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Author Topic: What's the difference between genome-wide data and mitochondrial genomes?
Ase
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 -

Is one more comprehensive than the other? Because the way this illustration looks, mtdna could reflect as little as 1/16th of your overall ancestry...

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capra
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They're quite different things, you can't really put a percentage on it. A mitochondrial chromosome is actually a kidnapped bacterial chromosome; it's structure is completely different and it is much much smaller than a nuclear chromosome. It has a small set of very important genes and very little 'junk', while your nuclear genome has a buttload of genes, some not all that important, and loads of 'junk DNA'.

mtDNA tells about one line of ancestry, so what percentage of your ancestors that is depends on how many generations back you go. If you go far enough back you could have no autosomal material whatsoever from your mitochondrial DNA ancestor, and they'd be one out of thousands.

Y DNA is a nuclear chromosome but similarly traces one line of ancestry. Thing is, they are very good at tracing that particular line of descent. Autosomal DNA represents all your ancestry (on average anyway), but it's scrambled together and much harder to make a neat tree of relationships with it like you can with uniparental markers.

In short there isn't any straightforward percentage you can put on it, just autosomal is much more informative overall if you can get it.

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Doug M
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An interesting related article:

 -
quote:

For a species whose numbers show no signs of collapsing, humans have a shockingly high mutation rate. Each of us is born with about 70 new genetic errors that our parents did not have. That’s much more than a slime mold, say, or a bacterium. Mutations are likely to decrease an organism’s fitness, and an avalanche like this every generation could be deadly to our species. The fact that we haven’t gone extinct suggests that over the long term, we have some way of taking out our genetic garbage. And a new paper, recently published in Science, provides evidence that the answer may be linked to another fascinating procedure: sex.

For about three decades, one of the senior authors of that paper, Alexey Kondrashov, a biologist at University of Michigan, has explored how populations might shed such mutations. The question poses more of a conundrum than you might think. One model of natural selection is that it acts on mutations one by one: letting this one stay, forcing that one out. Another, though, is that the fates of mutations can be linked—an effect that population geneticists call synergistic, or narrowing, epistasis. This might happen if having one mutation can compound the effects of another: for instance, a system that’s able to limp along with one defective piece will fail with the loss of a second or a third. In this way of thinking, for an individual, having more mutations is not just additively worse, but closer to exponentially worse.

To Kondrashov and others, that prediction suggests an escape route from the trap of rapidly accumulating mistakes, both for humans and other multicellular organisms prone to mutations: As the number of nasty genetic errors in a population rises, natural selection will sweep large rafts of them out of the genome together. And in sexual organisms, because of the ways that mutations from each parent can recombine randomly onto the same chromosomes, the synergistic elimination of bad mutations can happen even faster.

Kondrashov has investigated the implications of synergistic epistasis with theoretical studies. Other researchers have taken the experimental route, trying to detect whether, in real life, mutations can interact with each other this way. Those tests yielded mixed results, though, perhaps because the effect would not have to be very large to keep a population from succumbing.

Now, however, Kondrashov and his co-authors have put together a statistical case, pulled from the genomes of about 2,000 people and about 300 wild fruit flies, that the effect has been quietly acting on us and other organisms all along. Drawing on knowledge of the species’ mutation rates and other factors, the scientists began by calculating what the distribution of mutations in populations of humans and flies ought to be in the absence of this purging effect. Certain numbers of individuals in the group, for example, ought to show 100, 50 or 30 mutations. Then the group of researchers turned to the genomic data, looking for the distribution of mutations in real-world populations.

https://www.wired.com/story/what-if-sex-is-just-a-garbage-dump-for-genetic-mutations/
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Ase
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So in theory you could have something like this?

 -

Egyptians and blacks in the Americas with white ancestors have left me a little puzzled about genetics. I'm wondering if genetically people who've mixed can have European or Near Eastern haplogroups, while technically having most of their ancestry come from elsewhere. And if that's the case, how is that measured. Is that where K clustering comes in? Bear in mind I'm being very simplistic here with the picture right above. I only state "African" and "Asiatic" because both populations throughout the entire duration of history involved populations in multiple climate zones and ecological systems.

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Elmaestro
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Make life easy and treat different forms of genetic analysis as its own discipline.

K clustering? Like STRUCTURE or ADMIXTURE plots? Arent affected by uniparental haplogroups. In fact a lot of time we remove the sex chromosome reads in preprocessing.

You've been on this site for quite a while, I'm pretty sure you know the answer to you own questions most of the time. In that example you have above the Jx/U5 boy can be as much as 99% African. I believe you know that already aswell...

...so what's going on here... Idk for sure but I'm pretty confident in my guess that you're being a about what you think is going on with the Abusir mummies and their 90+ mtDNA haplogroups.

[ 21. July 2017, 09:40 AM: Message edited by: Punos_Rey ]

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Ase
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If you read the post above you, I actually do say my interest with respect to Egypt was part of why I asked (the other part being the implications DNA testing has on Afro Americans). I was not being a "pussy" about anything. In my example the person can have as much as 99% African ancestry, but the question for those with more experience with genetics is: Was the example I illustrated a proper way to understand how this works? And if that's true, would K clustering be a better way to understand the series of lineages that make up a person's background? Like, if I wanted to find out what groups I'm mixed with globally and to what extent, k clustering or a genome wide analysis would be more relevant than ydna mtdna analysis?

And since we're talking about Egypt: Would for that for instance explain why a few people were upset a genome wide analysis was only successfully preformed for 3 remains? My only thing about clustering tho is didn't they kinda do that here (assuming that'd show a bigger picture than simply showing their haplogroups:

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I guess one of the things I imagine some could complain about though with this is that Yoruba is the "Africa" proxy despite having being a population of Africans with no known relevance to Ancient Egypt. But then when you see the bit above it they seem to have a graph comparing AE to plots of more specific ethnicities. They seem to plot more with the Bedouin. One other thing: Applying ancient Egypt to genetics is because it makes genetics more fun for me. I don't think genetics should any place in "race" conversation. I already said this but: Until black people are subjected to racism based on their genetic background instead of their phenotypes, throwing genetics into that sort of debate deserves all sorts of side eye. You have people roaming the world just as mixed as any mummy in Abusir and they will be treated as "negroes."

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Elmaestro
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@PR - Can you add the reason(s) or at least a one word summary of what you edited so people who respond (like Oshun) don't look crazy or out of context to third party readers please.

@Oshun
There's nothing "wrong" with your example in theory. What you've illustrated can and does happen. I don't know exactly where you're coming from with your inquiry on "K-clustering." However it goes without saying that autosomal "clustering" of any form can better explain who you are or where you from genetically.

I can't speak about others but I wasn't upset at what we got, cuz I was biased and set in stone from since I read the abstract. But I see how some other users who were expecting revelation based on what the 90 leaked mtHgs suggested can be disappointed. There's a certain way you have to look at these samples to really get a grasp of what might really be going on if you catch my drift....

In fact, the results shown in the actual paper is gimped, they only showed one K, and didn't even disclose if it had the best CV error value. They ran 19 Ks, (38 including non pruned LD variants) it ain't shit to give us a page with one full run as an image in the supp.

But that's besides the point, look at what bloggers and others are doing with the genomes they released to the public. That's the more important part. And I don't mind when people interject racial stuff in genetics... As long as I can understand where they're personally coming from and they're consistent

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Djehuti
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quote:
Originally posted by Doug M:
An interesting related article:

 -
quote:

For a species whose numbers show no signs of collapsing, humans have a shockingly high mutation rate. Each of us is born with about 70 new genetic errors that our parents did not have. That’s much more than a slime mold, say, or a bacterium. Mutations are likely to decrease an organism’s fitness, and an avalanche like this every generation could be deadly to our species. The fact that we haven’t gone extinct suggests that over the long term, we have some way of taking out our genetic garbage. And a new paper, recently published in Science, provides evidence that the answer may be linked to another fascinating procedure: sex.

For about three decades, one of the senior authors of that paper, Alexey Kondrashov, a biologist at University of Michigan, has explored how populations might shed such mutations. The question poses more of a conundrum than you might think. One model of natural selection is that it acts on mutations one by one: letting this one stay, forcing that one out. Another, though, is that the fates of mutations can be linked—an effect that population geneticists call synergistic, or narrowing, epistasis. This might happen if having one mutation can compound the effects of another: for instance, a system that’s able to limp along with one defective piece will fail with the loss of a second or a third. In this way of thinking, for an individual, having more mutations is not just additively worse, but closer to exponentially worse.

To Kondrashov and others, that prediction suggests an escape route from the trap of rapidly accumulating mistakes, both for humans and other multicellular organisms prone to mutations: As the number of nasty genetic errors in a population rises, natural selection will sweep large rafts of them out of the genome together. And in sexual organisms, because of the ways that mutations from each parent can recombine randomly onto the same chromosomes, the synergistic elimination of bad mutations can happen even faster.

Kondrashov has investigated the implications of synergistic epistasis with theoretical studies. Other researchers have taken the experimental route, trying to detect whether, in real life, mutations can interact with each other this way. Those tests yielded mixed results, though, perhaps because the effect would not have to be very large to keep a population from succumbing.

Now, however, Kondrashov and his co-authors have put together a statistical case, pulled from the genomes of about 2,000 people and about 300 wild fruit flies, that the effect has been quietly acting on us and other organisms all along. Drawing on knowledge of the species’ mutation rates and other factors, the scientists began by calculating what the distribution of mutations in populations of humans and flies ought to be in the absence of this purging effect. Certain numbers of individuals in the group, for example, ought to show 100, 50 or 30 mutations. Then the group of researchers turned to the genomic data, looking for the distribution of mutations in real-world populations.

https://www.wired.com/story/what-if-sex-is-just-a-garbage-dump-for-genetic-mutations/
Actually the advantage of sexual reproduction is that it yields more genetic diversity. Mutation is the original source of all genetic diversity in all organisms both in asexual and sexual reproducing organisms however sexual organisms have an additional source of diversity through genetic recombination in that although the offspring inherits only half the genes from each parent, these genes recombine in ways that make the offspring genetically unique which is why with the exception of monozygotic (identical) birth siblings even siblings born at the same time but from different eggs and sperm differ from each other. Asexual organisms because they are identical are an entire population if not species vulnerable to disease. Because they are identical, what affects one individual will effect all of that population. Sexual organisms do not have that problem because of the great genetic diversity. The only way asexual organisms have any hope of surviving any onslaught against them is through mutation, but even some mutations may be harmful with those carrying those harful mutations usually dying before they reproduce.
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Ish Geber
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quote:
Originally posted by Oshun:
https://anonimag.es/i/20108314_465413223816872_4515292004374876349_n97e98.jpg

Is one more comprehensive than the other? Because the way this illustration looks, mtdna could reflect as little as 1/16th of your overall ancestry...

I suggest you look up this site for any of your future questions.


quote:
Genome-wide association studies are a relatively new way for scientists to identify genes involved in human disease. This method searches the genome for small variations, called single nucleotide polymorphisms or SNPs (pronounced “snips”), that occur more frequently in people with a particular disease than in people without the disease. Each study can look at hundreds or thousands of SNPs at the same time. Researchers use data from this type of study to pinpoint genes that may contribute to a person’s risk of developing a certain disease.

Because genome-wide association studies examine SNPs across the genome, they represent a promising way to study complex, common diseases in which many genetic variations contribute to a person’s risk. This approach has already identified SNPs related to several complex conditions including diabetes, heart abnormalities, Parkinson disease, and Crohn disease. Researchers hope that future genome-wide association studies will identify more SNPs associated with chronic diseases, as well as variations that affect a person’s response to certain drugs and influence interactions between a person’s genes and the environment.

https://ghr.nlm.nih.gov/primer/genomicresearch/gwastudies
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beyoku
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I can give you a real world example with my child's 23andme Report.

Here is a screen shot showing the Childs Ancestry as passed on from the parents.

 -

This is the whole genome. You are able to get this split view because both parents have had their DNA sequenced and the proprietary programs form 23andme knows EXACTLY what parts of our ancestry was randomly passed to the child. This is somewhat of an easy case because My wife (Ethiopian) has no West African and I (African American) have no North African nor East African....so really you almost know what is what since our African ancestries are so distinct.

Now I have a cousin who's wife is Kenyan. His wife as far as whole genome ancestry is East African AND West African. Looking at the child's genome alone you wouldn't be able to tell which portions of West African were from the father or mother....and sometimes its not a clear 50% of all different ancestries down the line IE: If she is 50% West African, 25% Nilotic and 25% Cushitic the child's RANDOM recombination of Ancestry would inherit 50% but not in these exactly proportions. This this woman who hypothetically inherited ALL of Each parents white African ancestry instead of half of it and came out looking pretty mixed. Its like second nature to cut these figures in half but when with heterogeneous genomes its not quite that simple.

Here is another paining of Just the Child:
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When looking at Mtdna. It is ONLY the mothers line, mothers mothers mother...all the way back. The Child is East African L3f, but L3f sublades also show up in West African. I have a Zimbabwean frined that is E1b1a8a and L3f1b4a. His WHole genome is 95% West African and 5% East African. I have an Ivory Coast coworker that is E1b1a8a1a /L3f1b4a1 his whole genome is 100% West African. Obama kids carry a presumable a MTdna of West African or SSA origin, as I would presume his potential Sons BUT ONLY whole genome would tell us his kids are 25-35% or more European ancestry.

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xyyman
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That is why it is important to look at BOTH uniparental markers and autosomal markers. And NOT ONLY frequency of autosomal markers. Uniparental provides is the best indication of DIRECTION of migration. Of course in recent admixed populations like Obama's kids and yours. The story is incomplete when only considering autosomal makers. Interesting you said that West Africans carry "sub-clades" of L3f found in East Africa. I have no proof of that but that is again indicative of there being no such thing as a Bantu Expansion.

That is why the FREQUENCY nonsense in the New Kingdom mummies is a slieght of hands. Deep analysis is needed to determine migration route, frequency cannot tells us anything, and they know it that is why the paper is written like that. .

--------------------
Without data you are just another person with an opinion - Deming

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Elmaestro
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^so when you say frequency, what exactly are you referring too...I'm talking about in relationship to abusir mummies. From the get we have pointed out how relatively diverse the mtdna samples were, and it turns out they're even more diverse than expected when the actual paper dropped.

I know you're itching to say that these lineages represent indigenous African haplogroup diversity...but, till this day you haven't answered how it's possible for such a diverse set of lineages to have such low L frequencies. Would you expect this result If these lineages are coming from inner Africa?

Sleight of hand or not, we know more now than we did before, just apply the data.

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Clyde Winters
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^It is not necessary to see a high frequency of L mtDNA to support the African heritage of the Egyptians and Abusir mummies, because African maternal lineages should not be solely delegated to L branches. This is due to the fact Eurocentrists are constantly tinkering with names of L3 and L3(M,N) clades to deny the African origin of many so-called Asian lineages. This is supported by the change in the name of the mtDNA L3c group. The group L3c of Watson et al. (1997) was renamed U6 (Richards et al. 1998). This along with changing Y-Chromosomes R1b1 and R1b1a found in Africans into R-L278 and R-L754/L761 respectively , while Europeans carrying these clades are simply referred to as R1b1 and R1b1a, to make it appear the these clades do not exist in Africa and promote the idea that R-V88 is of non-African origin.

.
 -

.

Because few people who do genetics research study history and anthropology, they fail to realize that the skeletons dating between 950-750 BC, would represent Egyptians not Asians. This is supported by the fact that Abusir has been recognized as an early center of Egyptian civilization, and the Hyksos was a Kushite dynasty: See http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=18;t=000042

As a result, the Abusir mummies dating between 750-950 BC indicate that the so-called Eurasian haplogroups are in reality African haplogroup. Click on the video below:

' '
 -

.

--------------------
C. A. Winters

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the lioness,
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quote:
Originally posted by Clyde Winters:
Two thirds of the sample in the study were individual mummies of people who were the descendants of the Greeks, Romans and Turks that drove many Egyptians into Nubia and West Africa. Given the sample of mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

Clyde, stop making up stuff
What is this non-African DNA you are talking about ? what haplogroups?

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Clyde Winters
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quote:
Originally posted by the lioness,:
quote:
Originally posted by Clyde Winters:
Two thirds of the sample in the study were individual mummies of people who were the descendants of the Greeks, Romans and Turks that drove many Egyptians into Nubia and West Africa. Given the sample of mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

Clyde, stop making up stuff
What is this non-African DNA you are talking about ? what haplogroups?

This would be the haplogroups carried by the Turks, Greco-Romans and etc. skeletons, beginning with the Ptolemaic period of Egypt.

Click on the following video:

.
 -

.

--------------------
C. A. Winters

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the lioness,
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quote:
Originally posted by Clyde Winters:
quote:
Originally posted by the lioness,:
quote:
Originally posted by Clyde Winters:
Two thirds of the sample in the study were individual mummies of people who were the descendants of the Greeks, Romans and Turks that drove many Egyptians into Nubia and West Africa. Given the sample of mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

Clyde, stop making up stuff
What is this non-African DNA you are talking about ? what haplogroups?

This would be the haplogroups carried by the Turks, Greco-Romans and etc. skeletons, beginning with the Ptolemaic period of Egypt.

Click on the following video:

.
 -

.

quote:
Originally posted by Clyde Winters:

The C-Group founded the Kerma dynasty of Kush.
The Temehus or C-Group people began to settle Kush around 2200 BC.


quote:
Originally posted by Clyde Winters:

blacks carry Eurasian DNA because the first Eurasians were black Kushite.



So Eurasia was not populated until after 2200 BC ?

The video says blacks carry Eurasian DNA because the first Eurasians were black Kushites.

If the first Eurasians were black Kushites why would they be carrying Eurasian DNA? They would be carrying African DNA


And if for 2/3 of the mummies it was
"natural that the mummies would possess non-African DNA"
--Clyde Winters

what is the non-African haplogroups you are referring to?
The video does does not state which haplogroups are the non-Kushite aka non-African DNA

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Clyde Winters
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quote:
Originally posted by the lioness,:
quote:
Originally posted by Clyde Winters:
quote:
Originally posted by the lioness,:
quote:
Originally posted by Clyde Winters:
Two thirds of the sample in the study were individual mummies of people who were the descendants of the Greeks, Romans and Turks that drove many Egyptians into Nubia and West Africa. Given the sample of mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

Clyde, stop making up stuff
What is this non-African DNA you are talking about ? what haplogroups?

This would be the haplogroups carried by the Turks, Greco-Romans and etc. skeletons, beginning with the Ptolemaic period of Egypt.

Click on the following video:

.
 -

.

quote:
Originally posted by Clyde Winters:

The C-Group founded the Kerma dynasty of Kush.
The Temehus or C-Group people began to settle Kush around 2200 BC.


quote:
Originally posted by Clyde Winters:

blacks carry Eurasian DNA because the first Eurasians were black Kushite.



So Eurasia was not populated until after 2200 BC ?

The video says blacks carry Eurasian DNA because the first Eurasians were black Kushites.

If the first Eurasians were black Kushites why would they be carrying Eurasian DNA? They would be carrying African DNA


And if for 2/3 of the mummies it was
"natural that the mummies would possess non-African DNA"
--Clyde Winters

what is the non-African haplogroups you are referring to?
The video does does not state which haplogroups are the non-Kushite aka non-African DNA

LOL. The Kushites carried so-called Eurasian genes because they were the Eurasians who took these genes from the Levant into Eurasia. This is especially true of the R1 clade.

Eurocentrists confuse the origin of the CHG and EF populations in Europe. The African Y-Chromosomes R1b1 and R1b1a is called R-L278 and R-L754/L761 respectively , while Europeans carrying these clades are simply referred to as R1b1 and R1b1a. Eurocentrists do this to make it appear the these clades do not exist in Africa and promote the idea that R-V88 is of non-African origin.

.
 -

.

Mal'ta man belonged to the R1 clade. The First Europeans in Italy (14kya) and Samara were R1b1a and R1b1.

See: http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=18;t=000045

.

--------------------
C. A. Winters

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the lioness,
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quote:
Originally posted by Clyde Winters:
The Kushites carried so-called Eurasian genes because they were the Eurasians who took these genes from the Levant into Eurasia.

quote:
Originally posted by Clyde Winters:
Two thirds of the sample in the study were individual mummies of people who were the descendants of the Greeks, Romans and Turks that drove many Egyptians into Nubia and West Africa. Given the sample of mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

So Greek and Roman DNA is non-African Kushite DNA.

So which haplogroups are these?

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xyyman
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@ ELMaestro
Yes. These are indigenous Africans. I agree it is surprising with the low levels of mtDNA L. But M1 and T etc are found as far south of Tanzania. Also interesting is the LACK of H1 and H3. Typical North African and "European" female markers. These were NOT European women. This data set also opposes the Armana data which were clearly SSA along with yDNA E. So obviously we have to rethink who or what is an Eurasian vs a SSA. Geographically this dataset of the "new kingdom" mummies is typical of Great Lakes Africans like Kenyans and, yes, Horners' Swenets favorite people.

But undoubted these are not Europeans.

As I said I would like to the see the STR data.

Please, fools, do not respond.

What are the STR profile of the New Kingdom mummies? Understand the game being played.

The STR Profile of the New Kingdom mummies will show they are undoubtedly African. That is why they switched from STR to SNPs....FREQUENCY.
----

Multi-locus inference of population structure a comparison between single nucleotide polymorphisms and microsatellites
R J Haas

Although growing numbers of single nucleotide polymorphisms (SNPs) and microsatellites (short tandem repeat polymorphisms or STRPs) are used to infer population structure, their relative properties in this context remain poorly understood. SNPs and STRPs mutate differently, suggesting multi-locus genotypes at these loci might differ in ability to detect population structure. Here, we use coalescent simulations to measure the power of sets of SNPs and STRPs to identify population structure. To maximize the applicability of our results to empirical studies, we focus on the popular STRUCTURE analysis and evaluate the role of several biological and practical factors in the detection of population structure. We find that (1) fewer unlinked STRPs than SNPs are needed to detect structure at recent divergence times greater than 0.3 Ne generations; (2) accurate estimation of the number of populations requires many fewer STRPs than SNPs; (3) for both marker types, declines in power due to modest gene flow (Nem=1.0) are largely negated by increasing marker number; (4) variation in the STRP mutational model affects power modestly; (5) SNP haplotypes (θ=1, no recombination) provide power comparable with STRP loci (θ=10); (6) ascertainment schemes that select highly variable STRP or SNP loci increase power to detect structure, though ascertained data may not be suitable to other inference; and (7) when samples are drawn from an admixed population and one of its parent populations, the reduction in power to detect two populations is greater for STRPs than SNPs. These results should assist the design of multi-locus studies to detect population structure in nature.

--------------------
Without data you are just another person with an opinion - Deming

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Clyde Winters
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quote:
Originally posted by the lioness,:
quote:
Originally posted by Clyde Winters:
The Kushites carried so-called Eurasian genes because they were the Eurasians who took these genes from the Levant into Eurasia.

quote:
Originally posted by Clyde Winters:
Two thirds of the sample in the study were individual mummies of people who were the descendants of the Greeks, Romans and Turks that drove many Egyptians into Nubia and West Africa. Given the sample of mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

So Greek and Roman DNA is non-African Kushite DNA.

So which haplogroups are these?

It would be R1 clades. Epigravettian culture context in Italy (Villabruna) who lived circa 12,000 BC belonged to R1b1a, which is primarilly found in Africa.

--------------------
C. A. Winters

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xyyman
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cont-

Five-population simulations
For a divergence time of 0.16 Ne generations, 25-STRP data sets were the first to show marked peakedness at K=5, though other values of K were still broadly supported (Figure 2a). 100 STRP data sets showed an average rescaled ΔK of 0.98 for K=5 (values of rescaled ΔK close to 1 suggest strong support for a particular number of populations), whereas other values of K received little support (Figure 2a). 35-SNP data sets showed a bias toward low K-values (Figure 2b). Even 10 000-SNP data sets were less efficient at detecting five populations than 100 STRPs (Figure 2). However, 1000-SNP data sets in which all loci were ascertained based on the criterion of minor allele frequency >0.1 were near perfect at detecting the correct value of K (Figure 2b).

SNP haplotypes

15-SNP-haplotype data sets (θ=1, see Materials and methods) offered near identical performance to 15 STRP data sets in STRUCTURE analyses. Increasing marker number from 15 to 35 did less to improve the power of SNP haplotype data sets than STRP data sets (Figure 6a). The number of polymorphic loci comprising a simulated SNP haplotype varied from run to run.

Time scale
When a panmictic population splits into two isolated populations, all genetic diversity found within these daughter populations is initially descended from the parent population. Unless the daughter populations sample diversity from the parent population unevenly (due to a small parent population or other biological/ecological factors), genetic data will fail to distinguish the daughter populations from one another for some period of post-divergence time. In other words, spatial but not genetic structure exists. As long as gene flow is limited, genetic structure eventually arises through changes in allele frequencies due to drift and the emergence of derived alleles in one population or another.

STRP loci in the parent population should show greater allelic diversity than SNP loci, thereby providing greater opportunity for early genetic differentiation of the daughter populations due to random drift. In addition, the high rate of STRP mutation suggests private STRP variants should appear and accumulate more quickly than new SNPs. Our results support the general expectation that the greatest power gap between SNPs and STRPs is found when divergence times are small. For divergence times <0.24 Ne generations, detection of population structure with >0.95 power requires 5–15 times as many SNPs as STRPs (Figure 1). If gene flow and other complicating factors are ignored, the superior efficiency of STRP data decays rapidlyas divergence time increases; marker choice becomes nearly irrelevant for divergence times >0.40 Ne generations. Indeed, <50 SNPs are needed to detect structure with >0.95 power for divergence times >0.32 Ne generations. For populations with small Ne and short generation time, 0.32 Ne generations represent a relatively small number of years. Even for non-model organisms, the development of 50 unlinked SNP markers is a realistic objective

The exponential form of the SNP curves in Figure 1 suggests that detection of such recent population structure may require very large (perhaps impossible) numbers of unlinked SNPs. This corroborates a recent empirical result in maize (Hamblin et al., 2007

Interestingly, while the power of an individual SNP never approaches that of an individual STRP (Figure 3), multi-locus SNP and STRP data sets show roughly equal power for divergence times >0.3 Ne generations (Figure 1). This finding indicates that some SNP loci outperform the average SNP by a large margin,

--------------------
Without data you are just another person with an opinion - Deming

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the lioness,
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quote:
Originally posted by Clyde Winters:
quote:
Originally posted by the lioness,:
quote:
Originally posted by Clyde Winters:
The Kushites carried so-called Eurasian genes because they were the Eurasians who took these genes from the Levant into Eurasia.

quote:
Originally posted by Clyde Winters:
Two thirds of the sample in the study were individual mummies of people who were the descendants of the Greeks, Romans and Turks that drove many Egyptians into Nubia and West Africa. Given the sample of mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

So Greek and Roman DNA is non-African Kushite DNA.

So which haplogroups are these?

It would be R1 clades. Epigravettian culture context in Italy (Villabruna) who lived circa 12,000 BC belonged to R1b1a, which is primarilly found in Africa.
You said given the sample of 2/3 mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

so if R1b1a is primarily found in Africa what haplogroups are the non-African haplogroups of the 2/3 mummies ?

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Clyde Winters
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quote:
Originally posted by the lioness,:
quote:
Originally posted by Clyde Winters:
quote:
Originally posted by the lioness,:
quote:
Originally posted by Clyde Winters:
The Kushites carried so-called Eurasian genes because they were the Eurasians who took these genes from the Levant into Eurasia.

quote:
Originally posted by Clyde Winters:
Two thirds of the sample in the study were individual mummies of people who were the descendants of the Greeks, Romans and Turks that drove many Egyptians into Nubia and West Africa. Given the sample of mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

So Greek and Roman DNA is non-African Kushite DNA.

So which haplogroups are these?

It would be R1 clades. Epigravettian culture context in Italy (Villabruna) who lived circa 12,000 BC belonged to R1b1a, which is primarilly found in Africa.
You said given the sample of 2/3 mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

so if R1b1a is primarily found in Africa what haplogroups are the non-African haplogroups of the 2/3 mummies ?

Read the article!

--------------------
C. A. Winters

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Swenet
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quote:
Originally posted by xyyman:
Geographically this dataset of the "new kingdom" mummies is typical of Great Lakes Africans like Kenyans and, yes, Horners' Swenets favorite people.

Not at all. Cushitic speaking Horners are just a useful approximation. Truth is, Horners have more SSA ancestry than ancient Egyptians. So it's not about them being "favoured" by me; if anything, using equatorial Horners as an example has been sparing your emotional investment in your AE=SSA delusion. After all, even modern Cushitic speaking Horners as an approximation is too generous.

quote:
Originally posted by Swenet:
No one is talking about the Horn, except as a useful proxy in a global context. But when you zoom in and look at the region, the Horn lags behind also when compared to ancient Nubians.

I don't see what this has to do with favouritism.
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the lioness,
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quote:
Originally posted by Clyde Winters:
quote:
Originally posted by the lioness,:
quote:
Originally posted by Clyde Winters:
quote:
Originally posted by the lioness,:
quote:
Originally posted by Clyde Winters:
The Kushites carried so-called Eurasian genes because they were the Eurasians who took these genes from the Levant into Eurasia.

quote:
Originally posted by Clyde Winters:
Two thirds of the sample in the study were individual mummies of people who were the descendants of the Greeks, Romans and Turks that drove many Egyptians into Nubia and West Africa. Given the sample of mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

So Greek and Roman DNA is non-African Kushite DNA.

So which haplogroups are these?

It would be R1 clades. Epigravettian culture context in Italy (Villabruna) who lived circa 12,000 BC belonged to R1b1a, which is primarilly found in Africa.
You said given the sample of 2/3 mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA

so if R1b1a is primarily found in Africa what haplogroups are the non-African haplogroups of the 2/3 mummies ?

Read the article!
So when you said given the sample of 2/3 mummies of non-Egyptian origin in the study it was natural that the mummies would possess non-African DNA
then you agree with the article's opinion of what the non-African haplogroups are.
Ok. that concludes the investigation

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xyyman
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Again, from the study I cited, quote:

"The exponential form of the SNP curves in Figure 1 suggests that detection of such recent population structure may require very large (perhaps impossible) numbers of unlinked SNPs. This corroborates a recent empirical result in maize (Hamblin et al., 2007"


They said UNLINKED SNPs. Anyone!!!??? It is Impossible to determine population structure using SNPs. So what do they do, used FREQUENCY to assign population structure. But that model ASSUMES humans were isolated for 10's THOUSANDS of years then suddenly decided to admix. That is impossible. Understand the game being played.

The ONLY model the data supports is Isolation by Distance. Meaning there is no race and there never was!!! Meaning there was NEVER any back-migration. And they know this!!!

--------------------
Without data you are just another person with an opinion - Deming

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xyyman
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Unlinked SNPs=STR=haplotypes. That is why Berbers show up as "Negros" in CODIS. That is why these racialist Scientist stopped used STRs and macrosatellites . These results show Greeks are highly Africans, and this was confirmed by Arnaiz-Villens. That is why the Amarnas came out sub-Saharan Africans.

That is why they switched to SNP frequency(unlinked). Understand the game. Sleight of hands.

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Without data you are just another person with an opinion - Deming

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Thereal
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That includes the amazigh? As I thought the Berber was cultural groups and couldn't be specified as phenotype unless I'm not understanding the usage of negro in that context.
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Ase
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quote:
Originally posted by xyyman:
Again, from the study I cited, quote:

"The exponential form of the SNP curves in Figure 1 suggests that detection of such recent population structure may require very large (perhaps impossible) numbers of unlinked SNPs. This corroborates a recent empirical result in maize (Hamblin et al., 2007"


They said UNLINKED SNPs. Anyone!!!??? It is Impossible to determine population structure using SNPs. So what do they do, used FREQUENCY to assign population structure. But that model ASSUMES humans were isolated for 10's THOUSANDS of years then suddenly decided to admix. That is impossible. Understand the game being played.

The ONLY model the data supports is Isolation by Distance. Meaning there is no race and there never was!!! Meaning there was NEVER any back-migration. And they know this!!!

Can someone explain what he's trying to say in plain English?
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Ase
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quote:
Originally posted by beyoku:
I can give you a real world example with my child's 23andme Report.

Here is a screen shot showing the Childs Ancestry as passed on from the parents.

 -

This is the whole genome. You are able to get this split view because both parents have had their DNA sequenced and the proprietary programs form 23andme knows EXACTLY what parts of our ancestry was randomly passed to the child. This is somewhat of an easy case because My wife (Ethiopian) has no West African and I (African American) have no North African nor East African....so really you almost know what is what since our African ancestries are so distinct.

Now I have a cousin who's wife is Kenyan. His wife as far as whole genome ancestry is East African AND West African. Looking at the child's genome alone you wouldn't be able to tell which portions of West African were from the father or mother....and sometimes its not a clear 50% of all different ancestries down the line IE: If she is 50% West African, 25% Nilotic and 25% Cushitic the child's RANDOM recombination of Ancestry would inherit 50% but not in these exactly proportions. This this woman who hypothetically inherited ALL of Each parents white African ancestry instead of half of it and came out looking pretty mixed. Its like second nature to cut these figures in half but when with heterogeneous genomes its not quite that simple.

Here is another paining of Just the Child:
 -

When looking at Mtdna. It is ONLY the mothers line, mothers mothers mother...all the way back. The Child is East African L3f, but L3f sublades also show up in West African. I have a Zimbabwean frined that is E1b1a8a and L3f1b4a. His WHole genome is 95% West African and 5% East African. I have an Ivory Coast coworker that is E1b1a8a1a /L3f1b4a1 his whole genome is 100% West African. Obama kids carry a presumable a MTdna of West African or SSA origin, as I would presume his potential Sons BUT ONLY whole genome would tell us his kids are 25-35% or more European ancestry.

Beyoku you need to update your account to enable 3rd party hosting.
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xyyman
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Maybe someone else can better explain. Continuing, this is what Hamblin et al states.

Quote
----
Abstract

While Simple Sequence Repeats (SSRs) are extremely useful genetic markers, recent advances in technology have produced a shift toward use of single nucleotide polymorphisms (SNPs). The different mutational properties of these two classes of markers result in differences in heterozygosities and allele frequencies that may have implications for their use in assessing relatedness and evaluation of genetic diversity. We compared analyses based on 89 SSRs (primarily dinucleotide repeats) to analyses based on 847 SNPs in individuals from the same 259 inbred maize lines, which had been chosen to represent the diversity available among current and historic lines used in breeding. The SSRs performed better at clustering germplasm into populations than did a set of 847 SNPs or 554 SNP haplotypes, and SSRs provided more resolution in measuring genetic distance based on allele-sharing. Except for closely related pairs of individuals, measures of distance based on SSRs were only weakly correlated with measures of distance based on SNPs. Our results suggest that 1) large numbers of SNP loci will be required to replace highly polymorphic SSRs in studies of diversity and relatedness and 2) relatedness among highly-diverged maize lines is difficult to measure accurately regardless of the marker system.
---

What does it all mean? The Abusir mummies are not "Eurasian' if "Eurasian" means coming FROM Eurasia. They canNOT use frequency of SNPs to determine relatedness. Henn, Reich, Paabo etc . they ALL know this!!! It is a game played and laymen are caught up in the middle. Caught up in this "back-migration from Eurasia nonsense.

The author(Hamblin) is stating that an infinite amount of SNPs is need to determine relatedness which is impossible The only way to determine related is through STRs/SSRs or uniparental markers like what the JAMA report did and DNATribes exposed and what the FBI uses through CODIS. The FBI do NOT use SNPs frequency because it is meaningLESS and cannot be used to catch a criminal. The novice reader do NOT know this. That is why STR showed the Amarna's were SSA and if the autosomal STRs (CODIS) is revealed for the Abusir mummies they too will be African. It is a game and the novice readers are the one being fooled.

--------------------
Without data you are just another person with an opinion - Deming

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Thereal
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So what's the point in maintaining this lie? to convince everybody that Africans are incapable of developing advance societies? If race doesn't exist and people are only different because of time conditions and circumstances than why conduct these studies because the knowledge gained doesn't seem to be as enlightening as it should be.
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xyyman
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Be REAL. What do you mean what's the point. How long have been on this site. Doug says it many times. That is his mantra. To maintain the status quo and continued European dominance. To make Europeans in the Appalachians believe they are important than they really are.

That is why they still spin a WHITE Neanderthal even when they genetic evidence shows Neanderthals were black skinned with black hair and black eyes. These Appalachians will not pay good money at the Smithsonian to see a Black Negroid Neanderthal who roamed Europe for 400,0000 YEARS!! Why stop a good thing?

Obviously Some white scientist are struggling with these ethical issues. Henn is a good example. Helena Malmstrom also. White women caught between a rock and a hard place. See my thread on ESR.

--------------------
Without data you are just another person with an opinion - Deming

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xyyman
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Can someone post that plot showing Berbers are negros based on CODIS STRs?
------
Quote:
"5 SNP versus STR
In conclusion, the above numerical results of the comparative efficiency analysis of SNP and STR loci suggest that, without population data on SNP loci, a definite prescription regarding the required number of SNP loci cannot be given; to equal the power of the 13 STR loci with regard to genotypic match probability and/or paternity exclusion, however, somewhere in the range of 30±60 SNP loci would be needed, and they must be selected in such a manner that the assumption of independence across loci are met. Note that since SNP loci are biallelic (and hence, less mutable than the STR loci), the population substructure effect on SNP loci can be more severe than at the STR loci [37, 38]. Hence, more careful validation studies of SNP loci would be needed before implementing them for forensic and paternity analysis. In addition, the efficiency of SNP loci for interpreting DNA mixture evidence is far more reduced, necessitating a far

(on STRs) Above and beyond this, the population data collected in this context can address many of the broad questions of the human genome diversity studies, such as the evolutionary relationship of populations, the implications of reduced genetic variation in specific populations, as well as inference of the past demographic history of populations [39]. The availability of commercial kits for genotyping the STR loci [6, 7] offers the opportunity to conduct population genetic analysis by pooling data through interlaboratory comparisons of results. Worldwide allele frequency data at these 13 STR loci also raises some questions that could yield information as to the mechanism of maintenance of genetic variation at these tetranucleotide loci."

--------------------
Without data you are just another person with an opinion - Deming

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xyyman
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Swenet .....or Sage may remember the chart I posted when I schooled him on dendogram branch lengths and showed Berbers are Negros. I will try to find it on one of my many computers I post from.

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Without data you are just another person with an opinion - Deming

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Thereal
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I've been an active member on the site a little under a year and have browsed stuff here a little under 3 years,my points is whites already have the advantage of general ignorance and they control all the knowledge institutes,the flow of information in the Americas and Europe,sense there are not enough black owned and operated institutions to do those types studies,it doesn't matter if you're a black person in those fields because whites control your pay and they can discredit any work you've done and most people don't have good enough idea of certain groups which further obscures info not coming from the people themselves so why do these things if the knowledge acquired is being manipulate by whites or other people,its not hard to look online of people given misinformation.

No,I like using my tablet but sometimes it acts wonky.

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xyyman
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So Capra is correct and Beyoku's gave an example why Uniparental markers (mtDNA or YDNA) can also be misleading when looking at MODERN or EXTANT samples. In ancient times/ samples there was very little intercontinental travel therefore uniparental markers and their haplotypes or sub-clades are very informative. SNPs are useless without TreeMix which show migration edges or events. That is why ALL objective TreeMix studies show a 2nd migration event from SSA to Europe with Sardinians and Iberians being the closest. This trend is displayed also in STR analysis and NOT SNP analysis. This is why SNP analysis as a standalone is useless and misleading.

To Beyoku's point autosomal SNPs sometimes do NOT corroborate uniparental markers in "recent" admixed peoples like Obama and his offsprings. That may even apply to samples WITHIN Africa or even Europe. That is why aDNA is so important to understand migration history. There were no airplanes back then. Although some of us believe UFO/aliens built the pyramid and Africans could not have possible built it. lol!

quote:
Originally posted by capra:
[Q] They're quite different things, you can't really put a percentage on it. A mitochondrial chromosome is actually a kidnapped bacterial chromosome; it's structure is completely different and it is much much smaller than a nuclear chromosome. It has a small set of very important genes and very little 'junk', while your nuclear genome has a buttload of genes, some not all that important, and loads of 'junk DNA'.

mtDNA tells about one line of ancestry, so what percentage of your ancestors that is depends on how many generations back you go. If you go far enough back you could have no autosomal material whatsoever from your mitochondrial DNA ancestor, and they'd be one out of thousands.

Y DNA is a nuclear chromosome but similarly traces one line of ancestry. Thing is, they are very good at tracing that particular line of descent. Autosomal DNA represents all your ancestry (on average anyway), but it's scrambled together and much harder to make a neat tree of relationships with it like you can with uniparental markers.

In short there isn't any straightforward percentage you can put on it, just autosomal is much more informative overall if you can get it. [/QB]



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Without data you are just another person with an opinion - Deming

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xyyman
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Posting from your phone? I try to advise my pre-teen about importance of punctuation.

quote:
Originally posted by Thereal:
[Q] I've been an active member on the site a little under a year and have browsed stuff here a little under 3 years,my points is whites already have the advantage of general ignorance and they control all the knowledge institutes,the flow of information in the Americas and Europe,sense there are not enough black owned and operated institutions to do those types studies,it doesn't matter if you're a black person in those fields because whites control your pay and they can discredit any work you've done and most people don't have good enough idea of certain groups which further obscures info not coming from the people themselves so why do these things if the knowledge acquired is being manipulate by whites or other people,its not hard to look online of people given misinformation. [/QB]



--------------------
Without data you are just another person with an opinion - Deming

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beyoku
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@Oshun. Photobucket disabled hot linking.

Try here
http://s204.photobucket.com/user/beyoku/media/BabyB_zps396971ef.png.html

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Ase
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quote:
Originally posted by beyoku:
@Oshun. Photobucket disabled hot linking.

Try here
http://s204.photobucket.com/user/beyoku/media/BabyB_zps396971ef.png.html

You can't even see it clicking the direct link. You might have to do something with your account. Guess they're trying to cut corners. WTF did they think anyone used that site for. sigh...
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Swenet
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quote:
Originally posted by xyyman:
Swenet .....or Sage may remember the chart I posted when I schooled him on dendogram branch lengths and showed Berbers are Negros. I will try to find it on one of my many computers I post from.

Sometimes when you can't find the name of a paper, you can just google your old posts. If you can remember how you phrased your comments and the keywords you used, it's a good way to find old papers. Here is your paper:

quote:
Originally posted by xyyman:
Get to work guys...

http://i46.tinypic.com/28gtcvq.jpg


Genetic structure of north-west Africa revealed by STR analysis

http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=008329;p=1#000011
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Forty2Tribes
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http://www.nytimes.com/1985/04/16/science/intact-genetic-material-extracted-from-an-ancient-egyptian-mummy.html?pagewanted=all&mcubz=2

Do you think this study will ever be released? Quite some time ago.

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xyyman
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You the man Swenet.

--------------------
Without data you are just another person with an opinion - Deming

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the lioness,
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quote:
Originally posted by Fourty2Tribes:
http://www.nytimes.com/1985/04/16/science/intact-genetic-material-extracted-from-an-ancient-egyptian-mummy.html?pagewanted=all&mcubz=2

Do you think this study will ever be released? Quite some time ago.

 -
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Forty2Tribes
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I asked Paabo about the successful sample in 1995. To paraphrase he said pffft that ole thing we misplaced it but we have this new sample that was just released.
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the lioness,
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quote:
Originally posted by Fourty2Tribes:
I asked Paabo about the successful sample in 1995. To paraphrase he said pffft that ole thing we misplaced it but we have this new sample that was just released.

The article was published in 1985 and I have read it.
Iy so not about ancestral analysis of the DNA it is about DVA recovery methods. This was before they even were doing mtDNA analysis

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Ase
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Okay I hear that you need more SNPs, but they're saying:

quote:
"Using in solution enrichment for 1.2 million genome-wide SNPs, we obtained between 3,632 and 508,360 target SNPs per sample (Supplementary Data 2)."
I'm hearing you need 30-60 SNP for 13 SSRs but but they collected a minimum of 3.6k SNPs per sample. Wouldn't they have more than enough? I mean if people are arguing the STR of the Amarna (8 loci), could prove relatedness etc, wouldn't 3.6k SNPs be more than enough to fit that 13:60 ratio? I'm very confused.
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Ase
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quote:
Originally posted by xyyman:
Unlinked SNPs=STR=haplotypes. That is why Berbers show up as "Negros" in CODIS. That is why these racialist Scientist stopped used STRs and macrosatellites . These results show Greeks are highly Africans, and this was confirmed by Arnaiz-Villens. That is why the Amarnas came out sub-Saharan Africans.

That is why they switched to SNP frequency(unlinked). Understand the game. Sleight of hands.

Links to these findings? Or an older thread??


quote:
Originally posted by xyyman:
That is why it is important to look at BOTH uniparental markers and autosomal markers. And NOT ONLY frequency of autosomal markers. Uniparental provides is the best indication of DIRECTION of migration. Of course in recent admixed populations like Obama's kids and yours. The story is incomplete when only considering autosomal makers. Interesting you said that West Africans carry "sub-clades" of L3f found in East Africa. I have no proof of that but that is again indicative of there being no such thing as a Bantu Expansion.

That is why the FREQUENCY nonsense in the New Kingdom mummies is a slieght of hands. Deep analysis is needed to determine migration route, frequency cannot tells us anything, and they know it that is why the paper is written like that. .

So they can perhaps discuss coalescence, but not which genetic components would've been older or native, and which would've been the result of foreigners? Because they seem to imply their findings were able to establish when the populations had a surge mixture attributed to post-OOA lineages.
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xyyman
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I always site sources. Read over my posts. I don't blow smoke from my azz. The key word here is "unlinked SNP". Reason? Blocks of genes are linked ie they do NOT break apart during meiosis/recombination. (this is high school biology by the way). So in other words the only way to research population structure is through these blocks of genes that are NOT break apart during meiosis. ie STRs or haplotypes or microsatellites .

Think of the human genome as a long city block with houses. During recombination maybe 3 ADJACENT houses will never be unlinked and will recombine as a unit. 200 generations later those same 3 house will still be linked together. Those same 3 ADJACENT houses will be found in all Africans including Berbers. These same 3 ADJACENT houses will be found in ancient Greeks per Arnaiz-Villen using microsatellite data. SNP analysis do NOT take that into consideration. It assumes there is no linked allele which is false. That is why the FBI do not use it because it cannot tell the FBI investigator if the person is an African or European or Asian. SNP cannot tell the difference and therefore NOT used by criminal investigator. It is used by these "political" scientist to spin their BS to the unsuspecting and gullible web readers.

As I said Paabo, Henn, Reich etc ...they all know this!!!

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Without data you are just another person with an opinion - Deming

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Forty2Tribes
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quote:
Originally posted by the lioness,:
quote:
Originally posted by Fourty2Tribes:
I asked Paabo about the successful sample in 1995. To paraphrase he said pffft that ole thing we misplaced it but we have this new sample that was just released.

The article was published in 1985 and I have read it.
Iy so not about ancestral analysis of the DNA it is about DVA recovery methods. This was before they even were doing mtDNA analysis

I'm not talking about the 85 sample I'm talking about the 93 (my mistake I said 95) sample that yielded the often quoted never tangibly cited test.

Paabo, S., and A. Di Rienzo, A molecular approach to the study of Egyptian history. In Biological Anthropology and the Study of Ancient Egypt. V. Davies and R. Walker, eds. pp. 86-90. London: British Museum Press. 1993
quote:
identified multiple lines of descent, some of which originated in Sub-Saharan Africa.
Even if I didnt think Beyoku was honest I would give him the benefit of the doubt on those 42 haplogroups. Something was bound to leak.
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