Population genomics provide insight into ancestral relationships and diversity of the feral horses of Theodore Roosevelt National Park

Theodore Roosevelt National Park (TRNP) manages a herd of feral horses (Equus caballus) which was present on the landscape prior to the establishment of the park. The population presents a unique scenario in that it has experienced fairly intensive and well-documented management since the park's establishment, including herd size reductions, intentional introduction of diversity, and subsequent attempts to remove introduced lineages. This provides an interesting case study on the genetic effects of diverse evolutionary forces on an isolated feral population. To explore the effects of these forces and clarify the relationship of this feral herd with other horses, we used genome-wide markers to examine the population structure of a combined dataset containing common established breeds. Using the Illumina Equine 70k BeadChip, we sampled SNPs across the genome for 118 TRNP horses and evaluated the inbreeding coefficient f and runs of homozygosity (RoH). To identify breed relationships, we compared 23 representative TRNP samples with 792 horses from 35 different breeds using genomic population structure analyses. Mean f of TRNP horses was 0.180, while the mean f for all other breeds in the dataset was 0.116 (SD 0.079). RoH analysis indicates that the TRNP population has experienced recent inbreeding in a timeframe consistent with their management. With Bayesian clustering, PCA, and maximum likelihood phylogeny, TRNP horses show genetic differentiation from other breeds, likely due to isolation, historical population bottlenecks, and genetic drift. However, maximum likelihood phylogeny places them with moderate confidence (76.8%) among draft breeds, which is consistent with the known history of breeds used on early North Dakota ranches and stallions subsequently introduced to the park herd. These findings will help resolve speculation about the origins of the herd and inform management decisions for the TRNP herd.

Comparative Genomics Identifies the Evolutionarily Conserved Gene TPM3 as a Target of eca-miR-1 Involved in the Skeletal Muscle Development of Donkeys

Species within the genus Equus are valued for their draft ability. Skeletal muscle forms the foundation of the draft ability of Equus species; however, skeletal muscle development-related conserved genes and their target miRNAs are rarely reported for Equus. In this study, a comparative genomics analysis was performed among five species (horse, donkey, zebra, cattle, and goat), and the results showed that a total of 15,262 (47.43%) genes formed the core gene set of the five species. Only nine chromosomes (Chr01, Chr02, Chr03, Chr06, Chr10, Chr18, Chr22, Chr27, Chr29, and Chr30) exhibited a good collinearity relationship among Equus species. The micro-synteny analysis results showed that TPM3 was evolutionarily conserved in chromosome 1 in Equus. Furthermore, donkeys were used as the model species for Equus to investigate the genetic role of TPM3 in muscle development. Interestingly, the results of comparative transcriptomics showed that the TPM3 gene was differentially expressed in donkey skeletal muscle S1 (2 months old) and S2 (24 months old), as verified via RT-PCR. Dual-luciferase test analysis showed that the TPM3 gene was targeted by differentially expressed miRNA (eca-miR-1). Furthermore, a total of 17 TPM3 gene family members were identified in the whole genome of donkey, and a heatmap analysis showed that EaTPM3-5 was a key member of the TPM3 gene family, which is involved in skeletal muscle development. In conclusion, the TPM3 gene was conserved in Equus, and EaTPM3-5 was targeted by eca-miR-1, which is involved in skeletal muscle development in donkeys.

Genomic and comparative analysis of the T cell receptor gamma locus in two Equus species

The genus Equus is the only extant genus of the Equidae family, which belongs to Perissodactyla, an order of mammals characterized by an odd number of toes (odd-toes ungulates). Taking advantage of the latest release of the genome assembly, we studied, for the first time in two organisms belonging to the Equus genus, the horse (Equus caballus) and the donkey (Equus asinus), the T cell receptor gamma (TRG) locus encoding the gamma chain of the γδ T cell receptor. Forty-five Variable (TRGV) genes belonging to the seven IMGT-NC validated mammalian TRGV subgroups, 25 Joining (TRGJ) and 17 Constant (TRGC) genes organized in 17 V-J-(J)-C cassettes, in tandem on about 1100 Kb, characterize the horse TRG locus, making the horse TRG locus the one with the greatest extension and with a significantly higher number of genes than the orthologous loci of the other mammalian species. A clonotype analysis of an RNA-seq transcriptomic dataset derived from spleen of an adult healthy horse, using the complete set of the horse TRGJ germline gene sequences as a probe, revealed that, in addition to the most prominent V-J rearrangements within each cassette, there is a relevant proportion of trans-cassette V-J recombination, whereby the same TRGV genes can recombine with different TRGJ genes spliced to the corresponding TRGC genes. This recombinant event strongly contributes to the diversity of the γ chain repertoire. In the donkey TRG locus, 34 TRGV, 21 TRGJ and 14 TRGC genes distributed in 14 V-J-(J)-C cassettes were found in a region of approximately 860 kb. Although the donkey's TRG is smaller than that of the horse, in Equus genus, this is still the second largest locus so far found in any mammalian species. Finally, the comparative analysis highlighted differences in size and gene content between the horse and donkey TRG loci, despite belonging to the same genus, indicating a good level of diversification within Equus. These data is in agreement with the evolutionary idea of the existence of a Equus recent common ancestor in rapid evolution, for which a mutation rate between horses and donkeys is more comparable to that between species belonging to different genera rather than to species of the same genus.

Exploration of Parascaris species in three different Equus populations in China

BACKGROUND

The roundworms, Parascaris spp., are important nematode parasites of foals and were historically model organisms in the field of cell biology, leading to many important discoveries. According to karyotype, ascarids in Equus are commonly divided into Parascaris univalens (2n = 2) and Parascaris equorum (2n = 4).

METHODS

Here, we performed morphological identification, karyotyping and sequencing of roundworms from three different hosts (horses, zebras and donkeys). Phylogenetic analysis was performed to study the divergence of these ascarids based on cytochrome c oxidase subunit I (COI) and internal transcribed spacer (ITS) sequences.

RESULTS

Karyotyping, performed on eggs recovered from worms of three different Equus hosts in China, showed two different karyotypes (2n = 2 in P. univalens collected from horses and zebras; 2n = 6 in Parascaris sp. collected from donkeys). There are some differences in the terminal part of the spicula between P. univalens (concave) and Parascaris sp. (rounded). Additionally, it was found that the egg's chitinous layer was significantly thicker in Parascaris sp. (> 5 μm) than P. univalens (< 5 μm) (F₍₂₅₃₇₎ = 1967, P < 0.01). Phylogenetic trees showed that the sequences of Parascaris from Equus hosts were divided into two distinct lineages based on sequences of the COI and ITS.

CONCLUSIONS

Comparing the differences in roundworms collected from three different Equus hosts, this study describes a Parascaris species (Parascaris sp.) with six chromosomes in donkeys. It is worth noting that the thickness of the chitinous layer in the Parascaris egg may serve as a diagnostic indicator to distinguish the two roundworms (P. univalens and Parascaris sp.). The Parascaris sp. with six chromosomes in donkeys in the present study may be a species of P. trivalens described in 1934, but the possibility that it is a new Parascaris species cannot be ruled out. Both karyotyping and molecular analysis are necessary to solve the taxonomic problems in Parascaris species.

Hipparion tracks and horses' toes: the evolution of the equid single hoof

The traditional story of the evolution of the horse (family Equidae) has been in large part about the evolution of their feet. How did modern horses come to have a single toe (digit III), with the hoof bearing a characteristic V-shaped keratinous frog on the sole, and what happened to the other digits? While it has long been known that the proximal portions of digits II and IV are retained as the splint bones, a recent hypothesis suggested that the distal portion of these digits have also been retained as part of the frog, drawing upon the famous Laetoli footprints of the tridactyl (three-toed) equid Hipparion as part of the evidence. We show here that, while there is good anatomical and embryological evidence for the proximal portions of all the accessory digits (i.e. I and V, as well as II and IV) being retained in the feet of modern horses, evidence is lacking for the retention of any distal portions of these digits. There is also good ichnological evidence that many tridactyl equids possessed a frog, and that the frog has been part of the equid foot for much of equid evolutionary history.

Global prevalence and risk factors of Cryptosporidium infection in Equus: A systematic review and meta-analysis

Intoduction

Cryptosporidiosis is a zoonotic disease caused by Cryptosporidium infection with the main symptom of diarrhea. The present study performed a metaanalysis to determine the global prevalence of Cryptosporidium in Equus animals.

Methods

Data collection was carried out using Chinese National Knowledge Infrastructure (CNKI), VIP Chinese journal database (VIP), WanFang Data, PubMed, and ScienceDirect databases, with 35 articles published before 2021 being included in this systematic analysis. This study analyzed the research data through subgroup analysis and univariate regression analysis to reveal the factors leading to high prevalence. We applied a random effects model (REM) to the metadata.

Results

The total prevalence rate of Cryptosporidium in Equus was estimated to be 7.59% from the selected articles. The prevalence of Cryptosporidium in female Equus was 2.60%. The prevalence of Cryptosporidium in Equus under 1-year-old was 11.06%, which was higher than that of Equus over 1-year-old (2.52%). In the experimental method groups, the positive rate detected by microscopy was the highest (10.52%). The highest Cryptosporidium prevalence was found in scale breeding Equus (7.86%). The horses had the lowest Cryptosporidium prevalence (7.32%) among host groups. C. muris was the most frequently detected genotype in the samples (53.55%). In the groups of geographical factors, the prevalence rate of Cryptosporidium in Equus was higher in regions with low altitude (6.88%), rainy (15.63%), humid (22.69%), and tropical climates (16.46%).

Discussion

The search strategy use of five databases might have caused the omission of some researches. This metaanalysis systematically presented the global prevalence and potential risk factors of Cryptosporidium infection in Equus. The farmers should strengthen the management of young and female Equus animals, improve water filtration systems, reduce stocking densities, and harmless treatment of livestock manure.

Why wait to mark? Possible reasons behind latency from olfactory exploration to overmarking in four African equid species

Whereas most studies on overmarking in mammals analysed the rate of overmarking, that those investigate time between exploration of an olfactory stimulus and the response to it remain less common, with inconsistent results. We examined the latency in time between elimination by the sender and sniffing by the receiver, and from sniffing and overmarking, in four captive African equid species to explore differences among species, and among age and sex classes. We investigated these latency time periods in light of three potential hypotheses explaining overmarking behaviour in equids: social bonds, group cohesion, and intrasexual competition. Analysing 1684 events of sniffing and 719 of overmarking among 130 individuals, we found that (i) the time from elimination to overmarking was shorter among female friends and in parent-offspring dyads, proving support to the social bond hypothesis; (ii) intraspecific differences in time periods do not reflect the social organisation of species, thus not supporting the group cohesion hypothesis; (iii) males were more attracted to elimination of conspecifics than females, and female's eliminations were inspected longer, in line with the sexual competition hypothesis and/or reproductive behaviour. In addition, we found that the younger foals came to sniff eliminations faster than older ones, and in larger groups foals devoted longer time to sniffing the elimination before overmarking. We concluded that examination of the elimination could be driven by motivations other than the decision to overmark. Whereas overmarking serves to express bonds to a familiar individual, the latency of overmarking reflects more reproductive interests.

The Dmanisi Equus: Systematics, biogeography, and paleoecology

The Equus datum has been established as a geochronologic 'instantaneous' migratory event of a North American Equus species into Eurasia at the beginning of the Pleistocene (2.58 Ma). A remarkable radiation of Equus followed across Eurasia and Africa. Dmanisi includes excellent remains of Equus, well calibrated between 1.85 and 1.76 Ma. Our morphologic and morphometric analyses of the augmented Dmanisi Equus sample support the co-occurrence of Equus stenonis and Equus altidens in the sequence. Dmanisi E. stenonis is found to be morphologically similar to the European E. stenonis populations and represents the best well-dated easternmost occurrence of this species in Eurasia. The Dmanisi E. altidens represents the oldest well-calibrated occurrence of this species in Western Eurasia. Our analyses demonstrate that E. altidens extended its range westward from west Asia to Greece, Germany, Italy, Spain, and possibly France. Our results do not support distinguishing multiple subspecies of E. altidens, including E. altidens altidens, E. altidens granatensis and E. stenonis mygdoniensis. The Dmanisi cranial and postcranial samples exhibit morphologies close both to extant hemiones and zebras. Equus altidens is believed to have been well adapted to newly emergent arid environments in western Eurasia during the late Early and early Middle Pleistocene. The first occurrence of E. altidens at Dmanisi marks an important turnover in the horse communities of the late Early Pleistocene, with a dispersion of this species from West Asia to West Europe ca. 1.8 Ma.

Parasitic diseases of equids in Iran (1931-2020): a literature review

Parasitic infections can cause many respiratory, digestive and other diseases and contribute to some performance conditions in equids. However, knowledge on the biodiversity of parasites of equids in Iran is still limited. The present review covers all the information about parasitic diseases of horses, donkeys, mules and wild asses in Iran published as articles in Iranian and international journals, dissertations and congress papers from 1931 to July 2020. Parasites so far described in Iranian equids include species of 9 genera of the Protozoa (Trypanosoma, Giardia, Eimeria, Klossiella, Cryptosporidium, Toxoplasma, Neospora, Theileria and Babesia), 50 helminth species from the digestive system (i.e., 2 trematodes, 3 cestodes and 37 nematodes) and from other organs (i.e., Schistosoma turkestanica, Echinococcus granulosus, Dictyocaulus arnfieldi, Parafilaria multipapillosa, Setaria equina and 3 Onchocerca spp.). Furthermore, 16 species of hard ticks, 3 mite species causing mange, 2 lice species, and larvae of 4 Gastrophilus species and Hippobosca equina have been reported from equids in Iran. Archeoparasitological findings in coprolites of equids include Fasciola hepatica, Oxyuris equi, Anoplocephala spp. and intestinal strongyles. Parasitic diseases are important issues in terms of animal welfare, economics and public health; however, parasites and parasitic diseases of equines have not received adequate attention compared with ruminants and camels in Iran. The present review highlights the knowledge gaps related to equines about the presence, species, genotypes and subtypes of Neospora hughesi, Sarcocystis spp., Trichinella spp., Cryptosporidium spp., Giardia duodenalis, Blastocystis and microsporidia. Identification of ticks vectoring pathogenic parasites, bacteria and viruses has received little attention, too. The efficacy of common horse wormers also needs to be evaluated systematically.

Why the long face? Comparative shape analysis of miniature, pony, and other horse skulls reveals changes in ontogenetic growth

Background

Much of the shape variation found in animals is based on allometry and heterochrony. Horses represent an excellent model to investigate patterns of size-shape variation among breeds that were intentionally bred for extreme small and large sizes.

Methods

We tested whether ponies (wither height < 148 cm) have a diverging size-shape relationship in skull shape as compared to regular-sized horse breeds (wither height > 148 cm, here-after called horses) during ontogenetic growth. We used a dataset of 194 specimens from 25 horse and 13 pony breeds, two of which are miniature breeds (wither height < 96.5 cm)—Falabella, Shetland. We applied three-dimensional geometric morphometrics, linear measurements, and multivariate analyses (Procrustes ANOVAs) to quantitatively examine and compare the ontogenetic trajectories between pony and horse breeds with an emphasis on the miniature breeds as an extreme case of artificial selection on size. Additionally, we tested for juvenile characteristics in adult horse and miniature breeds that could resemble “paedomorphosis”—retention of juvenile characteristics in adult stage; e.g. large eyes, large braincase-to-face-relationship, and large head-to-body relationship.

Results

Allometric regression of size on shape revealed that 42% of shape variation could be explained by variation in size in all breeds. The ontogenetic trajectories of ponies and horses vary in slope and therefore in rate of change per unit size, and length. The differences in trajectory lengths and slopes result in ponies having a similar skull shape in an older age stage than horses of the same size in a younger age stage. This pattern could cause the generally perceived “paedomorphic” appearance of ponies. Miniature breeds have larger heads in relation to wither height compared to horses, a non-paedomorphic feature in horses specifically. Also, rostra (faces) are longer in adult individuals than in juveniles across all kinds of breeds. This pattern can be explained by the long-face hypothesis for grazing ungulates and could possibly be caused by the mismatch of selection by humans for shorter rostra and the dentition of ruminants.

Conclusions

Miniature breed specimens do not exhibit any of the classical mammalian “paedomorphic” features (large orbits, large heads), except for the adult Falabella that has enlarged orbits, possibly because they are herbivorous ungulates that are affected by functional and metabolic constraints related to low nutrient-food consumption. Instead ponies, including miniature breeds, have faster and shorter ontogenetic growth compared to horses, resulting in adult pony skulls looking in part like juvenile horse skulls.

Combining legacy data with new drone and DGPS mapping to identify the provenance of Plio-Pleistocene fossils from Bolt's Farm, Cradle of Humankind (South Africa)

Bolt’s Farm is a Plio-Pleistocene fossil site located within the southwestern corner of the UNESCO Hominid Fossil Sites of South Africa World Heritage Site. The site is a complex of active caves and more than 20 palaeokarst deposits or pits, many of which were exposed through the action of lime mining in the early 20th century. The pits represent heavily eroded cave systems, and as such associating the palaeocave sediments within and between the pits is difficult, especially as little geochronological data exists. These pits and the associated lime miner’s rubble were first explored by palaeoanthropologists in the late 1930s, but as yet no hominin material has been recovered. The first systematic mapping was undertaken by Frank Peabody as part of the University of California Africa Expedition (UCAE) in 1947–1948. A redrawn version of the map was not published until 1991 by Basil Cooke and this has subsequently been used and modified by recent researchers. Renewed work in the 2000s used Cooke’s map to try and relocate the original fossil deposits. However, Peabody’s map does not include all the pits and caves, and thus in some cases this was successful, while in others previously sampled pits were inadvertently given new names. This was compounded by the fact that new fossil bearing deposits were discovered in this new phase, causing confusion in associating the 1940s fossils with the deposits from which they originated; as well as associating them with the recently excavated material. To address this, we have used a Geographic Information System (GIS) to compare Peabody’s original map with subsequently published maps. This highlighted transcription errors between maps, most notably the location of Pit 23, an important palaeontological deposit given the recovery of well-preserved primate crania (Parapapio, Cercopithecoides) and partial skeletons of the extinct felid Dinofelis. We conducted the first drone and Differential Global Positioning System (DGPS) survey of Bolt’s Farm. Using legacy data, high-resolution aerial imagery, accurate DGPS survey and GIS, we relocate the original fossil deposits and propose a definitive and transparent naming strategy for Bolt’s Farm, based on the original UCAE Pit numbers. We provide datum points and a new comprehensive, georectified map to facilitate spatially accurate fossil collection for all future work. Additionally, we have collated recently published faunal data with historic fossil data to evaluate the biochronological potential of the various deposits. This suggests that the palaeocave deposits in different pits formed at different times with the occurrence of Equus in some pits implying ages of <2.3 Ma, whereas more primitive suids (Metridiochoerus) hint at a terminal Pliocene age for other deposits. This study highlights that Bolt’s Farm contains rare South African terminal Pliocene fossil deposits and creates a framework for future studies of the deposits and previously excavated material.

Grass greenness flush can influence breeding phenology and fertility in equatorial thoroughbred mares in the absence of photoperiod variation

Reproductive phenology is an important trait subjected to natural selection. Current horses in America belong to the Palearctic original populations after being introduced by European colonizers. Photoperiod variation is the main environmental factor for the adjustment of reproductive timing in horses, but is absent in equatorial areas. Here we hypothesize that seasonality of green-grass availability may influence breeding phenology in equatorial regions. We used data of 929 services to mares from 2006 to 2011 in a thoroughbred equine exploitation in Ecuador that experienced strong grass seasonality. Actual births could not be used to infer natural phenology because they were influenced by management decisions. Instead, we used variations in the probability of pregnancy after a service as a measure of the natural tendency of mares to show breeding phenology. We found that although managers tended to schedule pregnancies in two periods within the year, mares were more prone to become pregnant after the increase in grass greenness that takes place at the beginning of the year (February). Our finding has potential applications to improve the success of services and the welfare of animals, by providing green-grass stimuli in the appropriate season.

Long-term persistence of horse fecal DNA in the environment makes equids particularly good candidates for noninvasive sampling

Fecal DNA collected noninvasively can provide valuable information about genetic and ecological characteristics. This approach has rarely been used for equids, despite the need for conservation of endangered species and management of abundant feral populations. We examined factors affecting the efficacy of using equid fecal samples for conservation genetics. First, we evaluated two fecal collection methods (paper bag vs. ethanol). Then, we investigated how time since deposition and month of collection impacted microsatellite amplification success and genotyping errors. Between May and November 2014, we collected feral horse fecal samples of known age each month in a feral horse Herd Management Area in western Colorado and documented deterioration in the field with photographs. Samples collected and dried in paper bags had significantly higher amplification rates than those collected and stored in ethanol. There was little difference in the number of loci that amplified per sample between fresh fecal piles and those that had been exposed to the environment for up to 2 months (in samples collected in paper bags). After 2 months of exposure, amplification success declined. When comparing fresh (0–2 months) and old (3–6 months) fecal piles, samples from fresh piles had more matching genotypes across samples, better amplification success and less allelic dropout. Samples defecated during the summer and collected within 2 months of deposition had highest number of genotypes matching among samples, and lowest rates of amplification failure and allelic dropout. Due to the digestive system and amount of fecal material produced by equids, as well as their occurrence in arid ecosystems, we suggest that they are particularly good candidates for noninvasive sampling using fecal DNA.

Morphofunctional diversity of equine of varied genetic compositions raised in the Pantanal biome of Brazil

Evaluating phenotypic diversity makes it possible to identify discrepancies in aptitudes among animals of different genetic bases, which is an indicator of adaptive or selective differences between populations. The objective of this work was to evaluate the morphofunctional diversity of 452 male and female adult equines (Arabian, Quarter Mile, Pantaneiro, and Criollo breeds, and undefined crossbreeds of horses and mules) raised in the Pantanal biome (Brazil). Linear measurements were performed to estimate conformation indexes. Initially, a discriminant analysis was performed, regardless of the animal's size, followed by factor analysis. The factors were characterized and used as new variables. The diversity among equines and their relationship with the factors were evaluated using multivariate analysis. The factors were classified according to their decreasing importance: balance, rusticity, and robustness for the measurement factors; and load, ability, conformation, and equilibrium for the index factors. The genetic groups of equines have well-defined morphofunctional characteristics. The main differences are based on the rusticity and ability typologies in relation to those based on performance. Equines introduced to the Pantanal biome presented a more robust and compact body with good conformation. As a result, these horses may have superior athletic performance during equestrian activities when compared to the Pantaneiro local breed. However, this biotype may represent less rusticity (less adaptive capacity). Therefore, the regional breed can be equal or better in equestrian activities than breeds introduced to the Pantanal biome. Thus, breeders may cross horses from local breeds as an alternative to those introduced. Undefined crossbred male equines presented a different profile from the Pantaneiro breed, which may indicate little use of crossbreeds in breeding.

Asian horses deepen the MSY phylogeny

Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.

The evolution and anatomy of the horse manus with an emphasis on digit reduction

We revisit digit reduction in the horse and propose that all five digits are partially present in the modern adult forelimb. Osteological descriptions of selected tetradactyl, tridactyl and monodactyl equids demonstrate the evolution of the forelimb. Histological, osteological and palaeontological evidence suggest that the Equus distal forelimb is more complex than traditionally conceived. The current understanding is that the horse distal forelimb consists of one complete digit (III) and two reduced splint metacarpals (II and IV). Metacarpals II and IV each exhibit a ventral ridge, which we suggest represents the undifferentiated digits I and V. These ridges are present in the tridactyl Mesohippus, but are absent in the tetradactyl Hyracotherium. The carpal articulations of the five metacarpals match those of pentadactyl taxa. Distally, the frog, a V-shaped structure on the ventral hoof represents digits II and IV, and the wings and hoof cartilages of the distal phalanx are digits I and V. We relate this revised interpretation of the Equus forelimb to Laetoli footprints, and suggest the Hipparion side impressions are created from the hooves of I and V, rather than from II and IV. We show shades of pentadactyly within the Equus manus.

Reproductive phenology of Creole horses in Ecuador in the absence of photoperiod variation: The effects of forage availability and flooding affecting body condition of mares

Horse reproduction tends to be seasonal. The main adjusting factor in their original temperate ranges is photoperiod variation, although it is absent in equatorial areas where horses were introduced by European colonizers. Hence, dates of reproduction in these areas may be influenced by factors affecting mares' conditions and the success of foaling. Here we study reproductive timing in Creole horses in Ecuador reared in an extensive production system. We found that foaling peaked in August. Mares' conditions showed one peak in June-July, before the start of the breeding season, and another in December, and it was highly variable along the year. Mares' conditions increased after a period of vegetation growth and thus appeared negatively associated with the increment of grass greenness (normalized difference vegetation index data). Seasonal flooding of some pasturelands during March and April appeared to seriously impair mares' conditions and probably influenced the timing of foaling toward the dry season. Our results evidenced that horse breeding in these equatorial areas tended to be seasonal and point to some key factors that influence phenology by affecting body condition of mares, which may have implications for horse biology and management.

Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

The Plio-Pleistocene evolution of Equus and the subsequent domestication of horses and donkeys remains poorly understood, due to the lack of phenotypic markers capable of tracing this evolutionary process in the palaeontological/archaeological record. Using images from 345 specimens, encompassing 15 extant taxa of equids, we quantified the occlusal enamel folding pattern in four mandibular cheek teeth with a single geometric morphometric protocol. We initially investigated the protocol accuracy by assigning each tooth to its correct anatomical position and taxonomic group. We then contrasted the phylogenetic signal present in each tooth shape with an exome-wide phylogeny from 10 extant equine species. We estimated the strength of the phylogenetic signal using a Brownian motion model of evolution with multivariate K statistic, and mapped the dental shape along the molecular phylogeny using an approach based on squared-change parsimony. We found clear evidence for the relevance of dental phenotypes to accurately discriminate all modern members of the genus Equus and capture their phylogenetic relationships. These results are valuable for both palaeontologists and zooarchaeologists exploring the spatial and temporal dynamics of the evolutionary history of the horse family, up to the latest domestication trajectories of horses and donkeys.

Complete mitochondrial genome of an extinct Equus (Sussemionus) ovodovi specimen from Denisova cave (Altai, Russia)

Sussemionus is an extinct subgenus of Equus first characterized and delineated in 2010. The almost complete mitochondrial genome is available only for a single specimen of Sussemionus – a 40,000 years old E. ovodovi from Proskuryakova cave (Khakassia, Russia). Our studies of ancient horses from Denisova cave (Altai, Russia) revealed mitochondrial DNA of this species in a 32,000 years old sample. Using alignments to multiple mitochondrial genomes of non-caballine equids, we recovered 100% complete mitochondrial genome of E. ovodovi for the first time. Phylogenetic analysis demonstrates close relationship between this individual and the one previously described in Khakassia.

Small Ne of the Isolated and Unmanaged Horse Population on Sable Island

For small, isolated populations 2 common conservation concerns relate to genetic threats: inbreeding and negative consequences associated with loss of genetic diversity due to drift. Mitigating these threats often involves conservation actions that can be controversial, such as translocations or captive breeding programs. Although such actions have been successful in some situations, in others they have had undesirable outcomes. Here, we estimated the effective population size (N e ) of the Sable Island horses to assess the risk to this population of these genetic threats. We found surprising consistency of N e estimates across the 5 different methods used, with a mean of 48 effective individuals. This estimate falls below the 50 criterion of the "50/500 rule," below which inbreeding depression is a concern for population viability. However, simulations and knowledge of population history indicate that this population is still in its early stages of approaching equilibrium between mutation, drift, and genetic diversity; and no negative consequences have been identified that could be associated with inbreeding depression. Therefore, we do not recommend taking management action (such as translocations) at this stage. Rather, we propose continued monitoring of genetic diversity and fitness over time so that trends and any substantial changes can be detected. This represents one of the few unmanaged horse populations in the world, and therefore these data will not only alert us to serious concerns regarding their conservation status, but will also provide a wealth of information about how natural processes drive patterns of reproduction, mortality, and population growth over time.

Androgen receptor gene polymorphism in zebra species

Androgen receptor genes (AR) have been found to have associations with reproductive development, behavioral traits, and disorders in humans. However, the influence of similar genetic effects on the behavior of other animals is scarce. We examined the loci AR glutamine repeat (ARQ) in 44 Grevy's zebras, 23 plains zebras, and three mountain zebras, and compared them with those of domesticated horses. We observed polymorphism among zebra species and between zebra and horse. As androgens such as testosterone influence aggressiveness, AR polymorphism among equid species may be associated with differences in levels of aggression and tameness. Our findings indicate that it would be useful to conduct further studies focusing on the potential association between AR and personality traits, and to understand domestication of equid species.

Comparative analyses of tooth wear in free-ranging and captive wild equids

REASONS FOR PERFORMING STUDY

Captive breeding has played a crucial role in the conservation of threatened equid species. Grazing ruminants and rhinoceros in captivity have less abrasion-dominated tooth wear than their free-ranging conspecifics, with potential negative consequences for their health. However, a similar study on wild equids in captivity is missing.

OBJECTIVES

The aim was to establish if different tooth wear patterns are exhibited by free-ranging and captive equids.

STUDY DESIGN

Cross-sectional study of museum specimens comparing free-ranging and captive equids.

METHODS

Dental casts of maxillary cheek teeth of 228 museum specimens (122 from free-ranging and 106 from captive individuals) of 7 wild equid species were analysed using the extended mesowear method. Although teeth showing specific abnormalities were not scored, the presence of focal overgrowths (hooks) of the rostral premolars (106, 206) was recorded.

RESULTS

Captive Equus ferus przewalskii, E. grevyi, E. hemionus, E. quagga boehmi and E. zebra hartmannae have less abrasion-dominated tooth wear on their premolars than their free-ranging conspecifics (P<0.001). Fewer differences were exhibited between populations in the molars. No differences were exhibited in the distal cusp of the molars (110, 210) between populations, except in a small sample of E. kiang. Captive equids exhibited more homogeneous wear along the tooth row whereas free-ranging equids exhibited a tooth wear gradient, with more abrasion on premolars than molars. There were more rostral hooks on the premolars (106, 206) in the captive than the free-ranging population (P = 0.02).

CONCLUSIONS

Captive equids did experience less abrasion-dominated tooth wear than their free-ranging conspecifics, but the differences in tooth wear were less pronounced than those between captive and free-ranging wild ruminant and rhinoceros species. This indicates that feeding regimes for captive equids deviate less from natural diets than those for captive ruminants and rhinoceros but that factors leading to hook formation, in particular feeding height, should receive special attention. The Summary is available in Chinese - see Supporting information.