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

Widespread occurrence of botulinum and tetanus neurotoxin genes in ancient DNA

BACKGROUND

Ancient DNA collected from archaeological specimens not only provides a window into ancient human genetic diversity but also contains a rich mixture of associated microbial DNA including potential pathogens. In recent work, we identified C. tetani and tetanus neurotoxin (TeNT) genes in ancient DNA datasets collected from human archaeological specimens. However, the reasons underlying the occurrence of these toxin genes and the extent to which other toxin genes are present in ancient DNA is unclear.

METHODS

Here, we performed a large-scale analysis of 6435 ancient DNA (aDNA) sequencing datasets including human and non-human sources, searching for 49 clostridial neurotoxin types and subtypes, and 3 additional unrelated toxins.

RESULTS

Our search identified a total of 105 ancient DNA datasets (1.6 %) containing significant matches to one or more neurotoxin genes. Consistent with our earlier work, TeNT genes were most common, found in 50 ancient DNA datasets. In addition, we identified sequences encoding diverse botulinum neurotoxins including BoNT/C (40 samples), BoNT/D (6 samples), BoNT/B (4 samples), BoNT/E (1 sample), and the Enterococcus-associated BoNT/En (10 samples). TeNT genes were detected in a broad range of ancient samples including human and animal (horse, wild bear, chimpanzee, gorilla, dog) remains, whereas the largest diversity of toxins was detected in aDNA from Egyptian mummies. Phylogenetic and sequence analysis of the identified matches revealed close identity to modern forms of these toxins. Damage analysis revealed several toxin genes with hallmarks of ancient DNA associated damage, indicative of an ancient origin.

CONCLUSIONS

Our work reveals that clostridial neurotoxin genes occur frequently in aDNA samples, including human and animal-associated toxin variants. We conclude that the frequent association of these genes with aDNA likely reflects a strong ecological association of pathogenic clostridia with decaying human and animal remains and possible post-mortem colonization of these samples.

Performance of qpAdm-based screens for genetic admixture on graph-shaped histories and stepping stone landscapes

qpAdm is a statistical tool that is often used for testing large sets of alternative admixture models for a target population. Despite its popularity, qpAdm remains untested on 2D stepping stone landscapes and in situations with low prestudy odds (low ratio of true to false models). We tested high-throughput qpAdm protocols with typical properties such as number of source combinations per target, model complexity, model feasibility criteria, etc. Those protocols were applied to admixture graph-shaped and stepping stone simulated histories sampled randomly or systematically. We demonstrate that false discovery rates of high-throughput qpAdm protocols exceed 50% for many parameter combinations since: (1) prestudy odds are low and fall rapidly with increasing model complexity; (2) complex migration networks violate the assumptions of the method; hence, there is poor correlation between qpAdm P-values and model optimality, contributing to low but nonzero false-positive rate and low power; and (3) although admixture fraction estimates between 0 and 1 are largely restricted to symmetric configurations of sources around a target, a small fraction of asymmetric highly nonoptimal models have estimates in the same interval, contributing to the false-positive rate. We also reinterpret large sets of qpAdm models from 2 studies in terms of source-target distance and symmetry and suggest improvements to qpAdm protocols: (1) temporal stratification of targets and proxy sources in the case of admixture graph-shaped histories, (2) focused exploration of few models for increasing prestudy odds; and (3) dense landscape sampling for increasing power and stringent conditions on estimated admixture fractions for decreasing the false-positive rate.

Understanding horse domestication and horse health care in the ancient world

Many of the most important equine health problems - and their solutions - relate to the role of horses as a domestic animal, especially in riding and other kinds of transport. Recently, new discoveries from the archaeological sciences have rewritten our understanding of early horse domestication, suggesting that the first ancestors of domestic horses emerged in the Black Sea Steppes of western Eurasia at the turn of the second millennium BCE. This new chronology places horse domestication within a wider trajectory of early animal transport, including cattle and donkey, across western Asia and northern Africa beginning in the fourth millennium BCE. Archaeological data suggest that some health problems including musculoskeletal issues linked with transport, dental challenges, and disease emerged alongside horse transport, and that some of these issues solicited early veterinary care. Collaboration between archaeozoology and equine science has the potential to reveal much more about early human-horse dynamics, but doing so requires overcoming important obstacles, including contrasting methodology and incentives for those working in each discipline.

Effect of Alternative Splicing Euchromatic Histone Lysine Methyltransferase 2 (EHMT2/G9A) on Spermatogenesis in Mongolian Horses

The epigenetic regulation of gene expression through the covalent modification of histones is crucial for developing germline cells. To study the regulatory role of alternative splicing (AS) of euchromatic histone lysine methyltransferase 2 (EHMT2/G9A) in spermatogenesis in Mongolian horses, this study first examines the localization of the EHMT2 gene in testicular support cells and then predicts the higher-order structures of sequences with and without AS. Two types of lentiviral vectors for overexpression were subsequently constructed for the EHMT2 gene, one with AS and one without, to infect support cells. The proliferation and activity of infected cells were measured using CCK8, and the differential expression of spermatogenesis-related genes in the two types of support cells was analyzed via qRT-PCR. We analyzed the expression of EHMT2 by immunofluorescence staining. EHMT2 was expressed in the nuclei of Sertoli cells. The expression of spermatogenesis-related genes was measured in the two types of cells. The results reveal that the expression levels of the FSH, Stra8, CCNB2, CDC27, NRG1, PPP2R5C, CCNB2, and YWHAZ genes in the AS group were greater than those in the control group. These results indicate that AS events in EHMT2 affect gene expression and thus affect spermatogenesis.

Molecular Signatures of Exercise Adaptation in Arabian Racing Horses: Transcriptomic Insights from Blood and Muscle

Background/Objectives: Human-driven selection has shaped modern horse breeds into highly specialized athletes, particularly in racing. Arabian horses, renowned for their endurance, provide an excellent model for studying molecular adaptations to exercise. This study aimed to identify genes commonly influenced by physical exertion in the gluteus medius muscle and whole blood of Arabian horses during their first year of race training. Methods: RNA sequencing of sixteen pure-breed Arabian horses was used to analyze transcriptomic changes at three key training stages. Differentially expressed genes (DEGs) were identified to explore their role in endurance and metabolic adaptation. Results: Seven genes-RCHY1, PIH1D1, IVD, FABP3, ANKRD2, USP13, and CRYAB-were consistently deregulated across tissues and training periods. These genes are involved in muscle remodeling, metabolism, oxidative stress response, and protein turnover. ANKRD2 was associated with mechanosensing and muscle adaptation, FABP3 with fatty acid metabolism, and USP13 with ubiquitination-related pathways crucial for muscle recovery and energy regulation. The transcriptomic overlap between muscle and blood suggests potential systemic biomarkers for athletic performance and endurance. Conclusions: Our findings highlight the importance of multi-tissue transcriptomic profiling in understanding exercise-induced molecular adaptations. The identified genes warrant further investigation as potential molecular markers for monitoring training progression and athletic potential in endurance horses. This study contributes to the growing field of equine sports genetics and may offer translational insights into human sports performance.

Genetic testing as a tool for diagnosis of congenital stationary night blindness (CSNB) in white spotted breeds in Poland

Congenital stationary night blindness (CSNB) has been connected to the leopard complex spotting phenotype (LP) in various horse breeds. CSNB associated with LP is thought to be caused by a 1378 bp insertion in TRPM1, with homozygotes being nightblind and having few to no spots of pigment in their white patterned area. This study aimed to assess the prevalence of CSNB alleles in tarant-colored horses in Poland through a three-primer system for an allele-specific Polymerase Chain Reaction (PCR). The TRPM1 gene insertion was genotyped in 221 horses belonging to Małopolska, Felin and Shetland Ponies. The chi-square (χ²) test indicates, that χ2 <5.991 suggesting that the population is in Hardy-Weinberg equilibrium. Of the horses carrying the LP allele, 7 % of Małopolska horses, 4,8 % of Felin ponies and 6.25 % of the Shetland ponies were homozygous for the TRMP1 insertion, indicating low-light vision issues, crucial for horses working in dim conditions. This study highlights the utility of genetic testing for accurate phenotype evaluation, and clinical and breeding management.

Genomic Insights into Post-Domestication Expansion and Selection of Body Size in Ponies

Horse domestication revolutionizes human civilization by transforming transportation, agriculture, and warfare patterns. Despite extensive studies on modern domestic horse origins, the intricate demographic history and genetic signatures underlying pony size remain unexplored. Here, a high-quality genome assembly of the Chinese Debao pony is presented, and 452 qualified individuals from 64 horse breeds worldwide are extensively analyzed. The authors' results reveal the conservation of ancient components in East Asian horses and close relationships between Asian horses and Western pony lineages. Genetic analyses suggest an Asian paternal origin for European pony breeds. These pony-sized horses share close genetic affinities, potentially attributed to their early expansion and adaptation to local environments. In addition, promising cis-regulatory elements influencing horse withers height by regulating genes such as RFLNA and FOXO1 are identified. Overall, this study provides insightful perspectives on the dispersal history and genetic determinants underlying body size in ponies, offering broader implications for horse population management and improvement.

Running a genetic stop sign accelerates oxygen metabolism and energy production in horses

Horses are among nature's greatest athletes, yet the ancestral molecular adaptations fueling their energy demands are poorly understood. Within a clinically important pathway regulating redox and metabolic homeostasis (NRF2/KEAP1), we discovered an ancient mutation-conserved in all extant equids-that increases mitochondrial respiration while decreasing tissue-damaging oxidative stress. This mutation is a de novo premature opal stop codon in KEAP1 that is translationally recoded into a cysteine through previously unknown mechanisms, producing an R15C mutation in KEAP1 that is more sensitive to electrophiles and reactive oxygen species. This recoding enables increased NRF2 activity, which enhances mitochondrial adenosine 5'-triphosphate production and cellular resistance to oxidative damage. Our study illustrates how recoding of a de novo stop codon, a strategy thought restricted to viruses, can facilitate adaptation in vertebrates.

Detection of domestication signals through the analysis of the full distribution of fitness effects

Domestication is a process marked by complex interactions between demographic changes and selective pressures, which together shape genetic diversity. While the phenotypic outcomes of domestication are well documented, its genetic basis-particularly the dynamics of selection-remain less well understood. To investigate these dynamics, we performed simulations designed to approximate the demographic history of large domestic mammals. These simulations used selection coefficients as a modeling tool to represent changes in selection pressures, recognizing that such coefficients are abstractions rather than direct representations of biological reality. Specifically, we analyzed site frequency spectra (SFS) under varying distributions of fitness effects (DFE) and proportions of mutations with divergent selective pressures. Our results show that the discretized deleterious DFE can be reliably inferred from the SFS of a single population, but reconstructing the beneficial DFE and demographic history remains challenging, even when using the joint SFS of both populations. We further developed a novel joint DFE inference model to estimate the proportion of mutations with divergent selection coefficients (p c), although we found that signals of classic hard sweeps can mimic increases in p c, complicating interpretation. These findings underscore both the utility and limitations of DFE inference and highlight the need for caution when interpreting demographic histories in domesticated populations based on such modeling assumptions.

The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle

Cattle (Bos taurus) play an important role in the life of humans in the Iberian Peninsula not just as a food source but also in cultural events. When domestic cattle were first introduced to Iberia, wild aurochs (Bos primigenius) were still present, leaving ample opportunity for mating (whether intended by farmers or not). Using a temporal bioarchaeological dataset covering eight millennia, we trace gene flow between the two groups. Our results show frequent hybridisation during the Neolithic and Chalcolithic, likely reflecting a mix of hunting and herding or relatively unmanaged herds, with mostly male aurochs and female domestic cattle involved. This is supported by isotopic evidence consistent with ecological niche sharing, with only a few domestic cattle possibly being managed. The proportion of aurochs ancestry in domestic cattle remains relatively constant from about 4000 years ago, probably due to herd management and selection against first generation hybrids, coinciding with other cultural transitions. The constant level of wild ancestry (~20%) continues into modern Western European breeds including Iberian cattle selected for aggressiveness and fighting ability. This study illuminates the genomic impact of human actions and wild introgression in the establishment of cattle as one of the most important domestic species today.

Semi-Feral Horse Grazing Benefits the Grassland Diversity of Flowering Plants Including a Pollinator-Promoting Indicator Species

European grasslands and their biodiversity are declining rapidly due to land use changes, which highlight the need to develop effective restoration strategies. This study investigates the impact of reintroducing the Swedish national horse breed (the Gotland Russ) on grassland plant diversity and evenness in abandoned agricultural landscapes in Southeast Sweden. Twelve horses were introduced into three 10-13-hectare enclosure replicates (four horses per enclosure) in a three-year (2014-2016) rewilding experiment. Plant species richness, evenness, and diversity were investigated in both grazed and un-grazed conditions. The results indicate that horse grazing significantly increased grassland plant species diversity and richness, with higher Shannon and Simpson's diversity indices in grazed areas. In addition, the abundance of white clover (Trifolium repens), a signal species beneficial to pollinators, increased significantly in grazed areas. These findings emphasize the need for integrating large herbivore grazing into ecological restoration practices. Considering the recently enacted EU Nature Restoration Law, which aims to restore 20% of Europe's degraded ecosystems by 2030, this research provides critical insights into scalable restoration methods. The implementation of restoration strategies that include large herbivores may enhance the resilience and biodiversity of European grasslands, thereby aligning with the EU's restoration goals.

Unraveling the maternal heritage: identifying the complex origins of indigenous Indian horse and pony breeds through mitochondrial genome analysis

This study explored the maternal genetic diversity of six indigenous Indian horse and pony breeds (Bhutia, Kathiawari, Manipuri, Marwari, Spiti, and Zanskari) using comprehensive mitochondrial genome (mitogenome) analysis. Blood samples from 53 horses across diverse agro-climatic zones of India were analyzed, revealing 36 distinct haplotypes, with a haplotype diversity of 0.889 and nucleotide diversity of 0.00347. These indices suggest significant maternal genetic diversity in Indian equines. A median-joining (MJ) network, based on the hypervariable region of the D-loop along with sequences of Indian equids retrieved from the NCBI, identified 55 haplotypes, including shared haplotypes across 2-5 breeds. Hierarchical AMOVA analysis revealed that 95.20% of genetic variation was within populations, while only 4.80% was among different groups, indicating minimal genetic structuring based on geographic distribution. Phylogenetic analysis of these mitogenomes, alongside global sequences, revealed significant genetic variability without clear geographic clustering, highlighting extensive gene flow and interbreeding across regions. Median-Joining network based on D-loop sequence revealed that Indian horses conform to seven of the 18 globally recognized haplogroups (A, B, G, J, L, M, and P), with haplogroup A being the most frequent. This research contributes to the broader understanding of equine genetic diversity, aligning with global patterns of extensive maternal haplotype diversity, and underscores the intricate genetic backgrounds resulting from historical breeding practices.

Leveraging graphical model techniques to study evolution on phylogenetic networks

The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture. Computing the likelihood of data observed at the leaves is costly as the size and complexity of the phylogeny grows. Efficient algorithms exist for trees, but cannot be applied to networks. We show that a vast array of models for trait evolution along phylogenetic networks can be reformulated as graphical models, for which efficient belief propagation algorithms exist. We provide a brief review of belief propagation on general graphical models, then focus on linear Gaussian models for continuous traits. We show how belief propagation techniques can be applied for exact or approximate (but more scalable) likelihood and gradient calculations, and prove novel results for efficient parameter inference of some models. We highlight the possible fruitful interactions between graphical models and phylogenetic methods. For example, approximate likelihood approaches have the potential to greatly reduce computational costs for phylogenies with reticulations.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.

Performance of qpAdm-based screens for genetic admixture on admixture-graph-shaped histories and stepping-stone landscapes

qpAdm is a statistical tool that is often used for testing large sets of alternative admixture models for a target population. Despite its popularity, qpAdm remains untested on two-dimensional stepping-stone landscapes and in situations with low pre-study odds (low ratio of true to false models). We tested high-throughput qpAdm protocols with typical properties such as number of source combinations per target, model complexity, model feasibility criteria, etc. Those protocols were applied to admixture-graph-shaped and stepping-stone simulated histories sampled randomly or systematically. We demonstrate that false discovery rates of high-throughput qpAdm protocols exceed 50% for many parameter combinations since: 1) pre-study odds are low and fall rapidly with increasing model complexity; 2) complex migration networks violate the assumptions of the method, hence there is poor correlation between qpAdm p-values and model optimality, contributing to low but non-zero false positive rate and low power; 3) although admixture fraction estimates between 0 and 1 are largely restricted to symmetric configurations of sources around a target, a small fraction of asymmetric highly non-optimal models have estimates in the same interval, contributing to the false positive rate. We also re-interpret large sets of qpAdm models from two studies in terms of source-target distance and symmetry and suggest improvements to qpAdm protocols: 1) temporal stratification of targets and proxy sources in the case of admixture-graph-shaped histories; 2) focused exploration of few models for increasing pre-study odds; 3) dense landscape sampling for increasing power and stringent conditions on estimated admixture fractions for decreasing the false positive rate.

Higher order affordances

Affordances are opportunities for action for a given animal (or animals) in a given environment or situation. The concept of affordance has been widely adopted in the behavioral sciences, but important questions remain. We propose a new way of understanding the nature of affordances; in particular, how affordances are related to one another. We claim that many - perhaps most - affordances emerge from non-additive relations among other affordances, such that some affordances are of higher order relative to other affordances. That is, we propose that affordances form a continuous category of perceiveables that differ only in whether and how they relate to other affordances. We argue that: (1) opportunities for behaviors of all kinds can be described as affordances, (2) some affordances emerge from relations between animal and environment, whereas most affordances emerge from relations between other affordances, and (3) all affordances lawfully structure ambient energy arrays and, therefore, can be perceived directly. Our concept of higher order affordances provides a general account of behavioral phenomena that traditionally have been interpreted in terms of cognitive processes (e.g., remembering or imagining) as well as behavioral phenomena that have traditionally been interpreted in terms of cultural rules, such as conventions, or customs.

Rewilded horses in European nature conservation - a genetics, ethics, and welfare perspective

In recent decades, the integration of horses (Equus ferus) in European rewilding initiatives has gained widespread popularity due to their potential for regulating vegetation and restoring natural ecosystems. However, employing horses in conservation efforts presents important challenges, which we here explore and discuss. These challenges encompass the lack of consensus on key terms inherent to conservation and rewilding, the entrenched culture and strong emotions associated with horses, low genetic diversity and high susceptibility to hereditary diseases in animals under human selection, as well as insufficient consideration for the social behaviour of horses in wild-living populations. In addition, management of wild-living horses involves intricate welfare, ethics and legislative dimensions. Anthropocentric population-control initiatives may be detrimental to horse group structures since they tend to prioritise individual welfare over the health of populations and ecosystems. To overcome these challenges, we provide comprehensive recommendations. These involve a systematic acquisition of genetic information, a focus on genetic diversity rather than breed purity and minimal veterinary intervention in wild-living populations. Further, we advise allowing for natural top-down and bottom-up control - or, if impossible, simulating this by culling or non-lethal removal of horses - instead of using fertility control for population management. We advocate for intensified collaboration between conservation biologists and practitioners and enhanced communication with the general public. Decision-making should be informed by a thorough understanding of the genetic makeup, common health issues and dynamics, and social behaviour in wild-living horse populations. Such a holistic approach is essential to reconcile human emotions associated with horses with the implementation of conservation practices that are not only effective but also sustainable for the long-term viability of functional, biodiverse ecosystems, while rehabilitating the horse as a widespread wild-living species in Europe.

Does strain-level persistence of lactobacilli in long-term back-slopped sourdoughs inform on domestication of food-fermenting lactic acid bacteria?

Sourdoughs are maintained by back-slopping over long time periods. To determine strain-level persistence of bacteria, we characterized four sourdoughs from bakeries over a period of 3.3, 11.0, 18.0, and 19.0 years. One sourdough included isolates of Levilactobacillus spp. and Fructilactobacillus spp. that differed by fewer than 10 single-nucleotide polymorphisms (SNPs) from the isolates obtained 3.3 years earlier and thus likely represent the same strain. Isolates of Levilactobacillus parabrevis differed by 200-300 SNPs; their genomes were under positive selection, indicating transmission from an external source. In two other sourdoughs, isolates of Fructilactobacillus sanfranciscensis that were obtained 11 and 18 years apart differed by 19 and 29 SNPs, respectively, again indicating repeated isolation of the same strain. The isolate of Fl. sanfranciscensis from the fourth sourdough differed by 45 SNPs from the isolate obtained 19 years previously. We thus identified strain-level persistence in three out of four long-term back-slopped sourdoughs, making it possible that strains persisted over periods that are long enough to allow bacterial speciation and domestication.IMPORTANCEThe assembly of microbial communities in sourdough is shaped by dispersal and selection. Speciation and domestication of fermentation microbes in back-slopped food fermentations have been documented for food-fermenting fungi including sourdough yeasts but not for bacteria, which evolve at a slower rate. Bacterial speciation in food fermentations requires strain-level persistence of fermentation microbes over hundreds or thousands of years. By documenting strain-level persistence in three out of four sourdoughs over a period of up to 18 years, we demonstrate that persistence over hundreds or thousands of years is possible, if not likely. We thus not only open a new perspective on fermentation control in bakeries but also support the possibility that all humans, despite their cultural diversity, share the same fermentation microbes.

Expression and Analysis of TBX3 Gene in the Skin from Three Locations on Dun Mongolian Bider Horse

BACKGROUND/OBJECTIVES

The Mongolian horse, one of the oldest and most genetically diverse breeds, exhibits a wide variety of coat colors and patterns, including both wild-type and unique features. A notable characteristic of dun Mongolian horses is the presence of Bider markings-symmetrical, black-mottled patterns observed on the shoulder blades. These markings are also seen in Przewalski's horses. The dun coat color, a common wild-type phenotype in domestic horses, is characterized by pigment dilution with distinct dark areas and is regulated by mutations in the TBX3 gene. This study aimed to investigate the role of TBX3 in the development of Bider markings in dun Mongolian horses.

METHODS

Skin tissue samples were collected from three key anatomical regions of dun Mongolian horses with Bider markings: the croup, dorsal midline, and shoulder. Histological staining was conducted to examine the skin and hair follicle structure and pigment distribution. RT-qPCR was used to measure TBX3 mRNA expression, while immunoblotting and immunohistochemistry were employed to analyze TBX3 protein levels and localization.

RESULTS

Hematoxylin and eosin staining revealed the skin and hair follicle structures, including the epidermis, hair shaft, and hair bulb across different stages of the hair growth cycle. Differences in pigmentation were observed across the sampling sites. The croup and the light-colored area of the shoulder showed asymmetrical pigmentation, while the dorsal midline and dark-colored area of the shoulder displayed symmetrical pigmentation. TBX3 mRNA expression levels were significantly higher in the croup compared to the shoulder and dorsal midline; however, corresponding TBX3 protein expression did not show significant differences. Immunohistochemical analysis localized TBX3 protein predominantly in the hair bulb and epidermis.

CONCLUSIONS

This study demonstrates region-specific differences in TBX3 expression that correlate with pigmentation patterns in dun Mongolian Bider horses. These findings provide valuable insights into the molecular mechanisms underlying Bider markings, offering a deeper understanding of the genetic regulation of coat color and primitive markings in equines.

The global spread of Oriental Horses in the past 1,500 years through the lens of the Y chromosome

Since their domestication, horses have accompanied mankind, and humans have constantly shaped horses according to their needs through stallion-centered breeding. Consequently, the male-specific portion of the Y chromosome (MSY) is extremely uniform in modern horse breeds. The majority of stallions worldwide carry MSY haplotypes (HT) attributed to an only ~1,500-y-old, so-called, "Crown" haplogroup. The predominance of the Crown in modern horse breeds is thought to represent a footprint of the vast impact of stallions of "Oriental origin" in the past millennium. Here, we report the results of a fine-scaled MSY haplotyping of large datasets of patrilines comprising 1,517 males of 189 modern horse breeds, covering a broad phenotypic and geographic spectrum. We can disentangle the multilayered influence of Oriental stallions over the last few hundred years, exposing the intense linebreeding and the wide-ranging impact of Arabian, English Thoroughbred, and Coldblood sires. Iberian and New World horse breeds contain a wide range of diversified Crown lineages. Their broad HT spectrum illustrates the spread of horses of Oriental origin via the Iberian Peninsula after the Middle Ages, which is commonly referred to as the "Spanish influence." Our survey also revealed a second major historical dissemination of horses from Western Asia, attributed to the expansion of the Ottoman Empire. Our analysis shows that MSY analysis can uncover the complex history of horse breeds and can be used to establish the paternal ancestry of modern horse breeds.

Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages

The Indo-European languages are among the most widely spoken in the world, yet their early diversification remains contentious1-5. It is widely accepted that the spread of this language family across Europe from the 5th millennium BP correlates with the expansion and diversification of steppe-related genetic ancestry from the onset of the Bronze Age6,7. However, multiple steppe-derived populations co-existed in Europe during this period, and it remains unclear how these populations diverged and which provided the demographic channels for the ancestral forms of the Italic, Celtic, Greek, and Armenian languages8,9. To investigate the ancestral histories of Indo-European-speaking groups in Southern Europe, we sequenced genomes from 314 ancient individuals from the Mediterranean and surrounding regions, spanning from 5,200 BP to 2,100 BP, and co-analysed these with published genome data. We additionally conducted strontium isotope analyses on 224 of these individuals. We find a deep east-west divide of steppe ancestry in Southern Europe during the Bronze Age. Specifically, we show that the arrival of steppe ancestry in Spain, France, and Italy was mediated by Bell Beaker (BB) populations of Western Europe, likely contributing to the emergence of the Italic and Celtic languages. In contrast, Armenian and Greek populations acquired steppe ancestry directly from Yamnaya groups of Eastern Europe. These results are consistent with the linguistic Italo-Celtic10,11 and Graeco-Armenian1,12,13 hypotheses accounting for the origins of most Mediterranean Indo-European languages of Classical Antiquity. Our findings thus align with specific linguistic divergence models for the Indo-European language family while contradicting others. This underlines the power of ancient DNA in uncovering prehistoric diversifications of human populations and language communities.

Genomic insights into the genetic diversity, lateral gaits and high-altitude adaptation of Chakouyi (CKY) horses

Chakouyi (CKY) horses from the Qinghai‒Xizang Plateau are well known for their unique lateral gaits and high-altitude adaptation, but genetic mechanisms underlying these phenotypes remain unclear. This study presents a comparison of 60 newly resequenced genomes of gaited CKY horses with 139 public genomes from 19 horse breeds. Population structure analyses (admixture, PCA, and neighbor-joining tree) reveal a close genetic relationship between CKY and other highland breeds (Tibetan and Chaidamu horses). Compared with other Chinese breeds, CKY horses present reduced nucleotide diversity (θπ) and lower inbreeding (FROH coefficient), suggesting possible selective pressures. A key region on chromosome 23 (Chr23: 22.3 -22.6 Mb) is associated with the lateral gaits and harbors a highly prevalent nonsense mutation (Chr 23:22,391,254 C>A, Ser301STOP) in the DMRT3 gene, with an 88% homozygosity rate, which is strongly correlated with the distinctive gait of CKY horses. Furthermore, selection signals reveal that the EPAS1 gene is related to high-altitude adaptation, and the CAT gene contributes to altitude resilience in CKY horses. These findings suggest that preserving genetic diversity is essential for maintaining the unique gaits and high-altitude adaptations of CKY horses.

Archaeogenetics: Four letters from Pompeii

As archaeogenetics - the study of DNA from (pre-)historical samples - comes of age, it complements and contrasts historical and archaeological records in novel ways. DNA from victims of the eruption of Vesuvius that destroyed Pompeii provides an interesting case study.

The rise and transformation of Bronze Age pastoralists in the Caucasus

The Caucasus and surrounding areas, with their rich metal resources, became a crucible of the Bronze Age1 and the birthplace of the earliest steppe pastoralist societies2. Yet, despite this region having a large influence on the subsequent development of Europe and Asia, questions remain regarding its hunter-gatherer past and its formation of expansionist mobile steppe societies3-5. Here we present new genome-wide data for 131 individuals from 38 archaeological sites spanning 6,000 years. We find a strong genetic differentiation between populations north and south of the Caucasus mountains during the Mesolithic, with Eastern hunter-gatherer ancestry4,6 in the north, and a distinct Caucasus hunter-gatherer ancestry7 with increasing East Anatolian farmer admixture in the south. During the subsequent Eneolithic period, we observe the formation of the characteristic West Eurasian steppe ancestry and heightened interaction between the mountain and steppe regions, facilitated by technological developments of the Maykop cultural complex8. By contrast, the peak of pastoralist activities and territorial expansions during the Early and Middle Bronze Age is characterized by long-term genetic stability. The Late Bronze Age marks another period of gene flow from multiple distinct sources that coincides with a decline of steppe cultures, followed by a transformation and absorption of the steppe ancestry into highland populations.

Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history

Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.

Tracing horseback riding and transport in the human skeleton

Among the most widely used methods for understanding human-horse relationships in the archaeological record is the identification of human skeletal pathologies associated with mounted horseback riding. In particular, archaeologists encountering specific bony changes to the hip, femur, and lower back often assert a causal link between these features and prolonged periods of mounted horseback riding. The identification of these features have recently been used to assert the early practice of mounted horseback riding among the Yamnaya culture of western Eurasia during the third and fourth millennium BCE. Here, we summarize the methodological hurdles and analytical risks of using this approach in the absence of valid comparative datasets and outline best practices for using human osteological data in the study of ancient animal transport.

Testing times: disentangling admixture histories in recent and complex demographies using ancient DNA

Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches-firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes-and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudohaploidization. We observe that population differentiation is the primary factor driving qpAdm performance. Notably, while complex gene flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible among a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations.

Oxytocin homogenizes horse group organization

The oxytocinergic system has been suggested to make up an important part of the endocrine basis of group cohesion. However, controlled studies in open-group settings have not been performed. We here investigated the impact of exogenous intranasal oxytocin on the group-level social organization of 5 groups of horses (N = 58; 12 mares and 46 geldings) through GPS tracking and social network analysis. We find oxytocin flattened social differentiation across levels. Most strikingly, oxytocin did not simply reinforce existing bonds but selectively shifted social preferences toward homogenization - individuals and pairs who otherwise rarely associated spent more time close together, while individuals and pairs with the highest baseline association instead spent more time further apart. This resulted in a more distributed structure and lower clustering coefficient at the network level. These effects reinforce and extend oxytocin's role in collective behavior, social organization, and the evolution of group-based sociality across taxa.

Improving data archiving practices in ancient genomics

Ancient DNA is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is appropriately archived, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. Half of the studies archived incomplete datasets, preventing accurate replication and representing a loss of data of potential future use. No studies met all criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: (1) archive all sequencing reads, not just those that aligned to a reference genome, (2) archive read alignments too, but as secondary analysis files, (3) provide correct experiment metadata on samples, libraries and sequencing runs, (4) provide informative sample metadata, (5) archive data from low-coverage and negative experiments, and (6) document archiving choices in papers, and peer review these. Given the reliance on destructive sampling of finite material, ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.

What Is a Working Equid? Analysis of Current Terminology and a Suggested Definition

Equids are engaged in myriad types of work across the world, with contexts and industries varying widely between high-, middle- and low-income countries as classified by the World Bank. Through a comprehensive abstract search and literature review, we examined the usage and context of terms associated with working equids in high-income countries (HICs), upper-middle-income countries (UMICs), lower-middle-income countries (LMICs), and low-income countries (LICs). Analysis showed that the search term used was significantly associated with World Bank country income classification. All search terms except two returned a significantly higher number of papers for higher-income countries compared to lower-income countries. The two exceptions were "working equid" and "draft equid", which returned significantly more papers for lower-income countries than higher-income countries. Both terms also returned papers from high-income and upper-middle-income countries, but these were always in the context of low-resource settings and rural or marginalised communities, of which we provide examples in the discussion. We propose that the term "working equid" should be used to describe "any equid engaged in physical labour that provides a significant or direct contribution to the economic livelihood, sustenance or support of the owner/user's family, typically within a low resource setting". Our review highlights the intricate interplay between socioeconomic factors and examines how equids are described in the literature. The lack of a universally accepted definition leads to challenges in policy formulation, resource allocation, and welfare standards development, particularly in LMICs and LICs where working equids are crucial to livelihoods. This study underscores the need for a more inclusive and comprehensive approach to terminology, advocating for future research to bridge linguistic and cultural gaps in understanding working equids globally. Such efforts are vital for equitable and effective welfare standards and policy development for these animals.

A comparative analysis reveals the genomic diversity among 8 Muscovy duck populations

The Muscovy duck (Cairina moschata) is a waterfowl indigenous to the neotropical regions of Central and South America. It has low demand for concentrated feed and strong adaptability to different rearing conditions. After introduced to China through Eurasian commercial trade, Muscovy ducks have a domestication history of around 300 years in the Fujian Province of China. In the 1990s, the commodity Muscovy duck breed "Crimo," cultivated in Europe, entered the Chinese market for consumption and breeding purposes. Due to the different selective breeding processes, Muscovy ducks have various populational traits and lack transparency of their genetic background. To remove this burden in the Muscovy duck breeding process, we analyzed genomic data from 8 populations totaling 83 individuals. We identify 11.24 million single nucleotide polymorphisms (SNPs) and categorized these individuals into the Fujian-bred and the Crimo populations according to phylogenetic analyses. We then delved deeper into their evolutionary relationships through assessing population structure, calculating fixation index (FST) values, and measuring genetic distances. Our exploration of runs of homozygosity (ROHs) and homozygous-by-descent (HBD) uncovered genomic regions enriched for genes implicated in fatty acid metabolism, development, and immunity pathways. Selective sweep analyses further indicated strong selective pressures exerted on genes including TECR, STAT2, and TRAF5. These findings provide insights into genetic variations of Muscovy ducks, thus offering valuable information regarding genetic diversity, population conservation, and genome associated with the breeding of Muscovy ducks.

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.

Non-Synonymous Substitutions in Cadherin 13, Solute Carrier Family 6 Member 4, and Monoamine Oxidase A Genes are Associated with Personality Traits in Thoroughbred Horses

Retraining retired racehorses for various purposes can help correct behavioral issues. However, ensuring efficiency and preventing accidents present global challenges. Based on the hypothesis that a simple personality assessment could help address these challenges, the present study aimed to identify genetic markers associated with personality. Eight genes were selected from 18 personality-related candidate genes that are orthologs of human personality genes, and their association with personality was verified based on actual behavior. A total of 169 Thoroughbred horses were assessed for their tractability (questionnaire concerning tractability in 14 types of situations and 3 types of impressions) during the training process. Personality factors were extracted from the data using principal component analysis and analyzed for their association with single nucleotide variants as non-synonymous substitutions in the target genes. Three genes, CDH13, SLC6A4, and MAOA, demonstrated significant associations based on simple linear regression, marking the identification of these genes for the first time as contributors to temperament in Thoroughbred horses. All these genes, as well as the previously identified HTR1A, are involved in the serotonin neurotransmitter system, suggesting that the tractability of horses may be correlated with their social personality. Assessing the genotypes of these genes before retraining is expected to prevent problems in the development of a racehorse's second career and shorten the training period through individual customization of training methods, thereby improving racehorse welfare.

Mitochondrial DNA and Y chromosome reveal the genetic structure of the native Polish Konik horse population

Polish Konik remains one of the most important horse breeds in Poland. The primitive, native horses with a stocky body and mouse-like coat color are protected by a conservation program, while their Polish population consists of about 3,480 individuals, representing 16 dam and six sire lines. To define the population's genetic structure, mitochondrial DNA and Y chromosome sequence variables were identified. The mtDNA whole hypervariable region analysis was carried out using the Sanger sequencing method on 233 Polish Koniks belonging to all dam lines, while the Y chromosome analysis was performed with the competitive allele-specific PCR genotyping method on 36 horses belonging to all sire lines. The analysis of the mtDNA hypervariable region detected 47 SNPs, which assigned all tested horses to 43 haplotypes. Most dam lines presented more than one haplotype; however, five dam lines were represented by only one haplotype. The haplotypes were classified into six (A, B, E, J, G, R) recognized mtDNA haplogroups, with most horses belonging to haplogroup A, common among Asian horse populations. Y chromosome analysis allocated Polish Koniks in the Crown group, condensing all modern horse breeds, and divided them into three haplotypes clustering with coldblood breeds (28 horses), warmblood breeds (two horses), and Duelmener Pony (six horses). The clustering of all Wicek sire line stallions with Duelmener horses may suggest a historical relationship between the breeds. Additionally, both mtDNA and Y chromosome sequence variability results indicate crossbreeding before the studbooks closure or irregularities in the pedigrees occurred before the DNA testing introduction.

Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China

This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes.

Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region

Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from the Late Neolithic (∼4,100 cal BP) to historical times (∼1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.

An endothelial regulatory module links blood pressure regulation with elite athletic performance

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 racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.

Population structure and genomic diversity of the Einsiedler horse

The breeding history of the Einsiedler horse is closely connected with the Benedictine cloister Einsiedeln. In the mid-nineteenth century, it was decided to use European Warmblood stallions for cross-breeding and to abandon the selection of stallions. Since that time, it has only been possible to trace back the origin of Einsiedler horses using maternal ancestry information. Here, we collected high-density genotype data for European Warmblood horses (Selle Français, Swiss Warmblood and Einsiedler) and Franches-Montagnes horses, the last native Swiss horse breed, to unravel the current population structure of the Einsiedler horse. Using commonly applied methods to ascertain fine-scale population structures, it was not possible to clearly differentiate the Einsiedler from other European Warmblood horses. However, by means of runs of homozygosity (ROH) we were able to detect breed-specific ROH islands for the Einsiedler horse, including genes involved in domestication and adaptation to high altitude. Therefore, future breeding activities should involve the screening of these breed-specific ROH segments, the revival of cryopreserved sperm and the selection of Einsiedler stallions.

Unveiling the population genetic structure of Iranian horses breeds by whole-genome resequencing analysis

Preserving genetic diversity is pivotal for enhancing genetic improvement and facilitating adaptive responses to selection. This study focuses on identifying key genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs), while exploring the genomic evolutionary connectedness among seven Iranian horses representing five indigenous breeds: Caspian, Turkemen, DareShuri, Kurdish, and Asil. Using whole-genome resequencing, we generated 2.7 Gb of sequence data, with raw reads ranging from 1.2 Gb for Caspian horses to 0.38 Gb for Turkoman horses. Post-filtering, approximately 1.9 Gb of reads remained, with ~ 1.5 Gb successfully mapped to the horse reference genome (EquCab3.0), achieving mapping rates between 76.4% (Caspian) and 98.35% (Turkoman). We identified 2,909,816 SNPs in Caspian horses, constituting around 0.1% of the genome. Notably, 71% of these SNPs were situated in intergenic regions, while 8.5 and 6.8% were located upstream and downstream, respectively. A comparative analysis of SNPs between Iranian and non-Iranian horse breeds showed that Caspian horses had the lowest number of shared SNPs with Turkoman horses. Instead, they showed a closer genetic relationship with DareShuri, Quarter, Arabian, Standardbred, and Asil breeds. Hierarchical clustering highlighted Caspian horses as a distinct cluster, underscoring their distinctive genomic signature. Caspian horses exhibit a unique genetic profile marked by an enrichment of private mutations in neurological genes, influencing sensory perception and awareness. This distinct genetic makeup shapes mating preferences and signifies a separate evolutionary trajectory. Additionally, significant non-synonymous single nucleotide polymorphisms (nsSNPs) in reproductive genes offer intervention opportunities for managing Caspian horses. These findings reveal the population genetic structure of Iranian horse breeds, contributing to the advancement of knowledge in areas such as conservation, performance traits, climate adaptation, reproduction, and resistance to diseases in equine science.

A High-Coverage Mesolithic Aurochs Genome and Effective Leveraging of Ancient Cattle Genomes Using Whole Genome Imputation

Ancient genomic analyses are often restricted to utilizing pseudohaploid data due to low genome coverage. Leveraging low-coverage data by imputation to calculate phased diploid genotypes that enables haplotype-based interrogation and single nucleotide polymorphism (SNP) calling at unsequenced positions is highly desirable. This has not been investigated for ancient cattle genomes despite these being compelling subjects for archeological, evolutionary, and economic reasons. Here, we test this approach by sequencing a Mesolithic European aurochs (18.49×; 9,852 to 9,376 calBCE) and an Early Medieval European cow (18.69×; 427 to 580 calCE) and combine these with published individuals: two ancient and three modern. We downsample these genomes (0.25×, 0.5×, 1.0×, and 2.0×) and impute diploid genotypes, utilizing a reference panel of 171 published modern cattle genomes that we curated for 21.7 million (Mn) phased SNPs. We recover high densities of correct calls with an accuracy of >99.1% at variant sites for the lowest downsample depth of 0.25×, increasing to >99.5% for 2.0× (transversions only, minor allele frequency [MAF] ≥ 2.5%). The recovery of SNPs correlates with coverage; on average, 58% of sites are recovered for 0.25× increasing to 87% for 2.0×, utilizing an average of 3.5 million (Mn) transversions (MAF ≥2.5%), even in the aurochs, despite the highest temporal distance from the modern reference panel. Our imputed genomes behave similarly to directly called data in allele frequency-based analyses, for example consistently identifying runs of homozygosity >2 Mb, including a long homozygous region in the Mesolithic European aurochs.

Eimeria leuckarti in equid coprolites from the Sassanid Era (2nd-6th century CE) excavated in Chehrabad Salt Mine archaeological site, Iran

OBJECTIVE

This study reports coccidian oocysts in an equid coprolite dated to the Sassanid Empire (2nd-6th century CE) recovered in Chehrabad Salt Mine archaeological site, Iran.

METHODS

Between 2015 and 2017, an archaeoparasitological investigation led to the discovery of an equid coprolite in the Chehrabad Salt Mine archeological site, (Douzlakh), western Iran. Samples were rehydrated using trisodium phosphate solution and were examined by light microscopy.

RESULTS

Seven oocysts of Eimeria leuckarti (Flesch, 1883) were identified; they were in various stages of sporulation.

CONCLUSION

This is the first report of ancient coccidian oocysts from equids. The importance of this observation is discussed, and current knowledge of eimeriid oocysts at archaeological sites is reviewed.

SIGNIFICANCE

The observations of E. leuckarti increases current knowledge of parasite biodiversity in ancient Iran when it rested along the Silk Road, a network of trade routes connecting the East and West that was central to economic, cultural, political, and religious interactions between these regions, and to livestock movement that could contribute to the transmission of the parasites from/to other regions.

LIMITATIONS

The contextual information about animal species present in and around the Salt Mine during its working periods, including Achaemenid dynasty (6th to 4th century BCE) and Sassanid era (2nd to 6th century CE), is very limited and does not allow secure conclusions regarding the host origin of the coprolites.

SUGGESTIONS FOR FURTHER RESEARCH

Application of molecular biology tools to identify the correct host origin of the coprolites and to detect more parasite species is advocated.

Late History of Cattle Breeds in Central Europe in Light of Genetic and Archaeogenetic Sources-Overview, Thoughts, and Perspectives

Although Europe was not a primary centre of cattle domestication, its expansion from the Middle East and subsequent development created a complex pattern of cattle breed diversity. Many isolated populations of local historical breeds still carry the message about the physical and genetic traits of ancient populations. Since the way of life of human communities starting from the eleventh millennium BP was strongly determined by livestock husbandry, the knowledge of cattle diversity through the ages is helpful in the interpretation of many archaeological findings. Historical cattle diversity is currently at the intersection of two leading directions of genetic research. Firstly, it is archaeogenetics attempting to recover and interpret the preserved genetic information directly from archaeological finds. The advanced archaeogenetic approaches meet with the population genomics of extant cattle populations. The immense amount of genetic information collected from living cattle, due to its key economic role, allows for reconstructing the genetic profiles of the ancient populations backwards. The present paper aims to place selected archaeogenetic, genetic, and genomic findings in the picture of cattle history in Central Europe, as suggested by archaeozoological and historical records. Perspectives of the methodical connection between the genetic approaches and the approaches of traditional archaeozoology, such as osteomorphology and osteometry, are discussed. The importance, actuality, and effectiveness of combining different approaches to each archaeological find, such as morphological characterization, interpretation of the historical context, and molecular data, are stressed.

"Until death do us part". A multidisciplinary study on human- Animal co- burials from the Late Iron Age necropolis of Seminario Vescovile in Verona (Northern Italy, 3rd-1st c. BCE)

Animal remains are a common find in prehistoric and protohistoric funerary contexts. While taphonomic and osteological data provide insights about the proximate (depositional) factors responsible for these findings, the ultimate cultural causes leading to this observed mortuary behavior are obscured by the opacity of the archaeological record and the lack of written sources. Here, we apply an interdisciplinary suite of analytical approaches (zooarchaeological, anthropological, archaeological, paleogenetic, and isotopic) to explore the funerary deposition of animal remains and the nature of joint human-animal burials at Seminario Vescovile (Verona, Northern Italy 3rd-1st c. BCE). This context, culturally attributed to the Cenomane culture, features 161 inhumations, of which only 16 included animal remains in the form of full skeletons, isolated skeletal parts, or food offerings. Of these, four are of particular interest as they contain either horses (Equus caballus) or dogs (Canis lupus familiaris)-animals that did not play a dietary role. Analyses show no demographic, dietary, funerary similarities, or genetic relatedness between individuals buried with animals. Isotopic data from two analyzed dogs suggest differing management strategies for these animals, possibly linked to economic and/or ritual factors. Overall, our results point to the unsuitability of simple, straightforward explanations for the observed funerary variability. At the same time, they connect the evidence from Seminario Vescovile with documented Transalpine cultural traditions possibly influenced by local and Roman customs.

Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago

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 per cent, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here, we screen the sequenced data of 264 archaeological horse remains to detect the presence of EHV-4. We recover the first ancient EHV-4 genome with 4.2× average depth-of-coverage from a specimen excavated in the Southeastern Urals and dated to the Early Bronze Age period, approximately 3,900 years ago. The recovery of an EHV-4 virus outside the upper respiratory tract not only points to an animal particularly infected but also highlights the importance of post-cranial bones in pathogen characterisation. Bayesian phylogenetic reconstruction provides a minimal time estimate for EHV-4 diversification to around 4,000 years ago, a time when modern domestic horses spread across the Central Asian steppes together with spoke-wheeled Sintashta chariots, or earlier. The analyses also considerably revise the diversification time of the two EHV-4 subclades from the 16th century based solely on modern data to nearly a thousand years ago. Our study paves the way for a robust reconstruction of the history of non-human pathogens and their impact on animal health.

Population genomics of post-glacial western Eurasia

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 genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.

slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes

One of the goals of population genetics is to understand how evolutionary forces shape patterns of genetic variation over time. However, because populations evolve across both time and space, most evolutionary processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution of resources. This spatial dimension is often neglected, partly due to the lack of tools specifically designed for building and evaluating complex spatio-temporal population genetic models. To address this methodological gap, we present a new framework for simulating spatially-explicit genomic data, implemented in a new R package called slendr (www.slendr.net), which leverages a SLiM simulation back-end script bundled with the package. With this framework, the users can programmatically and visually encode spatial population ranges and their temporal dynamics (i.e., population displacements, expansions, and contractions) either on real Earth landscapes or on abstract custom maps, and schedule splits and gene-flow events between populations using a straightforward declarative language. Additionally, slendr can simulate data from traditional, non-spatial models, either with SLiM or using an alternative built-in coalescent msprime back end. Together with its R-idiomatic interface to the tskit library for tree-sequence processing and analysis, slendr opens up the possibility of performing efficient, reproducible simulations of spatio-temporal genomic data entirely within the R environment, leveraging its wealth of libraries for geospatial data analysis, statistics, and visualization. Here, we present the design of the slendr R package and demonstrate its features on several practical example workflows.

Interdisciplinary evidence for early domestic horse exploitation in southern Patagonia

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 from the site of Chorrillo Grande 1 in southern Argentina. Osteological and taphonomic analyses suggest that horses were pastorally managed and used for food by Aónikenk/Tehuelche hunter-gatherers before the onset of permanent European settlement, as early as the mid-17th century. DNA-based sex identifications suggest consumption of both male and female horses, while ceramic residue also shows use of guanaco products. Sequential isotope analyses on horse dentition reveal an origin in southern Patagonia and movement of these animals between the Río Coig and Río Gallegos basins. These results reinforce emerging evidence for rapid Indigenous-mediated dispersal of horses in the Americas and demonstrate that horses catalyzed rapid economic and social transformations.

Short review: Geographical distribution of equine-associated pVAPA plasmids in Rhodococcus equi in the world

Virulent Rhodococcus equi strains expressing virulence-associated 15-17 kDa protein (VapA) and having a large virulence plasmid (pVAPA) of 85-90 kb containing vapA gene are pathogenic for horses. In the last two decades, following pVAPA, two host-associated virulence plasmid types of R. equi have been discovered: a circular plasmid, pVAPB, associated with porcine isolates in 1995, and a recently detected linear plasmid, pVAPN, related to bovine and caprine isolates. Molecular epidemiological studies of R. equi infection in foals on horse-breeding farms in Japan and many countries around the world have been conducted in the last three decades, and the epidemiological studies using restriction enzyme digestion patterns of plasmid DNAs from virulent isolates have shown 14 distinct pVAPA subtypes and their geographical preference. This short review summarizes previous reports regarding equine-associated pVAPA subtypes in the world and discusses their geographic distribution from the standpoint of horse movements.

The Genetic Diversity of Horse Native Breeds in Russia

Horses were domesticated later than other farm animals. Horse breeds have been selectively developed by humans to satisfy different needs and purposes. The factory and indigenous breeds are of particular interest, having been bred in purity for many centuries without the addition of foreign blood. Data from 31 stud farms, as well as ranches, located in fifteen regions of the Russian Federation were used in this work. DNA was sampled from 102 stallions of 11 breeds: Arabian, Akhal-Teke, Don, Orlov Trotter, Vladimir Heavy Draft, Russian Heavy Draft, Soviet Heavy Draft, Kabardin, Yakut, Tuva, and Vyatka. Data on the origin of each animal from which the material was collected were taken into account. DNA genotyping was carried out using GGP Equine 70 k ® array chips (Thermo Fisher Scientific, USA). Genetic diversity of horse breeds was estimated using Admixture 1.3. and PLINK 1.9 software. FROH inbreeding was computed via the R detectRUNS package. The minimum length for ROH was set at 1 Mb to reduce the occurrence of false positives. We conducted PCA analysis using PLINK 1.9, and used the ggplot2 library in R for visualizing the results. Indigenous equine breeds, such as Vyatka, Tuva, and Yakut, are very hardy, and well adapted to local environmental and climatic conditions. They are employed as draft power, as well as for milk and meat. Both the Akhal-Teke breed and the Arabian breed have retained a minimum effective population size over many generations. We note significant accumulations of homozygosity in these breeds. In equestrian sports, performance is a top priority. ADMIXTURE and PCA analyses showed similarities between Don equine breeds and Kabardin, as well as some Arabian breed animals. Earlier research indicated the presence of thoroughbred traits in Don stallions. The Orlov Trotter breed stands out as a separate cluster in the structural and PCA analyses. Considering the small population size of this breed, our study found high FROH in all tested animals. The general reduction in the diversity of the horse breed gene pool, due to numerous crosses for breed improvement with thoroughbreds, has lead to a decline in the differences between the top sporting breeds. Our study presents new opportunities for exploring the genetic factors that influence the formation of adaptive traits in indigenous breeds, and for finding ways to preserve genetic diversity for effective population reproduction.