Several posters at Davidski's Eurogenes blog have noted that they've been banned from Anthrogenica for challenging the Kool-Aid drinking orthodoxy that infects that website.
The pattern almost always goes as follows. A regular Anthrogenica poster says something like, "Isn't the Kool-Aid grand?" A newcomer says, "I don't want to drink your Kool-Aid." The Anthrogenica regular says, "I'm right, you idiot." And then the newcomer says, "You're the idiot" -- and yep, you guessed it, only one of them gets banned.
It's gotten so bad that some of the best citizen-scientist minds, and almost all contrarian voices, are gone from that website. In the old days, the orthodoxy sought to excommunicate Galileo from the Catholic faith. Now they excommunicate posters from the major discussion websites. No dissent allowed.
With Dienekes inactive, Eurogenes is where many go for discussion. But Davidski has been very heavy with the censorship button there too. Post something he disagrees with? He removes your comment. It's really sad.
I myself have tried to post my most recent thread, about applying simple demographics to his "Conquest and Warfare" fantasies, and he always removes my comments asap.
What does that leave? Eupedia? Maciamo is a reductio ad absurdem idiot, who also doesn't hesitate to ban people with any contrarian viewpoint.
So, this is it. This is your thread. This thread (and this website) is for anyone Banned From Anthrogenica, or Censored by Eurogenes.
Post away. You will not be censored here.
Friday, May 12, 2017
Saturday, April 29, 2017
When Is A "Conquest" Not A Conquest?
When Is A Conquest Not A Conquest?
You are a scientist living in the year 4017, specializing in the ancient civilizations that existed between 1492 and 2200 A.D. Various cultures came and went, but alas, most written records were lost in the intervening centuries. So you study DNA.
Your fellow scientists know that in many different regions, the DNA record shows profound change over time, both in autosomal percentages and uniparental markers (Y-Chromosome, mtDNA).
Unfortunately, arrogant bloggers still exist in 4017, and three of them, one called Davidski Futurski (who blogs at Eurogenes-ski), a fellow named Maciamo-Futuriamo, and another named Rocca Futura, are examples of "a little knowledge can be dangerous."
They blindly state that all changes in DNA indicate evidence of conquest by some superior culture of badass men. (Nevermind that they all believe they descend from the people they assert to be superior; that's irrelevant, we're sure).
They blindly state that all changes in DNA indicate evidence of conquest by some superior culture of badass men. (Nevermind that they all believe they descend from the people they assert to be superior; that's irrelevant, we're sure).
Your boss at the university, someone who sees nuance better than the bloggers, asks you to model the record and various types of human interactions, and answer the question:
"When Might A 'Conquest' Not Really Be A Conquest?"
So you come up with the following four models, and re-create as best as you can some historical examples for the clueless:
"When Might A 'Conquest' Not Really Be A Conquest?"
So you come up with the following four models, and re-create as best as you can some historical examples for the clueless:
1. Refugees from a war-torn area flood into a nearby land (and even some faraway lands), overwhelming the demographics. The bloggers post that a people called the Syrians conquered the Lebanese, starting in 2011, but you're not so sure. Your research finds the opposite: that there was a horrendous war in Syria, causing 11 million people to lose all their belongings and flee. Therefore, you don't think these people were conquerors, but refugees. Nevertheless, the stubborn bloggers point out how the record shows a massive DNA shift in Lebanon, where the Syrian markers went from 5% to 25% of the population in just three years.
"It had to be conquest" they write, of powerful, rich, sophisticated men conquering the weak Lebanese.
Alas, you tell them: it was the opposite: a beaten-down people streaming into a nearby land (and also places like Sweden), altering the gene pool. In fact, Lebanon started with 5 million people, and absorbed an influx of 2.5 million refugees. Thus, the autosomal genetics and uniparental frequencies were both significantly changed. It's really as simple as that.
"It had to be conquest" they write, of powerful, rich, sophisticated men conquering the weak Lebanese.
Alas, you tell them: it was the opposite: a beaten-down people streaming into a nearby land (and also places like Sweden), altering the gene pool. In fact, Lebanon started with 5 million people, and absorbed an influx of 2.5 million refugees. Thus, the autosomal genetics and uniparental frequencies were both significantly changed. It's really as simple as that.
2. Disease. In 1598, slaves from Africa were brought to a place called Puerto Rico. They brought with them Yellow Fever, something the native American inhabitants did not have exposure or antibodies to.
Although the natives were, under the caste system at the time, a couple of rungs higher than the African slaves, and although the natives had better sources of food and systems for dealing with the native landscape, they were killed off in the thousands simply because they didn't have antibodies to the new disease.
But all the bloggers see is that Puerto Rico went from showing Native American DNA patterns to showing African (and European) DNA patterns. And they cry, their must have been a conquest, led by the African newcomers! You LOL, pointing out that these newcomers were slaves and vectors.
3. Economic Opportunity. The bloggers now discuss Los Angeles. They point out that the DNA record shows that in the 1950s, Los Angeles was 80% inhabited by an ancient culture called, "whites." By 2020, it was 60% Hispanic. The record thus showed profound shifts in autosomal frequencies and Y-chromosome patterns.
"There must have been a conquest!" the bloggers shout from the rooftops! War! Destruction! A supreme powerful tribe of men, with better tools!
No, you quietly assert. Your research shows that poor Hispanic immigrants simply migrated to Los Angeles, looking for better economic opportunities than what existed back home. Alas, the bloggers still don't grasp this example either.
4. Simple Cultural Differences in Birthrates. Palestinian women have vastly greater birthrates than their neighbors. In the 1960s, it was 8 children per every female. Even now, it's above 4.0 children for every woman. The Israeli birthrate, while still relatively high at 3.0, is not as high. By 2045, Palestinians may outnumber Israelis.
Our future bloggers, looking at this from the perspective of the year 4017, may try to argue that there was a conquest by the Palestinians. They must have had superior technology, they claim! Better weapons!
But again, your research (and history) shows this NOT to be the case.
Taking these four examples, you explain to the bloggers that many changes in DNA frequency, cannot be explained as "conquest" even though it's tempting for the simple-minded to do so.
There are even examples of multiple of the above factors explaining demographic shifts. For example, the Catholic Irish replacement of Anglo Saxons in many East Coast cities in the 1800s. That was due to the Irish being refugees, seeking greater economic opportunity en masse, and having higher birthrates.
Somewhere in the future, the intellectual heirs of Maciamo, Davidski, and many on Anthrogenica, are arguing that the Irish immigrants of the 1800s were in fact a technologically and militarily superior, overwhelming force of wealthy males who clearly conquered the British Americans of the time.
And you, and anyone with any degree of a nuances understanding of history, is still LOL'ing.
Although the natives were, under the caste system at the time, a couple of rungs higher than the African slaves, and although the natives had better sources of food and systems for dealing with the native landscape, they were killed off in the thousands simply because they didn't have antibodies to the new disease.
But all the bloggers see is that Puerto Rico went from showing Native American DNA patterns to showing African (and European) DNA patterns. And they cry, their must have been a conquest, led by the African newcomers! You LOL, pointing out that these newcomers were slaves and vectors.
3. Economic Opportunity. The bloggers now discuss Los Angeles. They point out that the DNA record shows that in the 1950s, Los Angeles was 80% inhabited by an ancient culture called, "whites." By 2020, it was 60% Hispanic. The record thus showed profound shifts in autosomal frequencies and Y-chromosome patterns.
"There must have been a conquest!" the bloggers shout from the rooftops! War! Destruction! A supreme powerful tribe of men, with better tools!
No, you quietly assert. Your research shows that poor Hispanic immigrants simply migrated to Los Angeles, looking for better economic opportunities than what existed back home. Alas, the bloggers still don't grasp this example either.
4. Simple Cultural Differences in Birthrates. Palestinian women have vastly greater birthrates than their neighbors. In the 1960s, it was 8 children per every female. Even now, it's above 4.0 children for every woman. The Israeli birthrate, while still relatively high at 3.0, is not as high. By 2045, Palestinians may outnumber Israelis.
Our future bloggers, looking at this from the perspective of the year 4017, may try to argue that there was a conquest by the Palestinians. They must have had superior technology, they claim! Better weapons!
But again, your research (and history) shows this NOT to be the case.
Taking these four examples, you explain to the bloggers that many changes in DNA frequency, cannot be explained as "conquest" even though it's tempting for the simple-minded to do so.
There are even examples of multiple of the above factors explaining demographic shifts. For example, the Catholic Irish replacement of Anglo Saxons in many East Coast cities in the 1800s. That was due to the Irish being refugees, seeking greater economic opportunity en masse, and having higher birthrates.
Somewhere in the future, the intellectual heirs of Maciamo, Davidski, and many on Anthrogenica, are arguing that the Irish immigrants of the 1800s were in fact a technologically and militarily superior, overwhelming force of wealthy males who clearly conquered the British Americans of the time.
And you, and anyone with any degree of a nuances understanding of history, is still LOL'ing.
Saturday, December 31, 2016
On the Need for More Interdisciplinariness in "Interdisciplinary" Studies
Ah, if they were all as good as Luigi Luca Cavalli-Sforza. The pioneer of interdisciplinary studies, and a Renaissance man, he would thoroughly immerse himself in genetics, demography, history, archaeology, and linguistics -- or find collaborators who could augment his knowledge. Thus, his work SAW THE BIG PICTURE.
A new paper out shows that modern "interdisciplinary" studies aren't so interdisciplinary at all.
It's called Mapping European Population Movement through Genomic Research by Patrick J. Geary and Krishna Veeramah. You can read it by clicking here.
The authors show that many geneticists writing about history simply pick up some bogus two-bit history book. That is why you get so much pseudo-science out there.
I once talked to a guy, a fairly educated scientist from another discipline, who felt he saw some marker in European genes. So he did some google searches as to which tribe had ever moved in the rough place where he found the markers. He then published a paper claiming he found a Cimbri-specific marker. But he didn't read the rest of the history; had he done so, he would have grasped perhaps that that tribe was wiped out by Gaius Marius in the first century BC....
The paper also points out that there isn't enough precision in genetics, because geneticists don't bother to understand that different regions have different histories. What good is knowing some person was French, without logging if that person is Provencal or Norman? Very little....
Best quote from the paper: "The Ralph and Coop study, while highly rigorous at the level of the population genetic analysis, included no historians or archaeologists, and the only historical literature cited, presumably to »identify« the Hunnic contribution to European population, was a general history of Europe, a survey of Slavic history, and two articles in the New Cambridge Medieval History. The Busby et al. study also included no historians or archaeologists on its team, and the only historical literature cited was a Penguin History of the World, Peter Heather’s survey of the Early Middle Ages, and a survey of Muslims in Italy. Unlike these studies, designed and executed exclusively by geneticists who then look through a few general historical handbooks to try to find stories that might explain their data..."
In other words, many scientific papers suffer from the same thing that plagues the Anthrogenica or even worse, Maciamo's horrifically bad Eupedia: "a LITTLE knowledge is dangerous." They don't bother grasping the big picture in genetics, demography, history, archaeology, and linguistics...
A new paper out shows that modern "interdisciplinary" studies aren't so interdisciplinary at all.
It's called Mapping European Population Movement through Genomic Research by Patrick J. Geary and Krishna Veeramah. You can read it by clicking here.
The authors show that many geneticists writing about history simply pick up some bogus two-bit history book. That is why you get so much pseudo-science out there.
I once talked to a guy, a fairly educated scientist from another discipline, who felt he saw some marker in European genes. So he did some google searches as to which tribe had ever moved in the rough place where he found the markers. He then published a paper claiming he found a Cimbri-specific marker. But he didn't read the rest of the history; had he done so, he would have grasped perhaps that that tribe was wiped out by Gaius Marius in the first century BC....
The paper also points out that there isn't enough precision in genetics, because geneticists don't bother to understand that different regions have different histories. What good is knowing some person was French, without logging if that person is Provencal or Norman? Very little....
Best quote from the paper: "The Ralph and Coop study, while highly rigorous at the level of the population genetic analysis, included no historians or archaeologists, and the only historical literature cited, presumably to »identify« the Hunnic contribution to European population, was a general history of Europe, a survey of Slavic history, and two articles in the New Cambridge Medieval History. The Busby et al. study also included no historians or archaeologists on its team, and the only historical literature cited was a Penguin History of the World, Peter Heather’s survey of the Early Middle Ages, and a survey of Muslims in Italy. Unlike these studies, designed and executed exclusively by geneticists who then look through a few general historical handbooks to try to find stories that might explain their data..."
In other words, many scientific papers suffer from the same thing that plagues the Anthrogenica or even worse, Maciamo's horrifically bad Eupedia: "a LITTLE knowledge is dangerous." They don't bother grasping the big picture in genetics, demography, history, archaeology, and linguistics...
Sunday, October 30, 2016
We Are Our Brother's Keeper: Are All Men Cousins? And Is This The Root Of Prejudice?
Many of you already know the following concepts. Humans intuit a sense of community and family with those with whom they are related. This has been confirmed in study after study, on child abuse, on ingroup-outgroup dynamics, and on racial prejudices.
The percentages of relatedness to trigger that feeling of kinship need not be large. As the following chart shows, many of us have folks over to Thanksgiving dinner with whom we only have 1-3% of identical DNA with. But that identical DNA is hugely significant. It's identical. And that of course makes one much more "related" than this "we share most DNA with all humans and even chimpanzees." Indeed, it's the margins that seem to count. And again, studies on stepfathers in particular, have confirmed this time and time again.
Parent / Child
Full Sibling 50%
The weird quality of the Y-Chromosome makes what I am about to post intriguing:
A human genome, including the X and Y chromosomes, is about 3771 cM long.
The Y Chromosome makes up about 2% of that, by length, and about 1% by SNPs.
Because men in certain haplogroups have IDENTICAL Y-Chromosomes (except for tiny combining parts), and because unlike the rest of DNA, those genes are passed on IDENTICALLY, then all men in the same haplogroup share as much DNA as, say, 2nd Cousins Once Removed.
Could this be the explanation why, for example, Western European males, which do not have much Y-chromosome diversity, exhibit a powerful ingroup dynamic with each other?
Fascinating, to be sure.
The percentages of relatedness to trigger that feeling of kinship need not be large. As the following chart shows, many of us have folks over to Thanksgiving dinner with whom we only have 1-3% of identical DNA with. But that identical DNA is hugely significant. It's identical. And that of course makes one much more "related" than this "we share most DNA with all humans and even chimpanzees." Indeed, it's the margins that seem to count. And again, studies on stepfathers in particular, have confirmed this time and time again.
Parent / Child
Full Sibling 50%
| Grandparent / Grandchild Aunt / Uncle Niece / Nephew Half Sibling |
25% | ||
| 1st Cousin | 12.5% | ||
| 1st Cousin once removed | 6.25% | ||
| 2nd Cousin | 3.13% | ||
| 2nd Cousin once removed | 1.5% | ||
| 3rd Cousin | 0.78% |
The weird quality of the Y-Chromosome makes what I am about to post intriguing:
A human genome, including the X and Y chromosomes, is about 3771 cM long.
The Y Chromosome makes up about 2% of that, by length, and about 1% by SNPs.
Because men in certain haplogroups have IDENTICAL Y-Chromosomes (except for tiny combining parts), and because unlike the rest of DNA, those genes are passed on IDENTICALLY, then all men in the same haplogroup share as much DNA as, say, 2nd Cousins Once Removed.
Could this be the explanation why, for example, Western European males, which do not have much Y-chromosome diversity, exhibit a powerful ingroup dynamic with each other?
Fascinating, to be sure.
Tuesday, October 11, 2016
How DNA Ancestry Testing Works and How Can I Know It's Accurate
When a commercial DNA testing site like Ancestry.com or 23andme or FTDNA tests your DNA, they do not know which snippet came from which of your parents.
For example, if at a given point (a gene, in popular parlance), you have a "C" from your dad and a "T" from you mom (meaning you have brown eyes, but carry the blue-eyes gene), the testing service doesn't know which "letter" came from which parent.
What they then do is try to guess, stringing your DNA out into small chunks or strings of letters.
They then compare these to DNA in their reference database. 23andme's reference database, which is one of the best, if not the best in the world, only has about 11,000 samples in it. To represent the whole world!
So if you have ancestry from a big country (like France or Germany) or a country that has pockets of deep isolation (like Italy), the odds -- that they have someone from your corner of the country, or your little isolated craggy valley in some mountain chain -- are small.
They then compare the little strings of letters and come up with a likelihood that you have ancestry from one of those reference populations.
23andme has the most scientific test in the business, but it gets French/German/Belgian/Dutch/Swiss/Austrian/Luxembourgisch ancestry wrong 92% of the time. It most often shows up as "generic Northwest European." Similarly, 23andme -- the best in the business -- can't identify Italian ancestry 50% of the time. It often shows up incorrectly as Middle Eastern or Generic Southern European.
The moral of this story is to be patient with the science. It's not 100% there yet.
If you have documented ancestry from one region, trust your documents.
If you don't have any cousins from a pool you were identified as, then chances are it was a miscall. (For example, if you have documented Italian ancestry, but it says you are 1/8 Middle Eastern or 1/8 Spanish), then unless you have a known great-grandparent that is 100% such, it's probably a miscall. (This would mean your parent would test as 1/4, by the way).
Finally, there is a series problem with testing sites, particularly FTDNA's, with the issue of timing. If you go back far enough, we are ALL Africans, right? Yet a DNA test telling you that you were African would not be too useful. Do they mean recently or in the past?
Similarly, as has been well-documented, most European ancestry can be broken down into 3 big chunks: ancient hunter gatherers (Ancient Western Europeans, most similar modern population = Lithuanians); ancient farmers (Ancient Near Easterners, most similar modern populations include Greeks, Sardinians, others); and ancient pastoralists/horse rearers (Ancient Eurasian Steppe Dwellers, most similar modern populations include Ukrainians). But the migrations were really, truly all over the place.
Ancient Near Easterners are NOT modern Near Easterners. Ancient hunter gatherers in France are NOT the modern French, etc.
If a test tells you that you have some Near Eastern blood, it often is sensing this ancient signal.
It doesn't do you much good for them to say that 6000 years ago, you had some ancestry in the Near East. Everyone did.
For example, if at a given point (a gene, in popular parlance), you have a "C" from your dad and a "T" from you mom (meaning you have brown eyes, but carry the blue-eyes gene), the testing service doesn't know which "letter" came from which parent.
What they then do is try to guess, stringing your DNA out into small chunks or strings of letters.
They then compare these to DNA in their reference database. 23andme's reference database, which is one of the best, if not the best in the world, only has about 11,000 samples in it. To represent the whole world!
So if you have ancestry from a big country (like France or Germany) or a country that has pockets of deep isolation (like Italy), the odds -- that they have someone from your corner of the country, or your little isolated craggy valley in some mountain chain -- are small.
They then compare the little strings of letters and come up with a likelihood that you have ancestry from one of those reference populations.
23andme has the most scientific test in the business, but it gets French/German/Belgian/Dutch/Swiss/Austrian/Luxembourgisch ancestry wrong 92% of the time. It most often shows up as "generic Northwest European." Similarly, 23andme -- the best in the business -- can't identify Italian ancestry 50% of the time. It often shows up incorrectly as Middle Eastern or Generic Southern European.
The moral of this story is to be patient with the science. It's not 100% there yet.
If you have documented ancestry from one region, trust your documents.
If you don't have any cousins from a pool you were identified as, then chances are it was a miscall. (For example, if you have documented Italian ancestry, but it says you are 1/8 Middle Eastern or 1/8 Spanish), then unless you have a known great-grandparent that is 100% such, it's probably a miscall. (This would mean your parent would test as 1/4, by the way).
Finally, there is a series problem with testing sites, particularly FTDNA's, with the issue of timing. If you go back far enough, we are ALL Africans, right? Yet a DNA test telling you that you were African would not be too useful. Do they mean recently or in the past?
Similarly, as has been well-documented, most European ancestry can be broken down into 3 big chunks: ancient hunter gatherers (Ancient Western Europeans, most similar modern population = Lithuanians); ancient farmers (Ancient Near Easterners, most similar modern populations include Greeks, Sardinians, others); and ancient pastoralists/horse rearers (Ancient Eurasian Steppe Dwellers, most similar modern populations include Ukrainians). But the migrations were really, truly all over the place.
Ancient Near Easterners are NOT modern Near Easterners. Ancient hunter gatherers in France are NOT the modern French, etc.
If a test tells you that you have some Near Eastern blood, it often is sensing this ancient signal.
It doesn't do you much good for them to say that 6000 years ago, you had some ancestry in the Near East. Everyone did.
Tuesday, May 24, 2016
Neandertals Never Died; Just Their Direct Sirelines and Matrilines
From a piece by Faye Flam in none other than Bloomberg, comes this wonderfully succinct nugget that expresses something that readers of this blog know I ascribe to:
"Scientists have also revised their view of Neanderthal extinction – long attributed to some deficit on their part. Maybe nothing dramatic happened at all, said Hawks. They would have made up a small fraction of the world’s population, and when larger groups of modern humans joined them in Europe they might have simply been absorbed."
(emphasis added)
This is what I coined the "Demography not Drama" explanation.
It is likely the Neandertal population was tiny, and when modern humans entered Europe, they simply absorbed them, perhaps even absorbed multiple sub-populations (which the genetics data now supports too).
With each generation, there is a great chance that a male line or a female line will disappear. All it takes is for a man to have only daughters, or a woman to have only sons. Older lines (which have been around for more generations) face longer odds of appearing to have survived, because each generation increases the chances a line will appear to have died out. The patrilines and matrilines from a group starting with a smaller population size will also appear to have died out over time.
We have seen this occur in the modern world, both in the example of surnames on isolated islands (the families didn't die out, but the surnames eventually greatly reduced in numbers because of the randomness of males having male children) and with thoroughbreds (the original thoroughbred founding population included 30+ male horses, but only 3 sirelines (akin to surnames or Y-chromosome haplogroups) have survived.
This doesn't mean the others "died out." Like Neandertals, their genes live on among us.
"Scientists have also revised their view of Neanderthal extinction – long attributed to some deficit on their part. Maybe nothing dramatic happened at all, said Hawks. They would have made up a small fraction of the world’s population, and when larger groups of modern humans joined them in Europe they might have simply been absorbed."
(emphasis added)
This is what I coined the "Demography not Drama" explanation.
It is likely the Neandertal population was tiny, and when modern humans entered Europe, they simply absorbed them, perhaps even absorbed multiple sub-populations (which the genetics data now supports too).
With each generation, there is a great chance that a male line or a female line will disappear. All it takes is for a man to have only daughters, or a woman to have only sons. Older lines (which have been around for more generations) face longer odds of appearing to have survived, because each generation increases the chances a line will appear to have died out. The patrilines and matrilines from a group starting with a smaller population size will also appear to have died out over time.
We have seen this occur in the modern world, both in the example of surnames on isolated islands (the families didn't die out, but the surnames eventually greatly reduced in numbers because of the randomness of males having male children) and with thoroughbreds (the original thoroughbred founding population included 30+ male horses, but only 3 sirelines (akin to surnames or Y-chromosome haplogroups) have survived.
This doesn't mean the others "died out." Like Neandertals, their genes live on among us.
Friday, February 5, 2016
The Sad Case of the Orthodoxy and the Posth Article on Pleistocene Demographics
Just a couple months ago, in the context of the peopling of Ireland, I
emphasized on Eupeida (and here) how important it is to put all the Theories Du Jour that are based on modern
uniparental distributions through a model based on population demographics and sound logic.
Specifically, I emphasized that ancient population sizes were minuscule compared to modern ones, and that if a population started a long long time ago, with a size that was way way small -- compared to subsequent waves -- that it would give a false signal that the original population was "conquered" or "outcompeted" or "never existed" or originated somewhere incorrect. I cautioned against those four errors.
This engendered quite the debate on Eupedia forums. When backed into a corner and shown the weakness of his "R1b Were Studly Conquerors Theory," the "blindly following the current orthodoxy" folks react badly.
Many "Interwebz Scientistz" fail to grasp these concepts. They favor their own wacky, biased theories based on what they see today only. If a land is populated by one people, they must be all conquering studs, right?
Today, Posth et. al put out an extensive paper on Pleistocene demographics.
Its shocking discovery? Just like Y DNA Hg C existed in Europe in tiny numbers among the very first Europeans, so did mtDNA Hg M.
M disappeared eventually, due to the simple fact that its initial population size was tiny, and that because it had been there so long, the odds that certain women didn't have daughters, each generation, eventually meant it was not passed on. Remember, we're talking uniparental markers here.
The authors commented exactly as I did: up to now, people mistakenly believed that Hg M never set foot in Europe -- or that if it did, it was killed off or whatever by a new wave. Sorry, both theories are wrong.
It is WONDERFUL to see another peer-reviewed, scholarly paper making this exact same point, and backing it up with newfound data.
As the paper indicates:
-These first hunter gatherers started with a TINY initial population size.
-There is a loss every generation of males having males or females having female offspring.
-I've calculated the approximate odds of a male not having a male child or a female not having a female child (i.e. looking like their uniparental marker was "conquered") at 12.5%, each generation, totally random.
-The longer a population has existed in a locale (and being free of mutations), the more generations go by, the greater the chance that random happenstance, chance, etc. will make it appear that a Hg either never existed or was slaughtered in a mass killing/enslavement/mate preference.
Now you have further proof of it.
I'm waiting to hear how Hg M died out because of some studly new more beautiful females who moved in. Oh woops, Maciamo doesn't post here. And he doesn't himself bear Hg M. And M is not linked to R1b...
Specifically, I emphasized that ancient population sizes were minuscule compared to modern ones, and that if a population started a long long time ago, with a size that was way way small -- compared to subsequent waves -- that it would give a false signal that the original population was "conquered" or "outcompeted" or "never existed" or originated somewhere incorrect. I cautioned against those four errors.
This engendered quite the debate on Eupedia forums. When backed into a corner and shown the weakness of his "R1b Were Studly Conquerors Theory," the "blindly following the current orthodoxy" folks react badly.
Many "Interwebz Scientistz" fail to grasp these concepts. They favor their own wacky, biased theories based on what they see today only. If a land is populated by one people, they must be all conquering studs, right?
Today, Posth et. al put out an extensive paper on Pleistocene demographics.
Its shocking discovery? Just like Y DNA Hg C existed in Europe in tiny numbers among the very first Europeans, so did mtDNA Hg M.
M disappeared eventually, due to the simple fact that its initial population size was tiny, and that because it had been there so long, the odds that certain women didn't have daughters, each generation, eventually meant it was not passed on. Remember, we're talking uniparental markers here.
The authors commented exactly as I did: up to now, people mistakenly believed that Hg M never set foot in Europe -- or that if it did, it was killed off or whatever by a new wave. Sorry, both theories are wrong.
It is WONDERFUL to see another peer-reviewed, scholarly paper making this exact same point, and backing it up with newfound data.
As the paper indicates:
-These first hunter gatherers started with a TINY initial population size.
-There is a loss every generation of males having males or females having female offspring.
-I've calculated the approximate odds of a male not having a male child or a female not having a female child (i.e. looking like their uniparental marker was "conquered") at 12.5%, each generation, totally random.
-The longer a population has existed in a locale (and being free of mutations), the more generations go by, the greater the chance that random happenstance, chance, etc. will make it appear that a Hg either never existed or was slaughtered in a mass killing/enslavement/mate preference.
Now you have further proof of it.
I'm waiting to hear how Hg M died out because of some studly new more beautiful females who moved in. Oh woops, Maciamo doesn't post here. And he doesn't himself bear Hg M. And M is not linked to R1b...
Saturday, January 30, 2016
In Praise of Roberta Estes and DNAeXplained.com
In a world of pseudo-science and echo chambers, a few blogs stick out for being mostly in touch with reality. In the world of Ancient DNA, Dienekes, although less active than before, has pioneered much in the field of DNA, and still has many serious scientists who comment there.
In the world of DNA for Genealogy, one blog sticks out. It is Roberta Estes' DNAeXplained.com. Of all the blogs and websites dedicated to disseminating information about DNA, hers is consistently factual, science-based, and yet easy to understand.
This scientist came across a few of her posts, and I daresay they are mandatory reading for anyone seeking a better understanding of their DNA. Below are links and highlights:
Step 1: Creation of the underlying population data base.
Don’t we wish this was as simple as it sounds. It isn’t. In fact, this step is the underpinnings of the accuracy of the ethnicity predictions. The old GIGO (garbage in, garbage out) concept applies here. . . .
The third way to obtain this type of information is by inference. Both Ancestry.com and 23andMe do some of this. Ancestry released its V2 ethnicity updates this week, and as a part of that update, they included a white paper available to DNA participants. In that paper, Ancestry discusses their process for utilizing contributed pedigree charts and states that, aside from immigrant locations, such as the United States and Canada, a common location for 4 grandparents is sufficient information to include that individuals DNA as “native” to that location. Ancestry used 3000 samples in their new ethnicity predictions to cover 26 geographic locations. That’s only 115 samples, on average, per location to represent all of that population. That’s pretty slim pickins. Their most highly represented area is Eastern Europe with 432 samples and the least represented is Mali with 16. The regions they cover are shown below. . .
No matter which calculations you use relative to acceptable Margin of Error and Confidence Level, Ancestry’s sample size is extremely light. . . .
"having Haplogroup Origins and Ancestral Origins indicating Native American ancestry does not necessarily mean you are Native American or have Native American heritage. This is a very pervasive myth that needs to be dispelled. . . .
The good news is that more and more people are DNA testing. The bad news is that errors in the system are tending to become more problematic, or said another way, GIGO – Garbage in, Garbage Out.
....
There are a very limited number of major haplogroups that include Native American results. For mitochondrial DNA, they are A, B, C, D, X and possibly M. I maintain a research list of the subgroups which are Native. Each of these base haplogroups also have subgroups which are European and/or Asian. The same holds true for Native American Y haplogroups Q and C.
In the Haplogroup Origins and Ancestral Origins, there are many examples where Non-Native haplogroups are assigned as Native American, such as haplogroup H1a below. Haplogroup H is European...
One of the problems we have today is that because there are so many people who carry the oral history of grandmother being “Cherokee,” it has become common to “self-assign” oneself as Native. That’s all fine and good, until one begins to “self-assign” those haplogroups as Native as well – by virtue of that “Native” assignment in the Family Tree DNA data base. That’s a horse of a different color.
In the world of DNA for Genealogy, one blog sticks out. It is Roberta Estes' DNAeXplained.com. Of all the blogs and websites dedicated to disseminating information about DNA, hers is consistently factual, science-based, and yet easy to understand.
This scientist came across a few of her posts, and I daresay they are mandatory reading for anyone seeking a better understanding of their DNA. Below are links and highlights:
Don’t we wish this was as simple as it sounds. It isn’t. In fact, this step is the underpinnings of the accuracy of the ethnicity predictions. The old GIGO (garbage in, garbage out) concept applies here. . . .
The third way to obtain this type of information is by inference. Both Ancestry.com and 23andMe do some of this. Ancestry released its V2 ethnicity updates this week, and as a part of that update, they included a white paper available to DNA participants. In that paper, Ancestry discusses their process for utilizing contributed pedigree charts and states that, aside from immigrant locations, such as the United States and Canada, a common location for 4 grandparents is sufficient information to include that individuals DNA as “native” to that location. Ancestry used 3000 samples in their new ethnicity predictions to cover 26 geographic locations. That’s only 115 samples, on average, per location to represent all of that population. That’s pretty slim pickins. Their most highly represented area is Eastern Europe with 432 samples and the least represented is Mali with 16. The regions they cover are shown below. . .
No matter which calculations you use relative to acceptable Margin of Error and Confidence Level, Ancestry’s sample size is extremely light. . . .
"having Haplogroup Origins and Ancestral Origins indicating Native American ancestry does not necessarily mean you are Native American or have Native American heritage. This is a very pervasive myth that needs to be dispelled. . . .
The good news is that more and more people are DNA testing. The bad news is that errors in the system are tending to become more problematic, or said another way, GIGO – Garbage in, Garbage Out.
....
There are a very limited number of major haplogroups that include Native American results. For mitochondrial DNA, they are A, B, C, D, X and possibly M. I maintain a research list of the subgroups which are Native. Each of these base haplogroups also have subgroups which are European and/or Asian. The same holds true for Native American Y haplogroups Q and C.
In the Haplogroup Origins and Ancestral Origins, there are many examples where Non-Native haplogroups are assigned as Native American, such as haplogroup H1a below. Haplogroup H is European...
One of the problems we have today is that because there are so many people who carry the oral history of grandmother being “Cherokee,” it has become common to “self-assign” oneself as Native. That’s all fine and good, until one begins to “self-assign” those haplogroups as Native as well – by virtue of that “Native” assignment in the Family Tree DNA data base. That’s a horse of a different color.
Monday, January 25, 2016
Calculating Matches on Gedmatch: Why CentiMorgans (cM) are more important than SNPs
I have discovered that very very very few people know this, so it is worth posting.
The different testing companies, 23andme, Ancestry, FTDNA, etc. all test slightly different SNPs. In other words, the "points" on the genome, the "genes" that are tested vary from company to company.
I have seen some people on Gedmatch dismiss a match because "it doesn't have enough SNPs." Or because "it's not above the SNP threshold."
Gedmatch itself uses a 7 cM and 700 SNPs match to qualify someone as a cousin.
The SNP part is faulty thinking.
Because the testing companies don't test the same SNPs, you can have long stretches that match with a low number of SNPs.
Case in point: Someone who tested on 23andme like I did matched me for 10.0 cM and 1024 SNPs. That same person on FTNDA matched me for 10.0 cM but just 510 SNPs. FTDNA tested half of the SNPs that 23andme did (or half of the same set).
This is key to grasp. Expect closer matches to you on Gedmatch if your kits start with the same letter (i.e. M for 23andme, F for FTDNA, and A for Ancestry.) DO NOT DISMISS LOW SNP MATCHES.
The different testing companies, 23andme, Ancestry, FTDNA, etc. all test slightly different SNPs. In other words, the "points" on the genome, the "genes" that are tested vary from company to company.
I have seen some people on Gedmatch dismiss a match because "it doesn't have enough SNPs." Or because "it's not above the SNP threshold."
Gedmatch itself uses a 7 cM and 700 SNPs match to qualify someone as a cousin.
The SNP part is faulty thinking.
Because the testing companies don't test the same SNPs, you can have long stretches that match with a low number of SNPs.
Case in point: Someone who tested on 23andme like I did matched me for 10.0 cM and 1024 SNPs. That same person on FTNDA matched me for 10.0 cM but just 510 SNPs. FTDNA tested half of the SNPs that 23andme did (or half of the same set).
This is key to grasp. Expect closer matches to you on Gedmatch if your kits start with the same letter (i.e. M for 23andme, F for FTDNA, and A for Ancestry.) DO NOT DISMISS LOW SNP MATCHES.
Monday, December 28, 2015
The Cassidy Earthquake: Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome
Lara Cassidy et al. just put out a paper that injects a bit of welcome science into the world of R1b fantasy theories. Those theories, of marauding bands of R1b warriors, are popular on online messenger boards. (One prominent board even maintains that most of Western Europe -- millions and millions of men -- are R1b because they are descended from royalty).
Here are the findings from this recent paper:
1. The very derived downstream clades of R1b like R1b1a2a1a2c were well-established in Ireland by 3750 before the present. There is no evidence the ancient specimens in the paper were the first generation in Ireland, so it is likely they were present by 2000 BCE.
7. R1b and this Western European expansion is strongly scientifically correlated to lactose persistence, which likely provided the demographic advantage to propagate in larger numbers in places like Hibernia.
Here are the findings from this recent paper:
1. The very derived downstream clades of R1b like R1b1a2a1a2c were well-established in Ireland by 3750 before the present. There is no evidence the ancient specimens in the paper were the first generation in Ireland, so it is likely they were present by 2000 BCE.
2. The population of the Central European migrants to Ireland, who were herders, and had some Steppe-derived ancestry, were MUCH higher, compared to hunter gatherers. In other words, R1b is so common in Ireland because of massive migration of such people.
3. This is emphatically NOT consistent with pioneer colonization and elite dominance.
4. The current distributions in many parts of Western Europe are due to a LACK of invasions since (no Anglo-Saxon or Roman penetration.) In other words, this was a second but more prounounced founder effect of sorts.
5. This is consistent with comparisons to more centrally located, easy to reach locales, like Italy, where the genomes show greater variability in
both autosomes and Y DNA, due to introgressions that occurred after the late Neolithic and early Bronze Age migrations. (Cavalli-Sforza's admonishment to understand the difference between an expansion and an "impansion" come to mind.)
6. In Western Europe, Bell Beaker culture is the most likely candidate for the spread of R1b and related autosomal genes.
7. R1b and this Western European expansion is strongly scientifically correlated to lactose persistence, which likely provided the demographic advantage to propagate in larger numbers in places like Hibernia.
8. As an addendum, the megaliths of Western Europe are indeed likely linked to early cardial cultures, who bore of mix of HG and farming genes, which correlate to I-M26 in Ireland and Sardinia.
WOW!
Wednesday, December 23, 2015
The Spread of Haplogroups in Europe, Especially R1b
This post is intended to
be a general foray into what I call "The Two -Ics" that explain
modern haplogroup distributions: demographics and mathematics. IMO,
both are poorly understood.
It's been said, "to be an R1b Fantasist, you have to believe that I2-M26 came to predominate Sardinia by chance (e.g., Founder Effect and Drift) -- but that R1b came to predominate other locales (e.g., Ireland or Spain) by merit (e.g., military superiority or sexual selection)."
It's also been said, "to be an R1b Fantasist, you have to now believe that R1b marks the spread of the first pastoralists, equestrians, and herders, and that you're now 100% correct that is right -- when just 2-3 years ago, you were 100% that Hg G2 was the mark of the first pastoralists and herders."
With respect to the first saying, I believe that most of the R1b apologists understand the former concepts (of chance as they apply to archaeogenetics), so this post is designed to build upon that knowledge, and add some demographics and mathematics too.
With respect to the second saying, I believe what is most key in a discipline like archaeogenetics is to recognize that theories and findings change from year to year, but the underpinnings of solid scientific method do not.
Let's get into it:
First, it is crucial to outline the possible outcomes. Every generation, every clade and subclade of every Haplogroup has three "options" (or three outcomes). Those are:
The "stakes" were more pronounced during prehistory than today, because the population sizes were so profoundly lower. If you don't grasp this and accept it as fact, you can't grasp what I will detail later.
Population of Europe Over Selected Times
In essence, you must remember that the population of Europe at the beginning of the time we are discussing (the post-glacial-maximum recolonization through the Bronze Age) was about 28,000 and peaked at maybe 100,000. This is hard for the modern mind to comprehend, I know. There were less people from Spain to Ukraine then, than there are in one city block in London now.
There are two takeaways:
Going back to our three outcomes for Y Haplogroups, every generation: the first "takeaway" above should inform several likely mechanisms of how R1b spread over time. If they entered a territory and had different disease resistance, it could have meant that large numbers of a tiny starting population would die off.
Similarly, because the initial population was so small, when larger populations migrated for whatever reason, indeed possibly even as refugees from other regions, the other haplogroups would seem to have shrunk in size, whereas it really is different population sizes.
All this is just build up. Our main focus, however, is the simple application of mathematics to Outcome 3 above.
This is what you need to know before we start:
1. Hunter/gatherer women space babies on average 4.5 years apart, whereas farmers and moderns space them 1.5 years apart.
2. The average paleolithic woman would have about 3.8 children.
3. Infant mortality among hunter/gatherers is 30 times higher than among "civilized", and reached approximately 25% at many points during history.
4. If the average hunter/gatherer family consisted of 3 children to live to adulthood, the odds of each family having just female kids survive was 12.5% each generation. (.5 x .5 x .5)
Now just these numbers by themselves (HGs having fewer kids than farmers or pastoralists) explain a LOT.
But the main point is thus: "older" non-mutated Y-chromosome haplogroups are found in lesser numbers simply because they are...older...
Every generation that a Hg exists and doesn't change, there is a 12.5% chance that those bearing it, in any one family, will not pass it along. To be very clear: if a Hg does not mutate into something else -- or does not die entirely -- its numbers and distribution will decrease over time. This applies to all except the most recent arrival, which is currently breeding like rabbits. For example:
Many people believe that C1a was the first Y Hg in Europe. There were probably just 5000-15,000 of them at any time. By definition, the Hg C1a are folks that did not go on to mutate into any of the downstream clades. Over time, the odds will catch up.
Many people believe that I2 was the next Y Hg in Europe. There were probably just 10,000 - 50,000 of them at any time. By definition, these are members of the IJ branch, and not members of F or K who mutated. Over time, the odds will catch up.
These very simple concepts explain much of the modern distribution of haplogroups in Europe. Is it more complex? Sure. Were there other factors? Absolutely. But over time, you cannot escape mathematics and demography being the biggest factors.
It's been said, "to be an R1b Fantasist, you have to believe that I2-M26 came to predominate Sardinia by chance (e.g., Founder Effect and Drift) -- but that R1b came to predominate other locales (e.g., Ireland or Spain) by merit (e.g., military superiority or sexual selection)."
It's also been said, "to be an R1b Fantasist, you have to now believe that R1b marks the spread of the first pastoralists, equestrians, and herders, and that you're now 100% correct that is right -- when just 2-3 years ago, you were 100% that Hg G2 was the mark of the first pastoralists and herders."
With respect to the first saying, I believe that most of the R1b apologists understand the former concepts (of chance as they apply to archaeogenetics), so this post is designed to build upon that knowledge, and add some demographics and mathematics too.
With respect to the second saying, I believe what is most key in a discipline like archaeogenetics is to recognize that theories and findings change from year to year, but the underpinnings of solid scientific method do not.
Let's get into it:
First, it is crucial to outline the possible outcomes. Every generation, every clade and subclade of every Haplogroup has three "options" (or three outcomes). Those are:
1. Mutate (i.e., become something else)
2. Propagate -- and, in more or less the same form, by having a male child who survives
3. Die out, by having only daughters, or by having male children who fail to themselves breed
2. Propagate -- and, in more or less the same form, by having a male child who survives
3. Die out, by having only daughters, or by having male children who fail to themselves breed
The "stakes" were more pronounced during prehistory than today, because the population sizes were so profoundly lower. If you don't grasp this and accept it as fact, you can't grasp what I will detail later.
Population of Europe Over Selected Times
(YBP = Years Before Present)
~50,000 YBP: No more than 10,000 (Neandertals)
~38,000 YBP - 19,000 YBP: No more than 37,000, likely population just 5,000
~12,000 YBP: About 28,000
~2000 YBP: About 35,000,000
-0 YBP: About 743,000,000
You can read more here.~50,000 YBP: No more than 10,000 (Neandertals)
~38,000 YBP - 19,000 YBP: No more than 37,000, likely population just 5,000
~12,000 YBP: About 28,000
~2000 YBP: About 35,000,000
-0 YBP: About 743,000,000
In essence, you must remember that the population of Europe at the beginning of the time we are discussing (the post-glacial-maximum recolonization through the Bronze Age) was about 28,000 and peaked at maybe 100,000. This is hard for the modern mind to comprehend, I know. There were less people from Spain to Ukraine then, than there are in one city block in London now.
There are two takeaways:
1. This made the population more susceptible to chance events, like a plague outbreak, or a famine in an area.
2. This made the population more susceptible to massive dilution, when population started on its massive upward trajectory, after people started drinking milk, wine, and beer, when they started making cheese, when they started farming cereals and living in one spot, and when they started herding animals and having meat at will.
2. This made the population more susceptible to massive dilution, when population started on its massive upward trajectory, after people started drinking milk, wine, and beer, when they started making cheese, when they started farming cereals and living in one spot, and when they started herding animals and having meat at will.
Going back to our three outcomes for Y Haplogroups, every generation: the first "takeaway" above should inform several likely mechanisms of how R1b spread over time. If they entered a territory and had different disease resistance, it could have meant that large numbers of a tiny starting population would die off.
Similarly, because the initial population was so small, when larger populations migrated for whatever reason, indeed possibly even as refugees from other regions, the other haplogroups would seem to have shrunk in size, whereas it really is different population sizes.
All this is just build up. Our main focus, however, is the simple application of mathematics to Outcome 3 above.
This is what you need to know before we start:
1. Hunter/gatherer women space babies on average 4.5 years apart, whereas farmers and moderns space them 1.5 years apart.
2. The average paleolithic woman would have about 3.8 children.
3. Infant mortality among hunter/gatherers is 30 times higher than among "civilized", and reached approximately 25% at many points during history.
4. If the average hunter/gatherer family consisted of 3 children to live to adulthood, the odds of each family having just female kids survive was 12.5% each generation. (.5 x .5 x .5)
Now just these numbers by themselves (HGs having fewer kids than farmers or pastoralists) explain a LOT.
But the main point is thus: "older" non-mutated Y-chromosome haplogroups are found in lesser numbers simply because they are...older...
Every generation that a Hg exists and doesn't change, there is a 12.5% chance that those bearing it, in any one family, will not pass it along. To be very clear: if a Hg does not mutate into something else -- or does not die entirely -- its numbers and distribution will decrease over time. This applies to all except the most recent arrival, which is currently breeding like rabbits. For example:
Many people believe that C1a was the first Y Hg in Europe. There were probably just 5000-15,000 of them at any time. By definition, the Hg C1a are folks that did not go on to mutate into any of the downstream clades. Over time, the odds will catch up.
Many people believe that I2 was the next Y Hg in Europe. There were probably just 10,000 - 50,000 of them at any time. By definition, these are members of the IJ branch, and not members of F or K who mutated. Over time, the odds will catch up.
These very simple concepts explain much of the modern distribution of haplogroups in Europe. Is it more complex? Sure. Were there other factors? Absolutely. But over time, you cannot escape mathematics and demography being the biggest factors.
Tuesday, December 15, 2015
A Review of All Theories, on Why R1b Is So Common in Western Europeans
The great Roman historian Tacitus begins the Germania by discussing how the Germans are separated from certain peoples by mountains, and separated from other peoples by rivers -- and where there were no rivers or mountains, the peoples were separated by Fear.
A similar, intangible concept applies today, to understanding why R1b is so common in Western Europe. Some of it can be gleaned by archaeology, some of it can be gleaned by DNA -- and where archaeology and DNA cannot provide an answer, we must resort to what makes us human: Logic.
Below is a review of all of possible models explaining why R1b and its subclades are common throughout Western Europe. After reading it, you decide which is the most logical.
1. The Bronze-Age Badasses.
The theory goes:R1b males were an awesome military force, who swept through Europe and killed the overwhelming majority of other males in their path. They started in modern Ukraine as bad-ass horsemen. But by the time they got to the coasts, they turned into bad-ass sailors and navigators. These horsemen built boats, and Ireland and England were next to be mowed down by their genocidal awesomeness. Despite traveling the length of Europe, they were still pure R1b by the time they reached Ireland. Sufficiently that some counties in Ireland are 80-98% R1b today. This R1b Empire was the largest that Europe ever knew. Not even Caesar's stretched from Ireland to Ukraine! Even though there was plenty of open space in Europe (the population being less than 1/1000th of what it is today), they decided to conquer an empire this vast expanse and risk the lives of themselves and their children, just because they were such badasses. They were such efficient killers they left no trace in archaeological records in Western Europe of destruction or razing. Despite well-established standards for evolution of language, the empire spoke vastly different languages (i.e. Latin and Ukrainian), despite this all happening just 1000 years or so before the beginnings of Rome and Greece.
Believe it or not, this theory is favored by some people today, who just happen to be R1b males.
2. The Irresistible Indo-Europeans
This theory goes: R1b males had uniformly gorgeous looks, tremendous wealth, and all-star qualities that made all hunter-gatherer women swoon with delight. Whether they had bright red hair, or looked like James Buchanan, cavewomen of all groups throughout Europe dropped their guys and decided to procreate with these R1b studs. None of the local guys resisted. They too were enamored by the R1b good looks, and some kind of genetic superiority that made them and their genes irresistible.
Believe it or not, this theory is favored by some people today. No, really. They actually posted it in comments below. And they just happen to be R1b males.
3. Colonizing Conquistadores
This theory is a variation of theory 1, minus the genocide. The theory is: just model the R1b spread after that of the Spanish conquest of the New World. Nevermind that the Spanish had guns, germs, and steel. Nevermind that they had cannon, smallpox, and boats that could traverse oceans. Nevermind that in most places in Latin America, the native haplogroups like Q and C still dominate. Just ignore these things and model R1b after the Spanish.
4. Lactase Persistence
At last we enter the realm of the plausible.
This theory goes as follows: very basal subclades of R1b were present throughout Europe in tiny pockets for a very long time.
This is why a slightly more downstream clade of R1b*, ancestral to modern lineages, was found, already in Els Trocs Spain, 7000 years ago.
I mean think about it. He couldn't have flown there. And in 5100 BC, he couldn't have even ridden a horse.
We know that R1 originated in Eurasia, and that it was present on both ends of Europe by 5100 BC.
If you adopt regular migration theories for on-foot migrations, these very basal R1b people in Spain were likely present in small pockets throughout Europe by 6000 BC. Perhaps in the modern Czech Republic, perhaps in France, perhaps in modern Germany. We only have ~400 aDNA samples from this epoch, and a smaller percentage of them have been tested for Y DNA.
Perhaps they lived in a moist climate less likely to preserve remains. Perhaps they cremated their dead. Perhaps archaeologists ignore their tiny region. But one thing is certain: Basal R1b was present in Europe, end to end, by about 6000 BC.
At some point, during a period of profound starvation, Western Europeans evolved a tremendous caloric advantage: the ability to digest milk. No more killing the cow to eat and therefore live: you can live off of turning grass into protein.
Let's assume the first humans to evolve this, living in some nameless, forgotten pocket of Germany or England or France or Spain were majority R1b, then their population would EXPLODE. In a time of mass starvation and famine, those with a caloric advantage would propagate exponentially.
(Perhaps these people come to worship the cow to some degree, creating taboos to killing it, as we see in modern lands, creating idols of bulls, as we saw in many ancient cultures, and creating elaborate drinking vessels in the shape of Bell Beakers -- but I digress...)
The population of Europe at this time was maybe a million people across the whole continent. If you figure that R1b people had a greater fertility rate (more kids per female, less time to wean because of cowmil availability, less time between kids, healthier kids, more kids reaching adulthood to propagate), then the simple math of exponential demography will show that within as few as 200 years, your uniparental markers will dominate the landscape.
It should be noted that the various genes for lactase persistence mirror closely the distribution of R1b-S21 even today.
5. Refugees and Different Cultural Attitudes
If you know a little about history or current events, this one is not hard to imagine. The historical example is the Goths; the modern example is what is happening in Lebanon with Syrian refugees.
People used to think the Goths were bad-ass, uncivilized, warlike, mighty (insert "supreme" adjective here) Germanic overlords who conquered much of the Roman world. But anyone who knows the history understands that the truth is a little kinder to them (kinder, depending on if you believe being peaceful and not purposefully killing people is a good thing).
The Goths were not some mighty tribe hell-bent on destruction, who willfully took over the Roman Empire. Just the opposite: they started out from modern South Sweden because of FAMINE. They were so weak, they were forced to WANDER for centuries. Finally, they invaded the Roman Empire, because the Huns EVICTED them from their steppe lands in modern Ukraine.
In other words, one of the baddest-ass people in most people's minds were refugees, forced to emigrate not because they wanted to conquer, but because they themselves had been evicted from their homelands by famine (first) and then another people (the Huns).
If that is too hard on you, let's imagine something happening today. The population of Lebanon is about 2 million people. Aside from the districts controlled by terrible people, many of the coastal folks are pretty wealthy, modern, and diverse. They don't have extraordinarily high birthrates.
All hell has broken loose near them, in a country you may have heard a lot of recently. It's called Syria. In the last two years, Lebanon...has been swamped with 2 million Syrian refugees.
In other words, the population of the country has doubled, in a generation, from an influx of refugees.
Now imagine the Lebanese bear Haplogroup L, we will call it. Imagine like many wealthier people today, they're not having 20 kids each. More like 1 or 2.
Imagine the Syrian refugees bear Haplogroup S, we will call it. Imagine like many poorer people today, they DO have many kids...
The "old" samples within this area we call Lebanon will all be Haplogroup L. A future archaeologist would find that to be the case.
The "new" samples, after a few generations, will be like 75-25%, with Haplogroup S clearly "winning out." The cause is a mix of migration -- plus different cultural attitudes toward having kids.
Did the Syrian refugees "conquer" the Lebanese? (No.)
Is it safe to say that the Syrian refugees genes were "selected for?" (No).
That the Syrian men were "more attractive" to women? (No).
That they bore some kind of genetic advantage, that made them fitter? (Again, no.)
6. Different Starting Population Sizes, Different In Time
This one is the hardest to fathom almost, because it is almost circular. It states simply that R1b is the most numerous in Western Europe because they started out more populous, and were the most recent immigrants.
Western Europe is a cul-de-sac for overland migrations. Almost all haplogroups originated in Africa or the Near East, but came into Western Europe via the eastern entry points into Europe. Iberia is the end of the cul-de-sac.
Imagine a 100-acre parcel. At first, it is a hunting preserve of sorts. It is inhabited by 5 families who own 20 acres each. They love the deer and geese they harvest from said land.
Next some farmers move in. 50 acres are used for farming. They support 10 farming families, who each have 5 acres.
The land is supporting 5 hunters and 10 farmers. (Have the farmers been "selected for?" No. They are more numerous and more recent migrants).
Finally, some others land in the area. There are 100 refugee families or maybe just people who tolerate living close to one another, so they squeeze into one acre of the land. They have metals, which they trade for food, so they are able to live in a much smaller parcel.
Have they been selected for? Again, no.
I just described something that has happened in recorded history several times, and surely in prehistory too.
Older, less numerous populations will appear to be "drowned out," unless you are careful. It's just simple math. Those who have been in a locale the longest will be diluted over time.
7. Disease
Many plagues in Western Europe entered through the east. Since R1b-bearing males were the largest migration from the east, it must be considered that different immune systems played a role in their spread.
In sum: R1b could be simply the most common haplogroup in Western Europe because it came there later, in greater numbers, and perhaps as part of a people who had different cultural attitudes toward having children.
In subsequent posts, I will link or recap demographic studies that show the clear power of exponential growth with even tiny differences in birthrates.
A similar, intangible concept applies today, to understanding why R1b is so common in Western Europe. Some of it can be gleaned by archaeology, some of it can be gleaned by DNA -- and where archaeology and DNA cannot provide an answer, we must resort to what makes us human: Logic.
Below is a review of all of possible models explaining why R1b and its subclades are common throughout Western Europe. After reading it, you decide which is the most logical.
1. The Bronze-Age Badasses.
The theory goes:R1b males were an awesome military force, who swept through Europe and killed the overwhelming majority of other males in their path. They started in modern Ukraine as bad-ass horsemen. But by the time they got to the coasts, they turned into bad-ass sailors and navigators. These horsemen built boats, and Ireland and England were next to be mowed down by their genocidal awesomeness. Despite traveling the length of Europe, they were still pure R1b by the time they reached Ireland. Sufficiently that some counties in Ireland are 80-98% R1b today. This R1b Empire was the largest that Europe ever knew. Not even Caesar's stretched from Ireland to Ukraine! Even though there was plenty of open space in Europe (the population being less than 1/1000th of what it is today), they decided to conquer an empire this vast expanse and risk the lives of themselves and their children, just because they were such badasses. They were such efficient killers they left no trace in archaeological records in Western Europe of destruction or razing. Despite well-established standards for evolution of language, the empire spoke vastly different languages (i.e. Latin and Ukrainian), despite this all happening just 1000 years or so before the beginnings of Rome and Greece.
Believe it or not, this theory is favored by some people today, who just happen to be R1b males.
2. The Irresistible Indo-Europeans
This theory goes: R1b males had uniformly gorgeous looks, tremendous wealth, and all-star qualities that made all hunter-gatherer women swoon with delight. Whether they had bright red hair, or looked like James Buchanan, cavewomen of all groups throughout Europe dropped their guys and decided to procreate with these R1b studs. None of the local guys resisted. They too were enamored by the R1b good looks, and some kind of genetic superiority that made them and their genes irresistible.
Believe it or not, this theory is favored by some people today. No, really. They actually posted it in comments below. And they just happen to be R1b males.
3. Colonizing Conquistadores
This theory is a variation of theory 1, minus the genocide. The theory is: just model the R1b spread after that of the Spanish conquest of the New World. Nevermind that the Spanish had guns, germs, and steel. Nevermind that they had cannon, smallpox, and boats that could traverse oceans. Nevermind that in most places in Latin America, the native haplogroups like Q and C still dominate. Just ignore these things and model R1b after the Spanish.
4. Lactase Persistence
At last we enter the realm of the plausible.
This theory goes as follows: very basal subclades of R1b were present throughout Europe in tiny pockets for a very long time.
This is why a slightly more downstream clade of R1b*, ancestral to modern lineages, was found, already in Els Trocs Spain, 7000 years ago.
I mean think about it. He couldn't have flown there. And in 5100 BC, he couldn't have even ridden a horse.
We know that R1 originated in Eurasia, and that it was present on both ends of Europe by 5100 BC.
If you adopt regular migration theories for on-foot migrations, these very basal R1b people in Spain were likely present in small pockets throughout Europe by 6000 BC. Perhaps in the modern Czech Republic, perhaps in France, perhaps in modern Germany. We only have ~400 aDNA samples from this epoch, and a smaller percentage of them have been tested for Y DNA.
Perhaps they lived in a moist climate less likely to preserve remains. Perhaps they cremated their dead. Perhaps archaeologists ignore their tiny region. But one thing is certain: Basal R1b was present in Europe, end to end, by about 6000 BC.
At some point, during a period of profound starvation, Western Europeans evolved a tremendous caloric advantage: the ability to digest milk. No more killing the cow to eat and therefore live: you can live off of turning grass into protein.
Let's assume the first humans to evolve this, living in some nameless, forgotten pocket of Germany or England or France or Spain were majority R1b, then their population would EXPLODE. In a time of mass starvation and famine, those with a caloric advantage would propagate exponentially.
(Perhaps these people come to worship the cow to some degree, creating taboos to killing it, as we see in modern lands, creating idols of bulls, as we saw in many ancient cultures, and creating elaborate drinking vessels in the shape of Bell Beakers -- but I digress...)
The population of Europe at this time was maybe a million people across the whole continent. If you figure that R1b people had a greater fertility rate (more kids per female, less time to wean because of cowmil availability, less time between kids, healthier kids, more kids reaching adulthood to propagate), then the simple math of exponential demography will show that within as few as 200 years, your uniparental markers will dominate the landscape.
It should be noted that the various genes for lactase persistence mirror closely the distribution of R1b-S21 even today.
5. Refugees and Different Cultural Attitudes
If you know a little about history or current events, this one is not hard to imagine. The historical example is the Goths; the modern example is what is happening in Lebanon with Syrian refugees.
People used to think the Goths were bad-ass, uncivilized, warlike, mighty (insert "supreme" adjective here) Germanic overlords who conquered much of the Roman world. But anyone who knows the history understands that the truth is a little kinder to them (kinder, depending on if you believe being peaceful and not purposefully killing people is a good thing).
The Goths were not some mighty tribe hell-bent on destruction, who willfully took over the Roman Empire. Just the opposite: they started out from modern South Sweden because of FAMINE. They were so weak, they were forced to WANDER for centuries. Finally, they invaded the Roman Empire, because the Huns EVICTED them from their steppe lands in modern Ukraine.
In other words, one of the baddest-ass people in most people's minds were refugees, forced to emigrate not because they wanted to conquer, but because they themselves had been evicted from their homelands by famine (first) and then another people (the Huns).
If that is too hard on you, let's imagine something happening today. The population of Lebanon is about 2 million people. Aside from the districts controlled by terrible people, many of the coastal folks are pretty wealthy, modern, and diverse. They don't have extraordinarily high birthrates.
All hell has broken loose near them, in a country you may have heard a lot of recently. It's called Syria. In the last two years, Lebanon...has been swamped with 2 million Syrian refugees.
In other words, the population of the country has doubled, in a generation, from an influx of refugees.
Now imagine the Lebanese bear Haplogroup L, we will call it. Imagine like many wealthier people today, they're not having 20 kids each. More like 1 or 2.
Imagine the Syrian refugees bear Haplogroup S, we will call it. Imagine like many poorer people today, they DO have many kids...
The "old" samples within this area we call Lebanon will all be Haplogroup L. A future archaeologist would find that to be the case.
The "new" samples, after a few generations, will be like 75-25%, with Haplogroup S clearly "winning out." The cause is a mix of migration -- plus different cultural attitudes toward having kids.
Did the Syrian refugees "conquer" the Lebanese? (No.)
Is it safe to say that the Syrian refugees genes were "selected for?" (No).
That the Syrian men were "more attractive" to women? (No).
That they bore some kind of genetic advantage, that made them fitter? (Again, no.)
6. Different Starting Population Sizes, Different In Time
This one is the hardest to fathom almost, because it is almost circular. It states simply that R1b is the most numerous in Western Europe because they started out more populous, and were the most recent immigrants.
Western Europe is a cul-de-sac for overland migrations. Almost all haplogroups originated in Africa or the Near East, but came into Western Europe via the eastern entry points into Europe. Iberia is the end of the cul-de-sac.
Imagine a 100-acre parcel. At first, it is a hunting preserve of sorts. It is inhabited by 5 families who own 20 acres each. They love the deer and geese they harvest from said land.
Next some farmers move in. 50 acres are used for farming. They support 10 farming families, who each have 5 acres.
The land is supporting 5 hunters and 10 farmers. (Have the farmers been "selected for?" No. They are more numerous and more recent migrants).
Finally, some others land in the area. There are 100 refugee families or maybe just people who tolerate living close to one another, so they squeeze into one acre of the land. They have metals, which they trade for food, so they are able to live in a much smaller parcel.
Have they been selected for? Again, no.
I just described something that has happened in recorded history several times, and surely in prehistory too.
Older, less numerous populations will appear to be "drowned out," unless you are careful. It's just simple math. Those who have been in a locale the longest will be diluted over time.
7. Disease
Many plagues in Western Europe entered through the east. Since R1b-bearing males were the largest migration from the east, it must be considered that different immune systems played a role in their spread.
In sum: R1b could be simply the most common haplogroup in Western Europe because it came there later, in greater numbers, and perhaps as part of a people who had different cultural attitudes toward having children.
In subsequent posts, I will link or recap demographic studies that show the clear power of exponential growth with even tiny differences in birthrates.
Another Way of Thinking About Ancient Populations (Autosomes versus just Y and mtDNA)
I don't think Neandertals died out at all.
No more so than any population that existed from 600,000 to 25,000 years ago.
If you tested ANY species of Homo that old, of course they wouldn't match us exactly. The genus has evolved.
Neandertal population size was tiny. Imagine that there were 40,000 of them in Europe. (That number is actually large. Many aDNA experts believe that there were never more than 10,000 Neanderthals alive at any one time!)
Now imagine that 1 million modern humans come into Europe, during various phases.
You mix them together, and you get the 4% of Neandertal autosomes in our populations.
You also get drastically smaller odds that their sex-linked DNA survives over time.
Never, ever forget population size.
This "study" has been replicated in modern times.
Imagine 100 men are marooned on an island. 4 have the surname "Rarityrareness."
After generations, it is likely that the sons of those 4 will have a generation or two that produces only daughters. In fact, it's almost certain.
So the odds are that there will be no Y chromosomes of the Rarityrareness males.
But did they survive? Yes. Their descendants through their daughters are very much alive in the population. And like Neandertals, large percentages of their genome would survive autosomally, perhaps as high as 80%!
Never ever forget initial and comparable population size. It explains just about every ratio of the newer versus older Y Chromosomes in Europe.
It explains the lack of Neandertal sex-linked DNA, and it explains the smaller number of the Old Europe haplogroups from small hunter-gatherer populations.
No more so than any population that existed from 600,000 to 25,000 years ago.
If you tested ANY species of Homo that old, of course they wouldn't match us exactly. The genus has evolved.
Neandertal population size was tiny. Imagine that there were 40,000 of them in Europe. (That number is actually large. Many aDNA experts believe that there were never more than 10,000 Neanderthals alive at any one time!)
Now imagine that 1 million modern humans come into Europe, during various phases.
You mix them together, and you get the 4% of Neandertal autosomes in our populations.
You also get drastically smaller odds that their sex-linked DNA survives over time.
Never, ever forget population size.
This "study" has been replicated in modern times.
Imagine 100 men are marooned on an island. 4 have the surname "Rarityrareness."
After generations, it is likely that the sons of those 4 will have a generation or two that produces only daughters. In fact, it's almost certain.
So the odds are that there will be no Y chromosomes of the Rarityrareness males.
But did they survive? Yes. Their descendants through their daughters are very much alive in the population. And like Neandertals, large percentages of their genome would survive autosomally, perhaps as high as 80%!
Never ever forget initial and comparable population size. It explains just about every ratio of the newer versus older Y Chromosomes in Europe.
It explains the lack of Neandertal sex-linked DNA, and it explains the smaller number of the Old Europe haplogroups from small hunter-gatherer populations.
Sunday, December 13, 2015
A Proposal for a New Lexicon for Ancient DNA "Components" Like WHG, EHG, EEF, ANE, and CHG
Some of us a few years back started to decry the ever-ongoing ISOGG
renaming process, which coupled with the discovery of new subclades,
meant that one year, someone might be deemed
R1b1b1a2bab2ba11babd12ba2b1c, and the next year
R1b1b2bab2f1faf1fafaf1f1f1a.
People started saying that it would probably be better to say the first couple letters and the major terminal SNP. For example, R1b-U106 or I2-M26. This was logical and good. Unlike the terminology, the SNPs never change. And they're shorter to write.
Here I humbly propose a new terminology for ancient autosomal samples. I think picking terms like, "WHG" was a mistake, and now that I read about EHG and CHG, I really think so. For the uninitiated, these acronyms stand for "Western Hunter Gatherer," "Caucasus Hunter Gatherer," etc.
People compare their modern genomes, or the genomes of modern populations or ethnic groups, to these ancient samples. And then they use the shorthand, like, "Scottish average 19% CHG." This is highly misleading.
Let me give the reasons why I think it is deficient, and tell me if you disagree.
1. As we get more samples over time, it will be hard to keep renaming the different samples, if they form a different component. We just saw this with the recent CHG finds. Imagine if we find a detectable signal of ancient genes from Iberia. What will we call that component? "Really Western Hunter Gatherer?"
2. The shorthand is deeply misleading (i.e., "Scottish are 19% CHG.") This to me is the most important point. Most people reading this are experts. But I see on so many other boards people who seem to think that some scientist somewhere took a survey of a bunch of ancient samples, "averaged" it, and that we are comparing populations to populations.
We're not. We are not comparing Scots to Western Hunter Gatherers. We are comparing Scots (or any other modern individual or group) to ONE SAMPLE. For WHG, it's Loschbour. For EEF, it's Stuttgart. For ANE, it's Mal'ta. Etc.
3. We don't know that that one sample will turn out to be representative of "Western Hunter Gatherers" any more than we know that taking Danny Devito or the harlequin model Fabio is a representative of a modern Italian. Indeed, as the number of samples we get grows, we know the situation is infinitely more complex.
We all remember, for example, when the first farmers sampled had very unique mtDNA. For a while, people tried to read too much into it. "OMG, what if all farmers bore this odd mtDNA?" was the refrain. But it turned out to be a one-off. This can and will happen again and again as we get more samples over time.
4. The acronyms will get repetitive real fast. We are talking about aDNA, remember? Before farming, the whole world were hunter gatherers. So, many (most) aDNA samples will eventually have -HG after them, if we follow the current convention.
I imagine a world where we have found 26 slightly different hunter gatherer samples, and thus we have one different -HG for every letter in the alphabet! That'd be just silly.
For these reasons, but primarily numbers 2 and 3, I think the current practice is misleading and doomed to failure. Europe is a very complicated place. We will find ancient samples with very unique genomes, which are detectable in modern populations. They will all be slightly different from one another, because one sample is, well, one sample... It is highly misleading to say that "John Smith..." or "Estonians are more Western Hunter Gatherer than..." because we have not sampled all, most, or even many Western Hunter Gatherers. (I don't mean to pick on WHG. This applies equally, indeed MORE, with EEF and ANE!)
So, what is the solution?
I think if we purport to be scientific, we need to speak with scientific precision.
If an individual or a modern population bears resemblance to an ancient genome, we should state that it has a percentage similarity to that one sample. And not try to make it more than it is, like the very official and extensive term like, "Eastern Hunter Gatherers."
As for the sample, we should also include the year discovered, the situs of the discovery, and the years Before Present (BP).
Remember, many of these sites are caves where there have been and will be more discoveries. In other words, I expect there will be many more Loschbours, more Stuttgarts, etc., and it will get quite confusing unless we speak with specificity about when something was discovered and when in time it came from.
Let's avoid a situation like we had with terms like R1b1b1b1a2a1b2bc3d, which lose meaning. Let's refer to things with scientific precision.
Examples:
Instead of, "Scots are 19% Ancient North Eurasian."
SAY: "On average 19% of the genes of the modern Scottish population match 2013Mal'ta-24,000BP."
Instead of, "Southern European populations have a lot more CHG blood than I expected."
SAY: "Southern European populations bear many genes matching 2015Kotias-10,000BP."
Instead of, "Sardinians are 45% WHG."
SAY: "Approximately 45% of the genes in the modern Sardinian population resemble 2013Loschbour-6000BP."
This convention is much more accurate.
People started saying that it would probably be better to say the first couple letters and the major terminal SNP. For example, R1b-U106 or I2-M26. This was logical and good. Unlike the terminology, the SNPs never change. And they're shorter to write.
Here I humbly propose a new terminology for ancient autosomal samples. I think picking terms like, "WHG" was a mistake, and now that I read about EHG and CHG, I really think so. For the uninitiated, these acronyms stand for "Western Hunter Gatherer," "Caucasus Hunter Gatherer," etc.
People compare their modern genomes, or the genomes of modern populations or ethnic groups, to these ancient samples. And then they use the shorthand, like, "Scottish average 19% CHG." This is highly misleading.
Let me give the reasons why I think it is deficient, and tell me if you disagree.
1. As we get more samples over time, it will be hard to keep renaming the different samples, if they form a different component. We just saw this with the recent CHG finds. Imagine if we find a detectable signal of ancient genes from Iberia. What will we call that component? "Really Western Hunter Gatherer?"
2. The shorthand is deeply misleading (i.e., "Scottish are 19% CHG.") This to me is the most important point. Most people reading this are experts. But I see on so many other boards people who seem to think that some scientist somewhere took a survey of a bunch of ancient samples, "averaged" it, and that we are comparing populations to populations.
We're not. We are not comparing Scots to Western Hunter Gatherers. We are comparing Scots (or any other modern individual or group) to ONE SAMPLE. For WHG, it's Loschbour. For EEF, it's Stuttgart. For ANE, it's Mal'ta. Etc.
3. We don't know that that one sample will turn out to be representative of "Western Hunter Gatherers" any more than we know that taking Danny Devito or the harlequin model Fabio is a representative of a modern Italian. Indeed, as the number of samples we get grows, we know the situation is infinitely more complex.
We all remember, for example, when the first farmers sampled had very unique mtDNA. For a while, people tried to read too much into it. "OMG, what if all farmers bore this odd mtDNA?" was the refrain. But it turned out to be a one-off. This can and will happen again and again as we get more samples over time.
4. The acronyms will get repetitive real fast. We are talking about aDNA, remember? Before farming, the whole world were hunter gatherers. So, many (most) aDNA samples will eventually have -HG after them, if we follow the current convention.
I imagine a world where we have found 26 slightly different hunter gatherer samples, and thus we have one different -HG for every letter in the alphabet! That'd be just silly.
For these reasons, but primarily numbers 2 and 3, I think the current practice is misleading and doomed to failure. Europe is a very complicated place. We will find ancient samples with very unique genomes, which are detectable in modern populations. They will all be slightly different from one another, because one sample is, well, one sample... It is highly misleading to say that "John Smith..." or "Estonians are more Western Hunter Gatherer than..." because we have not sampled all, most, or even many Western Hunter Gatherers. (I don't mean to pick on WHG. This applies equally, indeed MORE, with EEF and ANE!)
So, what is the solution?
I think if we purport to be scientific, we need to speak with scientific precision.
If an individual or a modern population bears resemblance to an ancient genome, we should state that it has a percentage similarity to that one sample. And not try to make it more than it is, like the very official and extensive term like, "Eastern Hunter Gatherers."
As for the sample, we should also include the year discovered, the situs of the discovery, and the years Before Present (BP).
Remember, many of these sites are caves where there have been and will be more discoveries. In other words, I expect there will be many more Loschbours, more Stuttgarts, etc., and it will get quite confusing unless we speak with specificity about when something was discovered and when in time it came from.
Let's avoid a situation like we had with terms like R1b1b1b1a2a1b2bc3d, which lose meaning. Let's refer to things with scientific precision.
Examples:
Instead of, "Scots are 19% Ancient North Eurasian."
SAY: "On average 19% of the genes of the modern Scottish population match 2013Mal'ta-24,000BP."
Instead of, "Southern European populations have a lot more CHG blood than I expected."
SAY: "Southern European populations bear many genes matching 2015Kotias-10,000BP."
Instead of, "Sardinians are 45% WHG."
SAY: "Approximately 45% of the genes in the modern Sardinian population resemble 2013Loschbour-6000BP."
This convention is much more accurate.
Saturday, December 12, 2015
How Little We Know About Ancient DNA - Part II
Earlier this year, I posted a series of maps graphically depicting the (at that time) exhaustive list of Ancient DNA finds, mapped out for both time and space.
The post, while now a bit dated due to additional finds, is still worth examining. When reading it, it should becomes very apparent to you, the concept in the title of this post: How Little We Know About Ancient DNA.
As you can see from the maps, it appears that people bearing certain Y Chromosome haplogroups "flew" across time and space. And that certain parts of Europe had nobody in them until someone flew across the distances.
Of course, this is impossible. It simply reflects the fact that we continue to have immense gaps in skeletal finds and in our knowledge.
Most importantly, it shows that today's conventional wisdom, popular at echo chambers like the Anthrogenica boards, will certainly change tomorrow -- revealing the adherents to such theories to be akin to arrogant fraudsters, peddling certainty where none is scientifically warranted.
Recently, a poster at Anthrogenica, with the handle Tomenable, posted an excellent visualization of the same gaps in knowledge that I referenced.
You can view a list of aDNA finds here, in chart form, courtesy of Tomenable.
And even better, here is a chart, in chronological order, showing the same.
What does the chart show? By applying *scientific* methods of taking things to their logical conclusions, and reducing our knowledge to a set of provable statements, you can easily see how little we know.
For starters, based on these chrono maps, it looks like Haplogroup C1 made it to Europe after I2. Yet almost everyone, from the scientific community to the "citizen" scientists (their term) on Anthrogenica, agree that C1 is a rare, likely "Cro-Magnon" marker, that represents the very first humans out of Africa and into Europe. On the other hand, it has been accepted for over a decade that Haplogroup I, notably I2, represents the second (or third) wave of the population of Europe, associated with the Gravettian dispersions.
But again, this is *not* "what the aDNA shows."
Ask the wiseguys on Anthrogenica, or search their posts. They express with certainty that C1 came first, followed by I2. And it probably is true. But it is NOT born out by the aDNA evidence. (Yet).
However, the same group of people turn to the aDNA evidence (blindly) to express 100% confidence in other theories, for example, everything from the notion that R1b xV88 couldn't be found west of modern Poland until the Indo-European expansions. (I find this notion laughable.)
They also rely on the aDNA evidence to express 100% confidence in wild notions of sex selection that have more in common with dimestore novels than anything scientific. The proponents of said theories also happen to be mostly males bearing R1b. Yes folks, in a world where racial identity is taboo, any sense of ingroup-outgroup dynamics for Western Europeans has simply been transferred to tiny markers on one chromosome.
In other words, many of these folks blindly turn to our meager aDNA evidence to justify their pet theory du jour, but choose to ignore what the aDNA evidence shows, when convenient.
They cite gaps in data (i.e., a lack of samples) as evidence for proving a negative, as if that was possible -- when they want to.
But they ignore the lack of samples when convenient, if it doesn't fit in their narrative for that time or place.
Doubt them, they revert to the argument "well, the aDNA shows..." but they are more than willing to fill in gaps in aDNA when convenient.
It's already been a rough year for the arrogantly certain in Ancient DNA. Notably, past theories on the dispersion of Haplogroup J2 have fallen by the wayside. Theories posted on Anthrogenica just a couple months ago, and accepted by the echo chamber as gospel fact, have been called into serious doubt by recent academic papers.
I've also posted repeatedly on how difference in culture and hyperlocal topography can affect what aDNA survives into modern times. The easiest example is one tribe burying their dead, while another tribe cremates it. Anyone who knows anything about written history understands that the reason why we don't have m(any) ethnic Roman skeletons is because they cremated their dead. To those who don't grasp this concept, it would be as if the Romans, a powerful, numerous, colonizing, widespread, important society -- didn't exist.
I can just see Anthrogenica in the year 2515: "but there are no Roman samples in aDNA," they would maintain adamantly. Yes, you would reply. But the Romans existed.
The point is simple: approach any theories explaining what happened before written history with caution. There are major gaps in the record, and it is far, far too early to approach things with the smug certainty one sees on these boards.
Look at the samples across time and space (geography). Don't hide behind relative, subjective terms like "Mesolithic" and "Neolithic." Instead, look at how Europe was populated, the way it was populated --- in gradations, over (real) time. You, too, will notice "How Little We Know (Still) About aDNA."
The post, while now a bit dated due to additional finds, is still worth examining. When reading it, it should becomes very apparent to you, the concept in the title of this post: How Little We Know About Ancient DNA.
As you can see from the maps, it appears that people bearing certain Y Chromosome haplogroups "flew" across time and space. And that certain parts of Europe had nobody in them until someone flew across the distances.
Of course, this is impossible. It simply reflects the fact that we continue to have immense gaps in skeletal finds and in our knowledge.
Most importantly, it shows that today's conventional wisdom, popular at echo chambers like the Anthrogenica boards, will certainly change tomorrow -- revealing the adherents to such theories to be akin to arrogant fraudsters, peddling certainty where none is scientifically warranted.
Recently, a poster at Anthrogenica, with the handle Tomenable, posted an excellent visualization of the same gaps in knowledge that I referenced.
You can view a list of aDNA finds here, in chart form, courtesy of Tomenable.
And even better, here is a chart, in chronological order, showing the same.
What does the chart show? By applying *scientific* methods of taking things to their logical conclusions, and reducing our knowledge to a set of provable statements, you can easily see how little we know.
For starters, based on these chrono maps, it looks like Haplogroup C1 made it to Europe after I2. Yet almost everyone, from the scientific community to the "citizen" scientists (their term) on Anthrogenica, agree that C1 is a rare, likely "Cro-Magnon" marker, that represents the very first humans out of Africa and into Europe. On the other hand, it has been accepted for over a decade that Haplogroup I, notably I2, represents the second (or third) wave of the population of Europe, associated with the Gravettian dispersions.
But again, this is *not* "what the aDNA shows."
Ask the wiseguys on Anthrogenica, or search their posts. They express with certainty that C1 came first, followed by I2. And it probably is true. But it is NOT born out by the aDNA evidence. (Yet).
However, the same group of people turn to the aDNA evidence (blindly) to express 100% confidence in other theories, for example, everything from the notion that R1b xV88 couldn't be found west of modern Poland until the Indo-European expansions. (I find this notion laughable.)
They also rely on the aDNA evidence to express 100% confidence in wild notions of sex selection that have more in common with dimestore novels than anything scientific. The proponents of said theories also happen to be mostly males bearing R1b. Yes folks, in a world where racial identity is taboo, any sense of ingroup-outgroup dynamics for Western Europeans has simply been transferred to tiny markers on one chromosome.
In other words, many of these folks blindly turn to our meager aDNA evidence to justify their pet theory du jour, but choose to ignore what the aDNA evidence shows, when convenient.
They cite gaps in data (i.e., a lack of samples) as evidence for proving a negative, as if that was possible -- when they want to.
But they ignore the lack of samples when convenient, if it doesn't fit in their narrative for that time or place.
Doubt them, they revert to the argument "well, the aDNA shows..." but they are more than willing to fill in gaps in aDNA when convenient.
It's already been a rough year for the arrogantly certain in Ancient DNA. Notably, past theories on the dispersion of Haplogroup J2 have fallen by the wayside. Theories posted on Anthrogenica just a couple months ago, and accepted by the echo chamber as gospel fact, have been called into serious doubt by recent academic papers.
I've also posted repeatedly on how difference in culture and hyperlocal topography can affect what aDNA survives into modern times. The easiest example is one tribe burying their dead, while another tribe cremates it. Anyone who knows anything about written history understands that the reason why we don't have m(any) ethnic Roman skeletons is because they cremated their dead. To those who don't grasp this concept, it would be as if the Romans, a powerful, numerous, colonizing, widespread, important society -- didn't exist.
I can just see Anthrogenica in the year 2515: "but there are no Roman samples in aDNA," they would maintain adamantly. Yes, you would reply. But the Romans existed.
The point is simple: approach any theories explaining what happened before written history with caution. There are major gaps in the record, and it is far, far too early to approach things with the smug certainty one sees on these boards.
Look at the samples across time and space (geography). Don't hide behind relative, subjective terms like "Mesolithic" and "Neolithic." Instead, look at how Europe was populated, the way it was populated --- in gradations, over (real) time. You, too, will notice "How Little We Know (Still) About aDNA."
Sunday, November 8, 2015
The Eerie Similarities Between Julius Caesar and Jesus Christ
Over
two-thousand years, some events happened. Tales of the events were
passed down orally by common people, in societies where over 80% of
the population was illiterate. The tales were modified over the
almost 100 years that they were passed down verbally. Local fathers
changed certain details to meet the local geography, to make the
story more relatable to their wide-eyed kids.
It
is well-known that the Epic of Gilgamesh of the Babylonians matches
almost exactly the Story of Noah's Flood from Genesis. Few credible
scholars deny there was quite a bit of borrowing from one to the
other.
This
theory below, by Francesco Carotta, is more controversial. But read the facts and determine whether you see the similarities.
Once
upon a time, a great man lived whose initials were J.C. He
was born quite poor, and lived among the common people, even though
he was descended from the great, foundational King
Romulus/King David. His aunt/his mother was named Maria.
Some claimed for him a miraculous birth/a birth by Caesarian
section. When he was still young, he was almost killed by the
tyrant Sulla/Herod.
His
deeds gained him significant fame during the early part of his public
career, when he was operating in the province just to the north,
called Gallia/Galilee. Everywhere he went, he was accompanied
by his 12 faithful Lictors/disciples. He spoke in
proverbs often, for example, “I came, I saw, I conquered/I
came, I saw, I washed.” He was close to a promiscuous woman
named Cleopatra/Magdalene and a righteous, powerful man named
Nicodemus of Bithynia/Nicodemus of Bethany.
Eventually,
his fate forced him to make a momentous decision and cross the
Rubicon/Jordan river. On the way, he was tested at and
performed miraculous deeds at a city called Corfinium/Cafarnaum.
Then, he was operational in the capital, Rome/Jerusalem.
There
had been a very similar man who he was close with, who had a
similar following and career. Eventually though, Pompey/John the
Baptist was beheaded by an Egyptian, and the head presented to
him.
He
was kind to the Caecilii (the blind), the Claudii
(the lame), and the Metellii (the disfigured). He was so
righteous that the common people started callimg him by the Greek
term, “chrestos.” After operating in the capital
for a while, his popularity was noticed by a jealous governing
body, the Senate/the Sanhedrin. He was accused of having
ambitions on becoming King.
He
was betrayed by someone very close to him named Junius/Judas.
The crowd is forced to choose between Brutus/Barabbas and him. A
powerful man named Pontifex Lepidus/Pontius Pilate washes his hands
of the matter. He is killed on March 15, wearing a Crown
of Grass/Crown of Thorns. Right before being killed, he is stabbed
between the ribs by someone named Cassius Longinus!
His body was displayed to
the people on a crucifix/he
was crucified.
His
followers were devastated, as predictions from all around the world
had said that a Savior and the King of the World would be born around
this time. So, he ascended into heaven and became a God. He took
his place in the pantheon as the son of God – son of Jupiter/son of
Jehovah.
Wednesday, October 28, 2015
What Is the Best and Most Accurate Ancestry Calculator (DNA Testing)?
What Is the Best and Most Accurate Ancestry or Admixture Calculator from DNA Testing?
We Review 23andme, AncestryDNA, Family Tree DNA (FTDNA), DNA.Land, Dodecad, Eurogenes, etc.
Judging from community discussions in online forums, "Admixture" tests, where a company or entity takes your raw DNA data, puts it into a calculator, and then purports to tell you where your ancestors came from -- these are all the rage. It is not rare for seemingly educated individuals to post on the Internet sheer and utter nonsense about their results, for example, assuming that a calculator identified their ancestry with something close to 100% accuracy.
In the online world, there is no such thing as perfect privacy. And in DNA, there is no such thing as 100% accuracy for ancestry calculators.
This is because all people are admixed, but not all ethnic groups form part of the samples. Put another way, if your ancestors come from a valley in Switzerland where no one has ever been tested, you might show up in a test as French, German, Italian, Austrian, but not Swiss.
You might say to yourself that you have documented ancestry back to the dawn of time that you are from Switzerland. You may match other Swiss people exactly. But because the Swiss are indeed mixes of the groups above, and because there are no specific, micro-targeted Swiss samples in the hypothetical database that match you more closely than those other nationalities, the test would be woefully inaccurate to YOU. After all, you don't want a test to tell you you might be Northern Italian, if you are Swiss. (For that matter, do you NEED a test to tell you that? See below.)
In the online privacy world, they've named protections that are scientifically the best (and do their job pretty darn well) "Pretty Good Privacy." In the DNA world, all we can hope for is "Pretty Good Accuracy" -- ancestry calculators that are scientifically grounded, don't make claims beyond what they can really do, and ones that get the broad regions correct in the very least.
The coolest benefit about living in a college town (Berkeley for this blogger) is that there are a ton of people from all over the world, with pretty well-defined ancestry. For example, that Danish exchange student with 500 years of documented ancestors in Denmark? That's a good candidate for testing some of these calculators. Enough friends of mine have taken DNA tests, and we've plugged the results in the calculators across several paysites (testing companies) like 23andme and AncestryDNA, and free calculators, like the ones available on Gedmatch. Who came out on top?
By far, the best and most accurate ancestry calculator is on 23andme. Like all good scientists, they are humble instead of full of hubris. They don't profess to give you one set of results and say, "this is it." Instead, they give you three different results: standard, conservative, and speculative. Each is pretty darn accurate for most of the people we know who have tested there and other sites. Bottom line: 23andme's "Ancestry Composition" feature is outstanding, and the best, most accurate one online we could find.
It is our opinion that the least accurate ancestry calculator is at the new site DNA.land. And the one on FTDNA is a close second. Both are terrible. Almost everyone who used the feature on DNA.land reported that the calculator is way off; just not ready for prime time at time of writing this post.
How do these calculators work? Well, remember, the data that comes out is only as good as the data that comes in. It is worth to always remember the concept that computer programmers call "GIGO: Garbage In, Garbage Out." What this means is that if the data on which a conclusion is based is faulty, the answer will also be faulty. With calculators, this manifests itself two ways: with a shifted focus, or faulty or incomplete baseline data.
By a different focus, we mean: Several calculators, for example, the MDLP Ethnicity Calculator, also offered (with Eurogenes and Dodecad and Gedrosia) at Gedmatch, stands for Magnus Ducatiae Lituania Project. As you might have guessed from its name, it focuses on the people from lands that used to form the Grand Duchy of Lithuania: places in Northeast Europe, including Poland, Estonia, etc.
MDLP seeks to be very good at calculating ethnic tidbits of interest to those populations. But is is good for determining the difference between, say, a Catalonian Spaniard and a Northern Italian? No, it's actually quite bad on that front. That's simply not its focus.
Similarly, there are other calculators on Gedmatch that exist to focus on and cater to Asians, Africans, even mixed race folks. And within European populations, you have other focuses, like Dodecad, which seems Grecocentric, for lack of a better word. None of these will do that great outside their focus areas. So take the results from those ones with a grain of salt, unless you happen to hail from their regions of focus.
Don't believe that? Think I'm being extreme? If you are European, try putting your data in a calculator that is focused on another population. Like the East Asian-focused calculators. It won't tell you that you are NOT East Asian. It will tell you which East Asian population you resemble the most. To be clear: if all a calculator has is East Asian samples, a European will be told he or she is Japanese or Chinese. This same concept applies within European focused calculators at the regional level.
In terms of bad baselines, recall the Swiss example above. Europe is filled with micropopulations that exhibit a high degree of population homogeneity (a little inbred, to use the pejorative term). If a calculator does not have a sample from your micropopulation (the narrow region where your ancestor lived for millennia), then you will get a faulty reading.
Put simply (to use a French example): It's a big country. Normans are not Basques, Provencals are not Bretagnes, etc. That is why the best calculators are HONEST. 23andme discloses quite readily that for the huge populations in the middle of Europe (French, Germans, but also Benelux countries, etc.), it cannot spot the DNA with certainty 92% of the time.
Does the 23andme website have any drawbacks? Sure it does. But they are minor compared to the others.
First, its "Countries of Ancestry" feature is not what it could be. But it's important to understand three things: (1) This is NOT their ancestry calculator, but another feature entirely, so perhaps it's unfair perhaps for us to even review it in this space. (2) It's experimental, and they state that. (3) They are wisely phasing it out. What was the problem with that feature? Well, it gave you the list of countries of people who have the most matches with you. Let's say for example you are half Italian, half Polish (a common mix in Chicago). In other parts of Chicago, another common mix is half Polish, half Irish. For whatever reason, people of Irish heritage have tested themselves at far greater numbers than the others. Your Polish DNA would overlap (match) with the people who reported they were half Polish, half Irish. And this feature would then tell you that "a high percentage of the people who have DNA similar to yours are from Ireland." Do you understand? It's a huge problem, especially for smaller populations, especially because so many Americans are now half this, half that. It's just not that edifying then.
23andme also suffers from the same sample issues as many of the other ancestry calculators. For example, 85% of Italian Americans (TRANSLATION: potential customers, since most people who test are from Britain or the US) hail from just 3 regions in the deep south of Italy: Campania (Naples), Calabria, and Sicily. Yet the population samples that most of these websites use are from Tuscany. Even though Dante tried to meld them, Tuscans are not Sicilians and vice-versa.
Often, these calculators when they see Sicilian or rural Southern Italian genes, they, in effect, say: we don't know what you are! you are kind of Italian but you also resemble, a little bit, people from Cyprus or Jews. So they give an odd result. And then you have someone tested who says, "I might be Jewish." No. The answer is that your people were not included in the data-set by which the baseline was developed. If they were, the calculator would recognize you as a run of the mill Sicilian.
All online ancestry alculators also suffer from lack of inter-operability and non-standardized terms. For example, among the calculators on Gedmatch, some use the term "Caucasian" to mean "generalized European" (which is how it used in common parlance, of course). Others use it to mean, the specific, like, from Soviet Georgia, Armenia, etc.
Here's the bottom line: don't expect any ethnicity or ethnic-origins calculator to be 100% correct. Don't expect new insights if you have confirmed records. In other words, if you look just like your dad (you're not a bastard), and you're not adopted, and you have records going back centuries -- why do you need an ethnicity calculator to begin with?
These admixture tests can help if you were adopted, and want to have a sense of where to start. But keep in mind, the largest plurality of Americans come from German heritage, and yet the best currently cannot identify German DNA 92% of the time.
Avoid the mythology and those who oversimplify. There are reliable sources out there in genetic genealogy, like Debbie Kennett -- and there are a lot of charlatans. Be careful whenever someone oversimplifies to the point of exaggeration, falls into stereotypes, or tells you what you want to hear. With DNA as with everything, the most parsimonious answer is often the best. The exotic is often wrong.
As the science improves, you can't go wrong using the Standard or Conservative setting on the 23andme Ancestry Composition test.
READ MORE:
Subscribe to:
Posts (Atom)