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This study investigated the effects of dietary mannan oligosaccharide (MOS) supplementation on growth performance, serum biochemistry, metabolomic profiles, and fecal microbiota in lactating Dezhou donkeys. Sixteen healthy jennies and their foals were randomly allocated to a control group (MCON), a group receiving no MOS, or an MOS-supplemented group (MMO; 0.5 g/kg diet) for 60 days. Compared with the MCON group, the MMO group showed a mitigation of lactational weight reduction, improved serum protein profiles, and favorable modulation of lipid metabolism. Furthermore, serum metabolomic analysis revealed 102 differentially abundant metabolites, which were enriched in 17 KEGG pathways involved in energy metabolism, bile secretion, and anti-inflammatory signaling. Key metabolites such as L-4-Chlorotryptophan, Gly-Trp, and cholylthreonine indicated enhanced nutrient metabolism and gut barrier function. Moreover, MOS supplementation significantly increased alpha diversity of the gut microbiota, altered community composition, and promoted the abundance of beneficial genera, including Clostridium and Bacteroides. Collectively, these results demonstrate that MOS supplementation improves metabolic health, modulates immune and antioxidant responses, and fosters a beneficial gut microbial ecosystem in lactating donkeys, suggesting its potential as an effective prebiotic in equine nutrition.

Despite over a century of interest, the function of zebra stripes has never been examined systematically. Here we match variation in striping of equid species and subspecies to geographic range overlap of environmental variables in multifactor models controlling for phylogeny to simultaneously test the five major explanations for this infamous colouration. For subspecies, there are significant associations between our proxy for tabanid biting fly annoyance and most striping measures (facial and neck stripe number, flank and rump striping, leg stripe intensity and shadow striping), and between belly stripe number and tsetse fly distribution, several of which are replicated at the species level. Conversely, there is no consistent support for camouflage, predator avoidance, heat management or social interaction hypotheses. Susceptibility to ectoparasite attack is discussed in relation to short coat hair, disease transmission and blood loss. A solution to the riddle of zebra stripes, discussed by Wallace and Darwin, is at hand. The function of zebra stripes remains unclear as none of the options have been validated ecologically. Here, the authors, matching striping patterns to environmental variables, test the main hypotheses against each other and find that biting fly avoidance best explains the presence of stripes in equids.

A new Early Eocene tapiromorph, Meridiolophus expansus gen. et sp. nov., from the Sanshui Basin, Guangdong Province, China, is described and discussed. It is the first reported Eocene mammal from the basin. The new taxon, represented by a left fragmentary mandible, is characterized by an expanded anterior symphyseal region, a long diastema between c1 and p1, a rather short diastema between p1 and p2, smaller premolars relative to molars, an incipient metaconid appressed to the protoconid on p3, a prominent entoconid on p4, molar metaconid not twinned, cristid obliqua extending mesially and slightly lingually from the hypoconid, inclined metalophid and hypolophid, and small hypoconulid on the lower preultimate molars. Meridiolophus is morphologically intermediate between basal Homogalax-like taxa and derived tapiromorphs (such as Heptodon). Phylogenetic analysis indicates Equidae is more closely related to Tapiromorpha than to Palaeotheriidae, although the latter is only represented by a single species Pachynolophus eulaliensis. 'Isectolophidae', with exception of Meridiolophus and Karagalax, has the closest affinity with Chalicotherioidea. Furthermore, the majority rule consensus tree shows that Meridiolophus is closer to Karagalax than to any other 'isectolophid', and both genera represent stem taxa to crown group Ceratomorpha.

The discovery of genomic imprinting through studies of manipulated mouse embryos indicated that the paternal genome has a major influence on placental development. However, previous research has not demonstrated paternal bias in imprinted genes. We applied RNA sequencing to trophoblast tissue from reciprocal hybrids of horse and donkey, where genotypic differences allowed parent-of-origin identification of most expressed genes. Using this approach, we identified a core group of 15 ancient imprinted genes, of which 10 were paternally expressed. An additional 78 candidate imprinted genes identified by RNA sequencing also showed paternal bias. Pyrosequencing was used to confirm the imprinting status of six of the genes, including the insulin receptor (INSR), which may play a role in growth regulation with its reciprocally imprinted ligand, histone acetyltransferase-1 (HAT1), a gene involved in chromatin modification, and lymphocyte antigen 6 complex, locus G6C, a newly identified imprinted gene in the major histocompatibility complex. The 78 candidate imprinted genes displayed parent-of-origin expression bias in placenta but not fetus, and most showed less than 100% silencing of the imprinted allele. Some displayed variability in imprinting status among individuals. This variability results in a unique epigenetic signature for each placenta that contributes to variation in the intrauterine environment and thus presents the opportunity for natural selection to operate on parent-of-origin differential regulation. Taken together, these features highlight the plasticity of imprinting in mammals and the central importance of the placenta as a target tissue for genomic imprinting.

The evolution of high-crowned molars among horses (Family Equidae) is thought to be an adaptation for abrasive diets associated with the spread of grasslands. The sharpness and relief of the worn cusp apices of teeth (mesowear) are a measure of dietary abrasion. We collected mesowear data for North American Equidae for the past 55.5 million years to test the association of molar height and dietary abrasion. Mesowear trends in horses are reflective of global cooling and associated vegetation changes. There is a strong correlation between mesowear and crown height in horses; however, most horse paleopopulations had highly variable amounts of dietary abrasion, suggesting that selective pressures for crown height may have been weak much of the time. However, instances of higher abrasion were observed in some paleopopulations, suggesting intervals of stronger selection for the evolution of dentitions, including the early Miocene shortly before the first appearance of Equinae, the horse subfamily in which high-crowned dentitions evolved.

A low-coverage draft genome sequence from a horse bone recovered from permafrost dated to approximately 560–780 thousand years ago is presented; this represents the oldest full genome sequence to date by almost an order of magnitude. Old horse DNA makes sense of Equus lineage A low-coverage draft genome sequence has been obtained from a horse bone recovered from a permafrost site in the Yukon Territory, Canada, dated to around 560,000–780,000 years before present. This is by far the earliest genome sequence so far determined. The data were compared to draft genome sequences for a Late Pleistocene horse, those of five contemporary domestic horse breeds, a Przewalski's horse and a donkey. Comparative genomics suggest that the Equus lineage that gave rise to all contemporary horses, zebras and donkeys originated about 4.0–4.5 million years ago — much earlier than previously suspected. The data support the contention that Przewalski's horses — an endangered subspecies native to the Mongolian steppes — represent the last surviving wild horse population. The rich fossil record of equids has made them a model for evolutionary processes 1 . Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560–780 thousand years before present (kyr bp ) 2 , 3 . Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr bp ), and modern genomes of five domestic horse breeds ( Equus ferus caballus ), a Przewalski’s horse ( E. f. przewalskii ) and a donkey ( E. asinus ). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0–4.5 million years before present (Myr bp ), twice the conventionally accepted time to the most recent common ancestor of the genus Equus 4 , 5 . We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski’s and domestic horse populations diverged 38–72 kyr bp , and find no evidence of recent admixture between the domestic horse breeds and the Przewalski’s horse investigated. This supports the contention that Przewalski’s horses represent the last surviving wild horse population 6 . We find similar levels of genetic variation among Przewalski’s and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski’s horse. Such regions could correspond to loci selected early during domestication.

Donkeys ( Equus asinus ) have played a vital role in agriculture, transportation, and companionship, particularly in developing regions where they are indispensable working animals. The domestication of donkeys marked a significant turning point in human history, as they became essential for transportation, agriculture, and trade, especially in arid and semi-arid areas where their resilience and endurance were highly valued. In modern society, donkeys are indispensable due to their diversified applications, including meat, dairy, medicine, and functional bioproducts, supporting economic, cultural, and medical industries. Despite their critical importance, research on donkeys has historically been overshadowed with studies on horses. However, recent advancements in high-throughput sequencing and bioinformatics have significantly deepened our understanding of the molecular landscape of donkey genome, uncovering their unique adaptations, genetic diversity, and potential therapeutic applications. Microsatellite and mitochondrial DNA (mtDNA) markers have proven effective in assessing the genetic diversity of donkeys across various regions of the world. Additionally, significant strides have been made in characterizing differentially abundant genes, proteins, and metabolic profiles in donkey milk, meat, and skin, and in identifying specific genes/proteins/metabolites associated with sperm quality, motility, and reproduction. Advanced genomic technologies, such as genome-wide association studies and the identification of selection signatures, have also been instrumental in delineating genomic regions associated with phenotypic and adaptive traits. This review integrates data from diverse studies, including those on genetic diversity, transcriptomics, whole genome sequencing, protein analysis, and metabolic profiling, to provide a comprehensive overview of donkey biology. It underscores the unique characteristics of donkeys and emphasizes the importance of continued research to improve their genetic management, conservation, and agricultural use, ensuring their ongoing contribution to human societies.

The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record. ‘The timing and ecological dynamics of extinction in the late Pleistocene are not well understood. Here, the authors use sediment ancient DNA from permafrost cores to reconstruct the paleoecology of the central Yukon, finding a substantial turnover in ecosystem composition between 13,500-10,000 years BP and persistence of some species past their supposed extinctions.’

Background The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. Results Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2 , DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager . The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1 , DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1 . Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3 . Conclusions The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB / DQB sub-regions in the Equidae .