Horse Lineage Research Articles

First approach to bone histology and skeletochronology of Equus hemionus

Histological approaches to extant mammalian life histories (LHs) provide the basis for reconstructing LHs of fossil mammals. They are of special interest in lineages such as perissodactyls that played a key role in fossil ecosystems. We studied an ontogenetic series of Equus hemionus (Asiatic wild ass), the most appropriate extant representative of fossil horses. We analyzed growth marks in femora of 10 specimens of different ontogenetic stages and habitats. Bone tissue types and vascular canal orientation vary both during ontogeny and within cross-sections. Skeletochronology generally fits previous age estimates from dental eruption patterns. Our wild adult female attained skeletal maturity at the age of four, the wild male at 5years. Our results do not only contribute to our knowledge of Asiatic wild ass but they also show that bone histology is a valid tool in reconstructing LH evolution in the horse lineage.

The Evolution of High Dental Complexity in the Horse Lineage

The horse lineage (family Equidae) represents one of the clearest acquisitions of complicated derived dental morphology from a more generalized ancestor. Here we investigate the change in dental complexity (orientation patch count rotated, OPCR) during the evolution of key members of this group. A clear linear increase in dental complexity over evolutionary time is apparent when complexity is measured at high resolution (125 to 175 rows per tooth). The taxa examined also show a linear scaling of OPCR with varying resolution. The slope of this relationship is also a key distinguishing factor among taxa, designated as OPCRS. We found that successive increases in dental complexity are due to the addition of finer-scale morphological features. The study sets the scene for a more detailed investigation into additional members of the Equidae.

Late Middle Pleistocene horse fossils from northwestern Europe as biostratigraphic indicators

Biostratigraphy provides a crucial tool for establishing temporal correlations between late Middle Pleistocene sites. The caballoid horse lineage is one of the few large mammal groups that underwent changes in size and morphology over this period. Here, univariate, bivariate and multivariate statistics are used to identify temporal affinities of late Middle Pleistocene horse remains from northwest Europe.Size and shape variation is limited in dental elements, but clear differences between sites can be observed in the limb bones. PCA and DFA on the same samples produce highly similar results, indicating the robusticity of the classifications found in the DFA. Thus, DFA on measurements of the limb bones of caballoid horses provides a reliable method to distinguish between sites dating from different marine oxygen isotope stages (MIS) and can give important clues to the temporal affinities of newly analysed faunal assemblages. The analyses have important consequences for the relative dates of the sites Bilzingsleben II and Schöningen II, which can be shown to date from different interglacials. The age of the sample from the Lower Travertine at Weimar-Ehringsdorf is confirmed as MIS 7. The Steinheim sample is highly distinct, implying variation at the oxygen isotope substage level that must be resolved in greater detail when more samples become available.

Discovery of lost diversity of paternal horse lineages using ancient DNA

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 from eight ancient wild horses and one 2,800-year-old domesticated horse. Both ancient and modern domestic horses form a separate branch from the ancient wild horses, with the Przewalski horse at its base. Our methodology establishes the feasibility of re-sequencing long ancient nuclear DNA fragments and demonstrates the power of ancient Y chromosome DNA sequence data to provide insights into the evolutionary history of populations.

A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses

The endangered Przewalski's horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski's horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski's horses have been sparse but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity of Przewalski's horses, we used massively parallel sequencing technology to decipher the complete mitochondrial and partial nuclear genomes for all four surviving maternal lineages of Przewalski's horses. Unlike single-nucleotide polymorphism (SNP) typing usually affected by ascertainment bias, the present method is expected to be largely unbiased. Three mitochondrial haplotypes were discovered—two similar ones, haplotypes I/II, and one substantially divergent from the other two, haplotype III. Haplotypes I/II versus III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski's horse maternal lineages, and were estimated to split 0.117–0.186 Ma, significantly preceding horse domestication. In the phylogeny based on autosomal sequences, Przewalski's horses formed a monophyletic clade, separate from the Thoroughbred domestic horse lineage. Our results suggest that Przewalski's horses have ancient origins and are not the direct progenitors of domestic horses. The analysis of the vast amount of sequence data presented here suggests that Przewalski's and domestic horse lineages diverged at least 0.117 Ma but since then have retained ancestral genetic polymorphism and/or experienced gene flow.

Implications of age variation and sexual dimorphism in modern equids for Middle Pleistocene equid taxonomy

ABSTRACTInterspecific variation in the equid lineage is limited when compared with other large mammal lineages, while a considerable amount of intraspecific ecomorphological variation occurs. This has led to considerable debate regarding the taxonomic status of palaeontological and archaeological equid remains. The possible confounding impact of sex and age variation on analyses of archaeological equid remains has so far remained untested. This could be especially problematic when it is unknown whether an assemblage contains more than one equid species, breed or hybrid. Here, sex and age variation in modern equid species is examined and compared to variation in Pleistocene equid assemblages from northwest Europe. Sex variation in the longbones of modern equid species was found to be lower than variation over time. Similarly, age variation in dental elements of the same species is predominantly lower than diachronic variation, although caution needs to be taken when an archaeological assemblages consists mostly of elements at a similar wear stage.To assess whether late Middle Pleistocene caballoid horse fossils should be assigned to multiple species or be considered to form a monospecific group, the coefficients of variation for measurements on fossil horse remains were compared with those for modern equid specimens. Results indicate that the fossil assemblages are similarly variable to samples of modern material. Taken as a whole, the late Middle Pleistocene caballoid horse lineage is equally variable to an assemblage of modern ponies of a variety of different breeds. This implies that the variation observed between samples dating from different parts of the Middle Pleistocene can be characterised as intraspecific variation within a single species reflecting ecomorphological adaptations to the changeable Pleistocene climate. Copyright © 2010 John Wiley & Sons, Ltd.

Mitochondrial DNA insertions in the nuclear horse genome

The insertion of mitochondrial DNA in the nuclear genome generates numts, nuclear sequences of mitochondrial origin. In the horse reference genome, we identified 82 numts and showed that the entire horse mitochondrial DNA is represented as numts without gross bias. Numts were inserted in the horse nuclear genome at random sites and were probably generated during the repair of DNA double-strand breaks. We then analysed 12 numt loci in 20 unrelated horses and found that null alleles, lacking the mitochondrial DNA insertion, were present at six of these loci. At some loci, the null allele is prevalent in the sample analysed, suggesting that, in the horse population, the number of numt loci may be higher than 82 present in the reference genome. Contrary to humans, the insertion polymorphism of numts is extremely frequent in the horse population, supporting the hypothesis that the genome of this species is in a rapidly evolving state.

Ecomorphological adaptations to climate and substrate in late Middle Pleistocene caballoid horses

Due to our limited knowledge of the precise causes and mechanisms shaping mammalian adaptations, there are still many unknowns regarding the processes underlying ecomorphological variation in large mammals. Ambient temperature and humidity affect skeletal morphology both directly through thermoregulation and indirectly through their influence on the character of vegetation and substrate. Oscillations in these factors contribute, in conjunction with evolutionary and behavioural factors, to morphological variation. An examination of dietary and locomotor adaptations in the context of climatic information can give insight into the effects of specific environmental conditions on particular adaptive traits. During the late Middle Pleistocene of Europe, the caballoid horse lineage occurred over a large geographic range and throughout glacial–interglacial cycles, except for the most extreme glacial maxima. The ecomorphological signature of horse fossils from late Middle Pleistocene archaeological and palaeontological sites from northwest Europe was analysed with univariate and multivariate statistical methods, in order to assess the reliability of correlations between particular skeletal adaptations in horses and specific aspects of the environment. The analyses show that in these animals large body size and robust limb bones are correlated with mosaic steppe habitats. Glacial horses were generally small and robust, while horses that lived in temperate oceanic conditions were slender and sometimes also small. Locomotor adaptations indicate a less mobile lifestyle than in modern equids. Dietary adaptations reflect the character of the vegetation and the amount of grit present in the environment. Differences between late Middle Pleistocene horse fossils from the British Isles and those found in continental northwest Europe illustrate the relationships between these adaptations and environmental factors.

Caballoid horses and late Middle Pleistocene biostratigraphy of the British Isles

Over the last decades, researchers have become increasingly aware of the complexity of the Quaternary glacial - interglacial cycles. Correlation of continental sites with (sub)stages of the oxygen isotope record and with other sites has proven to be difficult. In order to be able to address questions that go beyond analysis of single sites it is necessary to have a rigid chronological framework. For the British Isles, a biostratigraphic framework has been developed for the late Middle Pleistocene, incorporating geological, faunal and floral evidence. For the mammalian faunas, in particular, each interglacial stage was shown to have a characteristic fauna. The caballoid horse lineage under-goes a size reduction and morphological changes over its temporal range. These trends are well-documented for the Late Pleistocene. For the late Middle Pleistocene, the picture is less clear, in part because it has proven difficult to date sites from this period relative to each other. The robust and generally accepted biostratigraphic scheme for the British Isles provides an opportunity to address the evolution of the caballoid horses in the late Middle Pleistocene.

Restriction of Equine Infectious Anemia Virus by Equine APOBEC3 Cytidine Deaminases

The mammalian APOBEC3 (A3) proteins comprise a multigene family of cytidine deaminases that act as potent inhibitors of retroviruses and retrotransposons. The A3 locus on the chromosome 28 of the horse genome contains multiple A3 genes: two copies of A3Z1, five copies of A3Z2, and a single copy of A3Z3, indicating a complex evolution of multiple gene duplications. We have cloned and analyzed for expression the different equine A3 genes and examined as well the subcellular distribution of the corresponding proteins. Additionally, we have tested the functional antiretroviral activity of the equine and of several of the human and nonprimate A3 proteins against the Equine infectious anemia virus (EIAV), the Simian immunodeficiency virus (SIV), and the Adeno-associated virus type 2 (AAV-2). Hematopoietic cells of horses express at least five different A3s: A3Z1b, A3Z2a-Z2b, A3Z2c-Z2d, A3Z2e, and A3Z3, whereas circulating macrophages, the natural target of EIAV, express only part of the A3 repertoire. The five A3Z2 tandem copies arose after three consecutive, recent duplication events in the horse lineage, after the split between Equidae and Carnivora. The duplicated genes show different antiviral activities against different viruses: equine A3Z3 and A3Z2c-Z2d are potent inhibitors of EIAV while equine A3Z1b, A3Z2a-Z2b, A3Z2e showed only weak anti-EIAV activity. Equine A3Z1b and A3Z3 restricted AAV and all equine A3s, except A3Z1b, inhibited SIV. We hypothesize that the horse A3 genes are undergoing a process of subfunctionalization in their respective viral specificities, which might provide the evolutionary advantage for keeping five copies of the original gene.

Allele Frequency and Likely Impact of the Glycogen Branching Enzyme Deficiency Gene in Quarter Horse and Paint Horse Populations

Glycogen Branching Enzyme Deficiency (GBED), a fatal condition recently identified in fetuses and neonatal foals of the Quarter Horse and Paint Horse lineages, is caused by a nonsense mutation in codon 34 of the GBE1 gene, which prevents the synthesis of a functional GBE protein and severely disrupts glycogen metabolism. The aims of this project were to determine the mutant GBE1 allele frequency in random samples from the major relevant horse breeds, as well as the frequency with which GBED is associated with abortion and early neonatal death using the tissue archives from veterinary diagnostic laboratories. The mutant GBE1 allele frequency in registered Quarter Horse, Paint Horse, and Thoroughbred populations was 0.041, 0.036, and 0.000, respectively. Approximately 2.5% of fetal and early neonatal deaths in Quarter Horse‐related breeds submitted to 2 different US diagnostic laboratories were homozygous for the mutant GBE1 allele, with the majority of these being abortions. Retrospective histopathology of the homozygotes detected periodic acid Schiff's (PAS)‐positive inclusions in the cardiac or skeletal muscle, which is characteristic of GBED, in 8 out of the 9 cases. Pedigree and genotype analyses supported the hypothesis that GBED is inherited as a simple recessive trait from a single founder. The frequency with which GBED is associated with abortion and neonatal mortality in Quarter Horse‐related breeds makes the DNA‐based test valuable in determining specific diagnoses and designing matings that avoid conception of a GBED foal.

Allele Frequency and Likely Impact of the Glycogen Branching Enzyme Deficiency Gene in Quarter Horse and Paint Horse Populations

Glycogen Branching Enzyme Deficiency (GBED), a fatal condition recently identified in fetuses and neonatal foals of the Quarter Horse and Paint Horse lineages, is caused by a nonsense mutation in codon 34 of the GBE1 gene, which prevents the synthesis of a functional GBE protein and severely disrupts glycogen metabolism. The aims of this project were to determine the mutant GBE1 allele frequency in random samples from the major relevant horse breeds, as well as the frequency with which GBED is associated with abortion and early neonatal death using the tissue archives from veterinary diagnostic laboratories. The mutant GBE1 allele frequency in registered Quarter Horse, Paint Horse, and Thoroughbred populations was 0.041, 0.036, and 0.000, respectively. Approximately 2.5% of fetal and early neonatal deaths in Quarter Horse-related breeds submitted to 2 different US diagnostic laboratories were homozygous for the mutant GBE1 allele, with the majority of these being abortions. Retrospective histopathology of the homozygotes detected periodic acid Schiff's (PAS)-positive inclusions in the cardiac or skeletal muscle, which is characteristic of GBED, in 8 out of the 9 cases. Pedigree and genotype analyses supported the hypothesis that GBED is inherited as a simple recessive trait from a single founder. The frequency with which GBED is associated with abortion and neonatal mortality in Quarter Horse-related breeds makes the DNA-based test valuable in determining specific diagnoses and designing matings that avoid conception of a GBED foal.

Effects of induced lameness via carpal osteochondral fragmentation on plasma creatine kinase activity in horses

Objective To determine whether or not plasma creatine kinase (CK) values could be used as a reliable indicator for skeletal-based lameness. Design Pilot study. Animals Eight adult horses of Quarter Horse lineage. Procedure All 8 horses (4 treatment, 4 control) received arthroscopic surgery on bilateral carpal joints, with an osteochondral fragment created in 1 knee of the treatment group only. Two weeks post-operatively, horses began treadmill work. Pre-exercise and 4-hour post-exercise blood samples were obtained for plasma CK measurement from horses in both treatment and control groups. Results Horses that received a carpal chip fracture (treatment group) produced greater levels of change in plasma CK when pre- and post-exercise values were compared than did horses without osteochondral fragmentation. Although changes in CK activity were reported, none of the CK values were outside the normal range. Conclusions and clinical relevance Results of this study hoped to lend performance horse practitioners another reliable tool in diagnosing skeletal-based lameness, using elevations in the muscle enzyme CK as the marker. In addition, skeletal-based lameness and gait alteration as causes of increased muscle enzymes were ruled out. Changes in plasma CK values were greater for horses in the treatment group when pre- and post-exercise samples were compared. However, elevations in CK were too inconsistent to be considered diagnostic for correlating skeletal lameness, muscle health, and exercise.

Periodic paralysis in quarter horses: a sodium channel mutation disseminated by selective breeding.

We recently reported on a linkage study within a Quarter Horse lineage segregating hyperkalaemic periodic paralysis (HYPP), an autosomal dominant condition showing potassium-induced attacks of skeletal muscle paralysis. HYPP co-segregated with the equine adult skeletal muscle sodium channel alpha subunit gene, the same gene that causes human HYPP. We now describe the Phe to Leu mutation in transmembrane domain IVS3 which courses the horse disease. This represents the first application of molecular genetics to an important horse disease, and the data will provide an opportunity for control or eradication of this condition.

Observations on Structural Reduction in Evolution

The problem of structural reduction in evolution constitutes a special case of the more general problem of seemingly non-adaptive evolutionary changes. As Brace points out, many of the characters which differentiate species or higher categories appear trivial in that it is difficult to imagine how such characters in themselves directly contribute to the differences in adaptation. Numerous examples of such characters may easily be found by thumbing through analytic keys found in field guides to identification. Dobzhansky (1956) in discussing this same problem presents an impressive list of apparently trivial characters differentiating Drosophila species. The inability to understand or even imagine the direct adaptive significance of such structures immediately causes one to ask whether some evolutionary changes occur by means other than direct selection. The cases of structural reduction raise this question for the same reason. It is difficult to imagine the adaptive significance of the loss of the anthropoid tail or loss of the lateral digits in the horse lineage. If the adaptive significance of such changes were evident, then non-selective mechanisms for these changes