Well, Duh! More on Man's Best Friend

From The New York Times

Deeper Digging Needed to Decode a Best Friend’s Genetic Roots

By JAMES GORMAN
Published: May 21, 2012

As scientific puzzles go, the origin of dogs may not be as important as the origin of the universe. But it strikes closer to home, and it almost seems harder to answer.       

Cosmologists seem to have settled on the idea that 13.7 billion years ago the universe appeared with a bang (the big one) from nothing — albeit a kind of nothing that included the laws of physics.

With dogs, the consensus is that they came from wolves. Beyond that, there are varying claims. It seems dogs appeared sometime between 15,000 and 100,000 years ago, in Asia or Africa or multiple times in multiple places.

There is a reason for this confusion, according to Greger Larson at the University of Durham in England. In a new research paper, he argues that the DNA of modern dogs is so mixed up that it is useless in figuring out when and where dogs originated. “With the amount of DNA we’ve sequenced so far,” Dr. Larson said, “we’re lucky to get back a hundred years, max.” He says that only with the analysis of DNA from fossil dogs, now being done, will answers along this line emerge.

Dr. Larson, the first of 20 authors on a paper about the origin of dogs published Monday in The Proceedings of the National Academy of Sciences, argues that genetic study of modern breeds does not “get us any closer to understanding where and when and how dogs were domesticated.”

A Saluki, from article.

Adam Boyko of Cornell University, who has worked in the field of dog genetics but was not involved in the study, said that Dr. Larson’s group had a “fantastic data set,” and laid out clearly the current difficulties in nailing down the details of dog domestication. Dr. Larson and his colleagues analyzed 49,024 locations on dog DNA where the genetic code varies, so called SNPs (pronounced snips, for single nucleotide polymorphisms). They took the DNA from 1,375 dogs of 121 breeds, and 19 wolves.

What they found was that all the so-called modern breeds had been so mixed that their deep genetic history was obscured. [How can experts be so sure that this hasn't also happened with some "breeds" of humans???]

They also found six breeds that they called basal, meaning that their DNA was less mixed — the basenji, shar-pei, Saluki, Akita, Finnish spitz and Eurasier.       

Image from "The Dogs of Ancient Egypt" by Jimmy Dunn, Tour Egypt.

When they added these to eight breeds deemed ancient (older than 500 years) ["ancient" is only older than 500 years????] in other studies, what they found was that the dogs that were most genetically distinct were not from the places where the oldest archaeological and fossil evidence had been found. Dr. Larson said that the expectation was that if these breeds were closer genetically to the first domesticated dogs, they would be geographically closer as well, more likely to be found near the sites of early dog fossils, or archaeological records of ancient breeds.

Instead, the more genetically distinct dogs had been geographically isolated relatively recently in the history of domestication. For example, dingoes, basenjis and New Guinea singing dogs came from Southeast Asia and southern Africa, where dogs did not arrive until 3,500 and 1,400 years ago, respectively. Their distinctive genes were indications of relatively recent isolation. [This is fascinating. Didn't dog follow man?  And if dog followed so-called "modern man" out of Africa, for instance, some 100,000 years ago, wouldn't Africa be one of the hot spots of wide-spread 'original'  canine diversity, as it is said to be the hot spot for 'original' human genetic diversity?  Hmmmm, perhaps something is wrong with the entire model being used to interpret evidence.]

But, he said, all is not lost. Humans have buried their dogs for a long time, and as a result there are fossils of truly ancient dogs, in the neighborhood of 15,000 years old, from which DNA can be extracted. Just as DNA from Neanderthals has helped illuminate the origins of modern humans, DNA from ancient dog fossils should help illuminate the story of early dog domestication in the next few years. [Actually, any "differences" between so-called "Neanderthal" and "modern humans" were basically non-existent because many "modern humans" carry "Neanderthal" DNA.  If the "species" were that different, successful interbreeeding would not have been possible.  "Neanderthal" did not die out, he and she exist today within lots of us! 

“Let’s step back,” he said. “Let’s take a breath. We’re not a million miles away” from figuring out when and where dogs appeared. “We’re close.”         

*************************************

Yeah, right.  Close.  Ha ha ha!  You won't ever be close so long as you and other experts continue to insist that genetic diversity DECREASED over time for humans.  Think about that for a minute.  As humans spread across the globe, so current theory goes, isolated groups of humans that moved further and further away from the "parent group" developed distinct forms of DNA what-nots (I don't know all of the fancy terms) and they were less diverse than the "parent group," some of whom, I think, are said to have stayed back in Africa.  So, as humans spread around the globe, we moved from a greatly diverse population, genetically speaking, to a much less genetically diverse population. 

But our doggies, the genetic evidence is now showing, did the exact opposite.  Hmmmmm, is there something wrong with this picture?

Another Shot Across the Bow in the DNA Wars!

23 August 2011 Last updated at 19:15 ET
Study deals blow to theory of European origins
By Paul Rincon
Science editor, BBC News website
[Note: The title is wrong. The gist of the article is that this latest research study shows the opposite!]
A new study deals a blow to the idea that most European men are descended from farmers who migrated from the Near East 5,000-10,000 years ago.

The findings challenge previous research showing that the genetic signature of the farmers displaced that of Europe's indigenous hunters. The latest research leans towards the idea that most of Europe's males trace a line of descent to stone-age hunters. But the authors say more work is needed to answer this question.

The study, by an international team, is published in the journal Proceedings of the Royal Society B.
Archaeological finds show that modern humans first settled in Europe from about 40,000 years ago - during a time known as the Palaeolithic. [For convenience, I call these "the first settlers who became Europeans"].

These people survived an Ice Age some 20,000 years ago by retreating to relatively warm refuges in the south of the continent, before expanding into northern Europe again when the ice melted. But just a few thousand years after Europe had been resettled by these hunter-gatherers ['Europeans'], the continent underwent momentous cultural change. Farmers spread westwards from the area that is now Turkey, bringing with them a new economy and way of life. [See my comment below].

The extent to which modern Europeans are descended from these early farmers versus the indigenous hunter-gatherers who settled the continent thousands of years previously is a matter of heated debate. The results vary depending on the genetic markers studied and are subject to differing interpretations. [In other words, our technology is not up to the task of answering the question at present.  A refreshing change from most "scientific" articles that present the latest as the truth, the whole truth, and nothing but the truth!]

Family tree

The latest study focused on the Y chromosome - a package of DNA which is passed down more or less unchanged from father to son.  The Y chromosomes carried by people today can be classified into different types, or lineages, which - to some extent - reflect their geographical origins.

More than 100 million European men carry a type called R-M269, so identifying when this genetic group spread out is vital to understanding the peopling of Europe. R-M269 is most common in western Europe, reaching frequencies of 90% or more in Spain, Ireland and Wales.

But while this type reaches its highest distribution on the Atlantic fringe, Patricia Balaresque and colleagues at the University of Leicester published a paper in 2010 showing that the genetic diversity of R-M269 increases as one moves east - reaching a peak in Anatolia (modern Turkey). [Hmm...]

Genetic diversity is used as a measure of age; lineages that have been around for a long time accumulate more diversity. So this principle can be used to estimate the age of a population. [A clear and concise statement that diametrically opposes at least one other statement in an article discussing a DNA study that said diversity decreases in a given population over time.  That was so counter-intuitive to general principles of logic that I wrote to Mr. Don about it and asked him to read the article and see what he thought - and if I was just reading it wrong.  He read the article and agreed with me.  But tonight, I'm tired and I'm not going to go digging around in old archived emails to find the specific email and article!]

When the Leicester team estimated how old R-M269 was in different populations across Europe, they found the age ranges were more compatible with an expansion in Neolithic times (between 5,000 and 10,000 years ago). [In other words, some people from the Middle East followed their idea of 'farming' into the West some several thousands of years after that idea had already been spread - by whatever means - into Europe, beginning with "Old Europe" and eventually spreading westward all the way to the edges of 'Europe.']

The team's conclusions received support from papers published in August 2010 and in June this year. But one study which appeared last year backed the idea of a more ancient, Palaeolithic origin for R-M269.

Age estimates

Now, a team including Cristian Capelli and George Busby at Oxford University have explored the question.

Their results, based on a sample of more than 4,500 men from Europe and western Asia, showed no geographical trends in the diversity of R-M269. Such trends would be expected if the lineage had expanded from Anatolia with Neolithic farmers.

Furthermore, they suggest that some of the markers on the Y chromosome are less reliable than others for estimating the ages of genetic lineages. On these grounds, they argue that current analytical tools are unsuitable for dating the expansion of R-M269. [Damn right. If I'm reading this correctly, 50% of the most current research says "they came from the Middle East" and 50% of the research says "nope, they were "always" here. LOL!]

Indeed, Dr Capelli and his team say the problem extends to other studies of Y-chromosome lineages: dates based on the analysis of conventional DNA markers may have been "systematically underestimated", they write in Proceedings B.

But Dr Capelli stressed that his study could not answer the question of when the ubiquitous R-M269 expanded in Europe, although his lab is carrying out more work on the subject.

"At the moment it's not possible to claim anything about the age of this lineage," he told BBC News, "I would say that we are putting the ball back in the middle of the field."

Co-author Dr Jim Wilson from the University of Edinburgh explained: "Estimating a date at which an ancestral lineage originated is an interesting application of genetics, but unfortunately it is beset with difficulties."

The increasing frequency of R-M269 towards western Europe had long been seen by some researchers as an indication that Palaeolithic European genes survived in this region - alongside other clues.

A more recent origin for R-M269 than the Neolithic is also possible. But researchers point out that after the advent of agriculture, populations in Europe exploded, meaning that it would have been more difficult for incoming migrants to displace local people.

Interesting New Genetic Study Reveals Shared Sub-Saharan African Ancestry

Press Release at Eurekalert.org

Contact: David Cameron
david_cameron@hms.harvard.edu
617-432-0441
Harvard Medical School

Population genetics reveals shared ancestries
More than just a tool for predicting health, modern genetics is upending long-held assumptions about who we are. A new study by Harvard researchers casts new light on the intermingling and migration of European, Middle Eastern and African and populations since ancient times.

In a paper titled "The History of African Gene Flow into Southern Europeans, Levantines and Jews," published in PLoS Genetics, HMS Associate Professor of Genetics David Reich and his colleagues investigated the proportion of sub-Saharan African ancestry present in various populations in West Eurasia, defined as the geographic area spanning modern Europe and the Middle East. While previous studies have established that such shared ancestry exists, they have not indicated to what degree or how far back the mixing of populations can be traced.

Analyzing publicly available genetic data from 40 populations comprising North Africans, Middle Easterners and Central Asians were doctoral student Priya Moorjani and Alkes Price, an assistant professor in the Program in Molecular and Genetic Epidemiology within the Department of Epidemiology at the Harvard School of Public Health.

Moorjani traced genetic ancestry using a method called rolloff. This platform, developed in the Reich lab, compares the size and composition of stretches of DNA between two human populations as a means of estimating when they mixed. The smaller and more broken up the DNA segments, the older the date of mixture.

Moorjani used the technique to examine the genomes of modern West Eurasian populations to find signatures of Sub-Saharan African ancestry. She did this by looking for chromosomal segments in West Eurasian DNA that closely matched those of Sub-Saharan Africans. By plotting the distribution of these segments and estimating their rate of genetic decay, Reich's lab was able to determine the proportion of African genetic ancestry still present, and to infer approximately when the West Eurasian and Sub-Saharan African populations mixed.

"The genetic decay happens very slowly," Moorjani explained, "so today, thousands of years later, there is enough evidence for us to estimate the date of population mixture."

While the researchers detected no African genetic signatures in Northern European populations, they found a distinct presence of African ancestry in Southern European, Middle Eastern and Jewish populations. Modern southern European groups can attribute about 1 to 3 percent of their genetic signature to African ancestry, with the intermingling of populations dating back 55 generations, on average—that is, to roughly 1,600 years ago. Middle Eastern groups have inherited about 4 to 15 percent, with the mixing of populations dating back roughly 32 generations. A diverse array of Jewish populations can date their Sub-Saharan African ancestry back roughly 72 generations, on average, accounting for 3 to 5 percent of their genetic makeup today.

According to Reich, these findings address a long-standing debate over African multicultural influences in Europe. The dates of population mixtures are consistent with documented historical events. For example, the mixing of African and southern European populations coincides with events during the Roman Empire and Arab migrations that followed. The older-mixture dates among African and Jewish populations are consistent with events in biblical times, such as the Jewish diaspora that occurred in 8th to 6th century BC.

"Our study doesn't prove that the African ancestry is associated with migrations associated with events in the Bible documented by archeologists," Reich says, "but it's interesting to speculate."

Reich was surprised to see any level of shared ancestry between the Ashkenazi and non-Ashkenazi Jewish groups. "I've never been convinced they were actually related to each other," Reich says, but he now concludes that his lab's findings have significant cultural and genetic implications. "Population boundaries that many people think are impermeable are, in fact, not that way."

###

The Human Story Just Got More Interesting

One of the things about current DNA theory that is counter-intuitive to me is that human groups got less diverse the further away from Africa they moved.  One would think that as more people around the world had the opportunity to meet and breed our DNA signatures would get more complicated, not less complicated.  But the theory says that as people moved out of Africa (assuming the out of Africa theory is correct) and slowly travelled across and then filled the world, their DNA got less diverse. 

This story definitely contradicts that view and for a startling reason - well, startling to some people.

Story from Live Science
Humans Interbred with Neanderthals, Study Suggests
By Clara Moskowitz, LiveScience Senior Writer
posted: 29 April 2010 08:24 am ET

Humans today could be part Neanderthal, according to a new study that found our ancestors interbred with an extinct hominid species some millennia ago.

Neanderthals walked the Earth between about 130,000 and 30,000 years ago. While they co-existed with modern humans for a while, eventually they went extinct and we didn't. There has been intense scientific debate over how similar the two species were, and whether they might have mated with each other.

"The issue has been highly contentious for some time," said University of New Mexico genetic anthropologist Keith Hunley.

Last week at the annual meeting of the American Association of Physical Anthropologists in Albuquerque, N.M., Hunley and colleagues presented the results of a new study that found evidence for interbreeding between modern humans and some other extinct ancient human species – either Neanderthals (Homo neanderthalensis) or another group such as Homo heidelbergensis. The research was first reported by NatureNews.

The researchers looked at DNA samples from humans living today, and found signs of leftover Neanderthal genes introduced from this interbreeding. They looked at genetic data from almost 2,000 people around the world, and calculated how much genetic variation existed between samples. The results indicate that some extinct group of hominids mixed their genes with ours at two points in history, Hunley said.

One period of interbreeding probably occurred shortly after Homo sapiens migrated out of Africa around 60,000 years ago. The researchers found an excess of genetic diversity in all modern people except Africans, suggesting that the influx of Neanderthal-like DNA came after the exodus from Africa.

A second period of interbreeding is suggested by the fact that the researchers measured even more genetic diversity among people of Oceanic descent – people from Australia, New Zealand, New Guinea and other Pacific islands.

"I think we show there's clear evidence in the genome of living people of this mixture," Hunley told LiveScience. "The fact that there's a clear signal implies that there was some significant amount" of interbreeding, he said.

This work is the first time scientists have used DNA from living people to look at this question, Hunley said.

In an earlier study, Erik Trinkaus of Washington University in St. Louis found suggestions of Neanderthal and modern human interbreeding by comparing ancient bone fossils from the two species.

Trinkaus said the new work fits into his findings, though he hasn't reviewed the details yet since Hunley's paper has not yet been published in a peer-reviewed journal. "The conclusion makes sense and fits with the majority of the data available," Trinkaus said.

Another anthropologist who has studied Neanderthal anatomy agreed.

"I have been arguing for this position throughout my career, ever since I began to study Neandertals and other populations," said Milford Wolpoff of the University of Michigan. "It has always seemed clear that some Neandertal anatomy appears in living populations."

Not everyone, though, will be easily convinced yet, Hunley said.