Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi).

The composition of mammalian gut microbiomes is highly conserved within species, yet the mechanisms by which microbiome composition is transmitted and maintained within lineages of wild animals remain unclear. Mutually compatible hypotheses exist, including that microbiome fidelity results from inherited dietary habits, shared environmental exposure, morphophysiological filtering and/or maternal effects. Interspecific hybrids are a promising system in which to interrogate the determinants of microbiome composition because hybrids can decouple traits and processes that are otherwise co-inherited in their parent species. We used a population of free-living hybrid zebras (Equus quagga × grevyi) in Kenya to evaluate the roles of these four mechanisms in regulating microbiome composition. We analysed faecal DNA for both the trnL-P6 and the 16S rRNA V4 region to characterize the diets and microbiomes of the hybrid zebra and of their parent species, plains zebra (E. quagga) and Grevy's zebra (E. grevyi). We found that both diet and microbiome composition clustered by species, and that hybrid diets and microbiomes were largely nested within those of the maternal species, plains zebra. Hybrid microbiomes were less variable than those of either parent species where they co-occurred. Diet and microbiome composition were strongly correlated, although the strength of this correlation varied between species. These patterns are most consistent with the maternal-effects hypothesis, somewhat consistent with the diet hypothesis, and largely inconsistent with the environmental-sourcing and morphophysiological-filtering hypotheses. Maternal transmittance likely operates in conjunction with inherited feeding habits to conserve microbiome composition within species.

The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus).

We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6-6.4×. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass, secular name 'hydruntine'. Further, the Anatolian wild ass whole genome profiles fell outside the genomic diversity of other extant and past Asiatic wild ass (E. hemionus) lineages. These observations suggest that the three Anatolian wild asses represent hydruntines, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Our mitogenomic and genomic analyses indicate that E. h. hydruntinus was a clade belonging to ancient and present-day E. hemionus lineages that radiated possibly between 0.6 and 0.8 Mya. We also find evidence consistent with recent gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity suggest that the Anatolian wild ass population may have lost genetic diversity by the mid-first millennium BCE, a possible sign of its eventual demise.

Abortion storm of Yili horses is associated with Equus caballus papillomavirus 2 variant infection.

Nine different species of Equus caballus papillomavirus (EcPV) and three bovine papillomaviruses (BPVs) have been reported to infect horses. However, there are few descriptions of such infections in China. In our pioneer study on Chinese horses, we identified EcPV-2 in the nasal swabs (4/230, 1.7%) of Yili horses, and the semen (3/18, 16.7%) of thoroughbred horses. This indicated that EcPV is indeed hosted by horses in China, and that EcPV-2 might be transmitted though breeding. Further detection of EcPVs in the lung tissues of aborted fetuses of Yili horses, which were originally negative for equid herpes viruses, demonstrated EcPV-2 positivity in 19 of 50 samples, thereby indicating that EcPV-2 may be a new pathogen responsible for causing abortion. Thereafter, sequence analyses of the L1 genes of 26 EcPV-2 in China were performed, indicating that EcPV-2, which primarily infects horses in China, shared 98.3-99.9% nt identity with the published sequences for EcPV-2. These observations indicated that EcPV-2 identified in the current study were highly similar variants of the previously identified strains of EcPV-2. Phylogenetic analysis based on L1 gene sequences from GenBank showed that the EcPV-2 found in Chinese horses was closely related to and clustered together with an already known EcPV-2a lineage. Our study provides the first evidence related to EcPV-2 infection in Chinese horses, which can serve as a causative agent for Yili horse abortions, and may thus lay the foundation for a systematic and detailed epidemiological study of this infection in Chinese horses.

Horses discriminate between human facial and vocal expressions of sadness and joy.

Communication of emotions plays a key role in intraspecific social interactions and likely in interspecific interactions. Several studies have shown that animals perceive human joy and anger, but few studies have examined other human emotions, such as sadness. In this study, we conducted a cross-modal experiment, in which we showed 28 horses two soundless videos simultaneously, one showing a sad, and one a joyful human face. These were accompanied by either a sad or joyful voice. The number of horses whose first look to the video that was incongruent with the voice was longer than their first look to the congruent video was higher than chance, suggesting that horses could form cross-modal representations of human joy and sadness. Moreover, horses were more attentive to the videos of joy and looked at them for longer, more frequently, and more rapidly than the videos of sadness. Their heart rates tended to increase when they heard joy and to decrease when they heard sadness. These results show that horses are able to discriminate facial and vocal expressions of joy and sadness and may form cross-modal representations of these emotions; they also are more attracted to joyful faces than to sad faces and seem to be more aroused by a joyful voice than a sad voice. Further studies are needed to better understand how horses perceive the range of human emotions, and we propose that future experiments include neutral stimuli as well as emotions with different arousal levels but a same valence.

Horses form cross-modal representations of adults and children.

Recently, research on domestic mammals' sociocognitive skills toward humans has been prolific, allowing us to better understand the human-animal relationship. For example, horses have been shown to distinguish human beings on the basis of photographs and voices and to have cross-modal mental representations of individual humans and human emotions. This leads to questions such as the extent to which horses can differentiate human attributes such as age. Here, we tested whether horses discriminate human adults from children. In a cross-modal paradigm, we presented 31 female horses with two simultaneous muted videos of a child and an adult saying the same neutral sentence, accompanied by the sound of an adult's or child's voice speaking the sentence. The horses looked significantly longer at the videos that were incongruent with the heard voice than at the congruent videos. We conclude that horses can match adults' and children's faces and voices cross-modally. Moreover, their heart rates increased during children's vocalizations but not during adults'. This suggests that in addition to having mental representations of adults and children, horses have a stronger emotional response to children's voices than adults' voices.

What drives horse success at following human-given cues? An investigation of handler familiarity and living conditions.

Cues such as the human pointing gesture, gaze or proximity to an object are widely used in behavioural studies to evaluate animals' abilities to follow human-given cues. Many domestic mammals, such as horses, can follow human cues; however, factors influencing their responses are still unclear. We assessed the performance of 57 horses at a two-way choice task testing their ability to follow cues of either a familiar (N = 28) or an unfamiliar informant (N = 29). We investigated the effects of the length of the relationship between the horse and a familiar person (main caregiver), their social environment (living alone, in dyads, or in groups) and their physical environment (living in stalls/paddocks, alternating between paddocks and pastures, or living full time in pastures). We also controlled for the effects of horses' age and sex. Our results showed that horses' success rate at the task was not affected by the familiarity of the informant and did not improve with the relationship length with the familiar informant but did increase with the age of the horses. Horses living in groups had better success than the ones kept either in dyads or alone. Finally, horses housed in small paddocks had lower success than those living on pasture. These results indicate that with age, horses get better at following human-given indications regardless of who the human informant is and that an appropriate living and social environment could contribute to the development of socio-cognitive skills towards humans. Therefore, such aspects should be considered in studies evaluating animal behaviour.

Characteristic of Przewalski horses population from Askania-Nova reserve based on genetic markers.

Przewalski horses are considered the last living population of wild horses, however, they are secondarily feral offspring of herds domesticated ~ 5000 years ago by the Botai culture. After Przewalski horses were almost extinct at the beginning of the twentieth century, their population is about 2500 individuals worldwide, with one of the largest breeding centers in Askania-Nova Biosphere Reserve (Ukraine). The research aimed to establish the maternal variation of Przewalski horses population maintained in Askania-Nova Reserve based on mitochondrial DNA hypervariable 1 and hypervariable 2 regions profiling, as well as, analysis of Y chromosome single nucleotide polymorphism unique for Przewalski horses, and coat color markers: MC1R and TBX3. The mtDNA hypervariable regions analysis in 23 Przewalski horses allowed assigning them to three distinctly different haplotypes, showing the greatest similarity to the Equus caballus reference, the Equus przewalskii reference, and to extinct species-Haringtonhippus. The Y chromosome analysis using fluorescently labelled assays differentiated horses in terms of polymorphism (g731821T>C) characteristic of Equus przewalskii. All male individuals presented genotype C characteristics for Przewalski horses. The polymorphisms within the coat color genes indicated only native, wild genotypes. The Y chromosome and coat color analysis denied admixtures of the tested horses with other Equidae.

Age-specific effects of density and weather on body condition and birth rates in a large herbivore, the Przewalski's horse.

Reproduction in young females can show a particularly sensitive response to environmental challenges, although empirical support from individual-based long-term studies is scarce. Based on a 20-year data set from a free-roaming Przewalski's horse population (Equus ferus przewalskii), we studied effects of large-herbivore density (horses + cattle) and weather conditions experienced during different life stages on females' annual birth rates. Foaling probability was very low in 2-year-olds, reaching maximum values in 5 to 10-year-olds, followed by a decrease in older females indicating reproductive senescence. Mother's previous reproductive investment affected her current reproduction; young and old mothers (as opposed to middle-aged ones), which had nursed a foal for at least 60 days during the previous year, reproduced with a lower probability. Foaling probability and body condition of young females were lower when large-herbivore density was high. Reproduction was also influenced by interactive weather effects during different life stages. Low late-summer precipitation during the females' year of birth was associated with a pronounced decrease in foaling probability in response to harsh late-winter temperatures prior to the mating season. In turn, increased amounts of late-summer rain during this early age together with more late-summer rain during the females' current pregnancy led to an increased reproductive probability in 2-3-year-olds. These results were corroborated by the ameliorating effects of late-summer rain on body condition in such females. In conclusion, our findings highlight the interactive importance of weather conditions experienced during early life, and of density and weather during current pregnancy on foaling probability, particularly in young females.

Vulvo-vaginal epithelial tumors in mares: A preliminary investigation on epithelial-mesenchymal transition and tumor-immune microenvironment.

Vulvo-vaginal epithelial tumors are uncommon in mares, and data on the epithelial-to-mesenchymal transition (EMT) and the tumor-immune microenvironment (TIME) are still lacking. This is a study investigating the equus caballus papillomavirus type 2 (EcPV2) infection state as well as the EMT process and the tumor microenvironment in vulvo-vaginal preneoplastic/ benign (8/22) or malignant (14/22) epithelial lesions in mares. To do this, histopathological, immunohistochemical, transcriptomic, in situ hybridization, and correlation analyses were carried out. Immunohistochemistry quantification showed that cytoplasmic E-cadherin and ß-catenin expression as well as nuclear ß-catenin expression were features of malignant lesions, while benign/preneoplastic lesions were mainly characterized by membranous E-cadherin and ß-catenin expression. Despite this, there were no differences between benign and malignant equine vulvo-vaginal lesions in the expression of downstream genes involved in the canonical and noncanonical wnt/ß-catenin pathways. In addition, malignant lesions were characterized by a lower number of cells with cytoplasmic cytokeratin expression as well as a slightly higher cytoplasmic vimentin immunolabeling. The TIME of malignant lesions was characterized by more numerous CD204+ M2-polarized macrophages. Altogether, our results support the hypothesis that some actors in TIME such as CD204+ M2-polarized macrophages may favor the EMT process in equine vulvo-vaginal malignant lesions providing new insights for future investigations in the field of equine EcPV2-induced genital neoplastic lesions.

A retinoscopic survey of donkeys and goats.

PURPOSE: Assess the refractive states of donkeys and goats. METHODS: Forty-two donkeys and 28 goats were enrolled. The mean ± SD ages were 7.68 ± 7.33 years for donkeys and 4.26 ± 2.33 years for goats. Seven donkeys and one goat were <6 months old. Retinoscopy was performed in alert animals, following cycloplegia in goats but not in donkeys. Normality was determined using the Kolmogorov-Smirnov test. The two primary meridians and two eyes were compared using Pearson's correlation and paired Student's t-tests. The association between refractive states and age was examined using one-way ANOVA in donkeys and a paired Student's t-test in goats. One-sample t-tests were conducted to assess if the refractive error distributions were significantly different from "0". RESULTS: The mean ± SD spherical equivalent (SE) refractive errors of the right and left donkey eyes were -0.80 ± 1.03 D and -0.35 ± 0.95 D, respectively. The majority (86%) of the donkeys had an astigmatic refraction and eight (19%) had anisometropia. The mean SE refractive errors of the right and left goat eyes were -0.15 ± 1.1 D and -0.18 ± 1.2 D, respectively. The majority (54%) of the goat eyes had an astigmatic refraction and five (18%) had anisometropia. The right and left eye SE refractive errors were positively correlated in both species (both p = .9). Age was not correlated with refractive error in both donkeys (p = .09) and goats (p = .6). CONCLUSIONS: Both goats and donkeys are emmetropic.

Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line.

With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (FROH ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10-5 for Hardy-Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.

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.

A Satellite-Free Centromere in Equus przewalskii Chromosome 10.

In mammals, centromeres are epigenetically specified by the histone H3 variant CENP-A and are typically associated with satellite DNA. We previously described the first example of a natural satellite-free centromere on Equus caballus chromosome 11 (ECA11) and, subsequently, on several chromosomes in other species of the genus Equus. We discovered that these satellite-free neocentromeres arose recently during evolution through centromere repositioning and/or chromosomal fusion, after inactivation of the ancestral centromere, where, in many cases, blocks of satellite sequences were maintained. Here, we investigated by FISH the chromosomal distribution of satellite DNA families in Equus przewalskii (EPR), demonstrating a good degree of conservation of the localization of the major horse satellite families 37cen and 2PI with the domestic horse. Moreover, we demonstrated, by ChIP-seq, that 37cen is the satellite bound by CENP-A and that the centromere of EPR10, the ortholog of ECA11, is devoid of satellite sequences. Our results confirm that these two species are closely related and that the event of centromere repositioning which gave rise to EPR10/ECA11 centromeres occurred in the common ancestor, before the separation of the two horse lineages.

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.

Cutaneous epitheliotropic T-cell lymphoma in a donkey - a case report.

BACKGROUND: Cutaneous epitheliotropic T-cell lymphoma is a malignant tumour of the skin already reported in humans, dogs, cats, horses, and other species, but not previously in donkeys. The standard diagnosis is based on clinical, morphological and immunophenotypic data. Differentiation of malignant versus benign proliferation of lymphocytes is crucial; in ambiguous cases T-cell receptor gamma (TRG) molecular clonality should be tested. In the present paper, we report a case of mycosis fungoides diagnosed in a donkey whose diagnosis was based on clinical, histological and immunohistochemical aspects and a positive TRG clonality test. CASE PRESENTATION: A twenty-five-year-old donkey gelding was referred with a mildly pruritic, generalised and severe exfoliative dermatosis. Otherwise, the animal was clinically healthy, though mildly underweight. Dermatological examination revealed severe generalised alopecic and exfoliative dermatitis, occasionally eroded, with high number of large, thin, greyish scales. All mucocutaneous junctions except the hoofs were affected. Ectoparasites and dermatophytes were ruled out. The complete blood count and blood smear evaluation revealed mild normocytic normochromic anemia. The biochemistry panel showed mild hyperproteinemia with albumin within the normal range. Protein electrophoresis showed moderate polyclonal hypergammaglobulinemia. Histological findings were characterised by interface dermatitis with massive exocytosis in the epidermis of a homogenous population of lymphoid cells showing atypia. Clusters of neoplastic cells were present within the epidermis forming Pautrier "microabscesses". These findings are consistent with cutaneous epitheliotropic lymphoma. Immunohistochemical staining revealed uniform labelling of the neoplastic cells for CD3, and lack of expression of CD20 (a B cell lineage associated marker). Molecular clonality PCR (PARR) was performed using equine TRG primers; this revealed a clonal rearrangement in a heavy polyclonal background. Transmission electronic microscopy showed multiple lymphocytes with convoluted or cerebriform nuclei. CONCLUSIONS: This case report provides the first evidence of clinical, histopathological, immunophenotypic features, electron microscopy findings and molecular analysis of a cutaneous epitheliotropic T-cell lymphoma (mycosis fungoides) in a donkey. Our observations suggest that cutaneous T-cell lymphoma should be included in the differential diagnoses of exfoliative dermatitis, even those progressing in a chronic pattern and/or with few or no pruritus.

Molecular Dynamics and Evolution of Centromeres in the Genus Equus.

The centromere is the chromosomal locus essential for proper chromosome segregation. While the centromeric function is well conserved and epigenetically specified, centromeric DNA sequences are typically composed of satellite DNA and represent the most rapidly evolving sequences in eukaryotic genomes. The presence of satellite sequences at centromeres hampered the comprehensive molecular analysis of these enigmatic loci. The discovery of functional centromeres completely devoid of satellite repetitions and fixed in some animal and plant species represented a turning point in centromere biology, definitively proving the epigenetic nature of the centromere. The first satellite-free centromere, fixed in a vertebrate species, was discovered in the horse. Later, an extraordinary number of satellite-free neocentromeres had been discovered in other species of the genus Equus, which remains the only mammalian genus with numerous satellite-free centromeres described thus far. These neocentromeres arose recently during evolution and are caught in a stage of incomplete maturation. Their presence made the equids a unique model for investigating, at molecular level, the minimal requirements for centromere seeding and evolution. This model system provided new insights on how centromeres are established and transmitted to the progeny and on the role of satellite DNA in different aspects of centromere biology.

No size-dependent net particle retention in the hindgut of horses.

Sieve analyses of hindgut contents of horses as well as observations in horses where plastic markers had been applied to a caecal cannula suggested that there may be a discrimination by particle size in the passage or retention of digesta. Here, we performed a similar experiment with five caecum-cannulated horses (562 ± 31 kg) fed a constant amount (6.81 kg dry matter/day) of grass hay. Passage markers representing the liquid (Co-EDTA) as well as the particulate digesta phase (Yb-undefined; Cr mordanted fibre 1-2 mm; Ce-mordanted fibre 8 mm) were given as a pulse-dose into the cannula to measure their mean retention times (MRT). The MRTs were compared by repeated-measurements analysis of variance. The MRT in the hindgut was 22.2 ± 2.4 h for Co, 25.0 ± 3.4 h for Yb, 26.2 ± 1.6 h for Cr and 26.3 ± 1.5 h for Ce. Whereas differences between the particle marker MRTs were not significant (padj. > 0.05), significant differences were observed between the solute marker Co and each of the particle markers Cr and Ce (padj. < 0.009). The results confirm the well-known significant, albeit small, difference in MRT in horses between the fluid and the particle digesta phase, and corroborate another recent study that used a combination of whole, marked hay and individual marker analysis in different particle size fractions of the faeces, which also did not detect a selective retention of any particle size class.

Population structure, inbreeding and stripe pattern abnormalities in plains zebras.

One of the most iconic wild equids, the plains zebra occupies a broad region of sub-Saharan Africa and exhibits a wide range of phenotypic diversity in stripe patterns that have been used to classify multiple subspecies. After decades of relative stability, albeit with a loss of at least one recognized subspecies, the total population of plains zebras has undergone an approximate 25% decline since 2002. Individuals with abnormal stripe patterns have been recognized in recent years but the extent to which their appearance is related to demography and/or genetics is unclear. Investigating population genetic health and genetic structure are essential for developing effective strategies for plains zebra conservation. We collected DNA from 140 plains zebra, including seven with abnormal stripe patterns, from nine locations across the range of plains zebra, and analyzed data from restriction site-associated and whole genome sequencing (RAD-seq, WGS) libraries to better understand the relationships between population structure, genetic diversity, inbreeding, and abnormal phenotypes. We found that genetic structure did not coincide with described subspecific variation, but did distinguish geographic regions in which anthropogenic habitat fragmentation is associated with reduced gene flow and increased evidence of inbreeding, especially in certain parts of East Africa. Further, zebras with abnormal striping exhibited increased levels of inbreeding relative to normally striped individuals from the same populations. Our results point to a genetic cause of stripe pattern abnormalities, and dramatic evidence of the consequences of habitat fragmentation.

Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge.

The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0-0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875-625 and ~200-50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.

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.