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.
Chen J, Wang H, Li J, Liu S, Li B, Sun Y, Wang H, Manglai D.To date, the origins, domestication, and genetic structure of Chinese Mongolian horses (CMH) are poorly understood. Furthermore, there have been sparse reports on the genetic differences between CMH and Thoroughbred. In order to determine their genetic structure, understand their genetic relationships, and explore their domestication processes, we performed an extensive survey of creatine kinase (muscle isoenzyme; variations among six populations of indigenous CMH, cultivated Sanhe horses, and imported Thoroughbred. Twenty-three single-nucleotide polymorphisms were found among the 343 horse s...
Vincelette A.This article traces the characteristics, origin, distribution, and function of alternative lateral horse gaits, i.e., intermediate speed lateral-sequence gaits. Such alternative lateral gaits (running walk, rack, broken pace, hard pace, and broken trot) are prized by equestrians today for their comfort and have been found in select horse breeds for hundreds of years and even exhibited in fossil equid trackways. After exploring the evolution and development of alternative lateral gaits via fossil equid trackways, human art, and historical writings, the functional and genetic factors that led to...
Kusliy MA, Yurlova AA, Neumestova AI, Vorobieva NV, Gutorova NV, Molodtseva AS, Trifonov VA, Popova KO, Polosmak NV, Molodin VI, Vasiliev SK....This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic mark...
Yordanov G, Palova N, Mehandjyiski I, Hristov P.From a historical perspective, horse breeding in Bulgaria has been very well developed since the time of the Thracians (early Bronze Age c. 3000 BCE). Archaeological discoveries from this era present us with an extremely rich type diversity, including wild and local primitive horses, the prototype of heavy draft horses, and fine riding horses.The objective of this study was to investigate the genetic structure of unexamined populations of three closely related horse breeds - the Danubian Nonius Hungarian Nonius and Serbian Nonius horses. A 608?bp long fragment of the mtDNA D-loop region was am...
Sheikh A.The Arabian horse breed is well known for its purity and played a key role in the genetic improvement of other horses worldwide. The mitochondrial genome plays a vital role in maternal inheritance and it's helpful to evaluate its genetic diversity and conservation. It has higher mutation rates than nuclear DNA in vertebrates and therefore reveals phylogenetic relationships and haplotypes. In this study, the mitochondrial genome mutations in two Saudi horse strains, Kehilan and Hamdani demonstrated various changes in the gene and amino acid levels and included two other Saudi horses (Hadban and...
Bailey E.Native Americans of the Plains and Rocky Mountains are renowned for their horsemanship. Taylor et al. recently used ancient DNA and other bioarcheological approaches to document how horses dispersed throughout America and transformed Native American societies following their introduction by the Spanish in 1519, well before the arrival of European settlers.
Crosby B, Crespo ME.Venezuelan Equine Encephalitis Virus (VEEV) is the causative viral pathogen of Venezuelan Equine Encephalitis (VEE). Outbreaks frequently involve both equines – including horses, donkeys, mules, zebras – and humans. Outbreaks may range over a large geographic area and may last for several months to years. Sporadic epidemic outbreaks occur most commonly in Central and South America. VEEV exists as both a natural pathogen and a laboratory-developed biologic weapon. Outbreaks have been reported in several South and Central American countries, including Venezuela, Colombia, Peru, Ecuador, C...
Musiał AD, Ropka-Molik K, Stefaniuk-Szmukier M, Myćka G, Bieniek A, Yasynetska N.Przewalski horses are considered the last living population of wild horses, however, they are secondarily feral offspring of herds domesticated ~ 5000 years ago by the Botai culture. After Przewalski horses were almost extinct at the beginning of the twentieth century, their population is about 2500 individuals worldwide, with one of the largest breeding centers in Askania-Nova Biosphere Reserve (Ukraine). The research aimed to establish the maternal variation of Przewalski horses population maintained in Askania-Nova Reserve based on mitochondrial DNA hypervariable 1 and hypervariable 2 r...
Vincelette AR, Renders E, Scott KM, Falkingham PL, Janis CM.The traditional story of the evolution of the horse (family Equidae) has been in large part about the evolution of their feet. How did modern horses come to have a single toe (digit III), with the hoof bearing a characteristic V-shaped keratinous frog on the sole, and what happened to the other digits? While it has long been known that the proximal portions of digits II and IV are retained as the splint bones, a recent hypothesis suggested that the distal portion of these digits have also been retained as part of the frog, drawing upon the famous Laetoli footprints of the tridactyl (three-toed...
Langsjoen RM, Key A, Shariatzadeh N, Jackson CR, Mahmood F, Arkun K, Alexandrescu S, Solomon IH, Piantadosi A.Eastern equine encephalitis virus (EEEV) is a relatively little-studied alphavirus that can cause devastating viral encephalitis, potentially leading to severe neurological sequelae or death. Although case numbers have historically been low, outbreaks have been increasing in frequency and scale since the 2000 s. It is critical to investigate EEEV evolutionary patterns, especially within human hosts, to understand patterns of emergence, host adaptation, and within-host evolution. To this end, we obtained formalin-fixed paraffin-embedded tissue blocks from discrete brain regions from five contem...
Machmoum M, Badaoui B, Petit D, Germot A, El Alaoui MA, Boujenane I, Piro M.Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a subset of the Kingdom of Saudi Arabia (KSA), United Arab Emirates (UAE) and Bahrain (BAH), the Straight Egyptian (EG) and the Polish bloodline (PL), and (ii) to assess the accuracy of the traditional strain classification system based on maternal lines, as stated by the Bedouin cultur...
Todd ET, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury JM, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T....Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with high...
Mousavi SF, Razmkabir M, Rostamzadeh J, Seyedabadi HR, Naboulsi R, Petersen JL, Lindgren G.Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Ar...
Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D.LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant peris...
Bozlak E, Radovic L, Remer V, Rigler D, Allen L, Brem G, Stalder G, Castaneda C, Cothran G, Raudsepp T, Okuda Y, Moe KK, Moe HH, Kounnavongsa B....The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the wor...
Gu J, Li S, Zhu B, Liang Q, Chen B, Tang X, Chen C, Wu DD, Li Y.Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed horse SVs using a multi-assembly approach. Our findings suggest that SVs with the accumulation of mammalian-wide interspersed repeats related to long interspersed nuclear elements might be a horse-specific mechanism to modulate genome-wide gene regulato...
Sharman P, Wilson AJ.Several studies over recent decades have reported a lack of contemporary improvement in thoroughbred racehorse speed, despite apparent additive genetic variance and putatively strong selection. More recently, it has been shown that some phenotypic improvement is ongoing, but rates are low in general and particularly so over longer distances. Here we used pedigree-based analysis of 692,534 records from 76,960 animals to determine whether these phenotypic trends are underpinned by genetic selection responses, and to evaluate the potential for more rapid improvement. We show that thoroughbred spe...
Spotin A, Dalir F, Hazratian T, Shekarchi AA, Mahami-Oskouei M, Farmani M, Dolatkhah A, Ahmadpour E.The genetic variability of apicomplexan parasite Babesia species is a principal strategy used by piroplasma to evade their hosts' immune responses. The purpose of this review was to evaluate our current knowledge on global haplotype distribution and phylogeography of Babesia ovis derived from sheep, goat, horse and ixodid (hard) ticks. Bibliographic English databases were searched from 2017 to 2023, identifying a total of 11 publications. The 18S ribosomal RNA (18S rRNA) sequences of B. ovis from Asia, Europe, and Africa were retrieved and subjected to estimate the genetic diversity and phylog...
May-Davis S, Hunter R, White R.In this study, we examined the ventral process of C6 in extinct and extant (sister taxa to only) with the purpose of describing normal morphology and identifying anomalous variations relevant to recent studies describing a congenital malformation in . Overall, 83 specimens from 9 museums and 3 research/educational facilities were examined, totalling 71 extinct specimens from 12 species and 12 extant specimens from 5 species. The lateral view revealed that a large convexity exists in the ventral process between the cranial ventral tubercle (CrVT) and the caudal ventral tubercle (CVT) in the e...
Kang Z, Shi J, Liu T, Zhang Y, Zhang Q, Liu Z, Wang J, Cheng S.The study investigated the origin of the Akhal-Teke horse using genome-wide single-nucleotide polymorphism (SNP) data and mitochondrial hypervariable region 1 (HVR-1) nucleotide sequences. Methods: Genome-wide SNP data from 22 breeds (481 horses) and mitochondrial HVR-1 sequences from 24 breeds (544 sequences) worldwide to examine the origin of the Akhal- Teke horse. The data were analyzed using principal component analysis, linkage disequilibrium analysis, neighbor-joining dendrograms, and ancestry inference to determine the population relationships, ancestral source, genetic structure, and r...
Kalmykov NP.Morphological features of the teeth were studied in the three-toed horse Hipparion tchicoicum from the Pliocene of Western Transbaikalia (Russia). Several diagnostic signs of the Chicoi hipparion were described for the first time to provide criteria for distinguishing the taxon among other fossils of three-toed horses and estimating their real diversity at the final stage of their distribution in Inner Asia.
Science (New York, N.Y.)March 30, 2023
Volume 379, Issue 6639 1316-1323 doi: 10.1126/science.adc9691
Taylor WTT, Librado P, American Horse CJ, Shield Chief Gover C, Arterberry J, Afraid of Bear-Cook AL, Left Heron H, Yellow Hair RM, Gonzalez M....The horse is central to many Indigenous cultures across the American Southwest and the Great Plains. However, when and how horses were first integrated into Indigenous lifeways remain contentious, with extant models derived largely from colonial records. We conducted an interdisciplinary study of an assemblage of historic archaeological horse remains, integrating genomic, isotopic, radiocarbon, and paleopathological evidence. Archaeological and modern North American horses show strong Iberian genetic affinities, with later influx from British sources, but no Viking proximity. Horses rapidly sp...
Salamanca-Carreño A, Parés-Casanova PM, Crosby-Granados RA, Vélez-Terranova M, Bentez-Molano J.The skull is divided into neurocranium and splanchnocranium, and its variation allows ecomorphological studies to learn about possible evolutionary and adaptive characteristics. The basicranial organization of the neurocranium and splanchnocranium modules was studied in a sample of 31 skulls from adult Araucanian horses by means of 2D geometric morphometric techniques. The neurocranium and splanchnocranium modules on the ventral aspect were analyzed separately using a set of 31 landmarks. The RV coefficient (the multivariate analog of a correlation) was estimated to analyze the independence of...
Górecka-Bruzda A, Jaworska J, Stanley CR.In captivity, intact male horses, due to their sexual drive, are usually socially isolated from other horses. This lifestyle strongly contrasts with that experienced by horses living in free-roaming, feral, or semi-feral conditions, where adult stallions have several roles in their social group, with successful reproduction being their primary drive. Reproductive skew in wild populations is high; many stallions will fail to reproduce at all, while others achieve high levels of reproductive success, siring a large number of foals. Successful stallions are those with particular characteristics a...
Clauss M, Codron D, Hummel J.Like other members of the odd-toed ungulates (the perissodactyls), equids once had a higher species diversity in the fossil record than they have today. This is generally explained in comparison to the enormous diversity of bovid ruminants. Theories on putative competitive disadvantages of equids include the use of a single toe as opposed to two toes per leg, the lack of a specific brain cooling (and hence water-saving) mechanism, longer gestation periods that delay reproductive output, and in particular digestive physiology. To date, there is no empirical support for the theory that equids fa...
Wang H, Liu S, Lv Y, Wei W.Venezuelan equine encephalitis virus (VEEV) is an emerging zoonotic virus in the alphavirus genus. It can be transmitted to humans due to spillover from equid-mosquito cycles. The symptoms caused by VEEV include fever, headache, myalgia, nausea, and vomiting. It can also cause encephalitis in severe cases. The evolutionary features of VEEV are largely unknown. In this study, we comprehensively analyzed the codon usage pattern of VEEV by computing a variety of indicators, such as effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), on 130 VEEV ...
Bio SystemsFebruary 27, 2023
Volume 225 104871 doi: 10.1016/j.biosystems.2023.104871
Bhattacharjee S.Adaptations in equine limbs, including fusion of its bones, such as the metapodials II and IV (splint bones) with metapodial III (cannon bone), have been debated. It is argued that cursorial adaptations in equine limbs with a progressive reduction in the number of digits lighten up the limbs and facilitate fast running. Similar fusions in other bones, such as the radius and ulna, tend to exhibit similar traits. For example, the fusion often occurs in a disto-proximal direction while leaving sharp ridges. This article proposes a model to understand the biomechanical advantages that a fused symm...
White RT, Jelocnik M, Klukowski N, Haque MH, Sarker S.Chlamydia psittaci is a zoonotic pathogen that infects birds, humans, and other mammals. Notably, recent studies suggested the human-to-human transmission of C. psittaci, and this pathogen also causes equine reproductive loss in Australia. Molecular studies in Australia to date have focused on and described clonal sequence type (ST)24 strains infecting horses, wild psittacine, and humans. In contrast, the genetic identity of C. psittaci strains from captive psittacine hosts is scarce. In 2022, C. psittaci was detected in the faeces of a healthy captive blue-fronted parrot (Amazona aestiva). Ge...
Piras FM, Cappelletti E, Abdelgadir WA, Salamon G, Vignati S, Santagostino M, Sola L, Nergadze SG, Giulotto E.In mammals, centromeres are epigenetically specified by the histone H3 variant CENP-A and are typically associated with satellite DNA. We previously described the first example of a natural satellite-free centromere on Equus caballus chromosome 11 (ECA11) and, subsequently, on several chromosomes in other species of the genus Equus. We discovered that these satellite-free neocentromeres arose recently during evolution through centromere repositioning and/or chromosomal fusion, after inactivation of the ancestral centromere, where, in many cases, blocks of satellite sequences were maintained. H...
Caro T, Fogg E, Stephens-Collins T, Santon M, How MJ.Stripes deter horseflies (tabanids) from landing on zebras and, while several mechanisms have been proposed, these hypotheses have yet to be tested satisfactorily. Here, we investigated three possible visual mechanisms that could impede successful tabanid landings (aliasing, contrast and polarization) but additionally explored pattern element size employing video footage of horseflies around differently patterned coats placed on domestic horses. We found that horseflies are averse to landing on highly but not on lightly contrasting stripes printed on horse coats. We could find no evidence for ...
Science (New York, N.Y.)March 10, 2011
Volume 331, Issue 6021 1178-1181 doi: 10.1126/science.1196166
Mihlbachler MC, Rivals F, Solounias N, Semprebon GM.The evolution of high-crowned molars among horses (Family Equidae) is thought to be an adaptation for abrasive diets associated with the spread of grasslands. The sharpness and relief of the worn cusp apices of teeth (mesowear) are a measure of dietary abrasion. We collected mesowear data for North American Equidae for the past 55.5 million years to test the association of molar height and dietary abrasion. Mesowear trends in horses are reflective of global cooling and associated vegetation changes. There is a strong correlation between mesowear and crown height in horses; however, most horse ...
Waller BM, Julle-Daniere E, Micheletta J.Darwin observed that form, and in his view, meaning, of facial behaviour (observable changes in the appearance of the face, often termed facial 'expression') is similar between a wide range of species and concluded that this must be due to a shared ancestral origin. Yet, as with all social behaviours, exactly how to define similarity and determine homology is debated. Facial behaviour is linked to specific facial muscle movements, so one important factor in determining homology is the anatomical basis of facial behaviours that appear similar in both appearance and social function. The Facial A...
Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann KE, Kapranov P, Thompson JF, Zazula G, Froese D, Moltke I....Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first "true single molecule sequencing" of ancient DNA. We generated 115.9 Mb and 76.9 Mb of DNA sequences from a permafrost-...
Koolhaas JM, Van Reenen CG.This paper will argue that understanding animal welfare and the individual vulnerability to stress-related disease requires a fundamental understanding of functional individual variation as it occurs in nature as well as the underlying neurobiology and neuroendocrinology. Ecological studies in feral populations of mice, fish, and birds start to recognize the functional significance of phenotypes that individually differ in their behavioral and neuroendocrine response to environmental challenge. Recent studies indicate that the individual variation within a species may buffer the species for st...
Xu S, Luosang J, Hua S, He J, Ciren A, Wang W, Tong X, Liang Y, Wang J, Zheng X.To investigate genetic mechanisms of high altitude adaptations of animals living in the Tibetan Plateau, three mitochondrial genomes (mt-genome) of Tibetan horses living in Naqu (4,500 m) of Tibetan, Zhongdian (3,300 m) and Deqin (3,100 m) of Yunnan province were sequenced. The structures and lengths of these three mt-genomes are similar to the Cheju horse, which is related to Tibetan horses, but little shorter than the Swedish horse. The pair-wise identity of these three horses on nucleotide level is more than 99.3%. When the gene encoding the mitochondrial protein of Tibetan horses was analy...
Briefer EF, Maigrot AL, Mandel R, Freymond SB, Bachmann I, Hillmann E.Studying vocal correlates of emotions is important to provide a better understanding of the evolution of emotion expression through cross-species comparisons. Emotions are composed of two main dimensions: emotional arousal (calm versus excited) and valence (negative versus positive). These two dimensions could be encoded in different vocal parameters (segregation of information) or in the same parameters, inducing a trade-off between cues indicating emotional arousal and valence. We investigated these two hypotheses in horses. We placed horses in five situations eliciting several arousal level...
Morens DM, Taubenberger JK.To understand human influenza in a historical context of viral circulation in avian species, mammals, and in the environment. Methods: Historical review. Methods: Global events in a variety of circumstances over more than 3,000 years time. Methods: Comprehensive review of the historical literature including all major publications on pandemic and panzootic influenza. Methods: Influenza pandemics, panzootics, major epidemics and epizootics, and instances of interspecies transmission of influenza A. Results: Extensive documentation of human and animal influenza over many centuries suggests that i...
Powers AM, Oberste MS, Brault AC, Rico-Hesse R, Schmura SM, Smith JF, Kang W, Sweeney WP, Weaver SC.Venezuelan equine encephalitis (VEE) epidemics and equine epizootics occurred periodically in the Americas from the 1920s until the early 1970s, when the causative viruses, subtypes IAB and IC, were postulated to have become extinct. Recent outbreaks in Columbia and Venezuela have renewed interest in the source of epidemic/epizootic viruses and their mechanism of interepizootic maintenance. We performed phylogenetic analyses of VEE virus isolates spanning the entire temporal and geographic range of strains available, using 857-nucleotide reverse transcription-PCR products including the E3 and ...
Leroux C, Issel CJ, Montelaro RC.We have investigated the genetic evolution of three functionally distinct regions of the equine infectious anemia virus (EIAV) genome (env, rev, and long terminal repeat) during recurring febrile episodes in a pony experimentally infected with a well-characterized reference biological clone designated EIAV(PV). Viral populations present in the plasma of an EIAV(PV)-infected pony during sequential febrile episodes (18, 34, 80, 106, and 337 days postinfection) were amplified from viral RNA, analyzed, and compared to the inoculated strain. The comparison of the viral quasispecies showed that the ...
Mammalian centromeres are associated with highly repetitive DNA (satellite DNA), which has so far hindered molecular analysis of this chromatin domain. Centromeres are epigenetically specified, and binding of the CENPA protein is their main determinant. In previous work, we described the first example of a natural satellite-free centromere on Chromosome 11. Here, we investigated the satellite-free centromeres of by using ChIP-seq with anti-CENPA antibodies. We identified an extraordinarily high number of centromeres lacking satellite DNA (16 of 31). All of them lay in LINE- and AT-rich regio...
Huang ZY, de Boer WF, van Langevelde F, Olson V, Blackburn TM, Prins HH.Hosts species for multi-host pathogens show considerable variation in the species' reservoir competence, which is usually used to measure species' potential to maintain and transmit these pathogens. Although accumulating research has proposed a trade-off between life-history strategies and immune defences, only a few studies extended this to host species' reservoir competence. Using a phylogenetic comparative approach, we studied the relationships between some species' life-history traits and reservoir competence in three emerging infectious vector-borne disease systems, namely Lyme disease, W...
The Journal of hereditySeptember 1, 1991
Volume 82, Issue 5 369-377 doi: 10.1093/oxfordjournals.jhered.a111106
Wichman HA, Payne CT, Ryder OA, Hamilton MJ, Maltbie M, Baker RJ.We describe a molecular model for rapid chromosomal evolution that proposes tandemly repeated DNA sequences as a driving force. A prediction of this model is that when extensive rearrangements of euchromatin have been facilitated by heterochromatin, genomes will be characterized by tandemly repeated sequences that have actively changed chromosomal fields by intragenomic movement. Alternatively, it is proposed that in conservative chromosomal lineage each class of tandemly repeated sequences will be restricted to a specific chromosomal field. To provide baseline data to test this model we exami...
Wallner B, Vogl C, Shukla P, Burgstaller JP, Druml T, Brem G.The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most wi...
Reilly SM, McElroy EJ, Biknevicius AR.A reanalysis of locomotor data from functional, energetic, mechanical and ecological perspectives reveals that limb posture has major effects on limb biomechanics, energy-saving mechanisms and the costs of locomotion. Regressions of data coded by posture (crouched vs. erect) reveal nonlinear patterns in metabolic cost, limb muscle mass, effective mechanical advantage, and stride characteristics. In small crouched animals energy savings from spring and pendular mechanisms are inconsequential and thus the metabolic cost of locomotion is driven by muscle activation costs. Stride frequency appears...
Forrester NL, Wertheim JO, Dugan VG, Auguste AJ, Lin D, Adams AP, Chen R, Gorchakov R, Leal G, Estrada-Franco JG, Pandya J, Halpin RA, Hari K, Jain R....Venezuelan equine encephalitis (VEE) complex alphaviruses are important re-emerging arboviruses that cause life-threatening disease in equids during epizootics as well as spillover human infections. We conducted a comprehensive analysis of VEE complex alphaviruses by sequencing the genomes of 94 strains and performing phylogenetic analyses of 130 isolates using complete open reading frames for the nonstructural and structural polyproteins. Our analyses confirmed purifying selection as a major mechanism influencing the evolution of these viruses as well as a confounding factor in molecular cloc...
Janečka JE, Davis BW, Ghosh S, Paria N, Das PJ, Orlando L, Schubert M, Nielsen MK, Stout TAE, Brashear W, Li G, Johnson CD, Metz RP, Zadjali AMA....Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X-Y gametologs recorded in eutherians, in addition to novel Y-born and transp...
Gurgul A, Jasielczuk I, Semik-Gurgul E, Pawlina-Tyszko K, Stefaniuk-Szmukier M, Szmatoła T, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M.The genetic differentiation of the current horse population was evolutionarily created by natural or artificial selection which shaped the genomes of individual breeds in several unique ways. The availability of high throughput genotyping methods created the opportunity to study this genetic variation on a genome-wide level allowing detection of genome regions divergently selected between separate breeds as well as among different horse types sharing similar phenotypic features. In this study, we used the population differentiation index (FST) that is generally used for measuring locus-specifi...
Weaver SC, Hagenbaugh A, Bellew LA, Gousset L, Mallampalli V, Holland JJ, Scott TW.Evolution of viruses in the eastern equine encephalomyelitis (EEE) complex was studied by analyzing RNA sequences and oligonucleotide fingerprints from isolates representing the North and South American antigenic varieties. By using homologous sequences of Venezuelan equine encephalomyelitis virus as an outgroup, phylogenetic trees revealed three main EEE virus monophyletic groups. A North American variety group included all isolates from North America and the Caribbean. One South American variety group included isolates from the Amazon basin in Brazil and Peru, while the other included strain...
Steinrücken M, Bhaskar A, Song YS.The increased availability of time series genetic variation data from experimental evolution studies and ancient DNA samples has created new opportunities to identify genomic regions under selective pressure and to estimate their associated fitness parameters. However, it is a challenging problem to compute the likelihood of non-neutral models for the population allele frequency dynamics, given the observed temporal DNA data. Here, we develop a novel spectral algorithm to analytically and efficiently integrate over all possible frequency trajectories between consecutive time points. This advan...
Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, Elton D, Newton JR, Kellam P, Wood JL, Holmes EC, Murcia PR.The ability of influenza A viruses (IAVs) to cross species barriers and evade host immunity is a major public health concern. Studies on the phylodynamics of IAVs across different scales - from the individual to the population - are essential for devising effective measures to predict, prevent or contain influenza emergence. Understanding how IAVs spread and evolve during outbreaks is critical for the management of epidemics. Reconstructing the transmission network during a single outbreak by sampling viral genetic data in time and space can generate insights about these processes. Here, we ob...
Wallner B, Palmieri N, Vogl C, Rigler D, Bozlak E, Druml T, Jagannathan V, Leeb T, Fries R, Tetens J, Thaller G, Metzger J, Distl O, Lindgren G....The Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence diversity in horses has prevented the reconstruction of stallion genealogies [1, 2]. Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the male-specific region of the Y chromosome (MSY) in 52 horses from 21 breeds. Based on highly accurate pedigree data, we estimated the de novo mutation rate of the horse MSY and showed that various modern horse Y chromosome lineages split much later than the domestication of the species. Apart from few private northern Euro...
Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, Ludwig A, Rasmussen M, Cooper A, Weinstock J, Willerslev E, Shapiro B, Hofreiter M.Modern domestic horses display abundant genetic diversity within female-inherited mitochondrial DNA, but practically no sequence diversity on the male-inherited Y chromosome. Several hypotheses have been proposed to explain this discrepancy, but can only be tested through knowledge of the diversity in both the ancestral (pre-domestication) maternal and paternal lineages. As wild horses are practically extinct, ancient DNA studies offer the only means to assess this ancestral diversity. Here we show considerable ancestral diversity in ancient male horses by sequencing 4 kb of Y chromosomal DNA ...
Bower MA, McGivney BA, Campana MG, Gu J, Andersson LS, Barrett E, Davis CR, Mikko S, Stock F, Voronkova V, Bradley DG, Fahey AG, Lindgren G....Selective breeding for speed in the racehorse has resulted in an unusually high frequency of the C-variant (g.66493737C/T) at the myostatin gene (MSTN) in cohorts of the Thoroughbred horse population that are best suited to sprint racing. Here we show using a combination of molecular- and pedigree-based approaches in 593 horses from 22 Eurasian and North-American horse populations, museum specimens from 12 historically important Thoroughbred stallions (b.1764-1930), 330 elite-performing modern Thoroughbreds and 42 samples from three other equid species that the T-allele was ancestral and there...
Poole DC, Erickson HH.Evolutionary forces drive beneficial adaptations in response to a complex array of environmental conditions. In contrast, over several millennia, humans have been so enamored by the running/athletic prowess of horses and dogs that they have sculpted their anatomy and physiology based solely upon running speed. Thus, through hundreds of generations, those structural and functional traits crucial for running fast have been optimized. Central among these traits is the capacity to uptake, transport and utilize oxygen at spectacular rates. Moreover, the coupling of the key systems--pulmonary-cardio...
Wilkin S, Ventresca Miller A, Taylor WTT, Miller BK, Hagan RW, Bleasdale M, Scott A, Gankhuyg S, Ramsøe A, Uliziibayar S, Trachsel C, Nanni P....Dairy pastoralism is integral to contemporary and past lifeways on the eastern Eurasian steppe, facilitating survival in agriculturally challenging environments. While previous research has indicated that ruminant dairy pastoralism was practiced in the region by circa 1300 BC, the origin, extent and diversity of this custom remain poorly understood. Here, we analyse ancient proteins from human dental calculus recovered from geographically diverse locations across Mongolia and spanning 5,000 years. We present the earliest evidence for dairy consumption on the eastern Eurasian steppe by circ...
Imsland F, McGowan K, Rubin CJ, Henegar C, Sundström E, Berglund J, Schwochow D, Gustafson U, Imsland P, Lindblad-Toh K, Lindgren G, Mikko S....Dun is a wild-type coat color in horses characterized by pigment dilution with a striking pattern of dark areas termed primitive markings. Here we show that pigment dilution in Dun horses is due to radially asymmetric deposition of pigment in the growing hair caused by localized expression of the T-box 3 (TBX3) transcription factor in hair follicles, which in turn determines the distribution of hair follicle melanocytes. Most domestic horses are non-dun, a more intensely pigmented phenotype caused by regulatory mutations impairing TBX3 expression in the hair follicle, resulting in a more circu...
Linklater WL, Cameron EZ, Minot EO, Stafford KJ.Feral horse, Equus caballus, breeding groups, called bands, usually include one but sometimes up to five stallions. We found that mares were loyal to single-stallion (SS) or multistallion (MS) bands or were social dispersers (maverick mares, Mv). The spacing and social behaviour of mares and stallions in single- and multistallion bands was measured. Indices of mare well-being were also measured including activity budgets (feeding: MS>SS=Mv; resting: MSSS), maternal effort in maintaining contact with foals (MS=Mv>SS), parasite levels in faeces (MS>Mv>SS), body condition (MS=Mv<SS...
Raudsepp T, Frönicke L, Scherthan H, Gustavsson I, Chowdhary BP.Human chromosome specific libraries (CSLs) were individually applied to equine metaphase chromosomes using the fluorescence in situ hybridization (FISH) technique. All CSLs, except Y, showed painting signals on one or several horse chromosomes. In total 43 conserved chromosomal segments were painted. Homoeology could not, however, be detected for some segments of the equine genome. This is most likely related to the very weak signals displayed by some libraries, rather than to the absence of similarity with the human genome. In spite of divergence from the human genome, dated 70-80 million yea...
Bean WJ.The RNAs coding for the nucleoproteins of a panel of influenza isolates from human and nonhuman hosts were compared by RNA-RNA hybridization to determine the extent of genetic diversity of this protein and to determine if related nucleoproteins (NP) are consistently found in viruses from certain hosts. Five nucleoprotein groups were defined. Group 1 contains nearly all of the avian influenza viruses, group 2 includes only certain viruses isolated from gulls, group 3 includes all recent equine influenza strains, group 4 contains only equine/Prague/1/56, and group 5 contains all human and swine ...
