Domestication of animals and plants - genetic history

[lpetrich]

Genetics research has been shedding light not only on human prehistory but that of the numerous animal and plant species that we have domesticated.

•  List of domesticated animals
•  List of domesticated plants
•  List of domesticated fungi and microorganisms

The first domestic-animal species is the dog, domesticated in the late Paleolithic, before the invention of agriculture. Since then, dogs have been bred into a variety of sizes and shapes, and bred for a variety of tasks, like herding, hunting, guarding, and catching rats. In fact, a century ago, biologists could not agree on which wild canids are dogs' ancestors. Wolves? Jackals? Both?

But sequencing and comparison of genes, especially with the massive gene sequencing of recent decades, has resolved that issue. Dogs are descended from gray wolves, a species widely distributed across the Northern Hemisphere, most likely from a now-extinct Asian subspecies.  Origin of the domestic dog

 

[lpetrich]

Here is some recent research.

How did dogs become our best friends? New evidence - BBC News

Researchers studied DNA from three dogs found at archaeological sites in Germany and Ireland that were between 4,700 and 7,000 years old.

The ancient canines share ancestry with modern European dogs.

By looking at the rates of change to the DNA from the oldest specimen, scientists were able to place the timing of the domestication of dogs to between 20,000 and 40,000 years ago.

...
By 7,000 years ago, they were pretty much everywhere, although they were not the kind of dogs that we would consider pets.

''They would likely have resembled dogs we today call village dogs, which are free-breeding that did not live in specific people's houses and have a similar look to them across the world," said Dr Veeramah.

Dogs likely became domesticated from living off of leftovers from human hunting. The BBC article states that village dogs in the Americas and Pacific islands are mostly descended from European dogs, but that might be a misunderstanding of some of the research, because I find otherwise in the sources that I've found.

 

[lpetrich]

Ancient genomes heat up dog domestication debate : Nature News & Comment

Genetic data show that the ancestors of all modern dogs split into two populations: one that gave rise to East Asian breeds and another that would become modern European, South Asian, Central Asian and African dogs. Yet researchers still can’t pin down when this split occurred. And they can’t agree on whether dogs were domesticated once or twice.

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The researchers estimate that dogs and wolves diverged genetically between 36,900 and 41,500 years ago, and that eastern and western dogs split 17,500–23,900 years ago. Because domestication had to have happened between those events, the team puts it somewhere from 20,000 to 40,000 years ago.

This makes the two-event hypothesis unnecessary, because what seems like two events was an early split after one event.

Ancient European dog genomes reveal continuity since the Early Neolithic | Nature Communications
Breed dogs are interspersed within village dogs.

The East Asian dogs include village dogs from South China, Taiwan, Vietnam, and Borneo, and also dingos (Australian feral dog), and Chinese breeds chow chow and shar pei.

From the paper, "The larger SNP array reference data set shows that village dogs primarily separate into five distinct geographic clusters: Southeast Asia, India, Middle East, Europe and Africa. Breed dogs fall mostly within European village dogs’ variation with the exception of basal or ‘ancient’ breeds"

Breeds like the saluki and Afghan hound, which diverged as part of the main Eurasian divergence.

Of some other breed dogs, the basenji is among the village dogs of Egypt and Sub-Saharan Africa, and the boxer is among the village dogs of Portugal and Lebanon.

 

[lpetrich]

The paper finds (golden jackal, (wolf, dog))

with dog: (South China village dogs, (Indian village dogs, (Neolithic European dogs, European village dogs)))

Some more recent work:

Pontus Skoglund on Twitter: "In this ancient dog DNA study by Anders Bergström et al., we show that already 11,000 years ago there were ≥5 different dog groups across the world. ..." / Twitter

In this ancient dog DNA study by Anders Bergström et al., we show that already 11,000 years ago there were ≥5 different dog groups across the world. https://science.sciencemag.org/content/370/6516/557

We then trace the history written in dog & human DNA together, through the Holocene to global dogs today.

We see no evidence of multiple origins of dogs with respect to global wolf populations today.

There is no evidence of wolf>dog gene flow, but substantial dog>wolf gene flow. This could suggest that genetics underlying wolf behaviour was difficult to maintain in human societies.

With the great diversity at 11,000 years ago, dog origins must be traced to earlier than that, during the Paleolithic.

However, in our view the geographic region of origin is still unknown, and ancient DNA highlights how this question is hard to resolve with modern variation.

New dogs came into Europe during the agricultural expansion, meeting previous dogs already there, but a cline of Neolithic dog variation was replaced at some point in the past 4,000 years by a homogenization of ancestry found in European dog breeds today.

We compare the patterns of dog and human ancient DNA, and see hints of different ancestry impacts of steppe dogs in Europe vs East Asia compared to humans, similarities between early Iranian and Levantine dogs not seen in humans, and links between the Levant and African dogs.

This was a team effort with many collaborators in archaeology and ancient DNA from many countries and institutes.

What factors were behind the domestication event itself? Combining archaeological identification of early canids with new ancient DNA techniques might help find out.

Thanks to the project including Anders Bergström @Greger_Larson @LrFrantz @FlinkLinus @love_dalen @AndersGother @bigskybioarch @ErikErsmark @ArchaeOphelie & all the others whose accounts I don't have.

Did PS mix up dog-wolf gene-flow directions?

I found this paper: Gene Flow between Wolf and Shepherd Dog Populations in Georgia (Caucasus) | Journal of Heredity | Oxford Academic
From the abstract: "The results of the study suggest that wolf–dog hybridization is a common event in the areas where large livestock guarding dogs are held in a traditional way, and that gene flow between dogs and gray wolves was an important force influencing gene pool of dogs for millennia since early domestication events."

Not surprisingly, some present-day breeds of dogs continue to look much like wolves, like German shepherds and huskies.

 

[lpetrich]

Origins and genetic legacy of prehistoric dogs | Science

Dog domestication was multifaceted

Dogs were the first domesticated animal, likely originating from human-associated wolves, but their origin remains unclear. Bergstrom et al. sequenced 27 ancient dog genomes from multiple locations near to and corresponding in time to comparable human ancient DNA sites (see the Perspective by Pavlidis and Somel). By analyzing these genomes, along with other ancient and modern dog genomes, the authors found that dogs likely arose once from a now-extinct wolf population. They also found that at least five different dog populations ∼10,000 years before the present show replacement in Europe at later dates. Furthermore, some dog population genetics are similar to those of humans, whereas others differ, inferring a complex ancestral history for humanity's best friend.

Science, this issue p. 557; see also p. 522
Abstract

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

It's paywalled, so this is all I can get.

 

[lpetrich]

Aurochsen may seem like poor candidates for domestication. They were big, strong, fast, agile, and dangerous. I look at descriptions of American-bison behavior, and I find an uncanny resemblance. Yet they were among the first animals domesticated, and they became the ancestors of domestic bovines.

Domestication of cattle: Two or three events?

Between the late Pleistocene and early Holocene, the most commonly occurring cattle species was the aurochs (Bos primigenius), ranging from northern Africa to both the Atlantic and Pacific coasts of Eurasia (Zeuner, 1963). This formerly widespread wild species recently became extinct, with the last recorded herd found in 1627 AD in Poland (Götherström et al., 2005). Similar to sheep and goats, archaeological and genomic evidence suggests that the ancestors of taurine cattle (Bos taurus) were domesticated from Bos primigenius primigenius in the Fertile Crescent during the Neolithic, more than 10,000 years ago (YA; Bruford, Bradley, & Luikart, 2003; Ajmone‐Marsan, Garcia, & Lenstra, 2010; MacHugh, Larson, & Orlando, 2017). However, approximately 1,500 years later a second domestication event took place in the Indus Valley from Bos primigenius nomadicus, separated from the taurine branch ~250–330,000 YA, eventually giving rise to the extant indicine cattle (Bos indicus), often also termed zebu cattle (Loftus, MacHugh, Bradley, Sharp, & Cunningham, 1994).

Despite support for the extant distribution of cattle arising from two main domesticated lineages, a third domestication event has been hypothesized to have occurred in north‐east Africa about 8,000–9,000 YA, giving rise to the divergent African taurine cattle.

The authors then compared the genes of African bovines to European and Indian ones and found that this third domestication is an unnecessary hypothesis, that those northeast African bovines were already-domesticated European ones from the Middle East.

Indian cattle likely got into Africa by being taken across the Strait of Hormuz into southern Arabia, then across the Bab el Mandeb Strait to East Africa.

 

[lpetrich]

Taurine cattle = European ones, from the Middle East
Indicine cattle = Indian ones, from the Indus Valley

Modern Taurine Cattle Descended from Small Number of Near-Eastern Founders | Molecular Biology and Evolution | Oxford Academic

We report mtDNA sequences from 15 Neolithic to Iron Age Iranian domestic cattle and, in conjunction with modern data, use serial coalescent simulation and approximate Bayesian computation to estimate that around 80 female aurochs were initially domesticated. Such a low number is consistent with archaeological data indicating that initial domestication took place in a restricted area and suggests the process was constrained by the difficulty of sustained managing and breeding of the wild progenitors of domestic cattle.

So European bovines are descended from a single herd of Middle Eastern aurochsen.

Genetic origin, admixture and population history of aurochs ( Bos primigenius ) and primitive European cattle | Heredity - "We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations."

 

[lpetrich]

• The taming of the pig took some wild turns | Science | AAAS
• Insights into early pig domestication provided by ancient DNA analysis | Scientific Reports
• Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe | PNAS

From the first one,

For one, archaeological evidence now indicates that pigs were domesticated at least twice, once in China’s Mekong valley and once in Anatolia, the region in modern-day Turkey between the Black, Mediterranean, and Aegean seas. For another, a 2007 study of genetic material from 323 modern and 221 ancient pigs from western Eurasia suggests that pigs first came to Europe from the Near East, but that Europeans subsequently domesticated local wild boar, which seemed to replace those original pigs.

...
Domesticated animals have a large number of wild ancestors, Frantz, Groenen, and their colleagues report online today in Nature Genetics. Their data support the idea that pigs originated in two places. But Europe’s modern pigs are mongrel mixes derived from multiple wild boar populations. Some of their genetic material does not match any wild boar DNA collected by the researchers, so they think that at least some ancestors came from either an extinct group or from another group in central Eurasia. This anomaly suggests that pigs were herded from place to place, where they mated with this “ghost” population. Moreover, at one point—most likely in the 1800s, when Europeans imported Chinese pigs to improve their commercial breeds—a little Asian pig blood entered the mix.

So as farmers went into Europe, they bred local wild pigs with their domestic pigs, to the point that most of their ancestry of European domesticated pigs became European wild pigs.

 

[Swammerdami]

Genetic studies of domesticated animals can tell a story about humans as well. For example, IIRC the cows of Tuscany are closer to Anatolian cows genetically than they are to other cows in West Central Europe. This has been used as evidence that the Etruscans immigrated (with their cattle) from the Eastern Mediterranean to Italy, presumably as part of the Sea Peoples migrations after the fall of the Hittite Empire.

If non-humans can also be said to "domesticate" creatures, then millions of species are "domesticated." For example the delicious  Termitomyces robustus mushrooms only sprout when grown by termites. Where I live, villagers keep track of these mushrooms and when the weather is just right for sprouting, take time off from other duties to go searching for the mushrooms in hills and forests.

 

[lpetrich]

History of the Horse: Ancient DNA Reveals Lost Lineages | Discover Magazine

The history of the horse is not quite what we thought: Among the findings of an unprecedented analysis of ancient DNA, today's Icelandic ponies (above) are some of the last vestiges of a European lineage nearly wiped out by horses from Persia. (Credit: G. Tarlach) In the largest-ever ancient DNA study of its kind, researchers have pieced together the history of the horse: It's an epic saga sprawling across continents and 5,000 years of evolution and domestication, and yes, it has plot twists. Among the finds: researchers uncovered two lost lineages of the animal on opposite ends of Eurasia and determined that the modern horse is very different than even its recent ancestors, thanks in part to geopolitics. The scope of the study included 278 samples of genetic material from more than 40,000 years of the horse family tree. In addition to the two known living branches, the domestic horse and the Central Asian Przewalski's horse, the team discovered two now-extinct lineages that are not closely related to any living horse. One of the newly discovered lineages called Siberia home; the other was native to the Iberian Peninsula. The team behind the new research compared the lost horse lineages to Neanderthals, Homo sapiens' closest evolutionary kin. But the horses lasted longer than Neanderthals: Both the Siberian and Iberian populations went extinct only in the last 4,000 or so years.

Horses have been domesticated for the last 5,000+ years, and the oldest known word for that animal is not recorded but reconstructed in Proto-Indo-European: *ek'wos

But the new research found that some of the traits we associate most closely with horses have only recently evolved. For example, the genetic variations associated with locomotive speed appear to be the product of selective breeding only in the last 1,000 or so years.

...
The genome-wide analysis also found that established populations of European horses were nearly wiped out in the 7th to 9th centuries thanks to the arrival and spread of horses with a Persian pedigree. The genetic switcheroo was likely due to waves of Islamic armies and explorers fanning out from the southwestern corner of Asia at the time. Horses originating in Persia eventually spread far beyond the battle lines through trade routes. Central Asian domestic horse populations also experienced an influx of Persian genes. Today, the last vestiges of the European lineage of horses can be found in small populations scattered around northwestern Europe, notably the shaggy ponies of Iceland.

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series: Cell

• Two now-extinct horse lineages lived in Iberia and Siberia some 5,000 years ago
• Iberian and Siberian horses contributed limited ancestry to modern domesticates
• Oriental horses have had a strong genetic influence within the last millennium
• Modern breeding practices were accompanied by a significant drop in genetic diversity

Concern about "purity" of breeds led to drops in genetic diversity, especially in Y chromosomes.

 

[lpetrich]

Genes to Genomes: a blog from the Genetics Society of America
noting
The Evolutionary Origin and Genetic Makeup of Domestic Horses | Genetics
and
The Evolutionary Origin and Genetic Makeup of Domestic Horses

From Genes and Genomes:

Remarkably, the majority of Y-chromosomes carried by modern domestic horses can be traced back to just a few stallions. This could be because only a few males were originally used in domestication, but it could also result from carefully controlled modern breeding practices where a single male sires a huge number of offspring. The ultimate cause of this very low Y-linked diversity is still debated, but strict selective breeding has almost certainly contributed. In contrast, a much larger number of females than males contributed ancestry to domestic horses. According to Librado and colleagues, it seems that wild mares were continuously introduced into human-controlled herds throughout the process of domestication.

Turning a wild animal into a domestic one that will tolerate humans involves a long process of selecting for traits like docility and friendliness. In the case of hard-working horses, desirable traits also included strength, endurance, and gait. This kind of selective breeding leaves a very clear mark in the genome. By comparing the genomes of modern domestic horses with very ancient domestic horses, geneticists were able to identify many genes linked to selected traits, including genes involved in coat color, skeletal structure, the circulatory system, and brain development and behavior.

From PubMed:

THE history of the domestication of the horse remains enigmatic in several aspects due to the absence of clear morphological and osteological differences between wild and early domestic individuals, but also due to the scarcity of paleontological records from some key periods, especially the one preceding the earliest evidence of domestication. This evidence is given by the ∼5500-year-old archaeological site of Botai (modern-day Kazakhstan) (Outram et al. 2009), at a considerable spatial and temporal distance from the Anatolian domestication centers for sheep and goats (Zeder et al. 2006). Unlike other ungulates, horses were not only used as a source of meat and milk, but their stamina and speed also revolutionized warfare and transportation. This also promoted cultural exchange, including the spread of Indo-European languages, religions, science, and art (Kelekna 2009; Anthony 2010). With the introduction of the horse collar and horseshoes in agriculture, the horse was increasingly used for tilling soils, incrementing farmland productivity in medieval Europe, and remains today an essential asset to the agriculture of the least-developed countries.

Like other domestic animals, horses have been bred in different directions.

The population structure resulting from selective breeding is characterized by high interbreed and low intrabreed genetic diversity (McCue et al. 2012), and reflected by a huge array of morphological and behavioral traits (Figure 1). The height at withers, for example, extends from 70 cm in miniature Falabella horses to over 2 m in Shire and Percheron horses; an intraspecific range that is only exceeded by height variation in domestic dogs (Brooks et al. 2010). Domestic horses also exhibit striking variation in coat coloration, including the bay or bay-dun wild-type phenotypes, other basic colors like chestnut and black, as well as dilution (e.g., cream and silver), and spotting patterns (e.g., leopard complex, tobiano, and sabino) (Ludwig et al. 2009). Horse locomotion has also been recurrently selected, including their ability to perform alternate gaits, such as four-beat, lateral, or diagonal ambling. These alternate gaits come in addition to the three natural gaits (walk, trot, and gallop), and are known to increase the comfort of the rider and positively influence racing performance (Andersson et al. 2012; Promerová et al. 2014). Due to pleiotropic and/or epistatic effects, some of the traits selected in domestic breeds are, however, indirectly associated with congenital diseases (Bellone et al. 2008; McCue et al. 2008; Sandmeyer et al. 2012). These undesirable associations can be magnified by the extensive level of linkage disequilibrium (LD) that results from the low effective population size (Ne) within breeds.

The article then discussed the declines and extinctions of horse species over the Late Pleistocene and early Holocene. Human hunting? Climate changes? A meteorite/comet impact at 11.7 kya?

With a few notable exceptions, such as the Arabian, Mongolian, and Icelandic horses, breeds are relatively recent human constructs on an evolutionary timescale. The earliest horse studbook, that of the Thoroughbred racing horses, was created in 1791. Therefore, within the last two centuries, humans have imposed strong diverging selection among breeds.

Multiple domestications? Like these:
Dogs may have been domesticated more than once | Science | AAAS
Were cats domesticated more than once? | Science | AAAS

 

[lpetrich]

Domestication rapidly decreased genetic diversity in horses | NOVA | PBS | NOVA | PBS
More on that paper in "Cell" about horse genomes.

“This study is brilliant,” says Vagheesh Narasimhan, a mathematical genomicist at Harvard University who was not involved in the study. “Just to see data of this scale being produced for a species other than humans is spectacular.”

...
“DNA is nature’s own written history,” says Samantha Brooks, a horse geneticist at the University of Florida who was not involved in the study. “Horses can’t write or speak their side of their story, but we can read a little bit about the events based on their DNA.”

...
Horses were first bridled by humans sometime between the fourth and third millennium BCE. Through their analysis, the researchers found that breeding priorities have undergone several revolutions in the centuries since. For instance, around 1,000 years ago, strong, sturdy builds came into fashion, ushering in the lasting age of the Arabian horses, which still frequent many a stable today. Traits like speed and the ability to amble—a medium-speed gait that’s considered more comfortable for riders—also became common fixtures in the equine lineage.

Despite these reproductive restrictions, the genomic time series showed that domesticated horses remained relatively genetically diverse for the first 4,000 years or so of their close coexistence with humans. It was only around 200 or 300 years ago that these levels took a sharp downturn.

“This is the moment that genetic diversity started to collapse,” says study author Antoine Fages, a paleogenomicist at the University of Toulouse. “It’s quite amazing that it happened so quickly and so recently.”

The turning point coincides neatly with the latter half of the 18th century, when horse racing began in earnest, paring down the list of “desirable” equine traits, Fages says. As agility and power skyrocketed in importance, breeders began to select only a handful of stallions to sire future generations, keeping large parts of the population from throwing their genetic hats into the ring.

The dip isn’t shocking, though, and it parallels what humans have seen in other domesticated species, like dogs and livestock, Brooks says. The timing, she says, also coincides with cultural and technological evolutions in our history. As humans became less dependent on horses for farming and transportation, the relationship between the two species began to change. Eventually, equines settled into a newer, more specialized niche—recreation—giving breeders less incentive to keep their stables stocked with a diverse set of animals.

Prehistoric genomes reveal the genetic foundation and cost of horse domestication | PNAS

The domestication of the horse revolutionized warfare, trade, and the exchange of people and ideas. This at least 5,500-y-long process, which ultimately transformed wild horses into the hundreds of breeds living today, is difficult to reconstruct from archeological data and modern genetics alone. We therefore sequenced two complete horse genomes, predating domestication by thousands of years, to characterize the genetic footprint of domestication. These ancient genomes reveal predomestic population structure and a significant fraction of genetic variation shared with the domestic breeds but absent from Przewalski’s horses. We find positive selection on genes involved in various aspects of locomotion, physiology, and cognition. Finally, we show that modern horse genomes contain an excess of deleterious mutations, likely representing the genetic cost of domestication.

I don't know if anyone has researched how to undo this genetic homogenization. One would likely want to use out-of-the-way breeds that did not suffer as much, and use them as breeding stock.

 

[lpetrich]

Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

Through their domestication and subsequent selection, sheep have been adapted to thrive in a diverse range of environments. To characterise the genetic consequence of both domestication and selection, we genotyped 49,034 SNP in 2,819 animals from a diverse collection of 74 sheep breeds. We find the majority of sheep populations contain high SNP diversity and have retained an effective population size much higher than most cattle or dog breeds, suggesting domestication occurred from a broad genetic base. Extensive haplotype sharing and generally low divergence time between breeds reveal frequent genetic exchange has occurred during the development of modern breeds. A scan of the genome for selection signals revealed 31 regions containing genes for coat pigmentation, skeletal morphology, body size, growth, and reproduction. We demonstrate the strongest selection signal has occurred in response to breeding for the absence of horns. The high density map of genetic variability provides an in-depth view of the genetic history for this important livestock species.

So the genetics behind hornlessness shows up in their genomes.

On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools | Genetics Selection Evolution | Full Text

In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation.

... We demonstrate the occurrence, from southeast to northwest Europe, of a continuously increasing ancestral component of up to 20% contributed by the European mouflon, which is assumed to descend from the original Neolithic domesticates. The overall patterns indicate that the Balkan region and Italy served as post-domestication migration hubs, from which wool sheep reached Spain and north Italy with subsequent migrations northwards. The documented dispersal of Tarentine wool sheep during the Roman period may have been part of this process. Our results also reproduce the documented 18th century admixture of Spanish Merino sheep into several central-European breeds.

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits | Nature Communications
Like making wool. Wild sheep are short-haired, as one might expect, but domestic sheep are best-known for their wool -- long hair.

Frontiers | Deep Genome Resequencing Reveals Artificial and Natural Selection for Visual Deterioration, Plateau Adaptability and High Prolificacy in Chinese Domestic Sheep | Genetics
"Breed-specific selected regions were determined including genes such as CYP17 for hypoxia adaptability in Tibetan sheep and DNAJB5 for heat tolerance in Duolang sheep." -- the Tibetan plateau has an altitude of about 4000 meters, giving it an atmospheric pressure of about 0.6 times that of sea level.

 

[lpetrich]

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent

Little is known regarding the location and mode of the early domestication of animals such as goats for husbandry. To investigate the history of the goat, Daly et al. sequenced mitochondrial and nuclear sequences from ancient specimens ranging from hundreds to thousands of years in age. Multiple wild populations contributed to the origin of modern goats during the Neolithic. Over time, one mitochondrial type spread and became dominant worldwide. However, at the whole-genome level, modern goat populations are a mix of goats from different sources and provide evidence for a multilocus process of domestication in the Near East. Furthermore, the patterns described support the idea of multiple dispersal routes out of the Fertile Crescent region by domesticated animals and their human counterparts.

Ancient genome analyses reveal mosaic pattern | EurekAlert!

An international team of scientists, led by geneticists from Trinity College Dublin, have sequenced the genomes from ancient goat bones from areas in the Fertile Crescent where goats were first domesticated around 8,500 BC. They reveal a 10,000-year history of local farmer practices featuring genetic exchange both with the wild and among domesticated herds, and selection by early farmers.

There is evidence of selection for coat color. Domestic animals have much more variety than their wild ancestors, and in some cases, at least, that was due to selection by their masters.

 

[lpetrich]

Convergent genomic signatures of domestication in sheep and goats | Nature Communications

The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species.

PDF at (PDF) Convergent genomic signatures of domestication in sheep and goats

(PDF) Ancient goat genomes reveal mosaic domestication in the Fertile Crescent

Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.

Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China | Molecular Biology and Evolution | Oxford Academic

Goats are one of the most widespread farmed animals across the world; however, their migration route to East Asia and local evolutionary history remain poorly understood. Here, we sequenced 27 ancient Chinese goat genomes dating from the Late Neolithic period to the Iron Age. We found close genetic affinities between ancient and modern Chinese goats, demonstrating their genetic continuity. We found that Chinese goats originated from the eastern regions around the Fertile Crescent, and we estimated that the ancestors of Chinese goats diverged from this population in the Chalcolithic period. Modern Chinese goats were divided into a northern and a southern group, coinciding with the most prominent climatic division in China, and two genes related to hair follicle development, FGF5 and EDA2R, were highly divergent between these populations. We identified a likely causal de novo deletion near FGF5 in northern Chinese goats that increased to high frequency over time, whereas EDA2R harbored standing variation dating to the Neolithic. Our findings add to our understanding of the genetic composition and local evolutionary process of Chinese goats.