 cal BC.

Response to the paper by Redfern and Clegg by Malin Holst

ABSTRACT In their paper, Redfern and Clegg draw attention to two key issues that have an adverse effect on English and Welsh osteological assemblages, including the commercial post-excavation analysis of human remains and academic research of human skeletons. This response to Redfern and Clegg’s paper is based on the experiences of these issues as a managing director of a commercial osteological company (York Osteoarchaeology Ltd) and as a lecturer in Bioarchaeology at the University of York and includes advice and suggestions from colleagues from both institutions.

Earlier Prehistoric Activity and a Later Iron Age and Roman Field System at Beacon Lagoons, Kilnsea, East Riding of Yorkshire

Abstract An archaeological strip, map and record exercise on behalf of the Environment Agency was undertaken as part of the Easington Wetlands Project. The excavations revealed earlier prehistoric activity, probably representing seasonal occupation at times of the year when intermittently available resources were abundant. This activity is dated by predominantly later Neolithic and early Bronze Age flints, two Bronze Age radiocarbon dates and later Bronze Age pottery. A Romano-British field system that may have had Iron Age origins was also identified. The pottery assemblage suggests the field system was in use up to the fourth century ad.