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Horses
#1
My father, grandparents, great-grandfather, uncles, cousins, etc were or are all deeply involved in riding and buying and selling horses, mostly quarter horses, so the history of horses is very interesting to me. I created this thread so information about genetics of horses can be posted.
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#2
Domestic horses promoted rapid and long-distance human mobility from ~2,200 BCE

https://www.ebi.ac.uk/ena/browser/view/PRJEB71445

2024-03-20 

Project: PRJEB71445
Horses revolutionized human history with fast mobility. However, the timeline between their domestication and widespread integration as a means of transportation remains contentious. Here, we assemble the largest collection of ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged ~2,200 BCE, through close kin mating and shortened generation times. It followed a severe domestication bottleneck starting not earlier than ~2,700 BCE, and coincided with a sudden expansion across Eurasia that ultimately replaced nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly-held narrative of large horse herds accompanying the massive migration of steppe peoples into Europe ~3,000 BCE and earlier. We detect significantly shortened generation times at Botai ~3,500 BCE, a settlement from Central Asia associated with corrals and a subsistence economy centered on horses. This supports local horse husbandry before the rise of modern domestic bloodlines.
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#3
Horse domestication as a multi-centered, multi-stage process: Botai and the role of specialized Eneolithic horse pastoralism in the development of human-equine relationships

HYPOTHESIS AND THEORY article
Front. Environ. Archaeol., 24 April 2023
Sec. Zooarchaeology
Volume 2 - 2023 | https://doi.org/10.3389/fearc.2023.1134068

Alan K. Outram*
Department of Archaeology and History, University of Exeter, Exeter, United Kingdom

For over a decade there has been general, but not universal, consensus that the earliest known evidence for horse husbandry was at Eneolithic Botai, Kazakhstan, circa 3,500 BCE. Recent ancient genomic analyses, however, indicate that Botai is not the source of modern domestic horse stock (DOM2 lineage), but is instead related to the Przewalski clade of horses. DOM2 appears to instead to have emerged in early Bronze Age (mid 3rd Mill. BCE) in the Pontic-Caspian steppe, and spread quickly replacing other horse lineages after approximately 2,000 BCE. Whilst the specific evidence for earlier husbandry at Botai is not diminished by this evidence, it has broken the consensus regarding the early stages of horse domestication, with some now viewing it as a later event. This paper argues that domestication is rarely an event, but instead a process that is ongoing. The case is made for a “prey pathway” initial phase of domestication in multiple localities during the Eneolithic, which was based around local subsistence pastoralist niche construction. This took different forms due to the presence or absence of ruminant domestic stock in the Eastern European or Central Asian steppes, respectively. Whilst “push” factors likely played a part in the development of horse specialist pastoralism at Botai, it is suggested that “pull” factors accelerated the spread of DOM2 lineages, replacing others, in the later Bronze Age. The DOM2 spread was principally driven, not by local subsistence needs, but wider social, economic and military desirability of equestrianism. The long-term process of horse domestication continues in modernity with major breed changes caused first by the post-medieval agricultural revolution and, more currently, the desire for sporting achievement.
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#4
This one is about cattle. Since horses are heavily used for cattle I feel this should be included.

Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas
Delsol, N., Stucky, B.J., Oswald, J.A. et al.
Sci Rep 13, 12444 (2023).
https://doi.org/10.1038/s41598-023-39518-3

Published01 August 2023

Abstract

Before the arrival of Europeans, domestic cattle (Bos taurus) did not exist in the Americas, and most of our knowledge about how domestic bovines first arrived in the Western Hemisphere is based on historical documents. Sixteenth-century colonial accounts suggest that the first cattle were brought in small numbers from the southern Iberian Peninsula via the Canary archipelago to the Caribbean islands where they were bred locally and imported to other circum-Caribbean regions. Modern American heritage cattle genetics and limited ancient mtDNA data from archaeological colonial cattle suggest a more complex story of mixed ancestries from Europe and Africa. So far little information exists to understand the nature and timing of the arrival of these mixed-ancestry populations. In this study we combine ancient mitochondrial and nuclear DNA from a robust sample of some of the earliest archaeological specimens from Caribbean and Mesoamerican sites to clarify the origins and the dynamics of bovine introduction into the Americas. Our analyses support first arrival of cattle from diverse locales and potentially confirm the early arrival of African-sourced cattle in the Americas, followed by waves of later introductions from various sources over several centuries.
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#5
The origins and spread of domestic horses from the Western Eurasian steppes.
Librado, P., Khan, N., Fages, A. et al.
Nature 598, 634–640 (2021).
https://doi.org/10.1038/s41586-021-04018-9

Published 20 October 2021

Abstract

Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2,3,4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture
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#6
Refining the evolutionary tree of the horse Y chromosome.
Bozlak, E., Radovic, L., Remer, V. et al.
Sci Rep 13, 8954 (2023)
https://doi.org/10.1038/s41598-023-35539-0

Abstract

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski’s horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.
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#7
I come from a horse racing family, many generations. Before the Internet, they'd sit around for hours reading Sires and Dams which was the genealogy and race performance of horses from the past. They'd try to figure out who to breed with who to produce a viable racing offspring.

They'd probably kill for what we can do with genetics today.
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#8
My dad's family are cowboys. They migrated from Texas to Montana before the railroad was finished, as cattle were still driven during the summers to Montana, then sold off on the track back to Texas, which lead many families to migrate to Montana to establish ranches. Once the railroad was finished, a lot of the the ranches went under, as there was no need to drive the cattle like they used to. My dad was actually working on horseback on a ranch in Wyoming when his draft letter came for Vietnam, and was about two days out in the back country. My grandfather had to drive out to the ranch and then take a horse out to find him and give him his draft notice. One could say that the relationship between man and horse is almost as magical as it is with dogs.
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#9
My sister had a horse when we were teenagers, and I used to ride her horse when she wasn't. It was a lot of fun. He was a very gentle gelding named Chief, so not real dangerous or challenging, but he could do a furious gallop when urged to do so.

Some time back, we got horseback riding lessons for our youngest daughter. While she was grooming her horse in the barn, which took a lot of time, I made friends with a big old Clydesdale who was blind. I used to pet him and talk to him. He was gigantic. Whenever I would momentarily stop petting him, he would nudge me to start petting him again, often nearly knocking me over. 

Horses are great.
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Let us now praise famous men, and our fathers that begat us.

- Wisdom of Sirach 44:1
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#10
Has there been any studies about the origins of the "Oriental horse"? The type would eventually become Arab, Akhal-Teke, Barb, etc.
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#11
(05-13-2024, 12:42 PM)Necrontyr Wrote: Has there been any studies about the origins of the "Oriental horse"? The type would eventually become Arab, Akhal-Teke, Barb, etc.

That's a good question. If I remember correctly one or more of those are mentioned in at least one of the previously mentioned studies. I'll try to remember to search when I have time.
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#12
Having been around and messed with horses myself, I am surprised by the "scholars" who think that Yamnaya did not or could not have ridden horses.

Jumping on a horse's back seems like a natural human thing to me. We even jumped on the backs of cows, but that was always boring (we knew enough not to try that with bulls, which would have been exciting).

I think Yamnayans rode horses but acted as "mounted infantry". In other words, they rode horses to a raid, but then dismounted and fought on foot. When the fighting or looting was over, they remounted and rode away. Locals without horses couldn't catch them.
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Let us now praise famous men, and our fathers that begat us.

- Wisdom of Sirach 44:1
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#13
(05-13-2024, 06:21 PM)rmstevens2 Wrote: We even jumped on the backs of cows, but that was always boring (we knew enough not to try that with bulls, which would have been exciting).

My father, myself, and my cousins also rode bulls.  One cousin does nothing but rent bulls for bull riding events. He doesn't even like riding horses. His life revolves around bull riding. The rest of the family is more into horses. I don't like putting too much personal info otherwise I would get into more detail about the events and how renowned my relatives were.
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#14
(05-13-2024, 12:42 PM)Necrontyr Wrote: Has there been any studies about the origins of the "Oriental horse"? The type would eventually become Arab, Akhal-Teke, Barb, etc.

These are the studies that I was able to find -

Remer, V.; Bozlak, E.; Felkel, S.; Radovic, L.; Rigler, D.; Grilz-Seger, G.; Stefaniuk-Szmukier, M.; Bugno-Poniewierska, M.; Brooks, S.; Miller, D.C.; et al. Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses. Genes 2022, 13, 229. https://doi.org/10.3390/genes13020229 

Abstract
The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.

Results from that study were used for the study in post #6 I suggest reading both of them and reading all of the supplementary information if it exists and looking up the reference studies. Here are two of those -

Radovic, L.; Remer, V.; Krcal, C.; Rigler, D.; Brem, G.; Rayane, A.; Driss, K.; Benamar, M.; Machmoum, M.; Piro, M.; et al. Y Chromosome Haplotypes Enlighten Origin, Influence, and Breeding History of North African Barb Horses. Animals 2022, 12, 2579. https://doi.org/10.3390/ani12192579

Abstract
In horses, demographic patterns are complex due to historical migrations and eventful breeding histories. Particularly puzzling is the ancestry of the North African horse, a founding horse breed, shaped by numerous influences throughout history. A genetic marker particularly suitable to investigate the paternal demographic history of populations is the non-recombining male-specific region of the Y chromosome (MSY). Using a recently established horse MSY haplotype (HT) topology and KASP™ genotyping, we illustrate MSY HT spectra of 119 Barb and Arab-Barb males, collected from the Maghreb region and European subpopulations. All detected HTs belonged to the Crown haplogroup, and the broad MSY spectrum reflects the wide variety of influential stallions throughout the breed’s history. Distinct HTs and regional disparities were characterized and a remarkable number of early introduced lineages were observed. The data indicate recent refinement with Thoroughbred and Arabian patrilines, while 57% of the dataset supports historical migrations between North Africa and the Iberian Peninsula. In the Barb horse, we detected the HT linked to Godolphin Arabian, one of the Thoroughbred founders. Hence, we shed new light on the question of the ancestry of one Thoroughbred patriline. We show the strength of the horse Y chromosome as a genealogical tool, enlighten recent paternal history of North African horses, and set the foundation for future studies on the breed and the formation of conservation breeding programs.

Cosgrove, E.J., Sadeghi, R., Schlamp, F. et al. Genome Diversity and the Origin of the Arabian Horse. Sci Rep 10, 9702 (2020). https://doi.org/10.1038/s41598-020-66232-1
 
Abstract
The Arabian horse, one of the world’s oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region. Also, contrary to popular belief, we could detect no significant genomic contribution of the Arabian breed to the Thoroughbred racehorse, including Y chromosome ancestry. However, we found strong evidence for recent interbreeding of Thoroughbreds with Arabians used for flat-racing competitions. Genetic signatures suggestive of selective sweeps across the Arabian breed contain candidate genes for combating oxidative damage during exercise, and within the “Straight Egyptian” subgroup, for facial morphology. Overall, our data support an origin of the Arabian horse in the Middle East, no evidence for reduced global genetic diversity across the breed, and unique genetic adaptations for both physiology and conformation.
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