by Beth Minnich, with Michael Bowling

Y Chromosome Ancestry in the Arabian Horse

by Beth Minnich with Michael Bowling

“The Arabian horse possesses a rich history, intimately connected to the physical environment of its ancestral homeland and culture of Bedouin caretakers who nurtured its development. It is unclear when and where the horse was introduced to the area historically known as ‘Arabia’. Yet, from a regional proto-Arabian that was developed over millennia, the nomadic horse breeding tribes cultivated the foundation of the breed now known as the Arabian horse.

From the mapping of the horse genome in 2007, genomic tools were developed that provide access to information offering expanded perspectives for viewing breed ancestry. These new observations provide a gateway to deeper understanding of the Arabian breed, helping to connect the threads of culture, history, and genetics. With these threads, we can weave a more detailed tapestry depicting the origins of the Arabian horse, to help guide preservation efforts of this iconic animal.”

If these words look familiar, they are the opening to “Genetic Diversity & Complex Ancestry in the Arabian Horse” (May 2021, Khamsat), which introduced findings from the scientific paper “Genome Diversity and the Origin of the Arabian Horse” (Cosgrove, et al. Scientific Reports, June 2020).1,2 Genomic studies are bringing about new ways of viewing DNA history of the Arabian horse and other breeds, helping to connect the past to the present. For a brief recap of this research, the main summary points across the study include: 1. The Arabian breed has a unique genetic profile marked by broad variation and underlying complex ancestry consistent with an ancient origin: • Globally, Arabian horses display a large degree of genetic diversity, more than many other breeds of horse. • Registered Arabian horses were identified in the Middle East that carry expanded genetic and phenotypic diversity. • Straight Egyptians have a distinct genetic signature and less genetic variation than other Arabian bloodline groups considered. 2. Genomic regions were identified that may be associated with important traits of the Arabian horse, such as head shape and athletic ability. 3. Little overall genetic similarity of Arabians to Thoroughbreds was detected, including lack of evidence for Arabian stallion Y chromosome ancestry. 4. Strong evidence was found for recent interbreeding of Thoroughbreds with Arabians used for flat racing.

As we continue the journey to better understand how DNA can assist in unlocking the mysteries of breed history and ancestry, we will take an introductory walk through the Y chromosome component of the study. To help set the stage for digesting this material, there will also be a brief overview on inheritance and ancestry of the equine Y chromosome. Important work from the lab of Dr. Barbara Wallner, from the Institute of Animal Breeding and Genetics at the University of Veterinary Medicine, Vienna, will also be included.

The goal of this article is to introduce equine Y chromosome research, with a focus on what has been learned (to date) about Y chromosome ancestry in the Arabian horse. Using modern scientific technology, we can gain greater understanding of the fascinating history of the Arabian horse. Keeping in mind ‘discovery’, by its nature, can yield unexpected results; some of the findings to be discussed are controversial. At the same time, good science should lead to more questions, and as we learn more about the background of the Arabian horse, further questions will arise. The additional perspective offered, alongside a basic explanation of how the conclusions have been drawn, will hopefully provide valuable context as work continues. This is important for the interpretation of data by researchers, as well as for development of narratives shared within the Arabian horse and broader equine communities. Y Chromosome Basics3,4

To establish a foundation to work from, let’s first review some Y chromosome basics. [Note: to assist with terminology, italicized terms appear in a glossary on page 18.]

Of a horse’s 64 chromosomes, two are sex chromosomes which are designated as X and Y. These chromosomes determine the sex of a horse, with females inheriting two copies of the X chromosome and males inheriting one X chromosome and one Y chromosome. Dams can only pass along an X chromosome to their offspring, and the Y chromosome can only be passed by the sire. But, because a stallion can contribute either an X or Y chromosome, his contribution is what determines the sex of offspring; an X chromosome from the sire produces a filly, while a Y chromosome results in a colt.

Though perhaps the smallest chromosome in the mammalian genome, the Y chromosome is one of the most distinct regions. Comprising <2% of the total haploid genome, the Y chromosome is male specific, and the horse Y chromosome contains 52 genes. Some of these genes have important functions, playing a role in the development of male characteristics, spermatogenesis and male fertility. For comparison, the X chromosome comprises about 5% of the total haploid genome, is the 3rd largest chromosome, and is estimated to contain >800 genes.

The Y chromosome structure includes two regions: 1) a pseudoautosomal region (PAR), the area where the X and Y chromosomes pair during meiosis, and 2) a Male-specific-Y region (MSY), that does not match with the X chromosome. While the PAR is shared between the X and the Y chromosome, the MSY region is present only on the Y chromosome. This article will focus on the MSY, which is passed from father to son without alteration (except for rarely occurring spontaneous mutations or gene conversions.)

Y Chromosome Diversity4-8

In previous studies, autosomal microsatellite markers and single nucleotide polymorphisms (SNPs), along with mtDNA, have been used to study the genetic diversity and origins of horse breeds, including the Arabian. It is now possible to utilize alterations in the Y chromosome to expand on these studies. Using MSY genealogies, identification of paternal ancestry and information about horse breeding history can be obtained.

Research shows there is a significant amount of genetic diversity in horse mtDNA, but little Y chromosome diversity in the modern horse. Because modern horse Y chromosome lineages are distinct from the Przewalski’s horse, and prehistoric horses show more diversity than modern horses, the low MSY diversity is not a result of a low mutation rate. In fact, several studies show a lot of Y chromosome diversity until 700-1,000 years ago. Horses and humans have shared a close connection going back thousands of years. Not surprisingly, when comparing the human historical record with significant changes in the horse genome, there is a direct relationship with the expansion of human cultures spanning from the Early Bronze Age into the Middle Ages.

In more recent history, strategic breeding in the past 300 years has resulted in the most dramatic change in the genetic make-up of horses. As noted in Horse Genetics, 3rd Edition (Bailey, Brooks) … “About that time, it appears stallions from the Middle East became popular in breeding programs throughout the world. One stallion must have been particularly popular and had a large impact on European horse populations. Extensive use of descendants of this stallion led to the modern disappearance of other Y chromosomes in most breeds. Only breeds in remote regions, such as Iceland, Norway, and North Eastern Asia preserved the ancient variants for the Y chromoThe Y chromosome is paternally inherited, making the MSY ideal for tracking genetic history through the tail male line. This same principle applies to mitochondrial DNA (mtDNA), which is inherited maternally and used for tracking genetic history through the tail female line. some.” In short - domestication, in combination with a limited number of founder stallions (extreme founder effect), has led to a significant reduction in Y chromosome diversity, as compared to mtDNA. Haplogroups and Haplotypes With application of genomic tools, natural variations (mutations) trace ancestry as they are passed in the DNA from one population to another over time. On the MSY these variations are classified into ‘haplotypes’ and ‘haplogroups’. Haplotype (HT) is short for ‘haploid genotype’ and is a group of closely linked DNA variations on one chromosome which are often inherited together. A haplogroup (HG) is a group of similar haplotypes which share a common ancestor. Through identification of HTs and HGs, a horse Y chromosome phylogenetic tree can be created to view relationships between different groupings and breeds. In 2013, research by Dr. Barbara Wallner in Vienna, Austria identified six Y chromosomal haplotypes for domestic horse breeds, identified as HT1, HT2, HT3, HT4, HT5, HT6, and two for the Przewalski horse (HTprz1 and HTprz2)9 [see Figure 1]. Each of the domestic horse HTs are separated by only one novel variant or gene conversion step, so there are no deep branches in the tree involving many genetic changes.

Figure 1: 2013 Network of Modern Domestic and Przewalski Horse Haplotypes.

Source: Wallner, et al. Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds. PLoS One. 2013;8(4):e60015. http://creativecommons.org/licenses/by/4.0/

Glossary of Terms

1. Allele - one of two or more forms of a gene or a genetic locus, typically differing in their DNA sequences. 2. Autosomal - residing on or due to chromosomes that are not the sex (X or Y) chromosomes. 3. Chromosome - threadlike structure that carries genetic information (DNA). Chromosomes come in pairs; horses have 31 pairs of autosomes (non-sex chromosomes) and one pair of sex chromosomes (X and Y). The sire and dam each contribute one copy of each chromosome. 4. Clustering - refers to patterns of relative genetic similarity among individuals and populations. 5. Deletion - a type of genetic variant in which a part of a chromosome or a sequence of DNA is lost during DNA replication.

Deletion size can vary from a single base to an entire piece of a chromosome. 6. Fixation - when an allele reaches 100% frequency in a population. 7. Founder Effect - the reduction in genetic variation that results when a new population is established by a very small number of individuals from a larger population. 8. Gene conversion - the replacement of one part of a chromosome with a copy of the homologous part on the sister chromosome – e.g., the transfer of a short sequence from the homologous, but non-recombining region on the X- to the Y chromosome. 9. Genetic diversity - genetic variability within a species or population. 10. Genetic variation - differences in alleles of genes between individual members of a population, or the frequency in which the various genetic variants are expressed. 11. Haploid – a set of one chromosome from each homologous pair. The haploid number of chromosomes is carried by gametes (sperm and eggs). 12. Haplogroup (HG) - a group of similar haplotypes which share a common ancestor. 13. Haplotype (HT) - a group of closely linked DNA sequences on one chromosome which are often inherited together. 14. Indel (insertion–deletion mutation) – the insertion and/or deletion of nucleotides into genomic DNA. 15. Insertion - the addition of one or more nucleotide base pairs into a DNA sequence. 16. Meiosis – the method of cell division during the production of gametes (sperm and eggs). 17. Microsatellite markers – also called short tandem repeats (STRs), they are segments of DNA where the nucleotide sequence repeats. Microsatellite markers are one type of genetic marker available to measure genetic variation. 18. Mitochondrial DNA (mtDNA) - the small circular chromosome found inside mitochondria; passed from mother to offspring. 19 Mutation – a synonym of genetic variant; a spontaneous mutation is a ‘naturally’ occurring mutation in the absence of a mutagen, such as radiation or a chemical substance. 20. Phylogenetic tree – a diagrammatic representation showing the relationships among various groups that have a common ancestor. 21. Private variants - mutations that have occurred in the line being tested, but not yet in other lines. 22. Single nucleotide polymorphism (SNP) – a DNA sequence variation that occurs when a single nucleotide (A, T, C, or G) in the genome sequence is altered. 23. Tail female line - the continuous, unbroken chain of females and their progression through the generations tracking on the dam side only. 24. Tail male line - the continuous, unbroken chain of males and their progression through the generations tracking on the sire side only. 25. Variant – an alteration in DNA sequence often used synonymously with allele. There are genetic variants in the individual nucleotides (single nucleotide polymorphisms or SNPs) as well as larger variations, such as deletions, insertions, and copy number variations. 26. Whole genome sequence - the complete DNA sequence of an individual.

Domestic horse haplotypes are clearly separated from the Przewalski’s horse. The ancestral haplotype in domestic horses was identified as HT1, with HT2, HT4, HT5 and H6 stemming from HT1 at various time points after domestication, and HT3 stemming from HT2 around 1,800 CE. HT1, as the most widespread, was distributed across almost all breeds. HT2 and HT3 are widely distributed at high frequencies among modern European horse breeds, though HT2 is not found in northern European breeds or horses from the Iberian Peninsula. HT4-6 are found exclusively, and in high frequency, in three local northern European breeds; HT4 in Icelandic horses, HT5 in Norwegian Fjord horses, and HT6 in Shetland ponies. In 2017, Dr. Wallner added whole genome sequencing of a further 52 male horses from 21 different breeds to her studies of the Y chromosome.10 From this, an additional 49 SNPs and three indels were discovered, resulting in identification of new haplotypes; increasing the number to 24 found in 57 different breeds. With this expansion also came a change in naming conventions [see Table 1]. With these HTs, the Central European and North American breeds cluster in a grouping designated as the ‘crown-haplogroup’ [see Figure 2]. Of the four ‘crown branches’ (A, L, S, and T), the A branch is found mainly in Original Arabians, with some Arabian samples clustered at the basal node of T [see Figure 3] in a grouping that would later be identified as HT Ta. The A and T branches will be discussed in greater detail further into this article.

In 2018, work by Dr. Sabine Felkel in the Wallner lab studied an additional 52 stallions from European, American, and Asian

Table 1: Changes in Haplogroup Naming Table 1: Changes in Haplogroup Naming

2013 → 2017

HT1 Ao, Ad, L, S HT2 Ta, Tu and all Tb except Tb-dW1 HT3 Tb-dW1 HT4 I HT5 Nf HT6 Ns

Figure 2: 2017 Horse MSY Phylogenetic Tree. HT-defining mutations are indicated on branches in grey. Haplogroups are distinguished by colors. Source breeds are listed for each haplogroup, with number of samples per breed in parentheses. Source: Wallner, et al. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions. Curr Biol. 2017 Jul 10;27(13):2029-2035.e5. doi: 10.1016/j.cub.2017.05.086.

Crown Haplogroup

breeds. From this group of samples, 101 new variants were detected, with 61 of these variants found only in Asian breeds. This work expanded the number of haplotypes in domestic horses to 42.12

The following year, their continued work increased the domestic horse haplotype count to 71, determined by 740 variants.13 Within the crown-group, 58 HTs (almost double the previous number) were identified across three major haplogroup branches: the branches include the previously described HG A and T, and a newly uncovered HG H (replacing the previously identified L and S groups) containing Iberian lines and a North African Barb Horse [see Figure 5]. The A and T Branches

With this short overview of the identification of horse Y chromosome haplogroups in hand, let’s take a closer look at the groups most relevant to the Arabian horse – the A and T branches. To better comprehend the mutations in the A and T haplogroups, see Table 2 and Figure 4 in sidebar “Haplotype Identification”. Arabian Haplotypes1,10,11

The Ao and Ta haplotypes have been designated as Arabian breed HTs [see Figure 5]. Derived from “Original Arabians”, the Ao grouping was named for initially genotyped Original Arabians. At the time HT Ao was named, it appeared to be specific for Arabians and was the only haplotype found in the Arabian breed.

However, as sample numbers increased, some Arabians were found to cluster at the root of the T branch, but distinctly separate from the Tu and Tb haplogroups. This discovery resulted in creation of a new haplotype, named Ta, being assigned to this group of horses. Dating of the Ta split is estimated at around 800 CE, shortly after formation of the crown-group in 500 CE. These two different and distantly related haplogroups have led to speculation by some that HT Ta horses are incorrectly identified as purebred Arabians. For additional perspective on why Ta is considered an Arabian haplotype, along with Ao, the following points are important to include in the discussion: • To date, the Ta haplotype has been found only in Arabian horses. • The Arab Bedouin tribes defined ‘Arabian horse’ and that definition was based on a framework steeped in their cultural values.

From a Bedouin perspective, the notion of breed purity is more cultural rather than biological.

Figure 3: MSY HTs Detected in 363 Purebred Horses of 57 Breeds. (A) The size of each circle reflects the sample size of each HT. Haplogroups with confirmed Original Arabian ancestry are indicated by a dotted green line, and those with English Thoroughbred ancestry are indicated in red. Mutations are given on the branches. (B) Relative frequency of MSY HTs in different breeds and groups of breeds. The number of samples for each group of breeds is given in parentheses.

Source: Wallner, et al. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions. Curr Biol. 2017 Jul 10;27(13):20292035.e5. doi: 10.1016/j.cub.2017.05.086.

o Several Ta sire line founders have backgrounds qualifying them as foundation horses in the Al Khamsa Roster — including Bairactar, Hamdani Semri, Mersuch, O’Bajan and Souakim.11 o The Bedouin perspective must be the primary consideration for defining ‘Arabian horse’, instead of working backward using modern genetic research as the determinant for breed identification of historical horses. • These two different haplotypes in Arabians can also be explained by source population substructures and the differences in the expeditions to Arabia (the region), regarding timing, location, tribes visited, horses available for purchase, and selection goals of expedition patrons.

Haplotype Identification

Categorizing haplotypes is based on discovery of mutations. As more horses are included in testing, study sample size increases, and the potential for unearthing newly detected mutations increases. As additional mutations are identified, new HTs are designated, we can examine the haplotypes with finer resolution, and the phylogenetic tree expands.

For a better visual explanation, the mutations associated with the HTs are shown on the branches in Figure 2 (grey letters). For a focus on the A and T branches, that are of most interest in Arabians, Table 2 and Figure 4 (shown below) detail the mutations associated with each of the currently known A and T haplotypes.11 Source: Eva Michaelis 2019 Master’s Thesis: Analysis of Arabian stallion lines with Y chromosomal markers. University of Veterinary Medicine Vienna.

Table 2: Ao and T Haplotypes with Corresponding Alleles.

Figure 4: 2018 Phylogenetic Tree Including Genetic Markers (shown in red) for A and T Branches.

Figure 5: 2019 Horse MSY Phylogenetic Tree. The Przewalski’s horses are shown in brown. Blueish clades correspond to early splitting Asian samples (O), Northern European breeds (N and I) and other autochthonous Asian samples (M, Y and J). The three clearly separated crown group clades are represented in pink (H), green (A) and orange (T) shades. Assigned haplogroups are shown on right.

Source: Felkel, et al. The horse Y chromosome as an informative marker for tracing sire lines. Sci Rep. 2019 Apr 15;9(1):6095. http://creativecommons.org/licenses/by/4.0/

The T Haplogroup10, 13

The T haplogroup was first detected in the Thoroughbred influenced breeds, hence the naming convention of ‘T’. Though as more horses were tested, non-Thoroughbred influenced breeds were identified in the T grouping and the nomenclature evolved. The HG T has four sub-branches, Ta (T Arabian), Tu (T Unknown), Tb-d (Thoroughbred-Darley) and Tb-o (Thoroughbred-Other). As already discussed, to date, HT Ta has been found only in the Arabian horse. The HT Tu has been identified in the Franches-Montagnes horse, a Swiss breed with no documented Thoroughbred paternal ancestry; as such, the Tu origin is currently unknown. The HG Tb, that over the past 300 years has been extensively spread by the Thoroughbred, has three sublines represented by the Darley Arabian (Tb-d), Godolphin Arabian (Tb-oB3b, was formerly Tb-g), and the Byerley Turk (Tb-oB1) [see Figure 6]. HT Tb-dW1 is specific to the Whalebone branch of the Darley Arabian sire line, tracing through the legendary racehorse Eclipse. The mutation responsible for this HT must have occurred either in the germline of Eclipse, his son Waxy, or grandson Pot8os (the sire of Whalebone), making this a haplotype of unique Thoroughbred origin.

Figure 6: Details of Haplogroup Tb. (a) Haplotype network of group Tb. Circle sizes correspond to the number of samples. Determining variants are given on branches. HTs derived from Darley Arabian are shown in red, Godolphin Arabian in orange, and Byerley Turk in yellow. (b) Pedigree reconstruction of English Thoroughbred descendants and the respective HTs. Dotted lines connect relatives where at least one ancestor is omitted.

Source: Felkel, et al. The horse Y chromosome as an informative marker for tracing sire lines. Sci Rep. 2019 Apr 15;9(1):6095. http://creativecommons.org/licenses/by/4.0/

Reconciling DNA with the Historical Record

Genomic studies are informative for documenting relationships, but human interpretation further defines the information. In other words, there is ‘data’, and then there is ‘interpretation of the data’. So, what happens when DNA appears to tell a different story from what is outlined in the historical record?

Commonly recited breed history regularly references Arabian influence in the Thoroughbred foundation stallions — the Byerley Turk, Godolphin Arabian, and Darley Arabian. Understandably, research indicating the three stallions are likely of Turcoman origin is unexpected and questioned. Granted, over the centuries the classification of these stallions has been fluid, with the Byerly being referred to as an Arabian or Turk, and the Godolphin as an Arabian or Barb. The exception is the Darley, who has been consistently referred to as an Arabian. v Of note – the Darley Arabian is identified with a source Bedouin tribe (Fid’an) and strain (Mu’niqi-Hadruj — which is an old strain). Thomas Darley has a documented history with the Fid’an Anazeh Bedouins near Palmyra. Unless this background information is shown to be incorrect, it should not be ignored or quickly dismissed. As discussed earlier, the Arab Bedouin tribes defined ‘Arabian horse’, so using DNA to determine breed identity of historical horses has limitations.

Nomenclature, especially in the era when these horses were imported, can be challenging to work through. Albeit history probably does overestimate the Arabian’s contribution to the founding of the Thoroughbred. With the longstanding debate on the history of Turcoman and Arabian horses, it is possible horses of either breed could have been identified as being of the ‘other’ breed. But before closing the door on this topic and reassigning all three stallions to Turcoman origin, there are a few points for consideration and further research: • Given the human history of the region, gene flow between the various horse populations (including the Arabian and Turcoman) would be expected. Shared ancestry could be the key for reconciling DNA findings with historical information. o As noted in the 2020 Cosgrove paper, “genomic markers do identify a small proportion of Thoroughbred ancestry shared with both modern Persian Arabian sub-groups and the Turkemen breed though the origins of this shared ancestry have yet to be discovered and are likely very old.” [Note: Turkemen refers to the present-day breed, descended from the extinct Turcoman horse] o In addition, with mtDNA of Arabian and Akhal-Teke horses being quite similar, it is possible the two breeds share common ancestry. o Historically, in all populations, there is a tendency for the loss of male lines. A population ancestral to both the Turcoman and the Arabian could have possessed an array of Y chromosomes, only a subset of which persists in the modern Arabian while others were transmitted to the Thoroughbred. • The modern Arabian horse is likely different from the population sampled in early Thoroughbred breeding: o The Arabian horse has experienced 400 years of selection with an unknown number of population bottlenecks due to wars and migrations. o With source populations varying in different time periods, horses exported from the region prior to the mid-1800’s were likely drawn from different tribal sources than those exported later. o The lack of evidence for modern Arabian stallion Y chromosome ancestry in the Thoroughbred could be the foundation stallions came from Arabian male lines that have since died out.

As additional horses are tested and focused historical context is added to the discussion, we will continue to learn more about the rich and fascinating genetic histories of these breeds.

Thoroughbred Founding Sires – Arabian or Turcoman?2,10

One of the conclusions drawn from the 2017 Wallner paper, is the HG Tb is likely of Turcoman origin; meaning the three Thoroughbred founder stallions, the Darley, Byerly and Godolphin were not Arabians. This finding is also described in the 2020 Cosgrove paper, in that little overall genetic similarity of Arabians to Thoroughbreds was detected, including lack of evidence for Arabian stallion Y chromosome ancestry. [see May 2021, Khamsat for perspective on DNA vs. the historical record1]

This conclusion is at odds with the extensively documented history of the Thoroughbred breed and raises the question - how was the determination of Turcoman origin made? From the DNA perspective: • The sub-branches of Tb (Tb-d, Tb-oB3b, and Tb-oB1) can be definitely attributed to the Thoroughbred, but the root Tb haplotype is also found in breeds (e.g., Hucul and Lipizzan) with no documented Thoroughbred ancestry. Historically used to refine the bone and structure of many modern breeds, the Arabian, Barb, and Spanish breeds do not carry HT Tb. As such, testing was expanded to include the Akhal-Teke (a breed considered a remnant of the now extinct Turcoman horse); with the results showing 81% of the tested Akhal-Tekes had the Tb haplotype. To address the question of how more recent infusion of Thoroughbred blood in the Akhal-Teke could impact these results — the researchers note the private clustering of the Tb-oB3a lineage (Akhal-Teke) suggests “an origin from a similar source population but

independent from the Thoroughbreds.” In other words, Thoroughbred infusion which occurred in the AkhalTeke in the early 1900’s would not account for this. • Other points raised include: 1) breeds influenced by Arabians carry either Ao or T haplotypes, not Tb, and 2) HG Tb is found in many European breeds with no documented Thoroughbred stallion ancestry; with support that Turcoman stallions influenced the development of these breeds provided by the geopolitical history of the region. All put together, the conclusion drawn from DNA is the HG Tb is likely of Turcoman origin.

But to go beyond DNA and expand the scope of this discussion — there are several questions that arise. In the age of genomic testing, what makes a historical breed identity ‘authentic’? How does DNA data influence development of narratives regarding horse breed history? What are the implications, especially for a breed identity directly tied to the culture of the people who developed it? For further context regarding these questions, see sidebar “Reconciling DNA with the Historical Record.” Tb Haplotypes in Arabians2

Perhaps the most emotive aspect of the 2020 Cosgrove paper involves identification of recent admixture of Thoroughbred genomic regions in some Arabian racehorses. To briefly summarize these results — Y chromosome haplotypes were examined for 10 racing Arabians and 29 non-racing Arabians. While all 29 of the non-racing samples carried one of the Y haplogroups associated with the Arabian breed (Ao-1, Ao-2, and Ta), only two of the 10 racing stallions carried any of these Arabian Y haplogroups. Five of the racing horses carried HG Tb-oB1 (Byerley Turk). As noted in the paper, “Tb-oB1* is found within a variety of breeds and lineages, including the Turkomen. It is possible these five horses may carry Y chromosomes derived from ancestors common to both racing Arabians and Thoroughbreds.” As such, hopefully the Tb-oB1 finding will become clearer as research continues, and we learn more about ancestral relationships between the ‘Oriental breeds’ and any shared ancestry.

Where things get contentious is with the three racing Arabian horses who carry HG Tb-dW1 (aka the ‘Whalebone haplotype’). As discussed earlier, this mutation occurred after the founding of the Thoroughbred stud book and is linked specifically to the Whalebone sire line. Further, the Tb-dW1 haplotype has not been reported in modern Arabians but is almost fixed in the Thoroughbred breed. In addition, large autosomal chromosomal blocks of Thoroughbred origin (totaling up to 62%) were detected in some racing Arabians. With the autosomal and Y chromosome data combined, this scenario is easier to interpret in that it suggests recent admixture of Thoroughbred blood in some Arabian horses. While this information raises many debates and questions about how this situation should be handled, that discussion falls outside the scope of this article. Identity in the Age of Ancestral DNA

This very condensed introduction to equine Y chromosome research is meant to act as a portal for further, more detailed discussion. With this information, a deep dive can begin into the Y chromosome haplotype and haplogroup representations in the Al Khamsa population. Although this research is specific to the tail male line, through this work we can enrich our understanding of the complexity and richness of the Arabian breed’s fascinating history.

While some of the results may be unexpected, DNA is not the entire story. DNA can help in connecting the past to the present, but the charismatic desert-Arabian horse should first and foremost be appreciated through the lens of the environment that shaped its development and the culture of its original custodian. This is a true journey of discovery, with the goal of this exploration being to grow our understanding and appreciation of the horse, the history, and the people — and how these relationships fit into our human experience.

Acknowledgements:

Special thank you to Dr. Barbara Wallner and Dr. Samantha Brooks, with great appreciation to Scott Benjamin for his continual inspiration.

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Wiley-Blackwell, Iowa. 4. Bailey and Brooks. Horse Genetics (3rd Edition). 2020, CABI,

Oxfordshire, UK. 5. Wallner, et al. (2003). Fixed nucleotide differences on the Y chromosome indicate clear divergence between Equus przewalskii and Equus caballus. Anim. Genet. 34, 453–456. 6. Lippold, et al. (2011). Discovery of lost diversity of paternal horse lineages using ancient DNA. Nat. Commun. 2, 450. 7. Librado, et al. (2015). Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments. Proc. Natl. Acad. Sci. USA 112, E6889–E6897. 8. Librado, et al. (2017). Ancient genomic changes associated with domestication of the horse. Science 356, 442–445. 9. Wallner, et al. Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds. PLoS One. 2013;8(4):e60015. 10. Wallner, et al. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions. Curr Biol. 2017 Jul 10;27(13):2029-2035.e5. 11. Michaelis, Eva. 2019 Master’s Thesis: Analysis of Arabian stallion lines with Y chromosomal markers. University of Veterinary Medicine Vienna. 12. Felkel, et al. Asian horses deepen the MSY phylogeny. Anim

Genet. 2018 Feb;49(1):90-93. doi: 10.1111/age.12635. 13. Felkel, et al. The horse Y chromosome as an informative marker for tracing sire lines. Sci Rep. 2019 Apr 15;9(1):6095.