A fertile mule and hinny in China

Modelling speciation: Problems and implications

Darwin's and Wallace's 1859 explanation that novel speciation resulted from natural variants that had been subjected to selection was refined over the next 150 years as genetic inheritance and the importance of mutation-induced change were discovered, the quantitative theory of evolutionary population genetics was produced, the speed of genetic change in small populations became apparent and the ramifications of the DNA revolution became clear. This paper first discusses the modern view of speciation in its historical context. It then uses systems-biology approaches to consider the many complex processes that underpin the production of a new species; these extend in scale from genes to populations with the processes of variation, selection and speciation being affected by factors that range from mutation to climate change. Here, events at a particular scale level (e.g. protein network activity) are activated by the output of the level immediately below (i.e. gene expression) and generate a new output that activates the layer above (e.g. embryological development), with this change often being modulated by feedback from higher and lower levels. The analysis shows that activity at each level in the evolution of a new species is marked by stochastic activity, with mutation of course being the key step for variation. The paper examines events at each of these scale levels and particularly considers how the pathway by which mutation leads to phenotypic variants and the wide range of factors that drive selection can be investigated computationally. It concludes that, such is the complexity of speciation, most steps in the process are currently difficult to model and that predictions about future speciation will, apart from a few special cases, be hard to make. The corollary is that opportunities for novel variants to form are maximised.

Experimental cross-species infection of donkeys with equine hepacivirus and analysis of host immune signatures

BACKGROUND

The Equine Hepacivirus (EqHV) is an equine-specific and liver-tropic virus belonging to the diverse genus of Hepaciviruses. It was recently found in a large donkey (Equus asinus) cohort with a similar seroprevalence (30%), but lower rate of RNA-positive animals (0.3%) compared to horses. These rare infection events indicate either a lack of adaptation to the new host or a predominantly acute course of infection.

METHODS

In order to analyze the susceptibility and the course of EqHV infection in donkeys, we inoculated two adult female donkeys and one control horse intravenously with purified EqHV from a naturally infected horse. Liver biopsies were taken before and after inoculation to study changes in the transcriptome.

RESULTS

Infection kinetics were similar between the equids. All animals were EqHV PCR-positive from day three. EqHV RNA-levels declined when the animals seroconverted and both donkeys cleared the virus from the blood by week 12. Infection did not have an impact on the clinical findings and no significant histopathological differences were seen. Blood biochemistry revealed a mild increase in GLDH at the time of seroconversion in horses, which was less pronounced in donkeys. Transcriptomic analysis revealed a distinct set of differentially expressed genes, including viral host factors and immune genes.

CONCLUSION

To summarize, our findings indicate that donkeys are a natural host of EqHV, due to the almost identical infection kinetics. The different immune responses do however suggest different mechanisms in reacting to hepaciviral infections.

What Demarks the Metamorphosis of Human Individuals to Posthuman Entities?

Humans often seek to improve themselves, whether through self-discipline or through the use of science and technology. At some point in the future, techniques might become available that will change humans to such a degree that they might have to be regarded as something other than human: posthuman. This essay tries to define the point at which such a human-to-posthuman metamorphosis may occur. This is achieved by discerning what is it that makes human substance distinct, i.e. what is the human essence. This is accomplished by examining the features of the human body, looking at the mode of human existence in society and trying to grasp the importance of the body-soul relationship. Throughout the process, humans are compared to animals as well as entities from literature, film, and the gaming world. These are used as case studies to shape and test the ideas developed throughout the essay. This essay's conclusions might become useful when decisions will have to be made as to the legal status of posthumans, by providing a tool for discerning when metamorphosis has occurred. Moreover, insights from this essay might also inform debates surrounding the ethical status of certain modalities of human enhancement.

Improved de novo genomic assembly for the domestic donkey

Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.

Testicular Characteristics and the Block to Spermatogenesis in Mature Hinny

Most hinnies (female donkey×male horse) and mules (female horse×male donkey) are sterile with few reports of equine fertile hybrids. The main cause of this sterility is thought to be a meiotic block to spermatogenesis and oogenesis. This study compared the developmental features of the testes and a histological analyses of spermatogenesis in a male hinny with those of a normal, fertile stallion and Jack donkey. Hinny testes showed a thicker tunica albuginea, fewer blood vessels and more connective tissue in the testis parenchyma than those of the stallion and Jack donkey. Although the mean number of seminiferous tubules was significantly higher in stallion and hinny than Jack donkey (p<0.01), the mean proportion of seminiferous tubules was lower in the hinny (p<0.01) which resulted in a smaller diameter of seminiferous tubules. The mean number of spermatogonia and spermatocytes per unit area were significantly lower in hinny testis (p<0.01) and no spermatids or mature spermatozoa cells were found during immunofluorescent analyses. These results indicated that defects in seminiferous tubule development and structure occur in the testis of hinnies. Furthermore, most spermatogonia and spermatocytes cease development in synapsis during mid-meiosis of spermatocytes, which results in a block to spermatogenesis that prevents the formation of spermatids and matured spermatozoa during meiosis in male hinnies.

Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms

Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

The role of chromosome variation in the speciation of the red brocket deer complex: the study of reproductive isolation in females

BACKGROUND

The red brocket deer, Mazama americana, has at least six distinct karyotypes in different regions of South America that suggest the existence of various species that are today all referred to as M. americana. From an evolutionary perspective, the red brockets are a relatively recent clade that has gone through intense diversification. This study sought to prove the existence of post-zygotic reproductive isolation in deer offspring between distinct chromosome lineages. To achieve this, inter-cytotype and intra-cytotype crosses were performed, which resulted in both F1 hybrid (n = 5) and pure offspring (n = 3) in captivity.

RESULTS

F1 females were analyzed in terms of their karyotypes, ovarian histology, estrous cycles and in vitro embryo production. Pure females presented parameters that were similar to those previously reported for M. Americana; however, the parameters for hybrid females were different. Two hybrids were determined to be sterile, while the remaining hybrids presented characteristics of subfertility.

CONCLUSIONS

The results support the existence of well-established reproductive isolation among the most distant karyotype lineages and elucidates the need to define all karyotype variants and their geographical ranges in order to define the number of species of red brocket.

Characterization of Prdm9 in equids and sterility in mules

Prdm9 (Meisetz) is the first speciation gene discovered in vertebrates conferring reproductive isolation. This locus encodes a meiosis-specific histone H3 methyltransferase that specifies meiotic recombination hotspots during gametogenesis. Allelic differences in Prdm9, characterized for a variable number of zinc finger (ZF) domains, have been associated with hybrid sterility in male house mice via spermatogenic failure at the pachytene stage. The mule, a classic example of hybrid sterility in mammals also exhibits a similar spermatogenesis breakdown, making Prdm9 an interesting candidate to evaluate in equine hybrids. In this study, we characterized the Prdm9 gene in all species of equids by analyzing sequence variation of the ZF domains and estimating positive selection. We also evaluated the role of Prdm9 in hybrid sterility by assessing allelic differences of ZF domains in equine hybrids. We found remarkable variation in the sequence and number of ZF domains among equid species, ranging from five domains in the Tibetan kiang and Asiatic wild ass, to 14 in the Grevy’s zebra. Positive selection was detected in all species at amino acid sites known to be associated with DNA-binding specificity of ZF domains in mice and humans. Equine hybrids, in particular a quartet pedigree composed of a fertile mule showed a mosaic of sequences and number of ZF domains suggesting that Prdm9 variation does not seem by itself to contribute to equine hybrid sterility.

Molecular and cytogenetic paternity testing of a male offspring of a hinny

An alleged male foal of a female mule, whose sire and grandparents were unknown, was identified for its pedigree. Parentage testing was conducted by comparing polymorphism of 12 microsatellite DNA sites and mitochondrial D-loop sequences of the male foal and the female mule. Both the sequence analysis of species-specific DNA fragments and a cytogenetic analysis were performed to identify the species of the foal and its parents. The results showed that the alleged female mule is actually a hinny, and the male foal, which possesses 62 chromosomes, qualifies as an offspring of the female hinny and a jack donkey.

Variability of plasma melatonin level in pony mares (Equus caballus), comparison with the hybrid: mules and with jennies (Equus asinus)

In long-day breeders like horses, the length of nocturnal melatonin secretion is the main messenger of photoperiod. Previous studies have shown that the nocturnal jugular melatonin concentration is lower in horses, than in mules but is unknown in donkeys. The aim of this study was to estimate the inter-animal variability of plasma melatonin concentration in domestic mares and to compare this concentration with those observed in domestic jennies and in their hybrid mules. In the autumn, blood samples were collected at 22 h, 23 h, 0 h and 1 h during 2 nights at 3 weeks intervals, in 110 pony mares, 10 jennies and 6 mules maintained under natural photoperiod. Melatonin was assayed by a validated RIA method. The statistical analysis of the measures was done with a specific unbalanced analysis of variance model. The effect of species and individuals (nested under species) was highly significant. The mean melatonin concentration was 24 pg.mL(-1) in mares and was significantly lower than in jennies and in mules which were 90 pg.mL(-1) and 169 pg.mL(-1) respectively. The melatonin plasma concentration was higher in jennies than in mares. These results suggest that the melatonin concentration is genetically determined.

Construction of chromosome-specific paints for meta- and submetacentric autosomes and the sex chromosomes in the horse and their use to detect homologous chromosomal segments in the donkey

A pilot study comparing horse and donkey karyotypes on a molecular basis was initiated using the chromosomal microdissection approach. All equine meta- and submetacentric chromosomes, viz. ECA1 to ECA13 and the X and Y chromosomes, were microdissected. The DNA was PCR amplified, non-radioactively labelled and used as probes on equine metaphase chromosomes to confirm their origin. Once tested, the paints were used as probes on donkey metaphase chromosomes to detect homologous chromosomal segments between the two species. The results not only detected conservation of whole chromosome and/or arm synteny between the two karyotypes, but also highlighted varying degrees of rearrangements. The findings also enable deduction of homology between parts of donkey and human karyotypes. In light of the molecular evidence, this study examines the accuracy of the available comparative cytogenetic data between horse and donkey.

The variety of sterility and gradual progression to fertility in hybrids of the horse and donkey

Generally speaking, the majority of F1 hybrids between the horse and donkey are sterile and do conform to the hypothesis of gametogenic breakdown. The results of our own research, nevertheless, lead us to conclude that there is variability in degree of sterility and fertility for both F1 and B1 individuals, with a gradual advance from sterility to fertility being seen. This is the subject we will discuss from the point of view of oestrus, ovulation, mating, pregnancy, spermatogenesis, endocrine activity, isozymes and karyotypic analysis in this paper.