Spotted phenotypes in horses lost attractiveness in the Middle Ages

DNA methylation-based profiling of horse archaeological remains for age-at-death and castration

Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature of the fossil record and the lack of universal skeletal markers for age. DNA methylation clocks offer new, albeit challenging, alternatives for estimating the age-at-death of ancient individuals. Here, we take advantage of the availability of a DNA methylation clock based on 31,836 CpG sites and dental age markers in horses to assess age predictions in 84 ancient remains. We evaluate our approach using whole-genome sequencing data and develop a capture assay providing reliable estimates for only a fraction of the cost. We also leverage DNA methylation patterns to assess castration practice in the past. Our work opens for a deeper characterization of past husbandry and ritual practices and holds the potential to reveal age mortality profiles in ancient societies, once extended to human remains.

EWF: simulating exact paths of the Wright-Fisher diffusion

MOTIVATION

The Wright-Fisher diffusion is important in population genetics in modelling the evolution of allele frequencies over time subject to the influence of biological phenomena such as selection, mutation and genetic drift. Simulating the paths of the process is challenging due to the form of the transition density. We present EWF, a robust and efficient sampler which returns exact draws for the diffusion and diffusion bridge processes, accounting for general models of selection including those with frequency dependence.

RESULTS

Given a configuration of selection, mutation and endpoints, EWF returns draws at the requested sampling times from the law of the corresponding Wright-Fisher process. Output was validated by comparison to approximations of the transition density via the Kolmogorov-Smirnov test and QQ plots.

AVAILABILITY AND IMPLEMENTATION

All softwares are available at https://github.com/JaroSant/EWF.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Basal Reactivity Evaluated by Infrared Thermography in the "Caballo de Deporte Español" Horse Breed According to Its Coat Color

Horses have been valued for their diversity of coat color since prehistoric times. In particular, the pleiotropic effect that coat color genes have on behavior determines the way the horse perceives and reacts to its environment. The primary aim of this study was to evaluate the influence of coat color on basal reactivity assessed with infrared thermography as eye temperature at rest (ETR), determine their relation with the results obtained by these horses in Show Jumping competitions and to estimate the genetic parameters for this variable to test its suitability for genetic selection. A General Linear Model (GLM) and Duncan post-hoc analysis indicated differences in ETR due to coat color, sex, age, location, and breed-group factors. A Spearman’s rank correlation of 0.11 (p < 0.05) was found with ranking, indicating that less reactive horses were more likely to achieve better rankings. Heritability values ranged from 0.17 to 0.22 and were computed with a model with genetic groups and a model with residual variance heterogeneity. Breeding values were higher with the last genetic model, thus demonstrating the pleiotropic effect of coat color. These results indicate that ETR has a suitable genetic basis to be used in the breeding program to select for basal reactivity due to coat color.

The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics

The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.

Genomics and the Evolutionary History of Equids

The equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by several waves of explosive radiations and extinctions, cross-continental migrations, and local adaptations. In recent years, genomic technologies have provided new analytical solutions that have enhanced our understanding of equine evolution, including the species radiation within Equus; the extinction dynamics of several lineages; and the domestication history of two individual species, the horse and the donkey. Here, we provide an overview of these recent developments and suggest areas for further research.

Detecting and Quantifying Natural Selection at Two Linked Loci from Time Series Data of Allele Frequencies with Forward-in-Time Simulations

Recent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time. This improvement provides an opportunity for us to study natural selection based on time serial samples of genomes while accounting for genetic recombination effect and local linkage information. Such time series genomic data allow for more accurate estimation of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel Bayesian statistical framework for inferring natural selection at a pair of linked loci by capitalising on the temporal aspect of DNA data with the additional flexibility of modeling the sampled chromosomes that contain unknown alleles. Our approach is built on a hidden Markov model where the underlying process is a two-locus Wright-Fisher diffusion with selection, which enables us to explicitly model genetic recombination and local linkage. The posterior probability distribution for selection coefficients is computed by applying the particle marginal Metropolis-Hastings algorithm, which allows us to efficiently calculate the likelihood. We evaluate the performance of our Bayesian inference procedure through extensive simulations, showing that our approach can deliver accurate estimates of selection coefficients, and the addition of genetic recombination and local linkage brings about significant improvement in the inference of natural selection. We also illustrate the utility of our method on real data with an application to ancient DNA data associated with white spotting patterns in horses.

Estimation of Natural Selection and Allele Age from Time Series Allele Frequency Data Using a Novel Likelihood-Based Approach

Temporally spaced genetic data allow for more accurate inference of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel likelihood-based method for jointly estimating selection coefficient and allele age from time series data of allele frequencies. Our approach is based on a hidden Markov model where the underlying process is a Wright-Fisher diffusion conditioned to survive until the time of the most recent sample. This formulation circumvents the assumption required in existing methods that the allele is created by mutation at a certain low frequency. We calculate the likelihood by numerically solving the resulting Kolmogorov backward equation backward in time while reweighting the solution with the emission probabilities of the observation at each sampling time point. This procedure reduces the two-dimensional numerical search for the maximum of the likelihood surface, for both the selection coefficient and the allele age, to a one-dimensional search over the selection coefficient only. We illustrate through extensive simulations that our method can produce accurate estimates of the selection coefficient and the allele age under both constant and nonconstant demographic histories. We apply our approach to reanalyze ancient DNA data associated with horse base coat colors. We find that ignoring demographic histories or grouping raw samples can significantly bias the inference results.

Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics

The horse was essential to past human societies but became a recreational animal during the twentieth century as the world became increasingly mechanized. As the author reviews here, recent studies of ancient genomes have revisited the understanding of horse domestication, from the very early stages to the most modern developments. They have uncovered several extinct lineages roaming the far ends of Eurasia some 4000 years ago. They have shown that the domestic horse has been significantly reshaped during the last millennium and experienced a sharp decline in genetic diversity within the last two centuries. At a time when no truly wild horses exist any longer, this calls for enhanced conservation in all endangered populations. These include the Przewalski's horse native to Mongolia, and the many local breeds side-lined by the modern agenda, but yet representing the living heritage of over five millennia of horse breeding.

Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds

Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic diversity by runs of homozygosity (ROH) utilizing a 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures of selection were identified by breed and similarities/dissimilarities between populations were evaluated. In the entire dataset, 180 ROH islands were identified, whilst 100 islands were breed specific, all other overlapped in 36 genomic regions with at least one ROH island of another breed. Furthermore, two ROH hot spots were determined at horse chromosome 3 (ECA3) and ECA11. Besides the confirmation of previously documented target genes involved in selection for coat color (MC1R, STX17, ASIP), body size (LCORL/NCAPG, ZFAT, LASP1, HMGA2), racing ability (PPARGC1A), behavioral traits (GRIN2B, NTM/OPCML) and gait patterns (DMRT3), several putative target genes related to embryonic morphogenesis (HOXB), energy metabolism (IGFBP-1, IGFBP-3), hair follicle morphogenesis (KRT25, KRT27, INTU) and autophagy (RALB) were highlighted. Furthermore, genes were pinpointed which might be involved in environmental adaptation of specific habitats (UVSSA, STXBP4, COX11, HLF, MMD).

Selection signatures in four German warmblood horse breeds: Tracing breeding history in the modern sport horse

The study of selection signatures helps to find genomic regions that have been under selective pressure and might host genes or variants that modulate important phenotypes. Such knowledge improves our understanding of how breeding programmes have shaped the genomes of livestock. In this study, 942 stallions were included from four, exemplarily chosen, German warmblood breeds with divergent historical and recent selection focus and different crossbreeding policies: Trakehner (N = 44), Holsteiner (N = 358), Hanoverian (N = 319) and Oldenburger (N = 221). Those breeds are nowadays bred for athletic performance and aptitude for show-jumping, dressage or eventing, with a particular focus of Holsteiner on the first discipline. Blood samples were collected during the health exams of the stallion preselections before licensing and were genotyped with the Illumina EquineSNP50 BeadChip. Autosomal markers were used for a multi-method search for signals of positive selection. Analyses within and across breeds were conducted by using the integrated Haplotype Score (iHS), cross-population Extended Haplotype Homozygosity (xpEHH) and Runs of Homozygosity (ROH). Oldenburger and Hanoverian showed very similar iHS signatures, but breed specificities were detected on multiple chromosomes with the xpEHH. The Trakehner clustered as a distinct group in a principal component analysis and also showed the highest number of ROHs, which reflects their historical bottleneck. Beside breed specific differences, we found shared selection signals in an across breed iHS analysis on chromosomes 1, 4 and 7. After investigation of these iHS signals and shared ROH for potential functional candidate genes and affected pathways including enrichment analyses, we suggest that genes affecting muscle functionality (TPM1, TMOD2-3, MYO5A, MYO5C), energy metabolism and growth (AEBP1, RALGAPA2, IGFBP1, IGFBP3-4), embryonic development (HOXB-complex) and fertility (THEGL, ZPBP1-2, TEX14, ZP1, SUN3 and CFAP61) have been targeted by selection in all breeds. Our findings also indicate selection pressure on KITLG, which is well-documented for influencing pigmentation.

The horse Y chromosome as an informative marker for tracing sire lines

Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.

Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis

The analysis of single-nucleotide polymorphisms (SNPs) has proven to be advantageous for addressing variation within samples of highly degraded or low-quality DNA samples. This is because only short fragments need to be amplified to analyze SNPs, and this can be achieved by multiplex PCR. Here, we present a sensitive method for the targeted sequencing of SNP loci that requires only small amounts of template DNA. The approach combines multiplex amplification of very short fragments covering SNP positions followed by sample barcoding and next-generation sequencing. This method allows generation of data from large sample sets of poorly preserved specimens, such as fossil remains, forensic samples, and museum specimens. The approach is cost-effective, rapid, and applicable to forensics, population genetics, and phylogenetic research questions.

Decline of genetic diversity in ancient domestic stallions in Europe

Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.

Coat colour adaptation of post-glacial horses to increasing forest vegetation

Wild horses unexpectedly survived terminal Pleistocene megafaunal extinctions until eventual European extirpation in the twentieth century. This survival is tied to either their occurrence in cryptic open habitats or their adaptation to forests. Our niche modelling inferred an increasing presence of horses in post-glacial forests, and our analysis of ancient DNA suggested significant selection for black phenotypes as indicating adaptation to forests.