Genetic Similarities Within and Between Human Populations
The proportion of human genetic variation due to differences between populations is modest, and individuals from different populations can be genetically more similar than individuals from the same population. Yet sufficient genetic data can permit accurate classification of individuals into populations. To resolve this apparent conflict, we analyzed the question "How often is a pair of random individuals from two different populations genetically more similar than a pair of individuals randomly selected from any single population"; We compared this frequency (w) with error rates for classification methods, using data sets that vary in number of loci, diversity of populations, and polymorphism ascertainment strategies. Classification methods achieve higher discriminatory power than the individual-based measure, w, because of their use of aggregate properties of populations. The number of loci analyzed is the most critical variable: with one hundred polymorphisms, accurate classification is possible, but w remains sizable, even when using populations as distinct as sub-Saharan Africans and Europeans. Phenotypes controlled by a dozen or fewer loci can be expected to show substantial overlap between human populations. This provides empirical justification for caution when using population labels in biomedical settings, with broad implications for personalized medicine, pharmacogenetics, and the meaning of race.
Posts: 2007 | From: Washington State | Registered: Oct 2006
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quote:Originally posted by Evergreen: Genetics. 2007 Mar 4
Genetic Similarities Within and Between Human Populations
The proportion of human genetic variation due to differences between populations is modest, and individuals from different populations can be genetically more similar than individuals from the same population. Yet sufficient genetic data can permit accurate classification of individuals into populations. To resolve this apparent conflict, we analyzed the question "How often is a pair of random individuals from two different populations genetically more similar than a pair of individuals randomly selected from any single population"; We compared this frequency (w) with error rates for classification methods, using data sets that vary in number of loci, diversity of populations, and polymorphism ascertainment strategies. Classification methods achieve higher discriminatory power than the individual-based measure, w, because of their use of aggregate properties of populations. The number of loci analyzed is the most critical variable: with one hundred polymorphisms, accurate classification is possible, but w remains sizable, even when using populations as distinct as sub-Saharan Africans and Europeans. Phenotypes controlled by a dozen or fewer loci can be expected to show substantial overlap between human populations. This provides empirical justification for caution when using population labels in biomedical settings, with broad implications for personalized medicine, pharmacogenetics, and the meaning of race.
This article sounds interesting. Is there anyway to get a copy of the entire article?
This morning BMC just published an article that contradicts this piece.
. Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms Dominic J Allocco , Qing Song , Gary H Gibbons , Marco F Ramoni and Isaac S Kohane
The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.
Background
Recent studies have shown that when individuals are grouped on the basis of genetic similarity, group membership corresponds closely to continental origin. There has been considerable debate about the implications of these findings in the context of larger debates about race and the extent of genetic variation between groups. Some have argued that clustering according to continental origin demonstrates the existence of significant genetic differences between groups and that these differences may have important implications for differences in health and disease. Others argue that clustering according to continental origin requires the use of large amounts of genetic data or specifically chosen markers and is indicative only of very subtle genetic differences that are unlikely to have biomedical significance.
Results
We used small numbers of randomly selected single nucleotide polymorphisms (SNPs) from the International HapMap Project to train naive Bayes classifiers for prediction of ancestral continent of origin. Predictive accuracy was tested on two independent data sets. Genetically similar groups should be difficult to distinguish, especially if only a small number of genetic markers are used. The genetic differences between continentally defined groups are sufficiently large that one can accurately predict ancestral continent of origin using only a minute, randomly selected fraction of the genetic variation present in the human genome. Genotype data from only 50 random SNPs was sufficient to predict ancestral continent of origin in our primary test data set with an average accuracy of 95%. Genetic variations informative about ancestry were common and widely distributed throughout the genome.
Conclusions
Accurate characterization of ancestry is possible using small numbers of randomly selected SNPs. The results presented here show how investigators conducting genetic association studies can use small numbers of arbitrarily chosen SNPs to identify stratification in study subjects and avoid false positive genotype-phenotype associations. Our findings also demonstrate the extent of variation between continentally defined groups and argue strongly against the contention that genetic differences between groups are too small to have biomedical significance.
posted
The study about Fst differences is bogus because you just cannot do a getic study for large landmasses like Africa and Asia, especially when the genetic diversity in Africa is greater than for any other arbitrarily demarcated landmasses such as the other continents.
What the Eurocentric researchers fail to realise is that "bootlenecks" may develop not only between the continents(arbitrary demarcations because continents are not small islands isoleted from some mainland. They are all conjoined, except perhaps Australia) but within within continents. The Genetics March 4 thesis seems more cogent than the March 10 piece.
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quote:Originally posted by lamin: The study about Fst differences is bogus because you just cannot do a getic study for large landmasses like Africa and Asia, especially when the genetic diversity in Africa is greater than for any other arbitrarily demarcated landmasses such as the other continents.
I don't agree.
Granted any study on any population - whether it relates genetics, political opionion or anything else, is of course inherently limited by the impossiblity of studying every one of millions of individuals.
All forms of statistical data on populations therefore are the result of sampling or polling.
But the specific point about genetic distances being great in Africa is easily validated by sampling *any* African population.
Africans are derived from older lineages from the main source of human origin and diversity.
All non Africans are the product of a small bottleneck in NorthEast Africa from recent times.
Take a sample of most any 100 Africans, and compare to any 100 non Africans and you will simply find that Africans have more allellic diversity.
This is a fact of genetics that may be hard to understand, but a fact nontheless.
What follows is a large excerpt from Spencer Wells Journey Man,
I will agree that it's bogus, *if* you can find a *geneticist* who contradicts it...
posted
^ The majority of genetic polymorphisms found within our species are found uniquely within Africans - Spencer Wells.
quote:What the Eurocentric researchers fail to realise is that "bootlenecks" may develop not only between the continents(arbitrary demarcations because continents are not small islands isoleted from some mainland. They are all conjoined, except perhaps Australia) but within within continents.
This is wrong because continents are *not* arbitrary to biology. They define very real biological boundaries.
It is also a specious statement, since, as I explained to you before - you yourself describe bottlenecks as either:
a) intercontinental or... b) intracontinental
*Both* terms validate the relevance of continents, athough you don't seem to get this?
Continents are real geographical bottlenecks which stimulate genetic variation and speciation.
Disagree?
Ok fine.
Human beings evolved in Africa 150~ thousand years ago. Until 60~ thousand years ago, there were no humans anywhere other than Africa, with the sole known venture beyound the contentental boundary making it as far as Israel, and then dieing out. This means that for most of human history, the human species is exclusively African, with no non Africans.
Spencer Wells can explain this, can you?
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posted
I've noticed that opinions have already been formed around the posted studies, but what specific markers are being discussed; autosomes, paternal, maternal, or some other monophyletic unit? Are the two studies discussing the very same "type" of 'monophyletic' unit(s)?
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posted
^ I haven't read the study. My comments are specially to the prior reply with regards the fact of African genetic diversity, and the legitmacy of fst distances in population genetics
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^ I haven't read the study. My comments are specially to the prior reply with regards the fact of African genetic diversity, and the legitmacy of fst distances in population genetics
...and so, the point of contention here is centered on the idea of "continents" being "arbitrary demarcations" as opposed to 'real demarcations' vis-à-vis demographic differences in genotype(s) at "continental" level?...because it does appear that Lamin acknowledges the fact of African diversity in his post.
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^ I haven't read the study. My comments are specially to the prior reply with regards the fact of African genetic diversity, and the legitmacy of fst distances in population genetics
...and so, the point of contention here is centered on the idea of "continents" being "arbitrary demarcations" as opposed to 'real demarcations' vis-à-vis demographic differences in genotype(s) at "continental" level?...because it does appear that Lamin acknowledges the fact of African diversity in his post.
On this point, I'd rather allow Lamin to respound to my reply, if he chooses to do so.
Did you read the excerpt from Journey of Man:
Wells mentions a trip to Luxor Egypt, and his wife being mistaken for some one else. The Egyptian told him: "Sorry, you all look alike to me." [pg 17]
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quote:Originally posted by rasol: Not if you don't read it, there isn't.
Well, Rasol, if you put an extract in front of me, there must be a reason for doing so. I take it that you did so, because of something I said or not have said?
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You're reading too much into it, while, at the same time...not actually reading it, which is a bit odd, don't you think?
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You're reading too much into it, while, at the same time...not bothering to reading it, which is a bit odd, don't you think?
Therein lies the confusion [on my part I guess]; I was under the impression it was meant for my consumption, and hence my **question(s)**, which you could have simply addressed earlier on by pointing to the fact that it was meant for Lamin. I don't jump to conclusions, I first ask questions.
No, I don't think it is odd that I didn't bother reading it, considering that I wasn't given a reason as to why I should, in terms of something new that is supposed to be brought to my attention, or whether it has any relationship with something I've said herein. I do think however, it is odd for you to "now" tell me, that you weren't addressing me when you asked:
On this point, I'd rather allow Lamin to respound to my reply, if he chooses to do so.
Did you read the excerpt from Journey of Man:
Wells mentions a trip to Luxor Egypt, and his wife being mistaken for some one else. The Egyptian told him: "Sorry, you all look alike to me." [pg 17]
You spoke of Lamin in the third person format while addressing my post, and then that question in the first person format. This is why I wrote my post in as a conditional one (with question mark in quotation marks), to the extent that it pertains to me. But now that you've said it has nothing to do with me, then the matter is settled. Posts: 5964 | Registered: Jan 2005
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posted
Sorry for belated reply--just away from the keyboard.
To answer the question, let's take the landmass known as Eurasia--home to 2 arbitrarily delineated continents:Asia and Europe.
It is evident that the flora and fauna of Europe and Asia vary widely from region to re gion because of the vagaries of genetic drift and geographic adaptation. Example: the flora and fauna of the British Isles differ radically from those of say, South Asia(India) or North East Asia(Siberia).
But these 2 continents occupy a continuous landmass yet we cannot deny that the variabilities in the flora and fauna of the Eurasian landmass developed on account of genetic drift pushed along by the random occurrence of "population bottlenecks".
But this is the case eeven when we look at Eurasia in terms of its 2 arbitrarily constructed continents. What's at work here, it seems, is that once population bootlenecks diverge from each other centrifugally then the determining factor for genetic differentiation is "geographic distance" or "geographic(niche) isolation".
The point is that for land masses as large and as geographically variable as Africa and Asia with both subjecvt to bottleneck centrifugal expansion there is no basis fro saying anything specific about the flora and fauna(this includes humans) of such large and geographically variable landmasses.
We can just as easily divide up the African continent into 15 geographical regions all approximately the size of Europe--in much the same way that Eurasia has been arbitrarily divided up into Asia and Europe.
So it would just beg the question to say that a particular regions reflect their own genetic peculiarities--knowing full well that the larger the landmass and geographic space the less likely such statements could be plausibly made.
Again, the larger the landmass and geographic space the more likely that there will be centrifugal genetic drifts each prompted by its own bottleneck and the less likely that such new niche groups would come contact with each other again--over time.
In the case of Africa, Asia and Europe we must note that these 3 arbitrarily defined landmasses are all conjoined and that the likelihood of bootlenecks developing inter-continentally are just as great as intra-continetally.
Case in point: the evident phenotypic distinction between South Asians and North East Asians.
Thus, in the case of Africa, it is quite probable that the average Fst distance between human samples from, say, Senegal(Wolof) and South Africa(Khoi-San) would be greater than that between the Senegal sample and, say, another sample from Portugal or Greece.
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quote:Originally posted by lamin: Sorry for belated reply--just away from the keyboard.
To answer the question, let's take the landmass known as Eurasia--home to 2 arbitrarily delineated continents:Asia and Europe.
Here the issue is geology and not genetics.
All geologists agree the continents exist.
Continents are neither arbitrary nor precise.
They are large masses of land that are either entirely or nearly-so bounded by water.
Imprecision enters into the matter for several reasons.
1st) Plate techtonics are the underlying factor behind the creation of continents - which *do exist* according to geologists. However the manner in which underground plate techtonics separate land massess isn't always contiguious the connection/separation of surface land masses.
2nd) Political consideration conflates Europe into the status of 'continenet', when in fact:
quote:It is evident that the flora and fauna of Europe and Asia vary widely from region to re gion because of the vagaries of genetic drift and geographic adaptation.
See above **anomoly**. Geologists well tell you that Europe is not a continent, so arguments pertaining its continental status are somewhat moot.
quote: But this is the case eeven when we look at Eurasia in terms of its 2 arbitrarily constructed continents. What's at work here, it seems, is that once population bootlenecks diverge from each other centrifugally then the determining factor for genetic differentiation is "geographic distance" or "geographic(niche) isolation".
No, and this long nonexplanation avoids my question:
Why did humans evolve in Africa, and not Eurasia?
Why did humans live in Africa for 100 thousand years....but not anywhere else?
What is this if not a continental bottleneck?
If you acknowledge this, then I don't see how you can pretend that continental bottlenecks are not realities of biology and moreover are of crucial importance to the history of the human species?
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quote:The point is that for land masses as large and as geographically variable as Africa and Asia with both subjecvt to bottleneck centrifugal expansion there is no basis fro saying anything specific about the flora and fauna(this includes humans) of such large and geographically variable landmasses.
Nonsense. The entiriety of biological flora and fauna classification is filled with definitions of species based ulimtately on the continents in which they are found.
There are literally millions of examples.
This leads back to my other question which you ignored - please refer us to a biologist who can affirm your view. Just one....please.
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quote:We can just as easily divide up the African continent into 15 geographical regions all approximately the size of Europe
No, you can't, because Africa is almost entirely devoid of constant geographical barriers that separate flora and fauna.
The best case for such a barrier would be the sahara, but the sahara [dessert] expands, contracts and virtually ceases to exist at times.
Morever, even if you could sub-divide continents into smaller zones...this does not support your claim that continents are arbitrary.
Which leads back to the third question I asked and which you also fail to address.
What is the basis for claiming that what you call "intra" continental bottlenecks are any less germane to continents that "extra" continental bottlenecks?
You claim continents are arbitrary, but they are in fact still the basis of your divisions.
I don't think your position is well reasoned.
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posted
Well, yes there are natural environmental barriers that could lead to floral and faunal bottlenecks in Africa. We have rivers, mountains, deserts, inland seas, dense forests, etc.--al of which have led to the very great floral and faunal diversity in Africa.
Consider the genomic intra-species differences between elephants and lions on the African continent. And the obvious inter-species differences one easily observe between the extremely diverse mammal and avian life forms we see on the Serengeti for examaple.
Why was it necessary for giraffes and zebras to have bottlenecked into specific herbal niches--if not for some natural barrier that led to their diverse faunal forms.
I say continents a re arbitrary but I cannot help but appeal to them in my discussion if only because most population geneticists are fixated on them and naively don't recognise that "continents" are not much more than normative constructs.
We a re not talking about geology here but flora and fauna--as they adapt to the vafaries of geological movement--as in the case of the differentials between mountain and valley dwelling members of the same species.
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I say continents a re arbitrary but I cannot help but appeal to them in my discussion if only because most population geneticists are fixated on them and naively don't recognise that "continents" are not much more than normative constructs.
You are so right. This is what makes their discussion of African, Eurasian (and etc.) populations--ludicris-- when you can eyeball differences between South African Bantu and Boers; and/or Chinese and Indonesians.
What about an American population?
.
-------------------- C. A. Winters Posts: 13012 | From: Chicago | Registered: Jan 2006
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posted
The genetic differences between continentally defined groups are sufficiently large that one can accurately predict ancestral continent of origin using only a minute, randomly selected fraction of the genetic variation present in the human genome. Genotype data from only 50 random SNPs was sufficient to predict ancestral continent of origin in our primary test data set with an average accuracy of 95%.
Again, it would be quite useful if the specificity of the markers in question was established, because it could make a difference in context. For instance, a mutation like say, E-M78 from the paternal line, is deemed to be of "African" [a continent] origin, but if this mutation alone was deemed to be the sole indicator of "genetic differences" between the different "continentally defined" groups sampled, then is it not safe to say that the results would be misleading, if the mutation transcends the "continentally defined" groups? Now in that same example, this would be different from say, determining the "ancestral continent of origin" based on the said marker alone. The "ancestral continent of origin" in this case may not be the same as the "continent" that the population is "attached/defined" with.
On the other hand, if this was based on autosomes, it would make sense that populations within geographical proximity are likely to be genetically closer, as a product of interbreeding between the populations and sharing of recent common ancestry. The likelihood of geographical close populations having closer genetic distances [in autosomal analysis] with respect to one another, but relatively greater genetic distances with populations from much greater geographical distance, is high. Intra-continental genetic variations ultimately translate into continental diversity. Certain lineages [even when they transcend continents] have trends in frequency and distribution [in the form of clusters] in geographical locations. If in the case of the ongoing example, the autosomal markers are largely associated with certain geographical region in a certain continent, then it is possible to trace the markers back to the "ancestral continent of origin".
For instance, in a place like coastal north Africa, which is geographically intermediate between northern Eurasia [notwithstanding greater barrier of water body like the Mediterranean sea] and the rest of Africa, if going by autosomal markers, would the markers predict either Europe or Africa as the "ancestral continent of origin", both, or will these coastal North Africans develop their own genotypic peculiarities that point to that region of Africa [in which case, goes back to "Africa"]?...If one or the other, or both, does this necessarily have any bearing on their "continental definition" as "Africans"?
On another note, populations that diverged relatively more recently with respect to one another than other groups, will likely have smaller genetic distances based on common recent ancestry and time depth of shared lineages [whether paternal, maternal, or perhaps autosomal] with respect to one another, than they would to populations that diverged from a common ancestor(s) at greater time depths.
Again, the need for understanding the specificity of the nature of the markers in question, as well as the parameters being used to note genetic differences, cannot be underestimated.
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posted
Speaking of so-called Eurasian continent, is it a Fruedian slip that India is commonly referred to as "the sub-continent."
Geologically, India is no more Eurasian than is the Arabian peninsula/Levant/"Mesopotamia."
Posts: 8014 | From: the Tekrur in the Western Sahel | Registered: Feb 2006
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....but you admit that they aren't. Bottom line really.
quote:We a re not talking about geology here but flora and fauna--
Incorrect. The basis for continent is geology. Geology separates landmass....the basis of specication in biology is isolation due to separation, hence the relevance of continent to biology.
Obfuscation and refusal to answer questions is causing this conversation to remain stuck at and elementary level.
Let's brush aside the obfuscation and get to the point then....
The human species at its root, can be denoted genetically by it's oldest, and hence most diverse lineage..... L1.
L1 arose in Africa at least 120 thousand years ago.
L1 has two daughters..... L2 and L3, which were born from L1 lineages bewtween 100~ and 70~ thousand years ago, also in Africa.
A single L3 has over half a dozen sublineages, labeled from L3a to L3h.
One of thise sub lineages, L3a, gives birth to two daughters, 60kya~ known as M and N...more properly L3aM and L3aN.
In the Nation of China there are over 1.2 billion Natives.
Every single one of them is a child of L3a.
In any village in Botswana you will find the natives are also children of L3a, but also several other sub lineages of L3, and L2....and L1.
When we search for unique markers among populations in China and Botswana, we find that a small group of people in Botswana have many markers that are not found anywhere in China [or anywhere else in Asia], amongst the over 1 billion people, but the billion plus Chinese have only a releative-few markers that are not found amongst the San, or virtually anwhere else in Africa.
In terms of mtdna, Africans are L1 and L2 and L3, 3 root lineages that are found in Ethiopia, in Egypt, and in Nigeria too.
Non Africans are L3aX only.
Africans have greater divesity because the human species is African in origin and non Africans are a product of a specific bottleneck, which I have just defined for you.
There is a genetic distinction due to continental bottlenecks between African and non African. There is no distinction in population genetics that is as fundamental, as clear, or as easy to define.
For better or worse, this is fact of genetics, it is not arbitrary.
Only the rheotric against the stated facts...is arbitrary.
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quote:Originally posted by alTakruri: Speaking of so-called Eurasian continent, is it a Fruedian slip that India is commonly referred to as "the sub-continent."
Geologically, India is no more Eurasian than is the Arabian peninsula/Levant/"Mesopotamia."
The problem I have with the reference to India as a 'sub-continent' is that it subliminally regurgiates the nasty conotation of 'sub-saharan' Africa. ie - sub-human.
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