Sex estimation using sexually dimorphic amelogenin protein fragments in human enamel

Parker, Glendon J.; Yip, Julia; Eerkens, Jelmer W.; Salemi, Michelle; Durbin‐Johnson, Blythe; Kiesow, Caleb; Haas, Randall; Buikstra, Jane E.; Klaus, Haagen D.; Regan, Laura A.; Rocke, David M.; Phinney, Brett S.

doi:10.1016/j.jas.2018.08.011

Cited by 88 publications

(109 citation statements)

References 70 publications

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“…An independent t-test found no significant difference in AMELX signal between the two groups (two-tailed, df = 53, p = 0.78). This supports a stable proteomic signal over this timeframe (roughly 2,000 years) and is consistent with previously published observations 33 .…”

Section: Sex Estimation As a Function Of Proteomic Data Quality To Esupporting

confidence: 93%

“…All proteomic male sex estimates were based on confident assignments of multiple AMELY peptides and were considered determinate 62 . Female assignments were more complex, but the calculated probabilities of female sex (Pr(F)) were generally high and lower probabilities were corroborated with high quality DNA data 33 .…”

Section: Discussionmentioning

confidence: 64%

“…Sex estimates fell into definitive or conditional categories. All proteomic estimates were definitive in this study, with all males having more than two unique AMELY_HUMAN (AMELY) peptides and females having a probability of female sex (Pr(F)) greater than 0.5 (Methods) 33,62,63 . DNA-based conditional, or "consistent with .…”

Section: Sensitivity Of Different Methodsmentioning

confidence: 66%

“…Amelogenin peptides adhere to the biomineral interface or are incorporated into the apatite matrix, reducing peptide flexibility and reactivity 33,75 . Over time, proteins that are less incorporated in the mineral matrix, such as extracellular matrix proteins, will degrade at a faster rate resulting in a less complex proteome that is relatively enriched with amelogenin peptides 33,35 . As a result, remaining amelogenin peptides are more likely to be targeted by the mass spectrometry instrument for fragmentation, increasing the cumulative signal.…”

Section: Discussionmentioning

confidence: 99%

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A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation

Buonasera

Eerkens

Flamingh

et al. 2020

Sci Rep

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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. Biological sex plays an important role in the human experience, correlating to lifespan, reproduction, and a wide range of other biological factors 1-5. Sex and gender are also fundamental in structuring an array of cultural behaviors, including residence patterns, kinship, economic roles, and identity construction and expression 6-9. How sex interacts with gender and these particular issues is not static and can vary in detail across societies and over time 10-12. It is not surprising that sex is one of the most basic and important measures in bioarchaeological and forensic analyses. Typically, osteological features are used to estimate sex of skeletal remains, and the most widely used marker is the morphology of the os coxae 13-16. However, appropriate markers are not always sufficiently expressed or preserved to estimate sex using morphological criteria 17. A lack of sexually-dimorphic markers is especially acute for skeletons of infants and children who have not undergone puberty. Mortuary practices, such as cremation or secondary burial in charnel houses, can also can impose limitations on the utility of osteological sex estimates 18. The advent of DNA sequencing made it possible to use skeletal remains to estimate the sex of very young individuals; it also expanded sex estimations for fragmentary, pathological, and degraded skeletal materials 19-21. More recently, development of massively parallel DNA sequencing greatly improved genome coverage in archaeological samples 22-25. In addition to providing detailed genetic information, this allows biological sex to be estimated from shotgun sequencing data 25-27. These approaches were an improvement over earlier PCR-based marker

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Section: Sex Estimation As a Function Of Proteomic Data Quality To Esupporting

confidence: 93%

Section: Discussionmentioning

confidence: 64%

Section: Sensitivity Of Different Methodsmentioning

confidence: 66%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation

Buonasera

Eerkens

Flamingh

et al. 2020

Sci Rep

Self Cite

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“…In addition to ancient DNA studies, the past few years have witnessed a multiplicity of analyses based on the extraction and characterisation of long-term persistent biomolecules: proteins [56][57][58][59][60][61] . Since their amino acid sequence is coded for by the DNA, proteins carry genetically derived features that allow researchers to propose phylogenetic relationships of extinct species [62][63][64][65] , sex attribution 66,67 or even characterisation of palaeopathogens 68 . The major protein of bone and teeth, type I collagen (constituting 90% of the organic phase of these materials), is composed of amino acid sequences that carry taxon-related differences in their order, allowing species discrimination 69 .…”

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confidence: 99%

Palaeoproteomics gives new insight into early southern African pastoralism

Meillour

Zirah

Zazzo

et al. 2020

Sci Rep

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The advent of domestication is a major step that transformed the subsistence strategies of past human societies. In Africa, domestic caprines (sheep and goat) were introduced in the northeastern part of the continent from the Near East more than 9000 years ago. However, their diffusion southwards was slow. They are thought to have made their first appearance in the southern part of the continent ca. 2000 years ago, at a few Later Stone Age sites, including Leopard Cave (Erongo region, Namibia), which provided the oldest directly dated remains assigned to sheep or goat on the basis of morphology of bones and teeth. However, similarities in morphology, not only between these two domesticated caprine species, but also between them and the small wild antelopes, raised questions about the morphological species attribution of these remains. Additionally, the high fragmentation of the site's osteological remains makes it difficult to achieve species-level taxonomic identification by comparative anatomy. In this paper, we report molecular species identification of the Leopard Cave remains using palaeoproteomics, a method that uses protein markers in bone and tooth collagen to achieve taxonomic identification of archaeological remains. We also report new direct radiocarbon dates. Wild antelope remains from museum collections were used to enrich the available protein record and propose de novo type I collagen sequences. Our results demonstrate that the remains morphologically described as domesticates actually belong to a wild antelope species and that domestic caprines first appeared at Leopard Cave 1500 years later than previously thought. This study illustrates that the use of palaeoproteomics coupled with direct radiocarbon dates is particularly suited to complement classic zooarchaeological studies, in this case concerning the arrival of the first herding practices in arid environments. Understanding how past human populations interacted with their environment, and particularly with other animals, allows understanding large parts of societies, their organisation and their economy. Climatic change is one of the factors that may have pressured human populations to adapt their subsistence strategy and diet. With Saharan and Sahelian aridification starting at the end of the African Humid Period (ca. 14,800-5500 years before present [BP] 1), Africa experienced its last major climatic change 2 and humans had to adapt to new environments 3. Thus, the inception of domestication may have been constrained by fewer food resources and their increased unpredictability 4. Given that they have no wild representatives on the continent, it is now commonly accepted that domestic sheep (Ovis aries) and goat (Capra hircus) were introduced from the Near East 5,6. The first archaeozoological evidence of these species dates from the end of the 9th and the beginning of the 8th millennium BP, in the eastern part of the Sahara 7-13. Yet, their diffusion across the continent was slow: the first

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Proteins in Fossil Biominerals

2020

Amino Acids and Proteins in Fossil Biominerals

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Sex estimation using sexually dimorphic amelogenin protein fragments in human enamel

Cited by 88 publications

References 70 publications

A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation

A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation

Palaeoproteomics gives new insight into early southern African pastoralism

Proteins in Fossil Biominerals

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