Genetic study of silkworm helps unravel its long history of domestication

July 3, 2018 by Bob Yirka, Phys.org report

A team of researchers affiliated with several institutions in China has conducted a genetic study of the silkworm in hopes of better understanding its long historical ties to humans. In their paper published in the journal Nature Ecology & Evolution, the group describes their study and what they found.

There are many varieties of silkworms, but only one makes silk that is mass-producible: Bombyx mori. Because of that unique characteristic, B. mori has a very long history of domestication by humans. Most scientists in the field suggest that the relationship began approximately 5000 years ago, and that it likely started in China. In this new effort, the researchers sought to trace the origins of the silkworm to its first domestication to learn more about its history over the past several thousand years.

The genetic study consisted of collecting silkworm samples representing 137 strains. Those samples included strains that were locally bred and even some representing recently improved strains. The team also collected samples of strains that have not been domesticated. They then sequenced the DNA of all the samples and compared them to one another. The group was able to use the DNA data to construct geographic maps that showed the history of the silkworm as it spread between geographic areas.

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Ancient DNA reveals how cats domesticated humans

June 20, 2017

by Chuck Bednar


While dogs are believed to be the first animal to be domesticated, cats – as one might expect from a feline – took their sweet time trying to decide whether or not they wanted to bond with humans, according to a new, comprehensive genetic analysis published this week.

The authors of the study, which appeared in the journal Nature Ecology & Evolution, looked at the DNA of around 200 feline species representing more than 9,000 years, including mummified Egyptian cats and modern-day African wildcats, National Geographic reported on Monday. Based on that analysis, the researchers concluded that felines lived alongside humans for several thousand years before actually becoming domesticated, and that the earliest ancestors of today’s housecats came to Europe from southwest Asia as early as 4400 BC, the publication added.

Lead author Claudio Ottoni, a paleogeneticist from the University of Leuven, and his colleagues analyzed DNA from the bones, teeth, skin and hair of 100 to 9,000-year-old felines discovered at archeological sites in Western Asia, Europe and Africa. They found that all modern-day cats can be traced back genetically to the African wildcat (Felis silvestris lybica), a subspecies of wildcat found in North Africa and the Near East, according to a press release.



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How domestication can change animals' facial features

Date: April 10, 2017

Source: Universitaet Tübingen

Domesticated animals, compared to their wild counterparts, have undergone numerous changes in physiology, behavior and morphology. These changes are commonly referred to as the domestication syndrome and include behavioral changes, such as increased docility as well as genetic alterations in size, color and facial characteristics. In attempting to find whether these changes have a single cause, Russian zoologist Dmitry Belyaev conducted a series of selection experiments with silver foxes, hypothesizing that behavior, specifically tameness, was the key driving factor behind the changes brought about by domestication. After generations of selecting foxes for tameness, they were found to display phenotypes similar to those observed in domesticated species. Since then, it has been further hypothesized that selection for social tolerance and reduced aggression may also have played an important role in shaping the modern human anatomy, which is remarkable for the reduced face and gracile overall features.

In parallel to his fox experiment, Belyaev also selected rats over 64 generations for their behavior: either tameness or defensive aggression towards humans. In the first ever quantitative study on the facial anatomy of Belyaev's selected rats, an international team of researchers from the Senckenberg Center for Human Evolution and Paleoenvironment at the University of Tübingen and Pennsylvania State University collected 3-D measurements on the skulls of both tame- and aggressive-selected rats, in order to evaluate Belyaev's hypothesis that tame behavior correlates with the facial changes similar to those seen in domesticated animals. The study found that rats selected for tame behavior show some -- though not all -- traits present in domesticated animals and the tame silver foxes. The findings are published in the latest Plos One.

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Dogs were domesticated not once, but twice ... in different parts of the world

Date: June 2, 2016

Source: University of Oxford

The question, 'Where do domestic dogs come from?', has vexed scholars for a very long time. Some argue that humans first domesticated wolves in Europe, while others claim this happened in Central Asia or China. A new paper, published in Science, suggests that all these claims may be right. Supported by funding from the European Research Council and the Natural Environment Research Council, a large international team of scientists compared genetic data with existing archaeological evidence and show that man's best friend may have emerged independently from two separate (possibly now extinct) wolf populations that lived on opposite sides of the Eurasian continent. This means that dogs may have been domesticated not once, as widely believed, but twice.

A major international research project on dog domestication, led by the University of Oxford, has reconstructed the evolutionary history of dogs by first sequencing the genome (at Trinity College Dublin) of a 4,800-year old medium-sized dog from bone excavated at the Neolithic Passage Tomb of Newgrange, Ireland. The team (including French researchers based in Lyon and at the National Museum of Natural History in Paris) also obtained mitochondrial DNA from 59 ancient dogs living between 14,000 to 3,000 years ago and then compared them with the genetic signatures of more than 2,500 previously studied modern dogs.

The results of their analyses demonstrate a genetic separation between modern dog populations currently living in East Asia and Europe. Curiously, this population split seems to have taken place after the earliest archaeological evidence for dogs in Europe. The new genetic evidence also shows a population turnover in Europe that appears to have mostly replaced the earliest domestic dog population there, which supports the evidence that there was a later arrival of dogs from elsewhere. Lastly, a review of the archaeological record shows that early dogs appear in both the East and West more than 12,000 years ago, but in Central Asia no earlier than 8,000 years ago.

Combined, these new findings suggest that dogs were first domesticated from geographically separated wolf populations on opposite sides of the Eurasian continent. At some point after their domestication, the eastern dogs dispersed with migrating humans into Europe where they mixed with and mostly replaced the earliest European dogs. Most dogs today are a mixture of both Eastern and Western dogs -- one reason why previous genetic studies have been difficult to interpret.

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Reshaping the horse through millennia: Sequencing reveals genes selected by humans in domestication

Date:

December 15, 2014

Source:

Faculty of Science - University of Copenhagen

Summary:

Whole genome sequencing of modern and ancient horses unveils the genes that have been selected by humans in the process of domestication through the last 5,500 years, but also reveals the cost of this domestication. An international research group reports that a significant part of the genetic variation in modern domesticated horses could be attributed to interbreeding with the descendants of a now extinct population of wild horses. This population was distinct from the only surviving wild horse population.

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Cat genome reveals clues to domestication​​

November 10th 2014

Cats and humans have shared the same households for at least 9,000 years, but we still know very little about how our feline friends became domesticated. An analysis of the cat genome led by researchers at Washington University School of Medicine in St. Louis reveals some surprising clues.

The research appears Nov. 10 in the Proceedings of the National Academy of Sciences Early Edition.

Cats have a relatively recent history of domestication compared with dogs; canines arose from wolves over 30,000 years ago.

"Cats, unlike dogs, are really only semidomesticated," said senior author Wes Warren, PhD, associate professor of genetics at The Genome Institute at Washington University​. "They only recently split off from wild cats, and some even still breed with their wild relatives. So we were surprised to find DNA evidence of their domestication."

One way scientists can understand the genetics of domestication is to look at what parts of the genome are altered in response to living together with humans, Warren added.

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Domestication of dogs may explain mammoth kill sites and success of early modern humans

Date:

May 29, 2014

Source:

Penn State

Summary:

A new analysis of European archaeological sites containing large numbers of dead mammoths and dwellings built with mammoth bones has led to a new interpretation of these sites -- that their abrupt appearance may have been due to early modern humans working with the earliest domesticated dogs to kill the now-extinct mammoth.

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Ancient Egyptian Kitten Skeletons Hint at Cat Domestication

By Stephanie Pappas, Senior Writer | March 17, 2014 07:51am ET

The skeletons of six cats, including four kittens, found in an Egyptian cemetery may push back the date of cat domestication in Egypt by nearly 2,000 years.

The bones come from a cemetery for the wealthy in Hierakonpolis, which served as the capital of Upper Egypt in the era before the pharaohs. The cemetery was the resting place not just for human bones, but also for animals, which perhaps were buried as part of religious rituals or sacrifices. Archaeologists searching the burial grounds have found everything from baboons to leopards to hippopotamuses.

The new find includes two adult cats and four kittens from at least two litters. The size of the bones and timing of the litters hints that humans may have kept the cats. The bones date back to between 3600 B.C. and 3800 B.C., which would be 2,000 years before the earliest known evidence of cat domestication in Egypt, archaeologists report in the May issue of the Journal of Archaeological Science. 

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Genomes of Modern Dogs and Wolves Provide New Insights On Domestication

Jan. 16, 2014 — Dogs and wolves evolved from a common ancestor between 9,000 and 34,000 years ago, before humans transitioned to agricultural societies, according to an analysis of modern dog and wolf genomes from areas of the world thought to be centers of dog domestication.

The study, published in PLoS Geneticson January 16, 2014, also shows that dogs are more closely related to each other than wolves, regardless of geographic origin. This suggests that part of the genetic overlap observed between some modern dogs and wolves is the result of interbreeding after dog domestication, not a direct line of descent from one group of wolves.

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Cat Domestication Traced to Chinese Farmers 5,300 Years Ago

Dec. 16, 2013 — Five-thousand years before it was immortalized in a British nursery rhyme, the cat that caught the rat that ate the malt was doing just fine living alongside farmers in the ancient Chinese village of Quanhucun, a forthcoming study in the Proceedings of the National Academy of Sciences has confirmed.

"At least three different lines of scientific inquiry allow us to tell a story about cat domestication that is reminiscent of the old 'house that Jack built' nursery rhyme," said study co-author Fiona Marshall, PhD, a professor of archaeology in Arts & Sciences at Washington University in St. Louis.

"Our data suggest that cats were attracted to ancient farming villages by small animals, such as rodents that were living on the grain that the farmers grew, ate and stored."

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Domestication of Dogs May Have Elaborated On a Pre-Existing Capacity of Wolves to Learn from Humans

Dec. 3, 2013 — Wolves can learn from observing humans and pack members where food is hidden and recognize when humans only pretend to hide food, reports a study for the first time in the open-access journal Frontiers in Psychology. These findings imply that when our ancestors started to domesticate dogs, they could have built on a pre-existing ability of wolves to learn from others, not necessarily pack members.

A paper published recently in the journal Science suggested that humans domesticated dogs about 18 thousand years ago, possibly from a European population of grey wolves that is now extinct. But it remains unknown how much the ability of dogs to communicate with people derives from pre-existing social skills of their wolf ancestors, rather than from novel traits that arose during domestication.

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Earliest Use of Mexican Turkeys by Ancient Maya

ScienceDaily (Aug. 8, 2012) — A new University of Florida study shows the turkey, one of the most widely consumed birds worldwide, was domesticated more than 1,000 years earlier than previously believed.

Researchers say discovery of the bones from an ancient Mayan archaeological site in Guatemala provides evidence of domestication, usually a significant mark of civilization, and the earliest evidence of the Mexican turkey in the Maya world. The study appears online in PLoS ONE.

The discovery of the turkey bones is significant because the Maya did not use a lot of domesticated animals. While they cultivated domesticated plants, most of their animal protein came mostly from wild resources, said lead author Erin Thornton, a research associate at the Florida Museum of Natural History on the UF campus and Trent University Archaeological Research Centre.

"We might have gotten the timing of the introduction of this species to the ancient Maya wrong by a significant chunk of time," Thornton said. "The species originates from central Mexico, outside the Maya cultural area. This is the species the Europeans brought back with them to Europe -- all domestic turkeys originated from Mexico."

Continued:  http://www.sciencedaily.com/releases/2012/08/120809090706.htm

Sake, Soy Sauce, and the Taming of the Microbes

ScienceDaily (July 12, 2012) — What do beer, dogs and cats, and corn all have in common? All of them are the end products of the process of domestication. Almost everybody knows that a number of different animals and plants have been bred for qualities that benefit humans. But few people realize that a number of microbes have undergone a similar transformation.

Take brewer's yeast, for example. It is the quintessential ingredient in beer making: genetically altered to convert the sugars in malted barley into alcohol and to produce metabolic byproducts that give beer its unique taste. In fact, dozens of specialized strains of yeast produce the wide variety of beers, lagers and ales that brewers have developed.

"Although people don't often think about it, we haven't only domesticated animals and plants, but we have also domesticated dozens of different microbes," said Assistant Professor of Biological Sciences Antonis Rokas, adding that it's hard to imagine what life would be like without beer, wine, leavened bread, cheese, yoghurt, soy sauce, sauerkraut and a number of other mainstays of the human diet that are produced by domesticated microbes.

Continued:  http://www.sciencedaily.com/releases/2012/07/120712131527.htm

Why Dogs' Origins Are Still Mysterious

Humans' close relationship to dogs has so far obscured their history so much that it's not yet possible to use genetic data to tease out the details of their domestication, new research indicates.

Their complicated history involves being interbred, as well as transported around the world.

"There's a central irony here which is that because we love them so much, we've completely obliterated their early history and made it more difficult to understand their origins," researcher Greger Larson, an evolutionary biologist at the University of Durham in the United Kingdom, told LiveScience in an email.

Dogs were the first domesticated animal; however, many major questions about their domestication remain. For instance, it's still not clear how many times they were domesticated, where in the Old World this happened, and how many different wolf populations contributed to the modern global population of dogs.


Continued: http://www.livescience.com/20480-dog-domestication-mystery.html

Mystery of the Domestication of the Horse Solved Competing Theories Reconciled

ScienceDaily (May 7, 2012) — New research indicates that domestic horses originated in the steppes of modern-day Ukraine, southwest Russia and west Kazakhstan, mixing with local wild stocks as they spread throughout Europe and Asia.

The research was published 07 May, in the journal PNAS.

For several decades scientists puzzled over the origin of domesticated horses. Based on archaeological evidence, it had long been thought that horse domestication originated in the western part of the Eurasian Steppe (Ukraine, southwest Russia and west Kazakhstan); however, a single origin in a geographically restricted area appeared at odds with the large number of female lineages in the domestic horse gene pool, commonly thought to reflect multiple domestication "events" across a wide geographic area.

In order to solve the perplexing history of the domestic horse, scientists from the University of Cambridge used a genetic database of more than 300 horses sampled from across the Eurasian Steppe to run a number of different modelling scenarios.

Their research shows that the extinct wild ancestor of domestic horses, Equus ferus, expanded out of East Asia approximately 160,000 years ago. They were also able to demonstrate thatEquus ferus was domesticated in the western Eurasian Steppe, and that herds were repeatedly restocked with wild horses as they spread across Eurasia.

Continue:  http://www.sciencedaily.com/releases/2012/05/120507154107.htm

Man's First Best Friend Might Have Been A Fox

by NPR Staff
February 19, 2011

In a dusty, ancient burial site in northern Jordan, archaeologists have made a startling discovery: a fox buried alongside human remains.

It seems some 16,000 years ago, several millennia before any animals were domesticated, humans may have been making an early attempt to keep pets. Red foxes, to be precise.

It's a surprising find, Cambridge researcher Lisa Maher tells NPR's Linda Wertheimer. "When we were first excavating the site, we thought it might have been a dog," she says. It wasn't until her team analyzed the animal's remains that it realized it was a fox.

That the fox was a pet is only one of several possibilities, however. It may instead have had totemic or spiritual significance to the culture. But Maher's team compared the burial site to sites from 4,000 years later, when domesticated dogs did accompany human burials. The similarities suggest "that it probably was a more emotional relationship of one particular fox to one particular person," she says.

Those similarities are also significant because they highlight a continuity in mortuary practices through time, Maher adds. "We're seeing these things, these similarities in mortuary practices and relationships to humans and animals in a much greater time depth than we had previously."

If the fox were indeed a pet, it would be a pretty big deal. "It's certainly a big deal for prehistoric archeology," Maher says, "but it's also a big deal for how we understand human-animal relationships today and in the past."

http://www.npr.org/2011/02/19/133898499/mans-first-best-friend-might-have-been-a-fox

Dogs domesticated in Middle East, not Asia

17 March 2010 19:37 GMT
By Steve Gorman

LOS ANGELES (Reuters) - From French poodles to German shepherds, domestic dogs likely trace most of their ancestry to the Middle East, as opposed to East Asian origins suggested by previous research, a genetic study reported on Wednesday.

The findings, published in the online edition of the scientific journal Nature, support an archaeological record that closely links the domestication of dogs in the Middle East with the rise of human civilization there, scientists said.

"It's significant because this is where civilization developed, and dogs were part of that," said Robert Wayne, professor of evolutionary biology at the University of California, Los Angeles, and a senior author of the study.

The region, often referred to as the Fertile Crescent, includes much of modern-day Iraq, Syria, Lebanon and Jordan --

"the same area where domestic cats and many of our livestock originated, and where agriculture first developed," he said.

The study is based on genetic comparisons between more than 900 dogs representing 85 breeds and over 200 wild gray wolves -- the closest living wild relative of dogs -- from around the globe, including North America, Europe, East Asia and the Middle East.

In the most extensive such analysis to date, scientists used molecular genetic techniques to examine more than 48,000 markers from across the entire genome -- or DNA sequence -- from each of the animals included in the study.

What they discovered was the vast majority of dogs share more unique genetic markers with gray wolves from the Mideast than with other wolf populations. A kinship to European wolves also was found, but to a lesser extent, Wayne said.

NUISANCE OR COMPANION?

One notable exception was the finding of a close genetic link between a small number of East Asian dog breeds and wolves from China, suggesting some intermingling between the two.

But the new research contradicts an earlier genetic study suggesting a close ancestry of all dogs to wolves from East Asia and China. That analysis was based on comparisons between a single, small DNA sequence taken from mitochondria -- tiny structures outside the nucleus of living cells that carry their own genes -- rather markers from entire genomes.

The newer research was far more comprehensive and "is much more consistent with the archaeological record," Wayne said.

"We know that dogs from the Middle East were closely associated with humans because they were found in human burial sites" there, he said. In one famous example, the remains of a puppy were found curled up in the arms of a human skeleton.

But the earliest bond between people and "man's best friend" was probably more often a love-hate relationship that persists in parts of the world to this day, and helps explain a cultural ambivalence towards dogs in the very region where they likely originated.

The archaeological record of dogs dates back 31,000 years to the remains of a Great Dane-like specimen found in Belgium. The first Mideast dogs appeared 12,000 to 13,000 years ago.

Although agriculture and animal husbandry go hand in hand, the first people to domesticate dogs from wild wolves probably were nomadic hunter-gatherers, who were followed at a distance by canine interlopers in search of scraps.

That relationship likely matured over thousands of years "to the point where these proto-dogs were living in close proximity with humans," and were often more of a nuisance than they were companions, Wayne said.

"Eventually dogs provided protection, an early warning system, maybe even helped out with the hunt, and then eventually, even closer in, provided companionship," he said.

While some dog breeds have ancient histories, 80 percent are modern varieties that have evolved since the explosion in dog breeding during the Victorian era, Wayne said.

(Editing by Dan Whitcomb and Vicki Allen)

http://news.stv.tv/oddly-enough/164262-dogs-domesticated-in-middle-east-not-asia/

Dogs First Tamed in China -- To Be Food?

John Roach
for National Geographic News
September 4, 2009

Wolves were domesticated no more than 16,300 years ago in southern China, a new genetic analysis suggests—and it's possible the canines were tamed to be livestock, not pets, the study author speculates.

"In this region, even today, eating dog is a big cultural thing," noted study co-author Peter Savolainen, a biologist at the Royal Institute of Technology in Stockholm, Sweden.

"And you can also see in the historical records as far back as you can go that eating dogs has been very common" in East Asia.

"Therefore, you have to think of the possibility that this was one of the reasons for domesticating dogs."

Dog Diversity

The new work, published Wednesday in the journal Molecular Biology and Evolution, bolsters the long-held theory that dogs first became "man's best friend" in East Asia.

That notion came under fire last month, based on a DNA analysis of so-called village dogs in Africa.

The highest level of genetic diversity in modern dogs should exist in the region where the animals first came under human control.

But the August study found that African village dogs have a similar amount of genetic diversity as those in East Asia, calling into question the origins of dog domestication.

For the new work, Savolainen and colleagues analyzed the entire mitochondrial genome—DNA passed down only from the mother—of 169 dogs, as well as portions of the genomes from 1,543 dogs from across Europe, the Middle East, and Asia.

These dogs all share at least 80 percent of their DNA, the team found. The animals' genetic diversity increased the farther east the scientists looked.

The greatest diversity was found in a region south of the Yangtze River in China.

According to Savolainen, the data make it "totally clear" that genetic variation in East Asian dogs is much higher than anywhere else in the world.

The analysis also suggests that wolves were domesticated from several hundred individuals sometime between 5,400 and 16,300 years ago.

This is around the time Asian hunter-gatherers were adopting a more settled agrarian lifestyle, which is part of what makes Savolainen think the canines might have been kept as food.

Support, But Not Proof?

Adam Boyko, a biologist at Cornell University in New York and co-author of the August study, agrees that the new work shows greater genetic diversity in East Asia than Africa.

But Boyko said he would like to see more genetic evidence before he calls the finding proof of domestication.

"But clearly, it is a very interesting result," he said. "There is a ton of data backing it up, [and] they put forth a really interesting hypothesis for dog domestication."

http://news.nationalgeographic.com/news/2009/09/090904-dogs-tamed-china-food.html