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Kimsis J, Petersone-Gordina E, Poksane A, Vilcāne A, Moore J, Gerhards G, Ranka R. Application of natural sciences methodology in archaeological study of Iron Age burials in Latvia: pilot study. Forensic Sci Med Pathol 2023; 19:8-15. [PMID: 36348137 DOI: 10.1007/s12024-022-00553-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Natural sciences provide several modern methodologies that could be successfully applied in archaeological studies. In this pilot study, archaeological human remains from two Iron Age cemeteries (7th-twelfth centuries AD), Lejasbitēni and Čunkāni-Dreņģeri, which are located in different regions of Latvia, were studied. We applied ancient DNA (aDNA) and tooth enamel peptide analysis to determine the biological sex of the individuals. In addition, aDNA analysis was used to perform mtDNA haplogroup analysis. In most cases, the results of aDNA analysis regarding the biological sex of individuals coincided with the gender assigned based on grave orientation and grave goods. The results of sex determination using peptide analysis in all four individuals for whom data were available matched the possible gender. Of the 17 samples that had sufficient DNA for sequencing, seven samples had enough reads to perform mtDNA haplogroup analysis. The H2a2a, I4a1, H2a2a1, and H16c mtDNA haplogroups were identified in the individuals from the Lejasbitēni cemetery, while the T2b and K1a + 150 mtDNA haplogroups were identified in the individuals from the Čunkāni-Dreņģeri cemetery. Overall, the obtained results demonstrated the feasibility of applying aDNA and tooth enamel peptide analysis for biological sex determination within archaeological studies. The availability of human aDNA data will be highly useful for investigating the demographic history and social structures in Iron Age Latvia.
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Affiliation(s)
- Janis Kimsis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Alise Poksane
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Antonija Vilcāne
- Institute of Latvian History, University of Latvia, Riga, Latvia
| | - Joanna Moore
- Department of Archaeology, Durham University, Durham, UK
| | - Guntis Gerhards
- Institute of Latvian History, University of Latvia, Riga, Latvia
| | - Renate Ranka
- Latvian Biomedical Research and Study Centre, Riga, Latvia.
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Buonasera T, Eerkens J, de Flamingh A, Engbring L, Yip J, Li H, Haas R, DiGiuseppe D, Grant D, Salemi M, Nijmeh C, Arellano M, Leventhal A, Phinney B, Byrd BF, Malhi RS, Parker G. A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation. Sci Rep 2020; 10:11897. [PMID: 32681049 PMCID: PMC7368048 DOI: 10.1038/s41598-020-68550-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/19/2020] [Indexed: 11/09/2022] Open
Abstract
Sex estimation of skeletons is fundamental to many archaeological studies. Currently, three approaches are available to estimate sex-osteology, genomics, or proteomics, but little is known about the relative reliability of these methods in applied settings. We present matching osteological, shotgun-genomic, and proteomic data to estimate the sex of 55 individuals, each with an independent radiocarbon date between 2,440 and 100 cal BP, from two ancestral Ohlone sites in Central California. Sex estimation was possible in 100% of this burial sample using proteomics, in 91% using genomics, and in 51% using osteology. Agreement between the methods was high, however conflicts did occur. Genomic sex estimates were 100% consistent with proteomic and osteological estimates when DNA reads were above 100,000 total sequences. However, more than half the samples had DNA read numbers below this threshold, producing high rates of conflict with osteological and proteomic data where nine out of twenty conditional DNA sex estimates conflicted with proteomics. While the DNA signal decreased by an order of magnitude in the older burial samples, there was no decrease in proteomic signal. We conclude that proteomics provides an important complement to osteological and shotgun-genomic sex estimation.
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Affiliation(s)
- Tammy Buonasera
- Department of Environmental Toxicology, University of California, Rm 5241B Meyer Hall, 1 Shields Ave, Davis, CA, 95616, USA. .,Department of Anthropology, University of California, Davis, USA.
| | - Jelmer Eerkens
- Department of Anthropology, University of California, Davis, USA
| | - Alida de Flamingh
- Program in Ecology, Evolution and Conservation Biology, University of Illinois, Urbana-Champaign, USA
| | - Laurel Engbring
- Far Western Anthropological Research Group, Inc, Davis, CA, USA
| | - Julia Yip
- Department of Environmental Toxicology, University of California, Rm 5241B Meyer Hall, 1 Shields Ave, Davis, CA, 95616, USA
| | - Hongjie Li
- Department of Anthropology, University of Illinois, Urbana-Champaign, USA
| | - Randall Haas
- Department of Anthropology, University of California, Davis, USA
| | | | - Dave Grant
- D&D Osteological Services, LLC, San Jose, CA, USA
| | - Michelle Salemi
- Proteomic Core Facility, Genome Center, University of California, Davis, CA, USA
| | - Charlene Nijmeh
- Muwekma Ohlone Tribe of the San Francisco Bay Area, Milpitas, CA, USA
| | - Monica Arellano
- Muwekma Ohlone Tribe of the San Francisco Bay Area, Milpitas, CA, USA
| | - Alan Leventhal
- Muwekma Ohlone Tribe of the San Francisco Bay Area, Milpitas, CA, USA.,Department of Anthropology, San Jose State University, San Jose, CA, USA
| | - Brett Phinney
- Proteomic Core Facility, Genome Center, University of California, Davis, CA, USA
| | - Brian F Byrd
- Far Western Anthropological Research Group, Inc, Davis, CA, USA
| | - Ripan S Malhi
- Program in Ecology, Evolution and Conservation Biology, University of Illinois, Urbana-Champaign, USA.,Department of Anthropology, University of Illinois, Urbana-Champaign, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, USA
| | - Glendon Parker
- Department of Environmental Toxicology, University of California, Rm 5241B Meyer Hall, 1 Shields Ave, Davis, CA, 95616, USA.
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