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.
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...
Kvist L, Honka J, Salazar D, Kirkinen T, Hemmann K.We used historical DNA samples to examine the history of a native horse breed, the Finnhorse. Samples were collected from private collections, museums, schools and excavations, representing the times prior to, during, and after the foundation of the breed; from the end of the 19th century and throughout the 20th century. We sequenced a fragment of mitochondrial DNA from these historical samples to study the history and evolution of maternal lineages of horses back to the early days of the breed, compared the mitochondrial DNA sequence diversity of different historical periods and modern day Fi...
Studies of horse evolution arose during the middle of the 19th century, and several hypotheses have been proposed for their taxonomy, paleobiogeography, paleoecology and evolution. The present contribution represents a collaboration of 19 multinational experts with the goal of providing an updated summary of Pliocene and Pleistocene North, Central and South American, Eurasian and African horses. At the present time, we recognize 114 valid species across these continents, plus 4 North African species in need of further investigation. Our biochronology and biogeography sections integrate Equinae...
Casanova E, Knowles TDJ, Outram AK, Stear NA, Roffet-Salque M, Zaibert V, Logvin A, Shevnina I, Evershed RP.Direct and accurate radiocarbon dating of lipid residues preserved in ceramics is a recently established method that allows direct dating of specific food products and their inception in human subsistence strategies. The method targets individual fatty acids originating from animal fats such as ruminant dairy, ruminant adipose, non-ruminant adipose and aquatic fats. Horse lipid residues found in Central Asian pottery vessels are also directly dateable using this new method. Here we present the identification of equine lipid residues preserved in two pottery assemblages from the Neolithic and E...
Schlindwein X, Werneburg I.We compared embryogenesis of five species of domesticated even-toed and one odd-toed ungulate and used a phylogenetic framework to contextualize such comparison. Organ systems that occur relatively earlier in embryogenesis generally have more time to develop and therefore are found to be more mature at birth when compared to structures that appear later in development. We hypothesized that the less mature the animals' organs are at birth, the more they are susceptible to artificial selection. The horse had the most mature organs at birth, followed by cattle, reindeer, sheep/goat, and pig. This...
Delsol N, Stucky BJ, Oswald JA, Reitz EJ, Emery KF, Guralnick R.Unlike other European domesticates introduced in the Americas after the European invasion, equids (Equidae) were previously in the Western Hemisphere but were extinct by the late Holocene era. The return of equids to the Americas through the introduction of the domestic horse (Equus caballus) is documented in the historical literature but is not explored fully either archaeologically or genetically. Historical documents suggest that the first domestic horses were brought from the Iberian Peninsula to the Caribbean in the late 15th century CE, but archaeological remains of these early introduct...
Colpitts J, McLoughlin PD, Poissant J.Understanding inbreeding and its impact on fitness and evolutionary potential is fundamental to species conservation and agriculture. Long stretches of homozygous genotypes, known as runs of homozygosity (ROH), result from inbreeding and their number and length can provide useful population-level information on inbreeding characteristics and locations of signatures of selection. However, the utility of ROH for conservation is limited for natural populations where baseline data and genomic tools are lacking. Comparing ROH metrics in recently feral vs. domestic populations of well understood spe...
Han L, Lan T, Lu Y, Zhou M, Li H, Lu H, Wang Q, Li X, Du S, Guan C, Zhang Y, Sahu SK, Qian P, Zhang S, Zhou H, Guo W, Chai H, Wang S, Liu Q, Liu H....The evolution of parasites is often directly affected by the host's environment. Studies on the evolution of the same parasites in different hosts are of great interest and are highly relevant to our understanding of divergence. Methods: Here we performed whole-genome sequencing of Parascaris univalens from different Equus hosts (horses, zebras and donkeys). Phylogenetic and selection analyses were performed to study the divergence and adaptability of P. univalens. Results: At the genetic level, multiple lines of evidence indicate that P. univalens is mainly separated into two clades (horse-de...
Gu J, Orr N, Park SD, Katz LM, Sulimova G, MacHugh DE, Hill EW.Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selec...
Daly JM, Lai AC, Binns MM, Chambers TM, Barrandeguy M, Mumford JA.Evolution of equine influenza a H3N8 viruses was examined by antigenic and genetic analysis of a collection isolates from around the world. It was noted that antigenic and genetic variants of equine H3N8 viruses cocirculate, and in particular that variants currently circulating in Europe and the USA are distinguishable from one another both in terms of antigenic reactivity and genetic structure of the HA1 portion of the haemagglutinin (HA) molecule. Whilst the divergent evolution of American and European isolates may be due to geographical isolation of the two gene pools, some mixing is believ...
Cieslak M, Pruvost M, Benecke N, Hofreiter M, Morales A, Reissmann M, Ludwig A.Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population r...
Lindgren G, Backström N, Swinburne J, Hellborg L, Einarsson A, Sandberg K, Cothran G, Vilà C, Binns M, Ellegren H.Genetic studies using mitochondrial DNA (mtDNA) have identified extensive matrilinear diversity among domestic horses. Here, we show that this high degree of polymorphism is not matched by a corresponding patrilinear diversity of the male-specific Y chromosome. In fact, a screening for single-nucleotide polymorphisms (SNPs) in 14.3 kb of noncoding Y chromosome sequence among 52 male horses of 15 different breeds did not identify a single segregation site. These observations are consistent with a strong sex-bias in the domestication process, with few stallions contributing genetically to the do...
Murcia PR, Wood JL, Holmes EC.Equine influenza viruses (EIVs) of the H3N8 and H7N7 subtypes are the causative agents of an important disease of horses. While EIV H7N7 apparently is extinct, H3N8 viruses have circulated for more than 50 years. Like human influenza viruses, EIV H3N8 caused a transcontinental pandemic followed by further outbreaks and epidemics, even in populations with high vaccination coverage. Recently, EIV H3N8 jumped the species barrier to infect dogs. Despite its importance as an agent of infectious disease, the mechanisms that underpin the evolutionary and epidemiological dynamics of EIV are poorly und...
Warmuth V, Eriksson A, Bower MA, Barker G, Barrett E, Hanks BK, Li S, Lomitashvili D, Ochir-Goryaeva M, Sizonov GV, Soyonov V, Manica A.Despite decades of research across multiple disciplines, the early history of horse domestication remains poorly understood. On the basis of current evidence from archaeology, mitochondrial DNA, and Y-chromosomal sequencing, a number of different domestication scenarios have been proposed, ranging from the spread of domestic horses out of a restricted primary area of domestication to the domestication of numerous distinct wild horse populations. In this paper, we reconstruct both the population genetic structure of the extinct wild progenitor of domestic horses, Equus ferus, and the origin and...
Schroeder DI, Jayashankar K, Douglas KC, Thirkill TL, York D, Dickinson PJ, Williams LE, Samollow PB, Ross PJ, Bannasch DL, Douglas GC, LaSalle JM.Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylated domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of hu...
Cooper KL, Sears KE, Uygur A, Maier J, Baczkowski KS, Brosnahan M, Antczak D, Skidmore JA, Tabin CJ.A reduction in the number of digits has evolved many times in tetrapods, particularly in cursorial mammals that travel over deserts and plains, yet the underlying developmental mechanisms have remained elusive. Here we show that digit loss can occur both during early limb patterning and at later post-patterning stages of chondrogenesis. In the 'odd-toed' jerboa (Dipus sagitta) and horse and the 'even-toed' camel, extensive cell death sculpts the tissue around the remaining toes. In contrast, digit loss in the pig is orchestrated by earlier limb patterning mechanisms including downregulation of...
Lewis NS, Daly JM, Russell CA, Horton DL, Skepner E, Bryant NA, Burke DF, Rash AS, Wood JL, Chambers TM, Fouchier RA, Mumford JA, Elton DM, Smith DJ.Equine influenza virus is a major respiratory pathogen in horses, and outbreaks of disease often lead to substantial disruption to and economic losses for equestrian industries. The hemagglutinin (HA) protein is of key importance in the control of equine influenza because HA is the primary target of the protective immune response and the main component of currently licensed influenza vaccines. However, the influenza virus HA protein changes over time, a process called antigenic drift, and vaccine strains must be updated to remain effective. Antigenic drift is assessed primarily by the hemagglu...
Leroy G, Mary-Huard T, Verrier E, Danvy S, Charvolin E, Danchin-Burge C.Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Results: Depending on breed and method, effective population sizes ranged from 15 to 133 ...
Carbone L, Nergadze SG, Magnani E, Misceo D, Francesca Cardone M, Roberto R, Bertoni L, Attolini C, Francesca Piras M, de Jong P, Raudsepp T....Centromere repositioning (CR) is a recently discovered biological phenomenon consisting of the emergence of a new centromere along a chromosome and the inactivation of the old one. After a CR, the primary constriction and the centromeric function are localized in a new position while the order of physical markers on the chromosome remains unchanged. These events profoundly affect chromosomal architecture. Since horses, asses, and zebras, whose evolutionary divergence is relatively recent, show remarkable morphological similarity and capacity to interbreed despite their chromosomes differing co...
Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A, Willerslev E, Knight R, McKenzie V, Orlando L.The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly modified. We investigated fecal microbiomes of Przewalski's horse (PH; Equus ferus p...
Haile J, Froese DG, Macphee RD, Roberts RG, Arnold LJ, Reyes AV, Rasmussen M, Nielsen R, Brook BW, Robinson S, Demuro M, Gilbert MT, Munch K....Causes of late Quaternary extinctions of large mammals ("megafauna") continue to be debated, especially for continental losses, because spatial and temporal patterns of extinction are poorly known. Accurate latest appearance dates (LADs) for such taxa are critical for interpreting the process of extinction. The extinction of woolly mammoth and horse in northwestern North America is currently placed at 15,000-13,000 calendar years before present (yr BP), based on LADs from dating surveys of macrofossils (bones and teeth). Advantages of using macrofossils to estimate when a species became extinc...
Arrigo NC, Adams AP, Weaver SC.The eastern equine encephalitis (EEE) complex consists of four distinct genetic lineages: one that circulates in North America (NA EEEV) and the Caribbean and three that circulate in Central and South America (SA EEEV). Differences in their geographic, pathogenic, and epidemiologic profiles prompted evaluation of their genetic diversity and evolutionary histories. The structural polyprotein open reading frames of all available SA EEEV and recent NA EEEV isolates were sequenced and used in evolutionary and phylogenetic analyses. The nucleotide substitution rate per year for SA EEEV (1.2 x 10(-4...
Doud MB, Ashenberg O, Bloom JD.Evolution drives changes in a protein's sequence over time. The extent to which these changes in sequence lead to shifts in the underlying preference for each amino acid at each site is an important question with implications for comparative sequence-analysis methods, such as molecular phylogenetics. To quantify the extent that site-specific amino acid preferences shift during evolution, we performed deep mutational scanning on two homologs of human influenza nucleoprotein with 94% amino acid identity. We found that only a modest fraction of sites exhibited shifts in amino acid preferences tha...
Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD....Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specim...
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-...
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 ...
Lippold S, Matzke NJ, Reissmann M, Hofreiter M.DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets. Results: In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds an...
Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SC, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM....The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further charact...
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...
Proops L, McComb K.Recent research has shown that domestic dogs are particularly good at determining the focus of human attention, often outperforming chimpanzees and hand-reared wolves. It has been suggested that the close evolutionary relationship between humans and dogs has led to the development of this ability; however, very few other domestic species have been studied. We tested the ability of 36 domestic horses to discriminate between an attentive and inattentive person in determining whom to approach for food. The cues provided were body orientation, head orientation or whether the experimenters' eyes we...
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...
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 ...
Kumar N, Bera BC, Greenbaum BD, Bhatia S, Sood R, Selvaraj P, Anand T, Tripathi BN, Virmani N.Equine influenza viruses (EIVs) of H3N8 subtype are culprits of severe acute respiratory infections in horses, and are still responsible for significant outbreaks worldwide. Adaptability of influenza viruses to a particular host is significantly influenced by their codon usage preference, due to an absolute dependence on the host cellular machinery for their replication. In the present study, we analyzed genome-wide codon usage patterns in 92 EIV strains, including both H3N8 and H7N7 subtypes by computing several codon usage indices and applying multivariate statistical methods. Relative synon...
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...
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...
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...
