Sex in the city: Uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France

Clavel, Benoît; Lepetz, Sébastien; Chauvey, Loreleï; Schiavinato, Stéphanie; Tonasso-Calvière, Laure; Liu, Xuexue; Fages, Antoine; Khan, Naveed; Seguin-Orlando, Andaine; Sarkissian, Clio Der; Clavel, Pierre; Estrada, Oscar; Alioğlu, Duha; Gaunitz, Charleen; Aury, Jean‐Marc; Barme, Maude; Bodu, Pierre; Olive, Monique; Bignon‐Lau, Olivier; Castel, Jean-Christophe; Boudadi‐Maligne, Myriam; Boulbes, Nicolas; Bourgois, Alice; Decanter, Franck; Foucras, Sylvain; Frere, S. S.; Gardeisen, Armelle; Jouanin, Gaëtan; Méla, Charlotte; Morand, Nicolás; Espinet, Ariadna Nieto; Perdereau, Aude; Putelat, Olivier; Rivière, Julie; Robin, Opale; Salin, Marilyne; Lamas, Sílvia Valenzuela; Vallet, Christian; Yvinec, Jean‐Hervé; Wincker, Patrick; Orlando, Ludovic

doi:10.1016/j.jasrep.2022.103341

Cited by 3 publications

(4 citation statements)

References 30 publications

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“…Most palaeoproteomic research in the fields of paleontology and zooarchaeology has focused on bone proteins to identify species using mass spectrometry (ZooMS) of previously identified collagen sequences [1][2][3][4][5][6][7][8][9][10][11][12] while aDNA sequencing has been used to identify species and/or sex [13][14][15] . However, recently researchers have turned to enamel proteins, and developed innovative methods for determination of species as well as sex by analyzing native peptides in the tooth enamel proteome using mass spectrometry techniques 16,17 .…”

Section: Introductionmentioning

confidence: 99%

A Peptidomics Method for Assessing Sex from Modern and Ancient Bovine Tooth Enamel.

Kotli,

Morgenstern,

Horwitz

et al. 2024

Preprint

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Identification of the sex of fossil and archaeological animal remains offers many insights into their demography, mortality profile and domestication pathways. However, sex determination of fossils is often impossible due to the absence of sex-specific diagnostic features on the remains or ambivalence in extrapolating dimorphism from body size and limited organic material preservation for analysis using aDNA. To counter this, we have developed an innovative protocol employing peptidomic techniques of tooth enamel in bovines. We discovered male-specific amino acid variations in AmelY (Asp44, Leu46, Tyr48 and Val58) unique to modern cattle and then successfully applied this same method to sex bovine tooth enamel from Neolithic sites in the Southern Levant (ca. 9,000 BP). We also compared diagenesis of AmelX using peptide length and site-specific post-translational modifications. Additionally, site-specific post-translational modifications (PTMs) of AmelX were identified and can be used to validate the antiquity of ancient enamel. Since teeth are usually better preserved than bones in the fossil and archaeological record, this innovative protocol has the potential to enable sex-determination is ancient bovine remains that currently cannot be sexed.

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Section: Introductionmentioning

confidence: 99%

A Peptidomics Method for Assessing Sex from Modern and Ancient Bovine Tooth Enamel.

Kotli,

Morgenstern,

Horwitz

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…Sexing paleofaunal remains can provide important data on a broad spectrum of issues. These include the animal's life history, extent of dimorphism, socio-ecological structure and behavior, as well as predator-prey relations and herd management strategies [1][2][3][4][5][6][7] . However, sex determination of fossil fauna is severely hampered by the often fragmentary nature of specimens, as it relies on the presence of sexspeci c morphological features (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…However, these methods also rely on the presence of well-preserved remains, while there is often ambivalence in interpreting the mechanism/s responsible for size patterning, since this may be confounded by factors such as climate change, nutrition and domestication 1,16 . While, the advent of aDNA analyses has offered revolutionary possibilities for sexing ancient fauna remains 7,11,13,17 , in many situations its application is limited by DNA degradation and contamination 18 . Clearly, additional tools that will enable sexing of fossil (and fragmentary modern) animal remains will be invaluable to researchers in zoology, archaeology, archaeozoology and paleontology.…”

Section: Introductionmentioning

confidence: 99%

A Label-Free Quantification Method for Assessing Sex from Modern and Ancient Bovine Tooth Enamel

Kotli

2024

Preprint

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Identification of the sex of modern, fossil and archaeological animal remains offers many insights into their demography, mortality profiles and domestication pathways. However, due to manifold factors, sex determination of osteological remains is often problematic. To overcome this, we have developed an innovative protocol to determine an animal’s sex from tooth enamel, by applying label-free quantification (LFQ) of two unique AmelY peptides ‘LRYPYP’ (AmelY;[M+2]2+ 404.7212 m/z) and ‘LRYPYPSY’ (AmelY;[M+2]2+ 529.7689 m/z) that are only present in the enamel of males. We applied this method to eight modern cattle (Bos taurus) of known sex, and correctly assigned them to sex. We then applied the same protocol to twelve archaeological Bos teeth from the Neolithic site of Beisamoun, Israel (8th–7th millennium BC) and determined the sex of the archaeological samples. Since teeth are usually better preserved than bones, this innovative protocol has potential to facilitate sex determination in ancient and modern bovine remains, that currently cannot be sexed.

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“…In this study, we selected eight ancient equine bone specimens from present-day France dating to the 1st-17th centuries CE (Common Era). These specimens were selected for their high equine DNA content (Clavel et al, 2021(Clavel et al, , 2022Lepetz et al, 2021), which allowed us to characterize the aforementioned methodological bias with minimal sequencing efforts. We constructed DNA libraries in the absence of or following USER treatment of ancient DNA extracts.…”

Section: Introductionmentioning

confidence: 99%

Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA

Suchan

Chauvey

Poullet

et al. 2022

Molecular Ecology Resources

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Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post-mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction.While both approaches have recently gained popularity in ancient DNA research, the impact of USER-treatment on capture efficacy still remains untested. In this study, we applied hyRAD capture to eight ancient equine subfossil specimens from France (1st-17th century CE), including horses, donkeys and their first-generation mule hybrids.We found that USER-treatment could reduce capture efficacy and introduce significant experimental bias. It differentially affected the size distribution of on-target templates following capture with two distinct hyRAD probe sets in a manner that was not driven by differences in probe sizes and DNA methylation levels. Finally, we recovered unbalanced proportions of donkey-specific and horse-specific alleles in mule capture sequence data, due to the combined effects of USER-treatment, probe sets and reference bias. Our work demonstrates that while USER-treatment can improve the quality of ancient DNA sequence data, it can also significantly affect hyRAD capture outcomes, introducing bias in the sequence data that is difficult to predict based on simple molecular probe features. Such technical batch effects may prove easier to model and correct for using capture with synthetic probes of controlled sizes and diversity content.

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Sex in the city: Uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France

Cited by 3 publications

References 30 publications

A Peptidomics Method for Assessing Sex from Modern and Ancient Bovine Tooth Enamel.

A Peptidomics Method for Assessing Sex from Modern and Ancient Bovine Tooth Enamel.

A Label-Free Quantification Method for Assessing Sex from Modern and Ancient Bovine Tooth Enamel

Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA

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