Historical management of equine resources in France from the Iron Age to the Modern Period

Lepetz, Sébastien; Clavel, Benoît; Alioğlu, Duha; Chauvey, Loreleï; Schiavinato, Stéphanie; Tonasso-Calvière, Laure; Liu, Xuexue; Fages, Antoine; Khan, Naveed; Seguin-Orlando, Andaine; Sarkissian, Clio Der; Clavel, Pierre; Estrada, Oscar; Gaunitz, Charleen; Aury, Jean‐Marc; Barme, Maude; 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; Valenzuela-Lamas, Sílvia; Vallet, Christian; Yvinec, Jean‐Hervé; Wincker, Patrick; Orlando, Ludovic

doi:10.1016/j.jasrep.2021.103250

Cited by 11 publications

(24 citation statements)

References 39 publications

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“…Regardless of the reference genome considered, we found that the sequence data generated from the two horse specimens almost exclusively showed horse‐specific alleles (Figure 4a,b). The reverse was true for the sequence data generated from the three donkey specimens, which supports the validity of our SNP assignment panel as well as the previous taxonomic identification of these specimens (Lepetz et al, 2021). Interestingly, the shotgun sequence data from the three mule specimens showed almost balanced proportions of horse‐ and donkey‐specific alleles.…”

Section: Resultssupporting

confidence: 86%

“…A previous study by Lepetz et al (2021) allowed us to identify a total of eight ancient equine subfossils from France (1st–17th centuries CE) showing excellent DNA preservation, including two horses, three mules and three donkeys (Table S1). Their high endogenous DNA content (37.9%–78.1%) guaranteed that a large number of equine DNA templates could be identified, and thus, the effect of capture following USER treatment assessed, even from limited sequencing efforts (289,599–1,997,334 reads; Table S1).…”

Section: Resultsmentioning

confidence: 99%

“…In a previous study, we used shallow DNA sequencing to screen a total of 874 equine subfossil specimens for DNA preservation levels (Lepetz et al, 2021). The sequence data collected were processed within the Zonkey pipeline (Schubert et al, 2017) to identify horses, donkeys and mules showing high levels of endogenous DNA (Table S1).…”

Section: Data Generationmentioning

confidence: 99%

“…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%

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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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Section: Resultssupporting

confidence: 86%

Section: Resultsmentioning

confidence: 99%

Section: Data Generationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…The abundance of donkeys at Boinville-en-Woëvre stands as an exception in Roman France, as mules dominated all other assemblages from this time ( 47 ). Contemporaneous Roman sites report mules of a large and uniform size, indicating selective breeding in the parental species for expensive animals of exceptional stature [Varro (2, 6)] ( 48 ).…”

Section: Romans Bred Improved Donkeys For Producing Mules Essential F...mentioning

confidence: 99%

The genomic history and global expansion of domestic donkeys

Todd

Tonasso-Calvière

Chauvey

et al. 2022

Science

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Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.

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Predictive use of modern reference osteological collections for disentangling the shape of Eurasian equid cheek teeth and metapodials in archaeological material

Mohaseb,

Cornette,

Zimmermann

et al. 2023

Intl J of Osteoarchaeology

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Equids have shaped past Eurasian societies in many ways. This applies in particular to domestic horses, donkeys, and their hybrids. Key to documenting modes of exploitation and cultural trajectories in past societies is the correct taxonomic classification of tooth and bone specimens found in archaeological sites. However, close osteomorphological resemblance of wild and domestic equids and their economically valuable hybrids, that is, mules and hinnies, complicates the identification of intentionally fragmented or naturally damaged archaeological specimens. Here, we apply geometric morphometrics (GM) to mandibular teeth and metapodials, two skeletal elements commonly found in archaeological collections and known for their diagnostic properties using traditional morphometric methods. We registered a statistically representative set of 2D and 3D coordinates on mandibular teeth (P3, P4, M1, and M2) and metapodials of 92 domestic horses (Equus caballus Linnaeus, 1758), 70 domestic donkeys (Equus asinus Linnaeus, 1758), 30 hybrids, and 63 Asiatic wild asses (Equus hemionus Pallas, 1775). Taxonomic classification of these 255 specimens considered both shape and form, applying linear discriminant analysis, k‐nearest neighbors algorithm, and artificial neural networks to seven combinations of taxa. We obtained correct classifications in over 87% and 80%, respectively, of the premolars and molars and in over 93% and 89%, respectively, of the metacarpals and metatarsals. This modern dataset was then used to classify equid specimens from three archaeological sites in the Middle East already analyzed morphologically. Taking into account the past zoogeography of wild equids and the historical distribution of their domesticated descendants and hybrids, the GM approach presented in this study offers the possibility to morphologically classify archaeological equids with far greater certainty than has been the case so far.

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Historical management of equine resources in France from the Iron Age to the Modern Period

Cited by 11 publications

References 39 publications

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

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

The genomic history and global expansion of domestic donkeys

Predictive use of modern reference osteological collections for disentangling the shape of Eurasian equid cheek teeth and metapodials in archaeological material

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