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Fathered by the Mailman? It's Mostly an Urban Legend
MATTER

Five days a week, you can tune into "Paternity Court," a television show featuring couples embroiled in disputes over fatherhood. It's entertainment with a very old theme: Uncertainty over paternity goes back a long way in literature. Even Shakespeare and Chaucer cracked wise about cuckolds, who were often depicted wearing horns.

But in a number of recent studies, researchers have found that our obsession with cuckolded fathers is seriously overblown. A number of recent genetic studies challenge the notion that mistaken paternity is commonplace.

"It's absolutely ridiculous," said Maarten H.D. Larmuseau, a geneticist at the University of Leuven in Belgium who has led much of this new research.

The term cuckold traditionally refers to the husband of an adulteress, but Dr. Larmuseau and other researchers focus on those cases that produce a child, which scientists politely call "extra-pair paternity."

Until the 20th century, it was difficult to prove that a particular man was the biological father of a particular child.

In 1304 a British husband went to court to dispute the paternity of his wife's child, born while he was abroad for three years. Despite the obvious logistical challenges, the court rejected the husband's objection.

"The privity between a man and his wife cannot be known," the judge ruled.

Modern biology lifted the veil from this mystery, albeit slowly. In the early 1900s, researchers discovered that people have distinct blood types inherited from their parents.

In a 1943 lawsuit, Charlie Chaplin relied on blood-type testing to prove that he was not the father of the actress Joan Barry's child. (The court refused to accept the evidence and forced Chaplin to pay child support anyway.)

It wasn't until DNA sequencing emerged in the 1990s that paternity tests earned the legal system's confidence. Labs were able to compare DNA markers in children to those of their purported fathers to see if they matched.

As the lab tests piled up, researchers collated the results and came to a startling conclusion: Ten percent to 30 percent of the tested men were not the biological fathers of their children.

Those figures were spread far and wide, ending up in many science books. But the problem with the lab data, Dr. Larmuseau said, was that it didn't come from a random sample of people. The people who ordered the tests already had reason to doubt paternity.

Dr. Larmuseau and other scientists developed other methods to get an unbiased look at cuckoldry.

In a 2013 study, Dr. Larmuseau and his colleagues used Belgium's detailed birth records to reconstruct large family genealogies reaching back four centuries. Then the scientists tracked down living male descendants and asked to sequence their Y chromosomes.

Y chromosomes are passed down in almost identical form from fathers to sons. Men who are related to the same male ancestor should also share his Y chromosome, providing that some unknown father didn't introduce his own Y somewhere along the way.

Comparing the chromosomes of living related men, Dr. Larmuseau and his colleagues came up with a cuckoldry rate of less than 1 percent. Similar studies have generally produced the same low results in such countries as Spain, Italy and Germany, as well as agricultural villages in Mali.

The scientists got the same results after trying a different tack. They studied men in Flanders, a part of Belgium to which French people emigrated in the late 1500s.

The Y chromosomes in Flemish men with French surnames, the researchers found, had the same genetic markers found in men who live today in the region of France where their ancestors originated. Had there had been a lot of cuckoldry over the centuries, the link between genetics and surnames should have been weaker, or disappeared altogether.

In a commentary in Trends in Ecology and Evolution, Dr. Larmuseau and his colleagues argue that it's long past time to toss out frequent cuckoldry as a myth. Studies relying on different methods in different cultures all point to cuckoldry rates of about 1 percent.

And because many of those studies are based on genealogies that reach back many generations, he argues, these rates must have been low for at least several centuries.

Beverly I. Strassmann, a University of Michigan anthropologist who gathered the data on paternity rates in Mali, agreed that widespread cuckoldry "was an urban legend. It seemed to have a life of its own."

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Science
Fathered by the Mailman? It's Mostly an Urban Legend

    87

Photo illustration by Stephen Webster
April 8, 2016
Carl Zimmer
Carl Zimmer
MATTER

Five days a week, you can tune into "Paternity Court," a television show featuring couples embroiled in disputes over fatherhood. It's entertainment with a very old theme: Uncertainty over paternity goes back a long way in literature. Even Shakespeare and Chaucer cracked wise about cuckolds, who were often depicted wearing horns.

But in a number of recent studies, researchers have found that our obsession with cuckolded fathers is seriously overblown. A number of recent genetic studies challenge the notion that mistaken paternity is commonplace.

"It's absolutely ridiculous," said Maarten H.D. Larmuseau, a geneticist at the University of Leuven in Belgium who has led much of this new research.

The term cuckold traditionally refers to the husband of an adulteress, but Dr. Larmuseau and other researchers focus on those cases that produce a child, which scientists politely call "extra-pair paternity."

Until the 20th century, it was difficult to prove that a particular man was the biological father of a particular child.

In 1304 a British husband went to court to dispute the paternity of his wife's child, born while he was abroad for three years. Despite the obvious logistical challenges, the court rejected the husband's objection.

"The privity between a man and his wife cannot be known," the judge ruled.

Modern biology lifted the veil from this mystery, albeit slowly. In the early 1900s, researchers discovered that people have distinct blood types inherited from their parents.

In a 1943 lawsuit, Charlie Chaplin relied on blood-type testing to prove that he was not the father of the actress Joan Barry's child. (The court refused to accept the evidence and forced Chaplin to pay child support anyway.)

Interactive Feature | A Week of Misconceptions We're using the first week of April as an opportunity to debunk some of the misconceptions about health and science that circulate all year round.

It wasn't until DNA sequencing emerged in the 1990s that paternity tests earned the legal system's confidence. Labs were able to compare DNA markers in children to those of their purported fathers to see if they matched.

As the lab tests piled up, researchers collated the results and came to a startling conclusion: Ten percent to 30 percent of the tested men were not the biological fathers of their children.

Those figures were spread far and wide, ending up in many science books. But the problem with the lab data, Dr. Larmuseau said, was that it didn't come from a random sample of people. The people who ordered the tests already had reason to doubt paternity.

Dr. Larmuseau and other scientists developed other methods to get an unbiased look at cuckoldry.

In a 2013 study, Dr. Larmuseau and his colleagues used Belgium's detailed birth records to reconstruct large family genealogies reaching back four centuries. Then the scientists tracked down living male descendants and asked to sequence their Y chromosomes.

Y chromosomes are passed down in almost identical form from fathers to sons. Men who are related to the same male ancestor should also share his Y chromosome, providing that some unknown father didn't introduce his own Y somewhere along the way.

Comparing the chromosomes of living related men, Dr. Larmuseau and his colleagues came up with a cuckoldry rate of less than 1 percent. Similar studies have generally produced the same low results in such countries as Spain, Italy and Germany, as well as agricultural villages in Mali.

The scientists got the same results after trying a different tack. They studied men in Flanders, a part of Belgium to which French people emigrated in the late 1500s.

The Y chromosomes in Flemish men with French surnames, the researchers found, had the same genetic markers found in men who live today in the region of France where their ancestors originated. Had there had been a lot of cuckoldry over the centuries, the link between genetics and surnames should have been weaker, or disappeared altogether.

In a commentary in Trends in Ecology and Evolution, Dr. Larmuseau and his colleagues argue that it's long past time to toss out frequent cuckoldry as a myth. Studies relying on different methods in different cultures all point to cuckoldry rates of about 1 percent.

And because many of those studies are based on genealogies that reach back many generations, he argues, these rates must have been low for at least several centuries.

Beverly I. Strassmann, a University of Michigan anthropologist who gathered the data on paternity rates in Mali, agreed that widespread cuckoldry "was an urban legend. It seemed to have a life of its own."

The evidence of low rates of cuckoldry comes not just from gene studies, she noted. In species where females mate with many males, the males tend to evolve sperm that are good at competing for fertilization. The males may produce large amounts of sperm, for example, and a high percentage swim well.

Humans, however, don't rate in the sperm department.

"It's of amazingly low quality," Dr. Strassmann said. "Half the sperm can be duds; they can have two heads; they can be defective in all sorts of ways."

The only way for men to have evolved comparatively ineffectual sperm, she added, was for them to have experienced high rates of paternity over time.

It's not that widespread cuckoldry doesn't exist in some cultures, Dr. Larmuseau said. Some South American tribes with high rates share a belief that more than one man can contribute to the formation of a fetus.

But Dr. Larmuseau suspects that these populations are the exception, not the rule. Humans have evolved to avoid cuckoldry, he said, because of our peculiar biology.

Human infants are born quite helpless, compared with the newborns of other animals, and they need a lot of food over a long period to fuel the growth of their calorie-hungry brains. Mothers needed fathers to help find the food.

"Babies really need good investment from the fathers," Dr. Larmuseau said, "and the paternity has to be very sure in order for them to make those investments."

http://mobile.nytimes.com/2016/04/12/science/extra-marital-paternity-less-common-than-assumed-scientists-find.html

[Valmy]

Yep. Women, and I guess men (not seducing all those married ladies) as well, were/are shockingly loyal in history. Weird. Or they just asked for anal.

I heard that if you had sex with a woman enough you would leave behind a lot of guardian sperm that strike down invaders, and obviously dissipate over time as the woman's defenses kill them all off.. So that might have had something to do with it if that is true.

[jimmy olsen]

First Phonecian sequenced truns out to be from an obscure European lineage. If true, it's not surprising given how mobile people were. However, very few ancient Africans have been sequenced due to the environment being bad for preservation.  This lineage could have originated in Africa long ago and then moved to Europe where we deteced their last descendants. We just can't tell until we get more data.

http://m.csmonitor.com/Science/2016/0529/Ancient-Phoenician-DNA-may-change-the-way-we-see-human-migration

[jimmy olsen]

Awesome article on dog evolution.  Seems like dogs in western Eurasia were mostly replaced by migrants, just as the human population has several times.

http://www.businessinsider.com/how-wolves-became-dogs-2016-6

Everything we know about how wolves became dogs

Ed Yong, The Atlantic

Jun. 4, 2016, 6:55 PM
   

Tens of thousands of years ago, before the internet, before the Industrial Revolution, before literature and mathematics, bronze and iron, before the advent of agriculture, early humans formed an unlikely partnership with another animal—the grey wolf. The fates of our two species became braided together.

The wolves changed in body and temperament. Their skulls, teeth, and paws shrank.

Their ears flopped. They gained a docile disposition, becoming both less frightening and less fearful. They learned to read the complex expressions that ripple across human faces. They turned into dogs.

Today, dogs are such familiar parts of our lives—our reputed best friends and subject of many a meme—that it's easy to take them, and what they represent, for granted.

Dogs were the first domesticated animals, and their barks heralded the Anthropocene. We raised puppies well before we raised kittens or chickens; before we herded cows, goats, pigs, and sheep; before we planted rice, wheat, barley, and corn; before we remade the world.



"Remove domestication from the human species, and there's probably a couple of million of us on the planet, max," says archaeologist and geneticist Greger Larson. "Instead, what do we have? Seven billion people, climate change, travel, innovation and everything. Domestication has influenced the entire earth. And dogs were the first." For most of human history, "we're not dissimilar to any other wild primate.

We're manipulating our environments, but not on a scale bigger than, say, a herd of African elephants. And then, we go into partnership with this group of wolves. They altered our relationship with the natural world."

Larson wants to pin down their origins. He wants to know when, where, and how they were domesticated from wolves. But after decades of dogged effort, he and his fellow scientists are still arguing about the answers. They agree that all dogs, from low-slung corgis to towering mastiffs, are the tame descendants of wild ancestral wolves. But everything else is up for grabs.

Some say wolves were domesticated around 10,000 years ago, while others say 30,000. Some claim it happened in Europe, others in the Middle East, or East Asia. Some think early human hunter-gatherers actively tamed and bred wolves. Others say wolves domesticated themselves, by scavenging the carcasses left by human hunters, or loitering around campfires, growing tamer with each generation until they became permanent companions.

Dogs were domesticated so long ago, and have cross-bred so often with wolves and each other, that their genes are like "a completely homogenous bowl of soup," Larson tells me, in his office at the University of Oxford. "Somebody goes: what ingredients were added, in what proportion and in what order, to make that soup?" He shrugs his shoulders. "The patterns we see could have been created by 17 different narrative scenarios, and we have no way of discriminating between them."



The only way of doing so is to look into the past. Larson, who is fast-talking, eminently likable, and grounded in both archaeology and genetics, has been gathering fossils and collaborators in an attempt to yank the DNA out of as many dog and wolf fossils as he can. Those sequences will show exactly how the ancient canines relate to each other and to modern pooches. They're the field's best hope for getting firm answers to questions that have hounded them for decades.

And already, they have yielded a surprising discovery that could radically reframe the debate around dog domestication, so that the big question is no longer when it happened, or where, but how many times.

On the eastern edge of Ireland lies Newgrange, a 4,800-year-old monument that predates Stonehenge and the pyramids of Giza. Beneath its large circular mound and within its underground chambers lie many fragments of animal bones. And among those fragments, Dan Bradley from Trinity College Dublin found the petrous bone of a dog.

Press your finger behind your ear. That's the petrous. It's a bulbous knob of very dense bone that's exceptionally good at preserving DNA. If you try to pull DNA out of a fossil, most of it will come from contaminating microbes and just a few percent will come from the bone's actual owner. But if you've got a petrous bone, that proportion can be as high as 80 percent. And indeed, Bradley found DNA galore within the bone, enough to sequence the full genome of the long-dead dog.

Larson and his colleague Laurent Frantz then compared the Newgrange sequences with those of almost 700 modern dogs, and built a family tree that revealed the relationships between these individuals. To their surprise, that tree had an obvious fork in its trunk—a deep divide between two doggie dynasties. One includes all the dogs from eastern Eurasia, such as Shar Peis and Tibetan mastiffs. The other includes all the western Eurasian breeds, and the Newgrange dog.

The genomes of the dogs from the western branch suggest that they went through a population bottleneck—a dramatic dwindling of numbers. Larson interprets this as evidence of a long migration. He thinks that the two dog lineages began as a single population in the east, before one branch broke off and headed west. This supports the idea that dogs were domesticated somewhere in China.

But there's a critical twist.

The team calculated that the two dog dynasties split from each other between 6,400 and 14,000 years ago.  But the oldest dog fossils in both western and eastern Eurasia are older than that. Which means that when those eastern dogs migrated west into Europe, there were already dogs there.

To Larson, these details only make sense if dogs were domesticated twice.

Here's the full story, as he sees it. Many thousands of years ago, somewhere in western Eurasia, humans domesticated grey wolves. The same thing happened independently, far away in the east. So, at this time, there were two distinct and geographically separated groups of dogs.

Let's call them Ancient Western and Ancient Eastern. Around the Bronze Age, some of the Ancient Eastern dogs migrated westward alongside their human partners, separating from their homebound peers and creating the deep split in Larson's tree. Along their travels, these migrants encountered the indigenous Ancient Western dogs, mated with them (doggy style, presumably), and effectively replaced them.

Today's eastern dogs are the descendants of the Ancient Eastern ones. But today's western dogs (and the Newgrange one) trace most of their ancestry to the Ancient Eastern migrants. Less than 10 percent comes from the Ancient Western dogs, which have since gone extinct.

This is a bold story for Larson to endorse, not least because he himself has come down hard on other papers suggesting that cows, sheep, or other species were domesticated twice. "Any claims for more than one need to be substantially backed up by a lot of evidence," he says. "Pigs were clearly domesticated in Anatolia and in East Asia. Everything else is once." Well, except maybe dogs.

Other canine genetics experts think that Larson's barking up the wrong tree. "I'm somewhat underwhelmed, since it's based on a single specimen," says Bob Wayne from the University of California, Los Angeles. He buys that there's a deep genetic division between modern dogs. But, it's still possible that dogs were domesticated just once, creating a large, widespread, interbreeding population that only later resolved into two distinct lineages.

In 2013, Wayne's team compared the mitochondrial genomes (small rings of DNA that sit outside the main set) of 126 modern dogs and wolves, and 18 fossils. They concluded that dogs were domesticated somewhere in Europe or western Siberia, between 18,800 and 32,100 years ago. And genes aside, "the density of fossils from Europe tells us something," says Wayne. "There are many things that look like dogs, and nothing quite like that in east Asia."

Peter Savolainen from the KTH Royal Institute of Technology in Stockholm disagrees. By comparing the full genomes of 58 modern wolves and dogs, his team has shown that dogs in southern China are the most genetically diverse in the world. They must have originated there around 33,000 years ago, he says, before a subset of them migrated west 18,000 years later.

That's essentially the same story that Larson is telling. The key difference is that Savolainen doesn't buy the existence of an independently domesticated group of western dogs. "That's stretching the data very much," he says. Those Ancient Western dogs might have just been wolves, he says. Or perhaps they were an even earlier group of migrants from the east. "I think the picture must seem a bit chaotic," he says understatedly. "But for me, it's pretty clear. It must have happened in southern East Asia. You can't interpret it any other way."

Except, you totally can. Wayne does ("I'm certainly less dogmatic than Peter," he says). Adam Boyko from Cornell University does, too: after studying the genes of village dogs—free-ranging mutts that live near human settlements—he argued for a single domestication in Central Asia, somewhere near India or Nepal. And clearly, Larson does as well.

Larson adds that his gene-focused peers are ignoring one crucial line of evidence—bones. If dogs originated just once, there should be a neat gradient of fossils with the oldest ones at the center of domestication and the youngest ones far away from it. That's not what we have. Instead, archaeologists have found 15,000-year-old dog fossils in western Europe, 12,500-year-old ones in east Asia, and nothing older than 8,000 years in between.

"If we're wrong, then how on earth do you explain the archaeological data?" says Larson. "Did dogs jump from East Asia to Western Europe in a week, and then go all the way back 4,000 years later?" No. A dual domestication makes more sense. Mietje Genompré, an archaeologist from the Royal Belgian Institute of Natural Sciences, agrees that the bones support Larson's idea. "For me, it's very convincing," she says.

But even Larson is hedging his bets. When I ask him how strong his evidence is, he says, "Like, put a number on it? If was being bold, I'd say it's a 7 out of 10. We lack the smoking gun."

Why is this so hard? Of all the problems that scientists struggle with, why has the origin of dogs been such a bitch to solve?

For starters, the timing is hard to pin down because no one knows exactly how fast dog genomes change. That pace—the mutation rate—underpins a lot of genetic studies. It allows scientists to compare modern dogs and ask: How long ago must these lineages have diverged in order to build up this many differences in their genes? And since individual teams use mutation rate estimates that are wildly different, it's no wonder they've arrived at conflicting answers.

Regardless of the exact date, it's clear that over thousands of years, dogs have mated with each other, cross-bred with wolves, travelled over the world, and been deliberately bred by humans. The resulting ebb and flow of genes has turned their history into a muddy, turbid mess—the homogeneous soup that Larson envisages.

Wolves provide no clarity. Grey wolves used to live across the entire Northern Hemisphere, so they could have potentially been domesticated anywhere within that vast range (although North America is certainly out). What's more, genetic studies tell us that no living group of wolves is more closely related to dogs than any other, which means that the wolves that originally gave rise to dogs are now extinct. Sequencing living wolves and dogs will never truly reveal their shrouded past; it'd be, as Larson says, like trying to solve a crime when the culprit isn't even on the list of suspects.

"The only way to know for sure is to go back in time," he adds.

The study informally known as the Big Dog Project was born of frustration. Back in 2011, Larson was working hard on the origin of domestic pigs, and became annoyed that scientists studying dogs were getting less rigorous papers in more prestigious journals, simply because their subjects were that much more charismatic and media-friendly. So he called up his longstanding collaborator Keith Dobney. "Through gritted teeth, I said: We're fucking doing dogs. And he said: I'm in."

Right from the start, the duo realized that studying living dogs would never settle the great domestication debate. The only way to do that was to sequence ancient DNA from fossil dogs and wolves, throughout their range and at different points in history. While other scientists were studying the soup of dog genetics by tasting the finished product, Larson would reach back in time to taste it at every step of its creation, allowing him to definitively reconstruct the entire recipe.

In recent decades, scientists have become increasingly successful at extracting and sequencing strands of DNA from fossils. This ancient DNA has done wonders for our understanding of our own evolution. It showed, for example, how Europe was colonized 40,000 years ago by hunter-gatherers moving up from Africa, then 8,000 years ago by Middle Eastern farmers, and 5,000 years ago by horse-riding herders from the Russian steppes. "Everyone in Europe today is a blend of those three populations," says Larson, who hopes to parse the dog genome in the same way, by slicing it into its constituent ingredients.

Larson originally envisaged a small project—just him and Dobney analyzing a few fossils. But he got more funding, collaborators, and samples than he expected. "It just kind of metastasized out of all proportion," he says. He and his colleagues would travel the world, drilling into fossils and carting chips of bone back to Oxford. They went to museums and private collections. ("There was a guy up in York who had a ton of stuff in his garage.") They grabbed bones from archaeological sites.

The pieces of bone come back to a facility in Oxford called the Palaeo-BARN—the Palaeogenomics and Bioarchaeology Research Network. When I toured the facility with Larson, we wore white overalls, surgical masks, oversoles, and purple gloves, to keep our DNA (and that of our skin microbes) away from the precious fossil samples. Larson called them 'spacesuits.' I was thinking 'thrift-store ninja.'

In one room, the team shoves pieces of bone into a machine that pounds it with a small ball bearing, turning solid shards into fine powder. They then send the powder through a gauntlet of chemicals and filters to pull out the DNA and get rid of everything else. The result is a tiny drop of liquid that contains the genetic essence of a long-dead dog or wolf. Larson's freezer contains 1,500 such drops, and many more are on the way. "It's truly fantastic the kind of data that he has gathered," says Savolainen.

True to his roots in archaeology, Larson isn't ignoring the bones. His team photographed the skulls of some 7,000 prehistoric dogs and wolves at 220 angles each, and rebuilt them in virtual space. They can use a technique calledgeometric morphometrics to see how different features on the skulls have evolved over time.

The two lines of evidence—DNA and bones—should either support or refute the double domestication idea. It will also help to clear some confusion over a few peculiar fossils, such as a 36,000 year old skull from Goyet cave in Belgium. Genompré thinks it's a primitive dog. "It falls outside the variability of wolves: it's smaller and the snout is different," she says. Others say it's too dissimilar to modern dogs. Wayne has suggested that it represents an aborted attempt at domestication—a line of dogs that didn't contribute to modern populations and is now extinct.

Maybe the Goyet hound was part of Larson's hypothetical Ancient Western group, domesticated shortly after modern humans arrived in Europe. Maybe it represented yet another separate flirtation with domestication. All of these options are on the table, and Larson thinks he has the data to tell them apart. "We can start putting numbers on the difference between dogs and wolves," he says. "We can say this is what all the wolves at this time period look like; does the Goyet material fall within that realm, or does it look like dogs from later on?"

Larson hopes to have the first big answers within six to twelve months. "I think it'll clearly show that some things can't be right, and will narrow down the number of hypotheses," says Boyko. "It may narrow it down to one but I'm not holding my breath on that." Wayne is more optimistic. "Ancient DNA will provide much more definitive data than we had in the past," he says. "[Larson] convinced everyone of that. He's a great diplomat."

Indeed, beyond accumulating DNA and virtual skulls, Larson's greatest skill is in gathering collaborators. In 2013, he rounded up as many dog researchers as he could and flew them to Aberdeen, so he could get them talking. "I won't say there was no tension," he says. "You go into a room with someone who has written something that sort of implies you aren't doing very good science... there will be tension. But it went away very quickly. And, frankly: alcohol."

"Everyone was like: You know what? If I'm completely wrong and I have to eat crow on this, I don't give a shit. I just want to know."

[The Minsky Moment]

First Phonecian sequenced truns out to be from an obscure European lineage. If true, it's not surprising given how mobile people were. However, very few ancient Africans have been sequenced due to the environment being bad for preservation.  This lineage could have originated in Africa long ago and then moved to Europe where we deteced their last descendants. We just can't tell until we get more data.

http://m.csmonitor.com/Science/2016/0529/Ancient-Phoenician-DNA-may-change-the-way-we-see-human-migration

Hmm I thought it was pretty much assumed that the Lebanese coast received invaders/migrants/refugees from the Aegean in bronze age collapse, thus wouldn't be totally surprising that European genes would be found in the iron age Phoenician population.

[Valmy]

Hmm I thought it was pretty much assumed that the Lebanese coast received invaders/migrants/refugees from the Aegean in bronze age collapse, thus wouldn't be totally surprising that European genes would be found in the iron age Phoenician population.

Yeah I thought that theory had strong support. This would, possibly, also support that pending further study.

[jimmy olsen]

The Red Wolf does not exist. At least not as a "natural" species, for whatever that's worth. It is a creation of man, due to the annhilation of the native wolves of the South. It's a 75% Coyote - 25% Grey Wolf mix.

The same is true of the Eastern Wolf, which is a more balanced 50/50 mix.

The Coyote it turns out is likely just a subspecies of wolf, diverging from the Grey Wolf just 50,000 years ago.

http://www.nytimes.com/2016/07/28/science/red-eastern-gray-wolves.html?_r=2

https://retrieverman.net/2016/08/01/north-american-canis-taxonomy-is-now-fubar/

I'm currently reading John Lane's excellent book, Coyote Settles the South. It is an excellent book, and I will be reviewing it here very soon. The whole time I've been reading it I thinking about my encounter with the male Eastern coyote I called in back in March.

He's not exactly the same coyote that Lane is writing about. He's a coyote of the gray woods, not the subtropical pine forests and river bottoms.

But in some ways, he is the same. He is the same creature that has adjusted to all that Western man can throw at him and thrived.

And he's thrived at the expense of the wolves that once roamed over the Northeastern US and the South. He's just the right size to live on a diet of rodents and rabbits but also has the ability to pack up and hunt deer. He can be an omnivore, enjoying wild apples and pears that fall to the ground, almost as much as he would if he came across a winter-killed deer.

The coyote is a survivor. I've written on this space several times that the reason he has thrived is because he has been here far longer than the wolves that once harried his kind. Until last week, it was assumed that the coyote split from the wolf some 1 million years ago. This million year split has been used for virtually every study that has examined the relationships between different populations or species in the genus Canis. It is used to set the molecular clock so that we can figure out when wolves and dogs split and perhaps give us some idea as to when dogs may have been domesticated.

This assumption has been directly challenged in a new study that was released in Science Advances last week. The paper examined full genome sequences of several different canids, and it can be argued that it pretty much ended the debate as to whether the red wolf and Eastern wolf are species. They aren't. Instead, they are the result of hybridization between wolves and coyotes. Most of the media attention has paid attention to this discovery in the study.

It's the most important practical implications, because the US Fish and Wildlife Service delisted the gray or Holarctic wolf in most of the Eastern, Southern, and Midwestern states in favor of protecting the Eastern and red wolves. Red wolves are called Canis rufus, and  Eastern wolf is Canis lycaon. With them being recognized as hybrids, this greatly complicates the issue of how to conserve them under the Endangered Species Act, which, as its name suggests, is meant to conserve actual species and not hybrids between species.

The authors of the study feel that these hybrid populations are still worth conserving, largely because the red wolf contains the last reservoir of genes belonging to the now extinct wolves of the Southeast.

But in order to make this work, we're probably going to have to rewrite the Endangered Species Act, and that is not going to happen any time soon.

However, the finding in the study that is worth discussing more is that not only showed that red and Eastern wolves were not some relict ancient species of wolf. It is the finding that coyotes and wolves split only 50,000 years ago.

Using a simple isolation model and a summary likelihood approach, we estimated a Eurasian gray wolf–coyote divergence time of T = 0.38 N generations (95% confidence interval, 0.376 to 0.386 N), where N is the effective population size. If we assume a generation time of 3 years, and an effective population size of 45,000 (24, 25), then this corresponds to a divergence time of 50.8 to 52.1 thousand years ago (ka), roughly the same as previous estimates of the divergence time of extant gray wolves.

This finding means that the studies that use that 1 million year divergence time to set the molecular clock for all those dog domestication studies need to be reworked. This is going to have some effect on how we think about dog domestication, and although the domestication dates have been moved back in recent years, the actual split between dogs and wolves is likely to be much later than when we see the first signs of domestication in subfossil canids.

That's one important finding that comes from this discovery that wolves and coyotes are much more closely related.

The other is that yes, it did pretty much end Canis rufus and Canis lycaon as actual species, but it probably also ends the validity of Canis latrans as a valid species. Coyotes could be classified as a subspecies of wolf. Indeed, they are much more closely related to wolves than Old World red foxes are to New World red foxes, which split 4oo,ooo years ago. And there is still some debate as to whether these two foxes are distinct species, because we've traditionally classified them as a single species. Plus, if we start splitting them into two species, we're likely to find the same thing exists with least weasels living in the Old and New World. And the same thing with stoats.

And then it's not long we're fighting over the house mouse species complex.

But if we're going to lump red foxes, it's pretty hard not to lump coyotes and wolves. It is true that wolves normally kill coyotes in their territory, but it also found that wolves in Alsaska and Yellowstone, wolves that were thought to be entirely free of any New World ancestry, also had some coyote genes.

So the coyote, like the extinct Honshu wolf and the current Arabian wolf, could be correctly thought of a small subspecies of wolf. We know from paleontology that in both North America and Eurasia there were various forms of canid that varied from jackal-like to wolf-like, and although we know the jackal-like form is the earliest form, these two types have ebbed and flowed across Eurasia and North America. We've assumed that the jackal-like forms gave became the coyote and the larger wolf-like forms have become the gray, red, and dire wolves.

But what we're looking at now is the coyote isn't the ancient species we thought it was. It's very likely that some ancestral wolf population came into North America, and instead assuming the pack-hunting behavior of Eurasian wolves, it tended toward the behavior of a golden jackal. When this ancient wolf walked into North America, it would have found that the pack-hunting niche was already occupied by dire wolves. There were many other large predators around as well, and evolving to the jackal-like niche would have made a lot more sense in evolutionary terms.

This is what the coyote is.

The pack-hunting modern wolf came into the continent and took it by storm, and the coyote exchanged genes with it. They lived together as sort of species-like populations in the West, but when wolves became rare from persecution following European settlement, the coyote and wolf began to exchange genes much more.

So with one study using complete genomes, the entire taxonomy of North American Canis is truly blown asunder.

And the implications for dog domestication studies and for the practical application of the Endangered Species Act could not be any more consequential.

Very rarely do you get studies like this one.

It changes so much, and the question about what a coyote is has become unusually unsettling but also oddly amazing.

I will never think of a coyote the same way.

The mystery is even more mysterious.

[jimmy olsen]

More proof that intelligence in modern society is being selected against by natural selection

http://www.pnas.org/content/early/2017/01/10/1612113114.full

Abstract

Epidemiological and genetic association studies show that genetics play an important role in the attainment of education. Here, we investigate the effect of this genetic component on the reproductive history of 109,120 Icelanders and the consequent impact on the gene pool over time. We show that an educational attainment polygenic score, POLYEDU, constructed from results of a recent study is associated with delayed reproduction (P < 10−100) and fewer children overall. The effect is stronger for women and remains highly significant after adjusting for educational attainment. Based on 129,808 Icelanders born between 1910 and 1990, we find that the average POLYEDU has been declining at a rate of ∼0.010 standard units per decade, which is substantial on an evolutionary timescale. Most importantly, because POLYEDU only captures a fraction of the overall underlying genetic component the latter could be declining at a rate that is two to three times faster.

    selection educational attainment genes fertility sequence variants

Epidemiological studies have estimated that the genetic component of educational attainment can account for as much as 40% of the trait variance (1). Recent meta-analyses (2, 3) yielded sequence variants contributing to the underlying genetic component. A negative correlation between educational attainment and number of children has been observed in many populations (4⇓⇓–7). A recent study of ∼20,000 genotyped Americans born between 1931 and 1953 provided direct evidence that the genetic propensity for educational attainment is associated with reduced fertility (8, 9), supporting previously postulated notions (10) that the population average of the genetic propensity for educational attainment and related traits must be declining. Here, using a population-wide sample that is both much larger and covers a substantially greater time span, and with additional auxiliary information, we aim to estimate the change of the genetic propensity of educational attainment in the Icelandic population over the last few decades, starting with an in-depth investigation of the relationship between a measurable genetic component of educational attainment and various aspects of reproduction (11⇓⇓–14).

[LaCroix]

  tim

[Valmy]

More proof that intelligence in modern society is being selected against by natural selection

Counter point is the impressive fecundity of BB and I right?

[grumbler]

I think that the assumption of this study, which is that changes in educational achievement is due to changes in the gene pool rather than changes in education, is unsupported.

[jimmy olsen]

 
University of California Television series of lectures on Ancient DNA begins here

https://www.youtube.com/watch?v=CH_GjaxNyZk&index=100&list=PL239FE2D62ECB3FD3

[jimmy olsen]

Neat. 

http://news.nationalgeographic.com/2017/02/chaco-canyon-pueblo-bonito-room-33/

DNA Offers Clues to Mysterious Crypt in Ancient Pueblo

It's a question that eluded answers for more than a century: Who were the 14 people buried in the tiny tomb known as Room 33?

By Andrew Curry

PUBLISHED February 21, 2017

Using DNA from skeletons excavated in New Mexico more than a century ago, researchers have shown that more than a dozen people buried in a small, hidden chamber were likely members of a powerful Native American dynasty related through their mothers.

New Mexico's Chaco Canyon was once the center of the most influential culture in the American Southwest. Between approximately 800 A.D. and 1100 A.D., the ancient Chacoans built settlements called pueblos with huge, five-story buildings and grand ceremonial plazas. Elaborate road networks connected the pueblos, and at its peak the culture covered most of modern New Mexico, along with parts of Utah, Colorado, and Arizona.

At the center of Chacoan society was Pueblo Bonito, Spanish for "beautiful town." Covering more than four acres, the elaborate pueblo was a honeycomb of nearly 650 rooms. Close to the pueblo's center was a hidden chamber measuring just six feet long by six feet wide and accessible only through a small hatch in the roof.

Archaeologists who excavated Room 33 in 1896 were stunned by the richness of the burial goods, including thousands of turquoise beads, as well as jewelry and instruments made from shells imported from the Pacific.
 
Archaeologists working for New York's American Museum of Natural History (AMNH) excavated Pueblo Bonito in 1896. Inside the tiny innermost chamber they discovered the remains of 14 people buried under the room's sandy floor, with grave stacked on grave in the tight space. The excavators labeled the mysterious chamber Room 33.

The two men buried at the bottom of the room were surrounded by stunning wealth. The first man buried in the chamber, known as Burial 14, was found with more than 12,000 turquoise beads and dozens of turquoise sculptures—more of the precious stone than in all the other Chacoan sites combined. A conch shell trumpet, likely from the Pacific, and other musical instruments rounded out the chamber's grave goods. Scarlet macaws imported from more than 1,000 miles away in Central America were found in a nearby room.

Female Power Line

The artifacts and human remains from Room 33 have been stored at the American Museum of Natural History since they were excavated in the 19th century. Since then the skeletons have remained a mystery: Who were these people, and why were they buried in a walled-off room in the middle of the mighty pueblo?

Recently, new radiocarbon dates and ancient DNA analysis of the millennia-old bones revealed that the burials may represent an early Native American dynasty. In a paper published today in the journal Nature Communications, researchers show that the men and women buried in the chamber are all related through their mothers, a connection known as a matriline. Many Native American groups still pass membership on through the mother's side, as do most of the world's Jewish communities.

"One pair may be a grandmother and her grandson, another two mother and daughter. They may not all have been rulers, but they were related," says University of Virginia archaeologist and study co-author Stephen Plog. "The evidence suggests it's a long matriline, in control for a long, long time."

Most researchers once thought Chacoan cultures were egalitarian, with no real hierarchy. Many modern Native American groups in the region are governed communally today.

But the grave goods show that Burial 14—a man who died around 880 A.D., likely killed by a blow to the head—was a big deal in life. And DNA evidence showing three centuries of relatives buried in the same room suggests that spending eternity with him was a high honor, one restricted to his matrilineal descendants.

Put together, the clues seem to indicate that Burial 14 was the founder of a political dynasty that lasted 300 or more years.

"It's likely Burial 14 is really the first individual to differentiate himself politically from other people in the canyon," Plog says. "I'm confident his matriline was the most powerful in Pueblo Bonito, and probably in Chaco Canyon. It was an elite group, able to control resources and have influence over broad areas of the Southwest."

Source of Status

The results are some of the first to use DNA to tackle a fundamental question in the study of human history: Where does status come from?

Hereditary leadership—power and status based on birth—is a hallmark of complex societies. In societies that use writing, evidence for hereditary leadership is easy to come by: In Europe, written histories hold the answers. In the Americas, Aztec and Maya ruling families have been indentified from carved inscriptions.

But without such records it's difficult to prove that leadership and power in ancient societies without writing was hereditary. "If these results hold up, I think it's a game changer," says American Museum of Natural History archaeologist David Thomas, who was not involved in the research.

Testing Ancestral Remains

For many groups who consider the people of Chaco Canyon their ancestors, the research may be controversial. Tribes including the Navajo, Hopi, Zuni, and Acoma all consider themselves descendants of the Chaco Canyon people, and some have religious objections to invasive, destructive testing on human remains.

Though the bones were excavated more than a century ago, curators at the American Museum of Natural History still weighed such concerns before authorizing the testing. "We can be sensitive and deal with communities in a respectful way and still do the best science we can do," says Thomas. "I think there's a middle ground."

[Razgovory]

First Phonecian sequenced truns out to be from an obscure European lineage. If true, it's not surprising given how mobile people were. However, very few ancient Africans have been sequenced due to the environment being bad for preservation.  This lineage could have originated in Africa long ago and then moved to Europe where we deteced their last descendants. We just can't tell until we get more data.

http://m.csmonitor.com/Science/2016/0529/Ancient-Phoenician-DNA-may-change-the-way-we-see-human-migration

Hmm I thought it was pretty much assumed that the Lebanese coast received invaders/migrants/refugees from the Aegean in bronze age collapse, thus wouldn't be totally surprising that European genes would be found in the iron age Phoenician population.

What's more interesting is where genes are associated with.  Iberia.

[katmai]

Hey Cal, are ancestry and 23and me the only two you've done?