TY - JOUR
T1 - A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation
AU - Buonasera, Tammy
AU - Eerkens, Jelmer
AU - de Flamingh, Alida
AU - Engbring, Laurel
AU - Yip, Julia
AU - Li, Hongjie
AU - Haas, Randall
AU - DiGiuseppe, Diane
AU - Grant, Dave
AU - Salemi, Michelle
AU - Nijmeh, Charlene
AU - Arellano, Monica
AU - Leventhal, Alan
AU - Phinney, Brett
AU - Byrd, Brian F.
AU - Malhi, Ripan S.
AU - Parker, Glendon
N1 - Funding Information:
We thank the Muwekma Ohlone Tribe of the San Francisco Bay Area for allowing us to conduct this analysis and for supporting this research. We also thank Drs. Jane Buikstra and Anne Stone for advice about the project and the manuscript, and Christopher Beckham, Samantha Cramer, Davis Watkins, and Lucia Diaz for help in preparing enamel samples. Analysis funding was provided by FWARG via an archaeological mitigation contract with the San Francisco Public Utilities Commission. FWARG thanks Kimberly Stern Liddell, Bryan Deassaure, and Deborah Craven-Green for their support. GJP and JWE acknowledge the support of the National Science Foundation (#BCS-1825022). RSM also acknowledges support of the National Science Foundation (#BCS-1518026). AF was supported by the Cooperative State Research, Education, and Extension Service, US Department of Agriculture, under project number ILLU 875–952.
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/12/1
Y1 - 2020/12/1
N2 - 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.
AB - 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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U2 - 10.1038/s41598-020-68550-w
DO - 10.1038/s41598-020-68550-w
M3 - Article
C2 - 32681049
AN - SCOPUS:85088100363
SN - 2045-2322
VL - 10
JO - Scientific Reports
JF - Scientific Reports
IS - 1
M1 - 11897
ER -