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.
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 ...
da Cruz AB, Hirata S, Dos Santos ME, Mendonça RS.Growing evidence shows a variety of sensorial and motor asymmetries in social and non-social interactions in various species, indicating a lateralized processing of information by the brain. Using digital video cameras on tripods and drones, this study investigated lateralization in frequency and duration of social behavior patterns, in affiliative, agonistic, and resting contexts, in a feral population of horses (Equus ferus caballus) in Northern Portugal, consisting of 37 individuals organized in eight harem groups. Affiliative interactions (including grooming) were more often performed, and...
Nishita Y, Amaike Y, Spassov N, Hristova L, Kostov D, Vladova D, Peeva S, Raichev E, Vlaeva R, Masuda R.The domestication of the horse began possibly more than 5000 years ago in the western part of the Eurasian steppe, and according to the leading hypothesis, horses first spread from the Steppe toward the region of the Thracian culture, starting in the second half of the 2nd millennium BCE and flourished from the fifth to first centuries BCE, mainly located in present-day Bulgaria. We analyzed 17 horse bone remains excavated from Thracian archaeological sites (fourth to first centuries BCE) in Bulgaria and successfully identified 17 sequences representing 14 different haplotypes of the mitocho...
Frontiers in geneticsJanuary 23, 2023
Volume 14 1099896 doi: 10.3389/fgene.2023.1099896
Capomaccio S, Ablondi M, Colombi D, Sartori C, Giontella A, Cappelli K, Mancin E, Asti V, Mantovani R, Sabbioni A, Silvestrelli M. The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene pool has been impacted by warfare and subsequent "colonization". In this study, using a comprehensive dataset for almost the entire Italian equine population, in addition to the most influential cosmopolitan breeds, we describe the current status of the modern Italian gene pool. The Italian dataset comprised 1,3...
He Z, Dai X, Lyu W, Beaumont M, Yu F.Novel technologies for recovering DNA information from archaeological and historical specimens have made available an ever-increasing amount of temporally spaced genetic samples from natural populations. These genetic time series permit the direct assessment of patterns of temporal changes in allele frequencies and hold the promise of improving power for the inference of selection. Increased time resolution can further facilitate testing hypotheses regarding the drivers of past selection events such as the incidence of plant and animal domestication. However, studying past selection processes ...
Han H, Randhawa IAS, MacHugh DE, McGivney BA, Katz LM, Dugarjaviin M, Hill EW.Thousands of years of natural and artificial selection since the domestication of the horse has shaped the distinctive genomes of Chinese Mongolian horse populations. Consequently, genomic signatures of selection can provide insights into the human-mediated selection history of specific traits and evolutionary adaptation to diverse environments. Here, we used genome-wide SNPs from five distinct Chinese Mongolian horse populations to identify genomic regions under selection for the population-specific traits, gait, black coat colour, and hoof quality. Other global breeds were used to identify r...
Li Y, Liu Y, Wang M, Lin X, Li Y, Yang T, Feng M, Ling Y, Zhao C.The Chakouyi horse is an ancient Chinese indigenous horse breed distributed in Gansu Province in northwestern China, and is also one of the key breeds protected by the government. However, the origin of the Chakouyi horse remains unclear. As it is distributed in a key region of the Silk Road, it was speculated that the origin of the Chakouyi horse might involve the foreign horse breeds found along this ancient commercial artery. In this study, whole-genome resequencing data of 12 horse breeds, including both indigenous and foreign horses, were applied to reveal the genetic relationships betwee...
Belyaev RI, Kuznetsov AN, Prilepskaya NE.The vertebral column is a hallmark of vertebrates; it is the structural basis of their body and the locomotor apparatus in particular. Locomotion of any vertebrate animal in its typical habitat is directly associated with functional adaptations of its vertebrae. This study is the first large-scale analysis of mobility throughout the presacral region of the vertebral column covering a majority of extant odd-toed ungulates from 6 genera and 15 species. In this study, we used a previously developed osteometry-based method to calculate available range of motion. We quantified all three directions ...
Sharif MB, Fitak RR, Wallner B, Orozco-terWengel P, Frewin S, Fremaux M, Mohandesan E.New Zealand has the fourth largest feral horse population in the world. The Kaimanawas (KHs) are feral horses descended from various domestic horse breeds released into the Kaimanawa ranges in the 19th and 20th centuries. Over time, the population size has fluctuated dramatically due to hunting, large-scale farming and forestry. Currently, the herd is managed by an annual round-up, limiting the number to 300 individuals to protect the native ecosystem. Here, we genotyped 96 KHs for uniparental markers (mitochondrial DNA, Y-chromosome) and assessed their genetic similarity with respect to other...
Schubert CL, Ryckewaert B, Pereira C, Matsuzawa T.This study aimed to use a computer-controlled touchscreen system to examine visual discrimination in Garrano horses (), an endangered breed of pony belonging to the Iberian horse family. This pilot study focused on the perceptual similarity among letters of the alphabet. We tested five horses in a one-male unit (OMU) living permanently in a semi-free enclosure near their natural habitat in Serra d'Arga, northern Portugal. Horses were trained to nose-touch black circles that appeared on the screen. Then, they were tested for discrimination of five letters of the Latin alphabet in Arial font, na...
Liu X, Zhang Y, Pu Y, Ma Y, Jiang L.Transposable elements (TEs) are diverse, abundant, and complicated in genomes. They not only can drive the genome evolution process but can also act as special resources for adaptation. However, little is known about the evolutionary processes that shaped horses. In this work, 126 horse assemblages involved in most horse breeds in China were used to investigate the patterns of TE variation for the first time. By using RepeatMasker and melt software, we found that the horse-specific short interspersed repetitive elements family, equine repetitive elements (ERE1), exhibited polymorphisms in hors...
Ren X, Liu Y, Zhao Y, Li B, Bai D, Bou G, Zhang X, Du M, Wang X, Bou T, Shen Y, Dugarjaviin M.Interspecific hybridization often shows negative effects on hybrids. However, only a few multicellular species, limited to a handful of plants and animals, have shown partial genetic mechanisms by which hybridization leads to low fitness in hybrids. Here, to explore the outcome of combining the two genomes of a horse and donkey, we analyzed the whole-genome sequences from an parent-offspring trio using Illumina platforms. We generated 41.39× and 46.21× coverage sequences for the horse and mule, respectively. For the donkey, a 40.38× coverage sequence was generated and stored in our laborat...
Salamanca-Carreño A, Parés-Casanova PM, Monroy-Ochoa NI, Vélez-Terranova M.This study examined paedomorphosis in PAH and F1 crossbreds. A sample of 99 horses was selected from 40 different breeders and consisted of three groups: stallions ( = 16), mares ( = 53), and geldings ( = 30), ranging from 10 months to 27 years in age. All horses presented a concave celloid lateral left head profile in the acquired photographic images. The hypothesis proposed in this study suggested the lateral profile of the head in juveniles was representational in the adult form due to the neonate's facial bones (part of the splanchnocranium) developing at a different rate to those of the s...
Nikbakhsh M, Varkoohi S, Seyedabadi HR.Kurdish horse is one of the most valuable horse genetic resources in the Middle East. To assess the genetic diversity of Kurdish horses, Mitochondrial DNA D-loop hyper-variable region1 (HVR1) was sequenced in 29 non-related Kurdish horses which were sampled from diverse geographic regions of Iran. Total DNA was extracted from the collected blood samples by modified salting out method. The HVR1 was amplified by PCR and then sequenced using ABI PRISM BigDyeTM Terminator Cycle Sequencing Ready Reaction Kit. Consequently, the sequences were trimmed to 294 bp using BIOEDIT to become comparable wit...
Hu D, Wang C, Ente M, Zhang K, Zhang D, Li X, Li K, Chu H.Intestinal microbiota play an important role in the survival of the host. However, no study to date has elucidated the adjustment of intestinal microbiota of the host during rewilding. Thus, this study aims to describe the intestinal bacterial community of reintroduced Przewalski’s horse (RPH) after being released into their original habitat for approximately 20 years in comparison with that of captive Przewalski’s horse (CPH), sympatric domestic horse (DH) and Mongolian wild ass (MWA) by sequencing the 16S rRNA gene. The results showed that the prevalent bacterial communities were differe...
Frontiers in geneticsOctober 5, 2022
Volume 13 944933 doi: 10.3389/fgene.2022.944933
Xu B, Yang G, Jiao B, Zhu H. The domestication of horses has played critical roles in human civilizations. The excavation of ancient horse DNA provides crucial data for studying horse domestication. Studies of horse domestication can shed light on the general mechanisms of animal domestication. We wish to explore the gene transcription regulation by long noncoding RNAs (lncRNAs) that influence horse domestication. First, we assembled the ancient DNA sequences of multiple horses at different times and the genomes of horses, donkeys, and Przewalski horses. Second, we extracted sequences of lncRNA genes shared in ancient ...
Leonardi M, Boschin F, Boscato P, Manica A.Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climati...
Radovic L, Remer V, Krcal C, Rigler D, Brem G, Rayane A, Driss K, Benamar M, Machmoum M, Piro M, Krischke D, Butler-Wemken IV, Wallner B.In horses, demographic patterns are complex due to historical migrations and eventful breeding histories. Particularly puzzling is the ancestry of the North African horse, a founding horse breed, shaped by numerous influences throughout history. A genetic marker particularly suitable to investigate the paternal demographic history of populations is the non-recombining male-specific region of the Y chromosome (MSY). Using a recently established horse MSY haplotype (HT) topology and KASP™ genotyping, we illustrate MSY HT spectra of 119 Barb and Arab-Barb males, collected from the Maghreb regio...
Open life sciencesSeptember 26, 2022
Volume 17, Issue 1 1269-1281 doi: 10.1515/biol-2022-0487
Pan J, Purev C, Zhao H, Zhang Z, Wang F, Wendoule N, Qi G, Liu Y, Zhou H.The Mongolian horses have excellent endurance and stress resistance to adapt to the cold and harsh plateau conditions. Intraspecific genetic diversity is mainly embodied in various genetic advantages of different branches of the Mongolian horse. Since people pay progressive attention to the athletic performance of horse, we expect to guide the exercise-oriented breeding of horses through genomics research. We obtained the clean data of 630,535,376,400 bp through the entire genome second-generation sequencing for the whole blood of four Abaga horses and ten Wushen horses. Based on the data an...
Guo R, Zhang S, Chen J, Shen W, Zhang G, Wang J, Zhang F, Pan Q, Xie T, Ai D, Dong J, Suo J, Sun Y, Liu S.Donkeys' gut microbe is critical for their health and adaptation to the environment. Little research has been conducted on the donkey gut microbiome compared with other domestic animals. The Tibetan Plateau is an extreme environment. In this study, 6 Qinghai donkeys (QH) from the Tibetan Plateau and 6 Dezhou donkeys (DZ) were investigated, and the contents of 4 parts-stomach, small intestine, cecum, and rectum-were collected. 16S rRNA sequencing and metagenomic sequencing were used to analyze the composition and diversity of gut microbial communities in donkeys. The results showed that the flo...
Landry Z, Roloson MJ, Fraser D.The metapodials of extinct horses have long been regarded as one of the most useful skeletal elements to determine taxonomic identity. However, recent research on both extant and extinct horses has revealed the possibility for plasticity in metapodial morphology, leading to notable variability within taxa. This calls into question the reliability of metapodials in species identification, particularly for species identified from fragmentary remains. Here, we use ten measurements of metapodials from 203 specimens of four Pleistocene horse species from eastern Beringia to test whether there are s...
Makowiecki D, Chudziak W, Szczepanik P, Janeczek M, Pasicka E.Knowledge about horses from early medieval (10th-13th c.) Poland has been largely based on historical and archaeological data. Archaeozoological information has only been used to a limited extent. Therefore, this article aims to present the current state of knowledge on this subject, drawing on archaeozoological data from studies of horse bones. Apart from confirming earlier reflections regarding the sacred significance of the horse, additional information was obtained about specific individuals who were the subject of magical treatments. It turned out that sites with horse skeletons and skull...
Bigler NA, Bruckmaier RM, Gross JJ.Maternal care is essential to optimally support survival of the offspring. During evolution of mammalian species, different phenotypes have evolved in relation to gestation length, number, size, and maturation stage of the offspring at parturition, as well as colostrum and milk composition. The aim of the present review is to describe relationships between placental function and colostrum and milk composition in different mammalian species. Species covered in this article include humans, rabbits, rodents (rat and mouse), carnivores (cats and dogs), and a variety of ungulate species (cattle, sh...
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...
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...
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...
Cunningham EP, Dooley JJ, Splan RK, Bradley DG.The thoroughbred (TB) horse is one of the oldest breeds of domestic animals, with pedigree records spanning three centuries. Because the population is essentially closed, there is concern about loss of genetic variation. Here we report two parallel analyses. In the first, genetic variation in the current population is measured using data from 13 microsatellite loci in 211 horses with relationships calculated based on allele sharing. In the second analysis, pedigree information is used to calculate genetic relationships between animals based on shared ancestry. These two measures of relationshi...
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...
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 ...
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...
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...
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...
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...
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...
Orlando L, Metcalf JL, Alberdi MT, Telles-Antunes M, Bonjean D, Otte M, Martin F, Eisenmann V, Mashkour M, Morello F, Prado JL, Salas-Gismondi R....The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 8...
Cosgrove EJ, Sadeghi R, Schlamp F, Holl HM, Moradi-Shahrbabak M, Miraei-Ashtiani SR, Abdalla S, Shykind B, Troedsson M, Stefaniuk-Szmukier M....The Arabian horse, one of the world's oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ances...
Lemasson A, Boutin A, Boivin S, Blois-Heulin C, Hausberger M.Many animal species that rely mainly on calls to communicate produce individual acoustic structures, but we wondered whether individuals of species better known as visual communicants, with small vocal repertoires, would also exhibit individual distinctiveness in calls. Moreover, theoretical advances concerning the evolution of social intelligence are usually based on primate species data, but relatively little is known about the social cognitive capacities of non-primate mammals. However, some non-primate species demonstrate auditory recognition of social categories and possess mental represe...
Li YY, Liu H, Fu SH, Li XL, Guo XF, Li MH, Feng Y, Chen WX, Wang LH, Lei WW, Gao XY, Lv Z, He Y, Wang HY, Zhou HN, Wang GQ, Liang GD.Getah virus (GETV) was first isolated in Malaysia in 1955. Since then, epidemics in horses and pigs caused by GETV have resulted in huge economic losses. At present, GETV has spread across Eurasia and Southeast Asia, including mainland China, Korea, Japan, Mongolia, and Russia. Data show that the Most Recent Common Ancestor (MRCA) of GETV existed about 145years ago (95% HPD: 75-244) and gradually evolved into four distinct evolutionary populations: Groups I-IV. The MRCA of GETVs in Group III, which includes all GETVs isolated from mosquitoes, pigs, horses, and other animals since the 1960s (fr...
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...
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 ...
