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Topic:Evolutionary Biology
Evolutionary biology and horses focus on the study of the evolutionary processes that have shaped the development, adaptation, and diversification of the Equus genus. This field examines the genetic, morphological, and ecological changes that have occurred over millions of years, leading to the modern horse. Researchers explore the transition from small, multi-toed ancestors to the large, single-toed horses of today, analyzing fossil records, genetic data, and environmental factors that influenced these changes. This page compiles peer-reviewed research studies and scholarly articles that investigate the evolutionary history, genetic adaptations, and ecological interactions of horses, providing insights into their development and survival strategies throughout history.
Comparative genomics of Standardbred horses reveals candidate regions under selection for harness racing performance. Harness racing performance in horses is a complex polygenic trait influenced by genetic background, breeding history, training, and environment. Understanding genomic patterns shaped by long-term artificial selection provides insights into performance-related traits and breed-specific genomic variation. Objective: This study aimed to characterize genomic differentiation, population structure, and candidate genomic regions potentially influenced by historical selection in Standardbred horses using comparative whole-genome sequencing involving diverse horse breeds. Methods: Whole-genome sequenci...
Comparative analysis of the karyotypes of Equus caballus and Equus asinus in the context of contemporary genomic data. Karyotypes of species within the genus Equus display considerable variation in chromosome number and are characterised by numerous structural rearrangements that have played a pivotal role in their evolutionary divergence and speciation. Equus caballus (horse), 2n = 64 and Equus asinus (donkey), 2n = 62, constitute particularly interesting models for comparative studies due to the diversified morphology of their chromosomes, including acrocentric and submetacentric pairs, documented Robertsonian translocations, and centric fusions. In recent decades, widely applied molecular cytogenetic techni...
Comparative genomic analysis of oxytocin and oxytocin receptor genes in the family Equidae. The oxytocin (OXT) - oxytocin receptor (OXTR) system regulates diverse biological processes including social behavior, stress responses, and processes related to domestication. While OXT is highly conserved, OXTR shows greater variability, which may contribute to species-specific adaptations. Methods: Comparative genomic analyses of OXT and OXTR coding sequences were performed across equid species using available genome assemblies and newly generated sequences obtained by next-generation sequencing. Phylogenetic relationships were inferred using maximum likelihood methods. Selection was assess...
Extreme male reproductive skew limits effective population size in American Standardbred horses. Standardbred horses are widely used for harness racing in North America, Europe, Australia, and New Zealand. In the U.S., two gaits (Pacers and Trotters) are genetically differentiated at a level typical for different horse breeds. We used the complete pedigree for all registered American Standardbred foals born 1970-2014 (>200 K Trotters and > 500 K Pacers) to calculate annual and lifetime reproductive skew and its consequences for the effective number of breeders per year (Nb) and effective size per generation (Ne). With rare exceptions, females can only produce 0 or 1 foal per year, w...
Characterization of Lipizzan Horse Population From Lipica Stud Using Molecular and Pedigree Data. In this study, we analysed genetic diversity, population structure and inbreeding in the Lipica Stud Farm population by integrating pedigree records, microsatellite (STR) and genome-wide SNP data generated using the GGP Equine 70K BeadChip. The dataset comprised 233 horses from the Lipica Stud Farm, which served as the reference population for comparisons of diversity estimates based on pedigree-, STR- and SNP data. The STR data were originally generated for routine parentage verification and were included here to compare inbreeding estimates based on pedigree, STR and genome-wide SNP data. Pe...
Genome-Wide Identification and Characterization of the Wnt Gene Family in Donkey (Equus asinus): Phylogenetic Analysis and Expression Profiling. The gene family encodes highly conserved signaling molecules involved in vertebrate development, tissue homeostasis, and cell fate regulation. However, the evolutionary characteristics and potential biological functions of genes in the domestic donkey () remain poorly understood. In this study, we performed the first genome-wide identification and comprehensive characterization of the donkey gene family. A total of 19 genes were identified, consistent with the conserved repertoire reported in other mammalian species. Phylogenetic and synteny analyses revealed strong evolutionary conservat...
Phased T2T horse and donkey assemblies from a mule reveal peculiar equid centromere evolution. We present telomere-to-telomere genome assemblies of a Thoroughbred horse and a donkey derived from their mule offspring. Now adopted and annotated by NCBI as reference genomes, these assemblies resolve previously inaccessible regions, including satellite arrays, duplications, and telomeres. Equids are known to exhibit an uncoupling between satellite DNA and centromeric function. The completeness of these assemblies enabled annotation of both satellite-based and satellite-free centromeres, as well as non-centromeric satellite loci, revealing notable centromeric plasticity. They also allowed de...
Demographic change and selection patterns in thoroughbred racing horses over the 20th century. The Thoroughbred horse is a legacy of centuries of selective breeding for speed, emerging from the admixture of British mares and imported Oriental stallions. While previous work explored its genetic diversity, inbreeding, and selection signatures, the breed demographic and selection dynamics during the 20-century remain poorly understood. Here, we sequenced the genome of Phar Lap, a late-1920s/early-1930s racing champion, and analyzed the largest time-series of Thoroughbred whole-genome sequences, within a global panel of 850 horse genomes. Demographic modeling reveals a marked decline in gen...
Genomic diversity and historical legacy of Baroque horses: a living cultural heritage. Baroque horses represent a distinctive group of breeds that emerged mainly between the 16th and 18th centuries, shaped by the demands of European royalty and their courts. Although recognised as separate breeds, they share common ancestry, breeding goals, and historical gene flow. This study aimed to evaluate their genomic diversity, population structure, and admixture patterns. We analysed 1 160 individuals from eight breeds - Lipizzan, Old Kladruby Horse, Pura Raza Española, Lusitano, Friesian, Criollo, Peruvian Paso, and Puerto Rican Paso Fino - using 34 026 single-nucleotide polymorphis...
Mitochondrial DNA reveals high maternal diversity within a weak breed structure in native Kazakhstani horses. Understanding the genetic diversity and evolutionary history of domestic horses () is essential for reconstructing their population dynamics and origins. In this study, we analyzed mitochondrial DNA variation (COI and cytb) in six Kazakhstani horse populations representing four native breeds (Kazakh, Kostanay, Adai, and Mugalzhar) to assess genetic diversity, population structure, and evolutionary relationships within a broader phylogenetic framework. High haplotype diversity combined with low nucleotide diversity revealed population expansion and admixture. Population structure analyses revea...
Genome-Wide Characterization of the TGF-β Gene Family in Donkey (Equus asinus) Reveals Lineage-Specific Gene Duplications and Deleterious Mutations. The transforming growth factor-beta (TGF-β) superfamily regulates diverse biological processes, including proliferation, differentiation, apoptosis, tissue remodeling, and reproductive signaling across metazoans. Here, we performed a genome-wide characterization of the TGF-β gene family in donkey (, ASM1607732v2) using comparative genomics and bioinformatics analyses, with horse (, EquCab3.0) as a reference to investigate evolutionary conservation and functional divergence. Genome assemblies and proteomes were retrieved from NCBI, and TGF-β genes were identified using BLASTp and HMMER searc...
Identification of Genomic Differences Resulting from Selection in Iranian Kurdish and Turkmen Horse Breeds Using Single Nucleotide Polymorphisms. Breakthroughs in genomic technologies have enabled the formulation of methods to identify genomic variation in domestic animal species. Detection of the variation is necessary because it is associated with breed characteristics and economic importance in domestic animal genetics. Unassigned: This study aimed to identify the genomic regions in Turkmen and Kurdish horse breeds that have been the target of different selections over many years. It also sought to locate the genes and Quantitative trait loci (QTL) in these regions that contributed to the differentiation of these two breeds or the di...
Integrative Advances in Equine Genomics From Reference Assemblies to Evolutionary History and Key Traits. Horses are major domestic animals and cultural symbols that have accompanied humans for millennia. They underpin transport, agriculture, warfare and sport, and also provide a model for studying domestication, complex traits and adaptive evolution. Recent work in equine genomics has now generated a much richer picture of how these roles are grounded in the genome. This review brings together advances in several connected areas: the construction and refinement of reference assemblies; genomic reconstructions of origin, domestication and dispersal; global and regional patterns of genetic diversit...
Observations on Anti-Predator Defense Behavior in Feral Horses in Venezuela. Apart from vigilance and flight, anti-predator defense behavior in horses has not been well documented despite its importance during natural selection. In this study, observations of a feral herd (around 140) of Venezuelan horses sympatric with puma and jaguar divided such defense into precaution and reaction. Group living and the avoidance of danger areas are precautionary measures enhanced by the stallion's vigilance and his actions to keep small foals with the band. Reactions to perceived threats comprise communication of alarm; bunching, or cohesion, as a primary response; massed flight fo...
Genetic diversity of horses of the Sargarinsko-Alexeevskaya and Irmen cultures of the Ob-Irtysh region of Western Siberia and their genetic proximity to modern horses of indigenous breeds. Genetic diversity of horses of the Sargarinsko-Alexeevskaya and Irmen cultures of the Ob-Irtysh region of Western Siberia and their genetic proximity to modern horses of indigenous breeds. Генетическое разнообразие лошадей саргаринско-алексеевской и ирменской культур Западной Сибири и их генетическое родство с современными лошадьми аборигенных пород.
Whole Genome Data Uncover the Complex Origins of Polish Konik Horses. Polish Konik is a native horse breed from Poland often regarded as living descendants of the extinct Tarpan, which has been crucial to the breed's conservation status and cultural importance. To evaluate Polish Konik origins, we sequenced 12 whole genomes and compared them with 148 horse genomes, including those of modern breeds, ancient Polish horses, Przewalski horses, and the Tarpan. The ADMIXTURE results showed that Polish Konik is dominated by a single ancestral component, which is also common among ancient Polish samples and several primitive breeds. The PCA places Polish Konik in a comp...
Extinct Dalian horse as a genetic bridge between Late Pleistocene North American and Eurasian equids. Pleistocene caballine horses exhibited considerable genetic diversity and maintained broad population connectivity across their range. The extinct Dalian horse (Equus dalianensis) from northeastern China likely contributed to this network. Here, we sequenced 20 complete mitochondrial and two nuclear genomes, establishing the Dalian horse as a distinct genetic clade within Northeast Eurasian caballines and extending its known geographic distribution. Ancestry component analyses revealed a distinctive component of Eastern Beringian (E-EBer), i.e. American ancestry in Dalian horses, absent from o...
Horse genetics, archaeology, and the beginning of riding. Recent papers argued that the domestication of horses can be equated with the appearance of favorable genetic mutations that are first evident in individuals in the DOM2 clade dated about ∼2200-2100 BCE. We challenge the idea that this genetic shift alone defines domestication. Evidence from archaeology, ancient DNA, osteology, and other disciplines shows that horses from multiple genetic backgrounds (DOM1, DOM2, and, as we suggest here, DOM3) were managed, milked, and ridden long before 2200 BCE. Yamnaya groups (∼3200-2600 BCE) rode DOM2 horses-the direct ancestors of modern domestic stoc...
Telomere-to-telomere Genome Assembly of Equus kiang (Tibetan wild donkey). The Tibetan wild donkey (Equus kiang) is an endemic equid species inhabiting the Qinghai-Tibet Plateau, exhibiting remarkable chromosomal diversity within the Equus genus. Here we present a chromosome-level, telomere-to-telomere genome assembly for E. kiang generated using Illumina short reads, PacBio HiFi long reads, and Hi-C sequencing data. The final assembly spans 4.02 Gb and comprises 27 pseudochromosomes. Specifically, 8 chromosomes are gapless, 8 chromosomes have one gap, 7 chromosomes have 2-4 gaps, and the remaining 4 chromosomes have five or more gaps. Benchmarking Universal Single...
Genomic diversity and structure in arabian horses revealed by whole-genome sequencing: establishment of an allele frequency database of common genetic variation. BACKGROUND: The Arabian horse is a culturally and historically influential breed that has contributed to the development of many modern horse populations. However, genomic resources for this breed remain limited, particularly population-level allele frequency datasets that support studies of genetic diversity, selection, and disease. The aim of this study was to generate a comprehensive allele frequency database for Arabian horses using representative sampling and high-coverage whole-genome sequencing. RESULTS: We generated the first publicly available allele frequency database for the Arabian...
Rocio virus sustained circulation in Brazil: first infection case in a horse highlights the need for enhanced arbovirus surveillance. Rocio virus (ROCV), a neurotropic arbovirus of the genus, caused Brazil’s largest encephalitis outbreak in the 1970s but has since been rarely detected. We report the first ROCV encephalitis clinical case after nearly 40 years and isolated and sequenced the virus from CNS tissue of a horse. Metatranscriptomics enabled full-genome sequencing, revealing divergence from the reference sequence at an evolutionary rate of 5.8–7.0 × 10⁻⁴, consistent with . Thirty-one non-synonymous substitutions were identified, with the envelope protein most affected. Findings indicate ROCV cryptic circula...
Fully Phased Telomere-to-Telomere Assemblies for Thoroughbred Horse and Donkey Haplotypes derived from a Mule Illuminate the Peculiar Evolution of Equid Centromeres. We present telomere-to-telomere genome assemblies of a Thoroughbred horse and a donkey derived from their mule offspring. Now adopted and annotated by NCBI as reference genomes, these assemblies resolve previously inaccessible regions, including satellite arrays, duplications, and telomeres. Equids are known to exhibit an uncoupling between satellite DNA and centromeric function. The completeness of these assemblies enabled annotation of both satellite-based and satellite-free centromeres, as well as non-centromeric satellite loci, revealing notable centromeric plasticity. They also allowed de...
Spatial strategies in non-territorial societies: how feral horses maintain boundaries with other groups. Encounters between competitive individuals or groups are common in social animals and can involve costly aggression; thus, animals often employ strategies to minimize direct conflict. However, research on whether and how animals adjust their group spatial structure when they encounter or spatially co-occur with a different group remains limited. We investigated how non-territorial units in feral horse multilevel societies manage spatial encounters with neighbouring units. We observed 25 reproductive units in northern Portugal, using drones, and employed statistical analyses to quantify spatial...
Sequencing and Analysis of mtDNA Genomes from the Teeth of Early Medieval Horses in Poland. This study presents the sequencing and analysis of mitochondrial DNA (mtDNA) genomes from nine early medieval horse remains excavated across archaeological sites in Silesia region in present day Poland. Methods: Using aDNA extraction protocols optimized for short fragments, combined with target enrichment and high-throughput sequencing, we reconstructed partial mtDNA sequences for seven of the specimens. Results: The authenticity of the aDNA was confirmed through damage pattern analysis. Phylogenetic reconstruction revealed that the specimens belonged to six distinct mtDNA lineages (B, D, E, G...
The petrosal and bony labyrinth of extinct horses (Perissodactyla, Equidae) and their implications for perissodactyl evolution. Perissodactyla, or odd-toed ungulates, are represented today by 16 species of rhinoceroses, tapirs, and horses. Perissodactyls were much more diverse in the past, having a rich fossil record spanning from the earliest Eocene (~56 Ma) to recent, including a myriad of extinct lineages. Despite over a century of study, the inter-relationships of some extinct perissodactyl families remain poorly resolved. New morphological characters are needed to help solve this issue. Recent studies suggest that the ear region, ., the petrosal and the bony labyrinth of the inner ear, is a valuable source of morp...
High-Altitude Extreme Environments Drive Convergent Evolution of Skin Microbiota in Humans and Horses. Unique skin microbial communities have been shaped by the harsh climatic conditions in high-altitude areas, such as intense ultraviolet radiation and low oxygen concentration. However, it is unknown whether high altitude contributes to shaping common microbiota inhabiting the skin across different mammals. The skin microbial communities of humans and horses living in high-altitude (Tibetan) and low-altitude areas were analyzed using full-length 16S rRNA sequencing technology. Alpha diversity differed between high- and low-altitude groups ( < 0.01). Skin microbial community composition also ...
Mitochondrial genome assembly of the Peruvian Paso horse through PacBio long-read sequencing. The complete mitochondrial genome of the Peruvian Paso Horse was assembled using PacBio HiFi long reads, resulting in a high-quality circular genome of 16,617 bp comprising 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Nucleotide composition and gene structure were consistent with other equine mitogenomes. Codon usage analysis revealed a bias toward CUA (Leu), AUA and AUC (Ile), suggesting translational optimization. Thirty-five heteroplasmic variants were identified, predominantly located in RNA genes (12 S rRNA and tRNA-Phe), with allele frequencies between 0.10 and 0.6...
Genome-Wide Characterization of the HOX Gene Family: Evolution and Expression Patterns in Donkey. The gene family plays an indispensable role in regulating embryonic development, cell differentiation, and morphogenesis. This study employed bioinformatics approaches for systematic analysis, ultimately identifying 33 gene family members from the donkey genome. Physicochemical property analysis revealed that the number of amino acids encoded ranged from 94 to 444, with 31 members classified as alkaline proteins. Their secondary structure was predominantly composed of random coils and alpha helices, and all members were localized to the nucleus. Conserved motif analysis further demonstrated ...
Comparison between SNP array and imputed data to estimate population structure and ROH hotspots in horse breeds. Single nucleotide polymorphism (SNP) arrays are commonly used for studying the genomic structure and diversity of livestock breeds, but whole-genome sequencing (WGS) provides higher-resolution genomic data. Genotype imputation has become a standard practice for increasing the genomic resolution of association studies. This work aimed to extend imputation to biodiversity analyses, comparing SNP array data before and after imputation. A 40 k SNP dataset of 281 horses from 12 breeds (DS) was imputed to sequence-level using a reference panel of 327 sequenced individuals, generating approximately 9...
