Ludovic Orlando

Université de Toulouse · Centre d'Anthropobiologie et de Génomique de Toulouse CAGT

Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to...

The domestication of animals led to a major shift in human subsistence patterns, from a hunter–gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have...

Revisiting the origins of modern horses The domestication of horses was very important in the history of humankind. However, the ancestry of modern horses and the location and timing of their emergence remain unclear. Gaunitz et al. generated 42 ancient-horse genomes. Their source samples included the Botai archaeological site in Central Asia, cons...

Ancient genomics of horse domestication The domestication of the horse was a seminal event in human cultural evolution. Librado et al. obtained genome sequences from 14 horses from the Bronze and Iron Ages, about 2000 to 4000 years ago, soon after domestication. They identified variants determining coat color and genes selected during the domestica...

The domestication of the horse and the development of new equestrian technologies have had a far-reaching impact on human history. Disentangling the respective role that horse males and females played during this process is, however, difficult based on iconography and osteological data alone. In this study, we leveraged an extensive ancient DNA tim...

The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication h...

The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to...

Domestic horses and donkeys played a key role in the initial colonization of the Atlantic seaboard of the Americas, a process partially chronicled by historical records. While Spanish colonists brought horses to the Caribbean and southern latitudes earlier, the transport of domestic horses to the English colony at Jamestown, Virginia in 1606 was am...

While few places on earth have been as deeply impacted by the human-horse relationship as the steppes of Mongolia and eastern Eurasia, gaps in the archaeological record have made it strikingly difficult to trace when and how the first domestic horses were integrated into ancient societies in this key region of the world. Recently, organic materials...

This paper reports a high-resolution isotopic study of medieval horse mobility, revealing their origins and in-life mobility both regionally and internationally. The animals were found in an unusual horse cemetery site found within the City of Westminster, London, England. Enamel strontium, oxygen, and carbon isotope analysis of 15 individuals prov...

Equine viral outbreaks have disrupted the socio-economic life of past human societies up until the late 19th century, and continue to be of major concern to the horse industry today. With a seroprevalence of 60-80%, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here...

Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genot...

Innovations in horse equipment during the early Middle Ages provided advantages to societies from the steppes, reshaping the social landscape of Eurasia. Comparatively little is known about the precise origin of these crucial advances, although the available evidence points to early adoption in East Asia. The authors present new archaeological disc...

The introduction of domestic horses transformed Indigenous societies across the grasslands of Argentina, leading to the emergence of specialized horse cultures across the Southern Cone. However, the dynamics of this introduction are poorly chronicled by historic records. Here, we apply archaeozoological and biomolecular techniques to horse remains...

Equine viral outbreaks have disrupted the socio-economic life of past human societies up until the late 19th century, and continue to be of major concern to the horse industry today. With a seroprevalence of 60-80%, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here...

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence...

Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation...

Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of a...

The horse is central to many Indigenous cultures across the American Southwest and the Great Plains. However, when and how horses were first integrated into Indigenous lifeways remain contentious, with extant models derived largely from colonial records. We conducted an interdisciplinary study of an assemblage of historic archaeological horse remai...

New excavations of an enclosure–related site at Ginnerup on Djursland, Denmark, in 2020 resulted in the identification of several features contain-ing depositions of marine shells. One of these, A4, is a natural depression with a fill comprised of four consecutively deposited layers, forming an un-disturbed stratigraphy, dated by several 14C dates...

An extensive genomic time series has been produced for 356 humans from across ice-age Europe. The data reveal how climate change affected the ranges of hunter-gatherer populations as they developed diverse cultures. Analysis of ancient DNA from 356 individuals.

Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ec...

Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature of the fossil record and the lack of universal skeletal markers for age. DNA methylation clocks offer new, albeit challenging, alternatives for estimating the age-at-death of ancient individuals. Here, we take ad...

A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate region approximately 50 kb downstream of the Endothelin 3 ( EDN3 ) gene. EDN3 and other endothelin family members are associated with blood pressure regulation in humans and other species, but similar association studies in horses are lacking. We hypothesiz...

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...

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day do...

Hybrids of horse and donkey, which have been valued in the Mediterranean basin since the Iron Age, became integrated into the animal world north of the Alps in the course of Romanization. Until now, however, their true contribution to the economic and military life in the northern Roman provinces Raetia, Noricum and Upper Pannonia (southern Germany...

Ancient DNA datasets are increasingly difficult to visualise for users lacking computational experience. Here, we describe mapDATAge, which aims to provide user-friendly automated modules for the interactive mapping of allele, haplogroup and/or ancestry distributions through space and time. mapDATAge enhances collaborative data sharing while assist...

A high-quality reference genome assembly, a biobank of diverse equine tissues from the Functional Annotation of the Animal Genome (FAANG) initiative, and incorporation of long-read sequencing technologies, have enabled efforts to build a comprehensive and tissue-specific equine transcriptome. The equine FAANG transcriptome reported here provides up...

The exceptionally-rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 arc...

Western Eurasia witnessed several large-scale human migrations during the Holocene. To investigate the cross-continental impacts we shotgun-sequenced 317 primarily Mesolithic and Neolithic genomes from across Northern and Western Eurasia. These were imputed alongside published data to obtain diploid genotypes from >1,600 ancient humans. Our analyse...

A new palaeogenetic study by Ludovic Orlando and his team at the Centre for Anthropobiology and Genomics of Toulouse, CNRS / Université Toulouse III-Paul Sabatier, in which also scientists from the DAI were involved, has now shed new light on the horse domestication. The study published in Nature 2021, which was carried out within the framework of...

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 D...

Determining the extent of overlap between modern humans and other hominins in Eurasia, such as Neanderthals and Denisovans, is fundamental to understanding the nature of their interactions and what led to the disappearance of archaic hominins. Apart from a possible sporadic pulse recorded in Greece during the Middle Pleistocene, the first settlemen...

Sex identification from fragmentary archeozoological assemblages is particularly challenging in the Equid family, including for horses, donkeys and their hybrids. This limitation has precluded in-depth investigations of sex-ratio variation in various temporal, geographic and social contexts. Recently, shallow DNA sequencing has offered an economica...

Visualisation and inference of population structure is increasingly important for fundamental and applied research. Here, we present Struct-f4, providing automated solutions to characterize and summarize the genetic ancestry profile of individuals, assess their genetic affinities, identify admixture sources and quantify admixture levels. Availabil...

Chinese ponies are endemic to the mountainous areas of southwestern China and were first reported in the archaeological record at the Royal Tomb of Zhongshan King, Mancheng, dated to approximately 2,100 YBP. Previous work has started uncovering the genetic basis of size variation in western ponies and horses, revealing a limited number of loci, inc...

Although the first ancient DNA molecules were extracted more than three decades ago, the first ancient nuclear genomes could only be characterized after high-throughput sequencing was invented. Genome-scale data have now been gathered from thousands of ancient archaeological specimens, and the number of ancient biological tissues amenable to genome...

Alongside horses, donkeys and their first-generation hybrids represent members of the Equidae family known for their social, economic and symbolic importance in protohistoric and historical France. However, their relative importance and their respective roles in different regions and time periods are difficult to assess based on textual, iconograph...

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 domestic...

During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1–8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across t...

Supplemental Information for: Suchan, T., Kusliy, M.A., Khan, N., Chauvey, L., Tonasso-Calvière, L., Schiavinato, S., Southon, J., Keller, M., Kitagawa, K., Krause, J., Bessudnov, A.N., Bessudnov, A.A., Graphodatsky, A.S., Lamas, S.V., Wilczyński, J., Pospuła, S., Tunia, K., Nowak, M., Moskal-delHoyo, M., Tishkin, A.A., Pryor, A.J.E., Outram, A.K.,...

The exceptionally-rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses and zebras represent three extant subgenus of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in Pleistocene. We sequenced 26 archaeol...

The development and dispersal of agropastoralism transformed the cultural and ecological landscapes of the Old World, but little is known about when or how this process first impacted Central Asia. Here, we present archaeological and biomolecular evidence from Obishir V in southern Kyrgyzstan, establishing the presence of domesticated sheep by ca....

DNA hybridization‐capture techniques allow researchers to focus their sequencing efforts on pre‐selected genomic regions. This feature is especially useful when analyzing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and de...

Horses and donkeys have had a far-reaching impact on human history, providing mechanical power for agriculture and transportation. Their F1-hybrids, especially mules, have also been of considerable importance due to their exceptional strength, endurance and resistance. The reconstruction of the respective role that horses, donkeys and mules played...

The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic...

Since the seminal paper in 1998 (Coolen and Overmann), sedimentary ancient DNA (sedaDNA) has become a powerful tool in paleoecology to reconstruct past changes in terrestrial and aquatic biodiversity. Still, sedaDNA is an emerging tool and there is a need for calibrations and validations to ensure the reliability of sedaDNA as a proxy to reconstruc...

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03328-2.

The 17th century plague epidemic had a particularly strong demographic toll in Southern Europe, especially Italy, where it caused long-lasting economical damage. Whether this resulted from ineffective sanitation measures or more pathogenic Yersinia pestis strains remains unknown. DNA screening of 26 skeletons from the 1629-1630 plague cemetery of L...

The equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by sever...

Although recognized as one of the most significant cultural transformations in North America, the reintroduction of the horse to the continent after AD 1492 has been rarely addressed by archaeological science. A key contributing factor behind this limited study is the apparent absence of equine skeletal remains from early historic archaeological co...

The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.¹ These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes²,³ into local populations, resulting from complex interactions between collapsing hunter-gatherers and exp...

Depuis longtemps, nous interrogeons les animaux avec des concepts définis du point de vue humain. Cela nous a fait confondre les versions humaines de l'intelligence, du langage, des émotions, etc., avec la définition générale de ces capacités. Cela nous a amené à conclure que les animaux ne possédaient pas ces capacités ou qu’ils n’en possédaient q...

Mules (Equus asinus x Equus caballus) represent first-generation hybrids between a female horse (mare) and a male donkey (jack). They are generally considered to have first appeared north of the Alps with Roman influence, a time period in which written and iconographic sources support their key role for transport and traction, both in farming and t...

Background: The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen bindin...

The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today,...

The maritime expansion of Scandinavian populations during the Viking Age (about ad 750–1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking pe...

Using the past to inform the future The late Quaternary paleorecord, within the past ∼130,000 years, can help to inform present-day management of the Earth's ecosystems and biota under climate change. Fordham et al. review when and where rapid climate transitions can be found in the paleoclimate record. They show how such events in Earth's history...