Performance and automation of ancient DNA capture with RNA hyRAD probes

DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analys- ing ancient DNA (aDNA) extracts, which are often dominated by exogenous environ- mental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic re- striction of fresh DNA extracts to produce RNA probes that cover only a fraction ofthe genome and can serve as baits for capturing homologous fragments from aDNA li- braries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing ex- tremely low endogenous content (20%¿30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensi- tive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypo- methylated regions, which improved data quality by reducing post-mortem DNA dam- age and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture process- ing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.This project received funding from: the University Paul Sabatier IDEX Chaire d’Excellence (OURASI); the CNRS Programme de Recherche Conjoint (PRC); the CNRS International Research Project (IRP AMADEUS); the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 797449; the Russian Foundation for Basic Research, project No. 19-59-15001 “Horses and their importance in the life of the ancient population of Altai and adjacent territories: interdisciplinary research and reconstruction”; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement 681605)

Widespread horse-based mobility arose around 2200 bce in Eurasia

Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2–4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 bce, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 bce, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 bce and earlier3, 5. Finally, we detect significantly shortened generation times at Botai around 3500 bce, a settlement from central Asia associated with corrals and a subsistence economy centred on horses6, 7. This supports local horse husbandry before the rise of modern domestic bloodlines

The origins and spread of domestic horses from the Western Eurasian steppes

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: All collapsed and paired-end sequence data for samples sequenced in this study are available in compressed fastq format through the European Nucleotide Archive under accession number PRJEB44430, together with rescaled and trimmed bam sequence alignments against both the nuclear and mitochondrial horse reference genomes. Previously published ancient data used in this study are available under accession numbers PRJEB7537, PRJEB10098, PRJEB10854, PRJEB22390 and PRJEB31613, and detailed in Supplementary Table 1. The genomes of ten modern horses, publicly available, were also accessed as indicated in their corresponding original publications57,61,85-87.NOTE: see the published version available via the DOI in this record for the full list of authorsDomestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 BC. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture

Diversité génétique des chevaux anciens et modernes de l'Altaï et des territoires adjacents

This study was one of the first to characterize the mitochondrial, nuclear, microbial genetic diversity of the horses of many archaeological cultures of Altai (Biiken, Pazyryk, Turkic) and adjacent territories (the Aldy-Bel culture (Tuva), the Khereksur and Deer Stone culture, the Xiongnu culture (Mongolia)) and modern horses of Altai. The mitochondrial genetic diversity of horses was determined by high-throughput sequencing of PCR fragments or enriched libraries of aDNA and subsequent phylogeographic and population genetic analyzes of the sequencing data. Nuclear and microbial genetic diversity was revealed by shotgun sequencing of the original genomic libraries and phylogeographic, statistical (Struct-f4, determination of sex, phenotype and genetic diseases), and metagenomic analyzes of the data obtained. The identified genetic diversity at the mitogenome level provided us with the opportunity to determine the phylogenetic relationships between the studied groups of ancient, medieval, and modern horses. It was shown: - slight overlap in the composition of mitogroups between horses of Altai and Mongolia of the Late Bronze – Eearly Iron Ages, while a moderate level of differentiation was determined between the groups of modern Altai horses of Southeastern Altai and the group of modern horses of the Mongolian breed; - the presence of close mitotypes between horses of the Biiken, Turkic cultures of Altai and modern Altai horses; - the presence of close mitotypes between the horses of the Khereksur and Deer Stone culture and the Xiongnu culture of Mongolia and modern Mongolian horses; - proximity of mitotypes of horses of Biiken, Pazyryk, Turkic cultures of Altai and many modern horses of native breeds of Central Asia and the Middle East; - similarity of mitotypes of the horses of Mongolia of the Late Bronze – Early Iron Ages and many horses of local breeds of China; The totality of these phylogeographic data may indicate a possible genetic continuity between the corresponding groups of horses and the migration routes of the studied horses. On the whole, the analysis of the high-throughput sequencing data of the non-enriched genomic libraries indicated the high degree of preservation of the studied horse bone samples and, thus, the prospects of the sites of Altai and adjacent territories for aDNA research. The analyzes results of the horse sex ratio and phenotypic composition of the horse groups under study for the most part confirmed the previously published data. The genome-wide phylogenetic reconstructions determined the presence of the geographic structure of horse populations before the beginning of domestication, the localization of the center of horse domestication in the Pontic-Caspian steppe, and not in Altai and adjacent territories, and the close genetic affinity between the horses of the Khereksur and Deer Stone culture of Mongolia and the Aldy-Bel culture of Tuva, which confirmed the presence of contacts between these cultures. The following microbes pathogenic for domestic animals were found in the studied horses of Altai and adjacent territories of the Eneolithic – Early Middle Ages: Erysipelothrix tonsillarum, Erysipelothrix rhusiopathiae, Staphylococcus lentus, Eimeria tenella. It is very important to continue the molecular genetic studies of the ancient and medieval horses of Altai and adjacent territories in order to assess whether the preliminary results obtained on genetic continuity, possible migration routes, and exchange could be confirmed.Cette étude a été l'une des premières à caractériser la diversité génétique mitochondriale, nucléaire et microbienne des chevaux de nombreuses cultures archéologiques de l'Altaï (biiken, de Pazyryk, turcique) et des territoires adjacents (Aldy-Bel, (Tyva), kheregsüür et pierres à cerf, Xiongnu (Mongolie)) et des chevaux contemporains de l'Altaï. La diversité génétique mitochondriale des chevaux a été déterminée à l'aide d'un séquençage à haut débit de fragments PCR ou de bibliothèques enrichies d'ADN ancien et du séquençage et de l'analyse phylogéographique et génétique des populations ultérieure des données de séquençage. La diversité génétique nucléaire et microbienne a été révélée par séquençage shotgun des bibliothèques génomiques sources et les analyses phylogéographiques, statistiques (Struct-f4, détermination du sexe, phénotype et maladies génétiques du cheval) et métagénomiques des données collectées. La révélation de la diversité génétique au niveau du mitogénome nous a donné la possibilité de déterminer les liens phylogénétiques entre les groupes étudiées de chevaux de l'antiquité, du Moyen Âge et contemporains. Il a été démontré : - un léger chevauchement dans la composition des mitogroupes entre les chevaux de l'Altaï et de la Mongolie aux siècles de l'âge du bronze final et du début de l'âge du fer, tandis qu'entre les groupes de chevaux contemporains de l'Altaï du Sud-Est et de la Mongolie il est observé un niveau modéré de différenciation ; - la présence de mitotypes proches entre les chevaux des cultures biiken, turcique de l'Altaï et les chevaux contemporains de l'Altaï ; - la présence de mitotypes proches entre les chevaux de la culture kheregsüür et pierres à cerf et de la culture xiongnu de Mongolie et les chevaux mongoles contemporains ; - une proximité des mitotypes des chevaux de cultures biiken, de Pazyryk, turcique de l'Altaï et de nombreux chevaux contemporains de races indigènes d'Asie centrale et du Moyen-Orient ; - une proximité des mitotypes des chevaux de Mongolie des siècles de l'âge du bronze final et du début de l'âge du fer et de nombreux chevaux de races locales de Chine ; L'ensemble de ces données phylogéographiques peut témoigner de la possibilité d'une continuité génétique entre les groupes correspondant de chevaux et des voies migratoires des chevaux étudiés. L'analyse des données du séquençage à haut débit des bibliothèques génomiques non-enrichies témoigne dans l'ensemble du haut niveau de conservation des échantillons osseux des chevaux étudiés, ce qui signifie une perspective de recherches d'ADN ancien du matériel ostéologique des sujets de l'Altaï et des territoires adjacents. Les résultats de l'analyse du rapport des sexes des chevaux et de la composition phénotypique des groupes de chevaux étudiés ont confirmé d'une manière générale les données précédemment publiées. Les reconstructions phylogénétiques du génome entier ont déterminé la présence d'une structure géographique des populations de chevaux avant le début de la domestication, la localisation du centre de domestication des chevaux dans la Steppe pontique-caspienne, et non en Altaï et les territoires adjacents, la relation génétique étroite entre les chevaux de la culture kheregsüür et des pierres de cerf de Mongolie et de la culture Aldy-Bel de Tyva, confirmant l'existence de contacts entre ces cultures. Chez les chevaux étudiés de l'Altaï et des territoires adjacents de l'énéolithique au début du Moyen Âge ont été découverts les microbes pathogènes suivants pour les chevaux domestiques : Erysipelothrix tonsillarum, Erysipelothrix rhusiopathiae, Staphylococcus lentus, Eimeria tenella. Il est très important de poursuivre les recherches moléculaires et génétiques des chevaux de l'Antiquité et du Moyen Âge de l'Altaï et des territoires adjacents pour vérifier l'exactitude des résultats préliminaires obtenus sur la continuité génétique, les possibles voies migratoires et le flux des gènes

Traces of Late Bronze and Early Iron Age Mongolian Horse Mitochondrial Lineages in Modern Populations

The Mongolian horse is one of the most ancient and relatively unmanaged horse breeds. The population history of the Mongolian horse remains poorly understood due to a lack of information on ancient and modern DNA. Here, we report nearly complete mitochondrial genome data obtained from five ancient Mongolian horse samples of the Khereksur and Deer Stone culture (late 2nd to 1st third of the 1st millennium BC) and one ancient horse specimen from the Xiongnu culture (1st century BC to 1st century AD) using target enrichment and high-throughput sequencing methods. Phylogenetic analysis involving ancient, historical, and modern mitogenomes of horses from Mongolia and other regions showed the presence of three mitochondrial haplogroups in the ancient Mongolian horse populations studied here and similar haplotype composition of ancient and modern horse populations of Mongolia. Our results revealed genetic continuity between the Mongolian horse populations of the Khereksur and Deer Stone culture and those of the Xiongnu culture owing to the presence of related mitotypes. Besides, we report close phylogenetic relationships between haplotypes of the Khereksur and Deer Stone horses and the horses of indigenous breeds of the Middle East (Caspian and Iranian), China (Naqu, Yunnan, and Jinjiang), and Italy (Giara) as well as genetic similarity between the Xiongnu Mongolian horses and those of the most ancient breeds of the Middle East (Arabian) and Central Asia (Akhal-Teke). Despite all the migrations of the Mongolian peoples over the past 3000 years, mitochondrial haplogroup composition of Mongolian horse populations remains almost unchanged

High genetic diversity of ancient horses from the Ukok Plateau.

A growing number of researchers studying horse domestication come to a conclusion that this process happened in multiple locations and involved multiple wild maternal lines. The most promising approach to address this problem involves mitochondrial haplotype comparison of wild and domestic horses from various locations coupled with studies of possible migration routes of the ancient shepherds. Here, we sequenced complete mitochondrial genomes of six horses from burials of the Ukok plateau (Russia, Altai Mountains) dated from 2.7 to 1.4 thousand years before present and a single late Pleistocene wild horse from the neighboring region (Denisova cave). Sequencing data indicates that the wild horse belongs to an extinct pre-domestication lineage. Integration of the domestic horse data with known Eurasian haplotypes of a similar age revealed two distinct groups: the first one widely distributed in Europe and presumably imported to Altai, and the second one specific for Altai Mountains and surrounding area

Performance and automation of ancient DNA capture with RNA hyRAD probes

International audienc

The origins and spread of domestic horses from the Western Eurasian steppes.

Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2-4 at Botai, Central Asia around 3500 BC3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture11,12