Hans-Ju ̈ rgen Bandelt,1 Yong-Gang Yao,2 Martin B. Richards,3 and Antonio Salas4* Summary The commercialization of ‘big science’ is in full swing, leading to situations in which the ethical principles of academia are beginning to be compromised. This is exemplified by the profitable business of genetic ances- try testing. The goals of this sort of ‘big science’ are not necessarily in any way novel, however. In particular, large genotyping projects have a certain start-up time when their design is frozen in, so that the projects often lag behind the development of genetic knowledge. On the other hand, extremely provisional knowledge about potential disease markers is being rapidly turned into questionable ‘tests’, purporting to determine risk factors for complex disorders, by private companies that are eager to get their share of a profitable market of the future. The flow of money generated by such concerns looks likely to erode traditional research operations and small- scale projects, which risk becoming pebbles on the ‘big science’ landscape. BioEssays 30:1246–1251, 2008. ß 2008 Wiley Periodicals,
Tukuler
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posted
Everything's a shade of grey, right?
The guy invented GPS is a geneticist. You can buy your GPS from his commercial lab like Mensa did. If you already have a file I think you just upload and get your GPS free. How robust is his African data? Can GPS "locate" the very recently infused diasporan Africans?
And that guy at Uppsala, Torsten, that found non-Amazigh non-Arab medieval Maghreb DNA. He has a nice write up on matching data from different bases requires remapping.
He also says technical artefacts can effect f stat related method results so it seems two populations share history they actually may not.
Gallego-Llorente accepted Skoglund's technical artefact find. But Mondal isn't going for it.
The field, tools, and methods are still very young.
posted
We are not sure what he found whether it is really non-Amazigh or Arab. He never published the study which is disconcerting.
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Tukuler
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posted
There was no paper. It was just a talk. He presented genetic results and discussed possibilities. But no formal paper.
The find is a political bomb burst.
Write him. Maybe he'll write back.
Meanwhile, what's your take on • GPS • remapping • technical artefacts
Tukuler
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posted
Oral Presentation Society for Molecular Biology and Evolution Conference 2016
Days Sunday, 3rd July Monday, 4th July Tuesday, 5th July Wednesday, 6th July Thursday, 7th July
Tracks Developmental and cellular genetics Ecological and conservation genetics Gene regulation and epigenetics Medical and human genetics
Search Speakers The genomic enigma of two Medieval North Africans (#243) Torsten Günther q , Cristina Valdiosera 2 , Juan Carlos Vera-Rodríguez 3 , Ricardo Rodriguez-Varela 4 , Emma Svensson 1 , Rafael M Martínez Sánchez 5 , Rafael Carmona Ávila 6 , Leonor Peña Chocarro 7 , Guillem Pérez Jordà 8 , Youssef Bokbot 9 , Eneko Iriarte 10 , Colin Smith 2 , Mattias Jakobsson 1
Uppsala University, Uppsala, Sweden La Trobe University, Melbourne, Australia Departamento de Historia, Geografía y Antropología, Universidad de Huelva, Huelva, Spain Universidad Complutense de Madrid, Madrid, Spain Departamento de Prehistoria y Arqueología, Universidad de Granada, Granada, Spain Museo Histórico Municipal, Córdoba, Spain Escuela Española de Historia y Arqueología en Roma/CSIC, Rome, Italy G. I. Arqueobiología, Instituto de Historia, Madrid, Spain Institut National des Sciences de l’Archéologie et du Patrimoine, Rabat, Morocco Departamento Historia, Geografía y Comunicación, Universidad de Burgos, Burgos, Spain
The trans-Saharan gold and salt trade as well as the trans-Saharan slave trade played an important role in population movements connecting sub-Saharan and Mediterranean economies during the Middle Ages. The slave trade alone is said to have transported more than 9 million slave soldiers and domestic servants along the trans-Saharan route. In this study, we present the genomic analysis of two human individuals from a cave site in the area of present-day Morocco which were directly dated to the Medieval period. The samples were processed in a designated ancient DNA lab and the genomic data obtained shows standard patterns of authentic ancient DNA with low levels of contamination. Both individuals – which represent the first ancient genome sequence data from North Africa – do not exhibit particular genetic affinities to modern North Africans or any other present-day population in published genotype data sets despite relatively extensive data has been produced from many areas of Africa. In fact, the most parsimonious way to model them genetically is as two-source admixture between Mediterranean Europeans and Southern Africans. The lack of archaeological context of the two individuals opens up various alternatives to explain their genomic pattern. Both individuals could represent a Medieval African population without population continuity to modern-day populations. Alternatively, both Mediterranean Europe and Southern Africa are known source regions in the Arab slave trade, thus they could potentially represent the offspring of slaves of different origin. The Arab slave trade extended over a longer period and may have involved more slaves than its transatlantic counterpart and our data might provide the first genetic insight into this historical process and the people who suffered in it. Our results highlight how archaeogenetic research can shed lights into historical events and long-distance population movements while opening new questions for the interpretation of the data.
posted
Agreed GPS is a new tool. Elhaik is being blasted by other researchers because GPS showed Ashkenazi are from Turkey and NOT indigenous to the Levant. (shoot the messenger). Many of us diasporans have no record or idea of our ancestral home. GPS is supposed to solve that problem. It looks promising to me.
Technical Artefact may be too cryptic words but I agree population can share history but not be related. Case in point Natuifians and Modern Europeans. Lazaridis suggested modern Europeans are not related to Natufians(although Euro-bloggers ignore that fact). And this is supported by many other studies which put Near Easterners(Bedoiuns) not related to modern Europeans from an "ancestral" point of view. The Turks in the Levant are not in the mix
I was trying to get my hands on Elhaik's software that is how I came across the HomeDNA-GPS. And they do charge for uploads. It is not free. Many of the free Software are Linux or Ubuntu based. I code and compile in Windows. Although I recently purchased a Mac. I still need to spend time play around with Mac and running these apps.
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Gps isn't that good. You can see the entire Python code in their supp. Its not useless but it isn't ground breaking by any means.
You make a decent point here though.
quote:Technical Artefact may be too cryptic words but I agree population can share history but not be related. Case in point Natuifians and Modern Europeans. Lazaridis suggested modern Europeans are not related to Natufians(although Euro-bloggers ignore that fact). And this is supported by many other studies which put Near Easterners(Bedoiuns) not related to modern Europeans from an "ancestral" point of view. The Turks in the Levant are not in the mix
Tukuler
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Member # 19944
posted
Obviously they don't know history. Indigenous Southern Africans (Khoe San) in a Indian Ocean to Maghreb slave trade?
But they did slide in a better guess "a medieval African population without population continuity to modern-day populations. "
One BellBleekerBlogger on the ISA connection:
quote:... Let me break this down. Two medieval genomes of North Africa are not immediately akin to Berbers. They appear to be a mixture of something Khoisan-like and something Southern Europe, Mediterranean-like.*
The authors interpret this in the most parsimonious way (at least from the abstract), that the Barbary-Moorish slave trade could have brought together these individuals' ancestries.
But...! "Both individuals could represent a Medieval African population without population continuity to modern-day populations" This has the potential to get very interesting, very quick.
The original inhabitants of the Saharan Early Neolithic 'wet phase' are generally called 'Roundheads' after their abundant rock art. These people inhabited a landscape and an ecology very similar to those of modern San-Khoisan peoples and their theorized ancient domains. Given that fact, I'd expect these people to be more similar to Khoi people than to Pygmy or West African peoples.
... The San-Khoisan element could be a substrate across much of the continent in addition to introgression from the Neolithic expansion, maybe in multiple places.
To put it directly, these Medieval individuals could be the remnants of native, North African ethnicities that were progressively destroyed in the Berber, and later Arab, expansions. I'm not saying that will be the case, but I'm satisfied knowing something I had predicted, that when the first genomes of North Africa start coming in, they'll be diverse and look neither Berber or Arab.
There is also a new paper by Zvelibil et al 2016 that I have lost for the moment. It proposes that ceramic pottery was independently invented in North Africa based on some very early sherds from Mali. While I'm always very deeply skeptical of 'independently' this or that, I think the North African Neolithic will soon become a very interesting place.
Me myself I'd like to see Algerian data from Wargla and for Haratin & 'vassal'. Can't really do NA genetics without them, and oh yeah, the Imraguen in Mauritania too.
quote:Originally posted by Tukuler: Oral Presentation Society for Molecular Biology and Evolution Conference 2016
The genomic enigma of two Medieval North Africans (#243)
The trans-Saharan gold and salt trade as well as the trans-Saharan slave trade played an important role in population movements connecting sub-Saharan and Mediterranean economies during the Middle Ages. The slave trade alone is said to have transported more than 9 million slave soldiers and domestic servants along the trans-Saharan route. In this study, we present the genomic analysis of two human individuals from a cave site in the area of present-day Morocco which were directly dated to the Medieval period. The samples were processed in a designated ancient DNA lab and the genomic data obtained shows standard patterns of authentic ancient DNA with low levels of contamination. Both individuals – which represent the first ancient genome sequence data from North Africa – do not exhibit particular genetic affinities to modern North Africans **or any other present-day population in published genotype data sets** despite relatively extensive data has been produced from many areas of Africa. In fact, the most parsimonious way to model them genetically is as two-source admixture between Mediterranean Europeans and Southern Africans. The lack of archaeological context of the two individuals opens up various alternatives to explain their genomic pattern. Both individuals could represent a Medieval African population without population continuity to modern-day populations. Alternatively, both Mediterranean Europe and Southern Africa are known source regions in the Arab slave trade, thus they could potentially represent the offspring of slaves of different origin. The Arab slave trade extended over a longer period and may have involved more slaves than its transatlantic counterpart and our data might provide the first genetic insight into this historical process and the people who suffered in it. Our results highlight how archaeogenetic research can shed lights into historical events and long-distance population movements while opening new questions for the interpretation of the data.
quote:Originally posted by Elmaestro:
Thats ode to an early split time for SanHG in general. All AMH populations can be seen as a subset of khoisan... with the exception of NC/Bantu & Mbuti. Mota is a downstream paraEurasian. which is why he retains East African, Eurasian Neolithic, and Eastern Eurasian HG signals... anything that can't be attributed to any of the latter is allocated to SanHG-like or rainforest HG signals. But even still, Mota is better fitted with SanHG than RHG due to RHG, like Mbuti having ancestry that Mota simply doesn't have.
Logically the story writes itself.
[...]
Skoglunds Admixture run basically reveal a gradient from Ju_Hoan to Sardinia (Neolithic Europe). Being that in the absene of YRI, the combination of heterogeneity and shared frequency within the Ju-Hoan gives the strongest likely hood for a singular population. Xyyman can show us another plot where the San HGs shows Eurasian signals at Low K... He used to spam that.
However I was gonna let him rock for the fact that the argument can be made about Early African-San HG-like populations representing a later expansion into Europe. I've been messing with the Idea for a while that there might be recent shared undetectable ancestry in SSA and west Eurasians. One of the few ways I find that achievable is if this mysterious population was relatively undifferentiated (from ancient founder) and possibly ancestral to both West Eurasians and SSAs. http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=009649;p=2#000053
This is possibly seen in the ancient Moroccan DNA. who I speculate to have introgressed Ibermaurasian HG DNA. They lack SSA admixture related to any modern African population which would be detectable via Dstats or even genetic distance however behaves like an intermediate population to SSAs and Neolithic Europeans. The Idea that an Ancient population is made closer to SSA populations by mixing with Eurasians is fun to play with when looking at the Neolithic Moroccans. See the transition between IAM -> KEB.
@Tukuler Does the story write itself?
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Tukuler
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posted
Oh, OK.
Technical Artefact is "program settings." Like when Skoglund saw Gallego-Llorente's conclusion about Africa didn't make sense. Skoglund found the technical error that falsely showed shared genetic histories.
GPS tracked the origin of the Siberian Kets. GPS successfully located Sardinians to their villages. GPS was excellent for locating Ashkenazi origins. It was supported by multidisciplinary evidence something some reports and most lay analysis aren't.
Elhaik admits GPS isn't so hot on western diasporan Africans and similar populations. ... if the admixture event was recent and the population did not maintain relative isolation, GPS prediction would be erroneous. (Figure S2).
This is the case of most North Americans, Israeli Jews (Elhaik 2016), and Caribbean populations (Elhaik et al . 2014), whose admixture proportions still reflect the massive Nineteenth and Twentieth centuries' mixture events involving Native Americans, West Europeans, and Africans.
posted
The link isn't working.
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
You can have the admix stuff This is the story i see writ
quote:Originally posted by Elmaestro:
quote:Originally posted by Tukuler: Both individuals could represent a Medieval African population without population continuity to modern-day populations.
quote:Originally posted by Elmaestro:
Logically the story writes itself. [...] ... the ancient Moroccan DNA. who I speculate to have introgressed Ibermaurasian HG DNA.
@Tukuler Does the story write itself?
Yes, I see Marusian possibilities. I think it'd be filtered by medieval times. But the archaeological context of the find is unknown.
I certain we can't know Maghreb and North Sahara genetics without data from Wargla and the Haratin and the "vassals" of the Algerian Oases and the isolated Imraguen "fishers" of Mauritania.
posted
Interesting read but I never saw that post but I sort of suspected that already that is why I paid no mind these statistical manipulation games...especially when it is based upon autosomal SNP FREQUENCY and not autosomal STR. I am surprised he included TreeMiIx because I thought it was based upon a totally different processing technique(or algorithm). I assumed TreeMix created some sort of "autosomal PhyloTree" like uniparental markers thus tracing migration. All the others uses str8up frequency which we know is nonsense. Many times you don't need these statistical gamesmanship to see the genetic history displayed in the Admixture Charts- Cluster Charts. As we go from K=2 to K=20 and beyond the separation and genetic history becomes clear. Thanks for the link but I was never convinced of the results from these statistical manipulation. Now it seems I am right. I always said. Genes mimic geography!!!!!! Sforza was correct! That will never change.....until the last 400years ...as we see with peoples of the new world. Oh! And yes, I picked up on Khoi-San being slaves. But the author needed to throw in the word "slave" in there at all cost even when it has no documented "historical" relevance.
--------------------------- Quote
"Do we always need to remap published aDNA data? Leave a comment The second step when another ancient human DNA paper is published (the first one is obviously to read it) is usually to download the genomic data in order to use it for our projects. Most papers (especially those concerned with Western Eurasian prehistory) try to include all previously published individuals, which is good for various reasons. The data comes in various shapes: unprocessed raw reads, trimmed/merged reads or bam files of already mapped reads or even genotype calls. The question is what kind of data to use. A recent discussion on whether to remap everything using our pipeline inspired me to this post.
Various forms of f statistics are widely used in the population genetic analysis of aDNA data. Essentially, they measure correlations between allele frequencies in different populations. The usual interpretation of correlated allele frequencies would be some shared ancestry. xyyman comment: WHICH IS WRONG!!!!! There is a certain risk that such correlations might arise from technical artefacts in the handling of different data sets and individuals. The results of at least two papers during the last year may have been substantially affected by some kind of technical artefacts (Gallego Llorente et al. and Mondal et al. see also here and here).
I downloaded the raw reads for 163 ancient individuals from Mathieson et al. and mapped the data to the human reference using bwa aln with two different settings for the -n parameter which controls the mismatch rate to the reference. I used both the default -n 0.04 and -n 0.01 which allows for more mismatches and helps to use more of the (potentially degraded) sequences in the library. Then I merged BOTH versions of each into one tped file by randomly choosing one read per SNP and bam file (~1.2 million captured SNP sites in total). Then, I used popstats to calculate the statistic D(Chimp, hg19_reference; IndividualX_n0.01, IndividualX_n0.04), so I tested whether the hg19 reference genome shares more alleles with either of two versions of the same individual. The answer should obviously be “no”.
dtest-hg19-out-hist (left) Histogram of the Z scores (zero as blue vertical line, the empirical mean is shown in red) and (right) QQ-plot of expected vs observed Z scores
Across all 163 individuals, the results show an enrichment of positive Z scores (expectation would be 0). In fact, the entire distribution seems to be shifted towards more positive values. The median is 0.59, the mean is 0.62 which is significantly different from zero (t-test, p=3e-11). Seventeen Z scores are larger than 2, three are even larger than 3, so there is quite some room to wrongly interpret the results of D tests when the samples have been processed differently. This setting is quite artificial as nobody will ask which individual is more or less “reference”, but the human reference sequence itself is closer to some populations than to others. So spurious effects like this could also make a test individual seem more similar to some populations. I know this effect is relatively small, but it is quite a difference whether we claim that population X traces 2% of its ancestry to population Y or if it’s actually 0%.
The results make sense: allowing for less mismatches introduces some inherent reference bias as the processing with more mismatches will accept the non-reference allele more often. The random sampling of one read per SNP position is based on the assumption that reference and alternative read would occur 50/50 at a heterozygous position, which seems to be violated due to the reference bias.
The reference bias is likely going to affect all sorts of f statistics and related methods (f3, f4, D, ABBA-BABA, qpAdm, TreeMix etc.) and it might affect others as well. So I’m definitely going make sure that all data is processed as equally as possible which means to process all samples through the same in silico pipeline even if that can be quite time-consuming for some big aDNA papers. I’m also assuming that other steps in the pipeline (e.g. different diploid genotype callers, base quality rescaling) could have similar effects of causing spurious correlations."
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So I had it right all along. Technical artefacts. They have switched from PCA using "haplogroup frequency" to PCA and new other statistical method using "autosomal allele frequency". Both are erroneous and they know it. That is why they use it. They know the best method to determine migration route and direction is to plot clades, sub-clade on some sort of geographic phylotree. When that is done it is obvious the path of migration. But I always thought TreeMix circumvented that frequency based error or technical artefact. Because TreeMixn uses some sort of diminishing frequency of specific alleles to draw the "events". Maybe the stats guys like ElMaestro or Swenet could chime in here. I am not a stat guy to that level. Anyways I called it when I posted on STR vs SNP. Maybe Lioness can bump that thread. I think the author concluded that it is impossible to draw migration path or related using SNPs. That is why the relatedness of the Abusir and "Near Easterners is a technical artefact. The game played by EuroNut researchers. If they used Treemix or sub-clades or autosomal STRs within the right population it will be easy to tell that Abusir mummies are closest realted to the Amarnas - People of the Great Lakes.
Quote "Various forms of f statistics are widely used in the population genetic analysis of aDNA data. Essentially, they measure correlations between allele frequencies in different populations. The usual interpretation of correlated allele frequencies would be some shared ancestry. There is a certain risk that such correlations might arise from technical artefacts in the handling of different data sets and individuals. The results of at least two papers during the last year may have been substantially affected by some kind of technical artefacts (Gallego Llorente et al. and Mondal et al. see also here and here)"
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posted
In other words I know they are wrong and they know they are wrong but it is not about right or wrong methods. It is about ostracizing the Sub-Saharan African and disenfranchised them from their rightful place in history and insert Europeans to the center piece. Have Europeans lie their way into grandiose and history. That is what it is about. "Eurasian" is the new Caucasian. Because Eurasians do NOT include "Asians" in the eyes of these racialist.
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i left a comment about the North African aDNA, maybe he will reply
hey xyyman why don't YOU actually try building a 'geographic phylotree of clades and subclades' and post it? would be cool. (problem is resolution and amount of data is so uneven everywhere, plus there's so much it's gets very messy when you try to plot it.)
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quote:Originally posted by capra: interesting article Tukuler
hey xyyman why don't YOU actually try building a 'geographic phylotree of clades and subclades' and post it? would be cool. (problem is resolution and amount of data is so uneven everywhere, plus there's so much it's gets very messy when you try to plot it.)
You don't need sophisticated computer ..eyeballing gives you an idea without much effort.
eg here are some. Clearly E-M35 is African and E-V13 is a subclade that migrated out same as E-123. This is not rocket science.
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You don't need to be a rocket scientist. Eg look at R0a. Clearly Arabia has a higher frequency of subclades of R0a but Africa carries much more unique version of R0a. Some can be seen in "west" Africa.. Same pattern is seen with mtDNA H and it subclades. In fact most haplogroups. Understand? They can't fool me with their games on PCA, and statistical rigging. If you truly want to be a white a liberal I can teach you a lot.
BTW - all this point to a very RECENT OOA. Just so you know. Ask me why.
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You see all these racialist bloggers repeating that the Abusir carry no African DNA. They go about thumping their chest that the Abusirs are "Eurasians" but they do not look closely at the data. They do not realize that the Abusir are clearly NOT related to modern Europeans and the Near East populations are Yemenis and Bedouins(not Syrians etc )....two geographically displaced Africans. But they are too rabid to understand that. And if the rightful population was included...game over. But it is about stroking the mis-directed ego and warped psyche of the modern European.
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quote:Originally posted by capra: interesting article Tukuler
i left a comment about the North African aDNA, maybe he will reply
hey xyyman why don't YOU actually try building a 'geographic phylotree of clades and subclades' and post it? would be cool. (problem is resolution and amount of data is so uneven everywhere, plus there's so much it's gets very messy when you try to plot it.)
posted
Quotes from: No evidence for unknown archaic ancestry in South Asia -Pontus Skoglund1,2*, Swapan Mallick1,2,3, Nick Patterson2, David Reich1,2,3 One possible explanation for the skew that the authors observe3 is batch artifacts, reflecting differences in laboratory or computer processing between the data newly reported by Mondal et al., and the data from non-Indians used for comparison10. Separate processing is known to be able to cause correlation of errors within datasets, and this could explain why the newly reported South Asian genomes appear (artifactually) to share fewer alleles with other modern humans. However, the data used by Mondal et al. have not been made available for independent reanalysis, and without this, a definitive explanation is not possible. Whatever the explanation, our analyses contradict the claim of unknown archaic ancestry in South Asians.
Further confirmation for unknown archaic ancestry in Andaman and South Asia. - Mayukh Mondal1 The existence of admixture with an extinct hominin has been challenged by Skoglund et al.4, as they were unable to replicate our results in their data sets. While we had used a wide variety of statistical methods and data sets from diverse populations to draw our inference, Skoglund et al.4 have used only one method (D-stats5, for the whole genome, not specifically for the relevant genomic regions) and compared only with the Asians, not even with the Europeans. Skoglund et al.4 have alleged that our statistical treatment of the data was faulty and have pointed out some possible sources of error. We have reexamined our data focusing on possible sources of error flagged by Skoglund et al4 . We have also performed new analyses. The reexamination and new analyses have bolstered our confidence that our earlier inferences were correct and have resulted in an improved model of introgression of modern humans with a hitherto unknown archaic ancestry. We also propose a possible reason for the inability of Skoglund et al.4 to validate our inference
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i love how you think circling the African R0a haplotypes will somehow magically convince people
did you try some crazy shit like actually counting how many basal branches are African vs Eurasian? of course not
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SMH. I think you are missing the point Capra. BASAL and exclusivity. Oh! And what is Eurasian?
Ok! Ok! I will give you a clue. Look at the blue=European. Do you see the pattern? As I said you don't need a computer. SMH! Why do I bother?
In other words look at the fugking PhytloTree within the chart(R0a). IT IS THERE! Damn! Am I the only one with a brain on here?
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Also if you the blue(European) sample is from Iberia or Italy then that also become African(North) and takes the total number of African up to 18. Genes mimic geography.
Plot this on a geographic map and the PhyloTree take shape as with YDNA E which you made no mention of. Lol! You don't need a fancy computer. I am unto their games.
16284 is questionable because the blue if Greek then may it(16284) may be Near East. If not that take African clades up to about 19
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posted
To those who can follow this stuff. Clearly this R0a pie chart mimic geography with R0a tree showing an African origin. Hit me up if you have any more questions. Simply plot the sub-clades on a Map of the Near East Africa and Europe. If the precise sample set location is known it will be more helpful but there is enough there. Forgot this FREQUENCY BS= Technical Artefact
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okay, there are 9 basal branches containing only Africans (North or East/West). then there are 9 which contain both Africans and Eurasians. now i expect you to count shared branches as African because circular reasoning, but why only 7 of them?
quote:Originally posted by xyyman: You see all these racialist bloggers repeating that the Abusir carry no African DNA. They go about thumping their chest that the Abusirs are "Eurasians" but they do not look closely at the data.
yeah they obviously are getting their info from some online circle jerk, since the analysis in the paper found that the Abusir mummies *did* have SSA ancestry. of course you are no better.
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posted
Finally we are making progress. I am tied up now . we will talk. Oh! And don't put me in the same class as the Euronuts on Abusir. I can read ..they cannot read and understand. Of course the Abusir has SSA ancestry.
quote:Originally posted by capra: okay, there are 9 basal branches containing only Africans (North or East/West). then there are 9 which contain both Africans and Eurasians. now i expect you to count shared branches as African because circular reasoning, but why only 7 of them?
quote:Originally posted by xyyman: You see all these racialist bloggers repeating that the Abusir carry no African DNA. They go about thumping their chest that the Abusirs are "Eurasians" but they do not look closely at the data.
yeah they obviously are getting their info from some online circle jerk, since the analysis in the paper found that the Abusir mummies *did* have SSA ancestry. of course you are no better.
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And yes you have to absolutely count the "mixed" as African. Why? The downstream-sub-clades are found outside Africa. If they were of Near East origin then the sub-clades will be found IN Africa which is NOT the case. Eg R0a2c. Six sub-clades are found outside Africa which means the upstream "mixed" has to be counted as African. ...this is not circular but logical. Same for R0a1a. There is only one "possible" back-migration from the Near East which I highlighted. As I said no computer is needed. Overlay this over a global map of the region and it will be clear to see R0a is of African origin. This is too easy.
The author tried to throw us for-a-loop with the discussion about FREQUENCY but ignore the fact that a PhyloTree can be created from his data just as yDNA E above.
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quote:Originally posted by Tukuler: Oral Presentation Society for Molecular Biology and Evolution Conference 2016
Days Sunday, 3rd July Monday, 4th July Tuesday, 5th July Wednesday, 6th July Thursday, 7th July
Tracks Developmental and cellular genetics Ecological and conservation genetics Gene regulation and epigenetics Medical and human genetics
Search Speakers The genomic enigma of two Medieval North Africans (#243) Torsten Günther q , Cristina Valdiosera 2 , Juan Carlos Vera-Rodríguez 3 , Ricardo Rodriguez-Varela 4 , Emma Svensson 1 , Rafael M Martínez Sánchez 5 , Rafael Carmona Ávila 6 , Leonor Peña Chocarro 7 , Guillem Pérez Jordà 8 , Youssef Bokbot 9 , Eneko Iriarte 10 , Colin Smith 2 , Mattias Jakobsson 1
Uppsala University, Uppsala, Sweden La Trobe University, Melbourne, Australia Departamento de Historia, Geografía y Antropología, Universidad de Huelva, Huelva, Spain Universidad Complutense de Madrid, Madrid, Spain Departamento de Prehistoria y Arqueología, Universidad de Granada, Granada, Spain Museo Histórico Municipal, Córdoba, Spain Escuela Española de Historia y Arqueología en Roma/CSIC, Rome, Italy G. I. Arqueobiología, Instituto de Historia, Madrid, Spain Institut National des Sciences de l’Archéologie et du Patrimoine, Rabat, Morocco Departamento Historia, Geografía y Comunicación, Universidad de Burgos, Burgos, Spain
The trans-Saharan gold and salt trade as well as the trans-Saharan slave trade played an important role in population movements connecting sub-Saharan and Mediterranean economies during the Middle Ages. The slave trade alone is said to have transported more than 9 million slave soldiers and domestic servants along the trans-Saharan route. In this study, we present the genomic analysis of two human individuals from a cave site in the area of present-day Morocco which were directly dated to the Medieval period. The samples were processed in a designated ancient DNA lab and the genomic data obtained shows standard patterns of authentic ancient DNA with low levels of contamination. Both individuals – which represent the first ancient genome sequence data from North Africa – do not exhibit particular genetic affinities to modern North Africans or any other present-day population in published genotype data sets despite relatively extensive data has been produced from many areas of Africa. In fact, the most parsimonious way to model them genetically is as two-source admixture between Mediterranean Europeans and Southern Africans. The lack of archaeological context of the two individuals opens up various alternatives to explain their genomic pattern. Both individuals could represent a Medieval African population without population continuity to modern-day populations. Alternatively, both Mediterranean Europe and Southern Africa are known source regions in the Arab slave trade, thus they could potentially represent the offspring of slaves of different origin. The Arab slave trade extended over a longer period and may have involved more slaves than its transatlantic counterpart and our data might provide the first genetic insight into this historical process and the people who suffered in it. Our results highlight how archaeogenetic research can shed lights into historical events and long-distance population movements while opening new questions for the interpretation of the data.
Europeans are obsessed with Africans and alleged slave trade. Meanwhile they themselves roamed all over the planet freely.
The word Hajj was not mention even one time, despite the islamic history in the region. Yet, Hajj is one of the pillars in orthodox islam. It gives away they are a bunch of clowns who serve the internet hype.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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posted
no, that does not make sense. but congratulations for the baby steps toward employing logic.
a long time ago there was only the root haplotype of R0a. in some, but not all, lines of descent one or more additional mutations occurred in the HVS-I. after 18 000 years or so any given line of descent will have an average of 1 HVS-I mutation (some will have none, some more than one). the older the haplogroup the smaller the proportion of the root haplotype will remain in modern descendants. estimated age of R0a is 20-25 000 years (not that i'd take that too seriously), the root haplotype and 1 step haplotypes are still very common.
okay so look at R0a2c. what is the most common kind of R0a2c? the root haplotype of R0a2c. if some R0a2c migrated from Asia into Africa, what kind would be most likely to migrate? the most common kind of course, which is the root haplotype. you need to think about what it actually means, not work with vague ideas of "upstream" and "downstream" that you don't understand.
now what if it originated in Africa. then what, all the R0a2c women who had a mutation in HVS-I just happened to migrate to Asia, leaving the root haplotype only there? no, that is nonsense. (but it could be that it is just a matter of luck in this small sample, that other branches of R0a2c do exist in Africa but they happened not to be found in this sample.)
Posts: 660 | From: Canada | Registered: Mar 2017
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Tukuler
multidisciplinary Black Scholar
Member # 19944
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
quote:Originally posted by Ish Gebor:
quote:Originally posted by Tukuler:
Oral Presentation Society for Molecular Biology and Evolution Conference 2016
The genomic enigma of two Medieval North Africans (#243) Torsten Günther q , Cristina Valdiosera 2 ,
Uppsala University, Uppsala, Sweden La Trobe University, Melbourne, Australia
The trans-Saharan gold and salt trade as well as the trans-Saharan slave trade played an important role in population movements connecting sub-Saharan and Mediterranean economies during the Middle Ages. The slave trade alone is said to have transported more than 9 million slave soldiers and domestic servants along the trans-Saharan route.
In this study, we present the genomic analysis of two human individuals from a cave site in the area of present-day Morocco which were directly dated to the Medieval period. The samples were processed in a designated ancient DNA lab and the genomic data obtained shows standard patterns of authentic ancient DNA with low levels of contamination.
Both individuals – which represent the first ancient genome sequence data from North Africa – do not exhibit particular genetic affinities to modern North Africans or any other present-day population in published genotype data sets despite relatively extensive data has been produced from many areas of Africa. In fact, the most parsimonious way to model them genetically is as two-source admixture between Mediterranean Europeans and Southern Africans. The lack of archaeological context of the two individuals opens up various alternatives to explain their genomic pattern. Both individuals could represent a Medieval African population without population continuity to modern-day populations.
Alternatively, both Mediterranean Europe and Southern Africa are known source regions in the Arab slave trade, thus they could potentially represent the offspring of slaves of different origin.
The Arab slave trade extended over a longer period and may have involved more slaves than its transatlantic counterpart and our data might provide the first genetic insight into this historical process and the people who suffered in it.
Our results highlight how archaeogenetic research can shed lights into historical events and long-distance population movements while opening new questions for the interpretation of the data.
Europeans are obsessed with Africans and alleged slave trade. Meanwhile they themselves roamed all over the planet freely.
The word Hajj was not mention even one time, despite the islamic history in the region. Yet, Hajj is one of the pillars in orthodox islam. It gives away they are a bunch of clowns who serve the internet hype.
This's how institutions of educational train minds. Afrikans schooled in cultural heritage won't be co-conspiritors to 19th and 20th century Euro-American doctrine that the Talented Tenth want us to believe is objective and unbiased science no oppression intended. They are buffers selling out for inclusion in the status quo. Or perhaps its just too painful realizing they can suffer the same fate at the whim of a cop as a hoodrat despite being the bestest negro or coon.
I'll be gone but the 2nd and 3rd generation of the next post's program will have the skills, tools, and most importantly independent Afrikan minds to free anthropology, genetics and the many disciplines genetics need in its support.
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
The collaborative African genomics network training program: a trainee perspective on training the next generation of African scientists
Busisiwe C. Mlotshwa MSc, Savannah Mwesigwa MSc[…] Sununguko W. Mpoloka PhD
Genetics in Medicine volume 19, pages 826–833 (2017)
Abstract Purpose: The Collaborative African Genomics Network (CAfGEN) aims to establish sustainable genomics research programs in Botswana and Uganda through long-term training of PhD students from these countries at Baylor College of Medicine. Here, we present an overview of the CAfGEN PhD training program alongside trainees’ perspectives on their involvement.
Background: Historically, collaborations between high-income countries (HICs) and low- and middle-income countries (LMICs), or North–South collaborations, have been criticized for the lack of a mutually beneficial distribution of resources and research findings, often undermining LMICs. CAfGEN plans to address this imbalance in the genomics field through a program of technology and expertise transfer to the participating LMICs.
Methods: An overview of the training program is presented. Trainees from the CAfGEN project summarized their experiences, looking specifically at the training model, benefits of the program, challenges encountered relating to the cultural transition, and program outcomes after the first 2 years.
Conclusion: Collaborative training programs like CAfGEN will not only help establish sustainable long-term research initiatives in LMICs but also foster stronger North–South and South–South networks. The CAfGEN model offers a framework for the development of training programs aimed at genomics education for those for whom genomics is not their “first language.”
Tukuler says Yep, ought to be a new era when they commence. Say bye-bye to lame historical interpretations with one of these guys on the team and demanding input or oversight of a write up.
posted
You are starting to sound like the faggy Ric on Davdski....Capra. We are going in circles. As a reminder, I don't argue hypotheticals. Try again!
quote:Originally posted by capra: no, that does not make sense. but congratulations for the baby steps toward employing logic.
a long time ago there was only the root haplotype of R0a. in some, but not all, lines of descent one or more additional mutations occurred in the HVS-I. after 18 000 years or so any given line of descent will have an average of 1 HVS-I mutation (some will have none, some more than one). the older the haplogroup the smaller the proportion of the root haplotype will remain in modern descendants. estimated age of R0a is 20-25 000 years (not that i'd take that too seriously), the root haplotype and 1 step haplotypes are still very common.
okay so look at R0a2c. what is the most common kind of R0a2c? the root haplotype of R0a2c. if some R0a2c migrated from Asia into Africa, what kind would be most likely to migrate? the most common kind of course, which is the root haplotype. you need to think about what it actually means, not work with vague ideas of "upstream" and "downstream" that you don't understand.
now what if it originated in Africa. then what, all the R0a2c women who had a mutation in HVS-I just happened to migrate to Asia, leaving the root haplotype only there? no, that is nonsense. (but it could be that it is just a matter of luck in this small sample, that other branches of R0a2c do exist in Africa but they happened not to be found in this sample.)
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
We got to do our part. The internet has leveled the playing field....sort of. But the liars are still in control.
quote:Originally posted by Tukuler: [QUOTE]Originally posted by Ish Gebor:
[QUOTE]Originally posted by Tukuler:
Or perhaps its just too painful realizing they can suffer the same fate at the whim of a cop as a hoodrat despite being the bestest negro or coon.
I'll be gone but the 2nd and 3rd generation of the next post's program will have the skills, tools, and most importantly independent Afrikan minds to free anthropology, genetics and the many disciplines genetics need in its support.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
I have my doubts, Mandela comes to mind. But we have no other choice but to try to correct the lies.
"Tukuler says Yep, ought to be a new era when they commence. Say bye-bye to lame historical interpretations with one of these guys on the team and demanding input or oversight of a write up"
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes - Francesca Gandini,
Bookmark
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
Why do people keep claiming the Khoisan were in North Africa or migrated Out of Africa?? There is NO PHYSICAL PROOF AT ALL> NO ONE IN EURASIAN CARRIES THEIR HAPLOGROUPS. There are NO Khoisan skulls found in North Africa or Europe or anywhere else. The FIRST MODERN PEOPLE EVERYWHERE LOOKED LIKE THIS:
Everyone originated from them including Negroids: Posts: 108 | From: UK | Registered: Jan 2018
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
For the resident geeks
quote:Günther blogged: Do we always need to remap published aDNA data?
The data comes in various shapes: • unprocessed raw reads, • trimmed/merged reads or • bam files of already mapped reads or • even genotype calls.
The question is what kind of data to use. A recent discussion on whether to remap everything using our pipeline inspired me to this post.
. . . .
There is a certain risk that such correlations might arise from technical artefacts in the handling of different data sets and individuals.
. . .
I tested whether the hg19 reference genome shares more alleles with either of two versions of the same individual. The answer should obviously be “no”.
. . .
Across all 163 individuals, the results show an enrichment of positive Z scores (expectation would be 0). In fact, the entire distribution seems to be shifted towards more positive values.
This setting is quite artificial as nobody will ask which individual is more or less “reference”, but the human reference sequence itself is closer to some populations than to others. So spurious effects like this could also make a test individual seem more similar to some populations. I know this effect is relatively small, but it is quite a difference whether we claim that population X traces 2% of its ancestry to population Y or if it’s actually 0%.
. . .
... reference bias is likely going to affect all sorts of f statistics and related methods • (f3, • f4, • D, • ABBA-BABA, • qpAdm, • TreeMix etc.) and it might affect others as well.
So I’m definitely going make sure that all data is processed as equally as possible which means to process all samples through the same in silico pipeline even if that can be quite time-consuming for some big aDNA papers. I’m also assuming that other steps in the pipeline (e.g. • different diploid genotype callers, • base quality rescaling) could have similar effects of causing spurious correlations."
Building a virtual ligand screening pipeline using free software: a survey
Virtual screening, the search for bioactive compounds via computational methods, provides a wide range of opportunities to speed up drug development and reduce the associated risks and costs.
While virtual screening is already a standard practice in pharmaceutical companies, its applications in preclinical academic research still remain under-exploited, in spite of an increasing availability of dedicated free databases and software tools.
In this survey, an overview of recent developments in this field is presented, focusing on free software and data repositories for screening as alternatives to their commercial counterparts, and outlining how available resources can be interlinked into a comprehensive virtual screening pipeline using typical academic computing facilities.
Finally, to facilitate the set-up of corresponding pipelines, a downloadable software system is provided, using platform virtualization to integrate pre-installed screening tools and scripts for reproducible application across different operating systems.
posted
you planning to back up any of the nonsense you're spouting with actual scientific literature, Dinkum? so far you're less credible than xyyman, which is one hell of a feat
Posts: 660 | From: Canada | Registered: Mar 2017
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
I left 3 or more slice pies (circles) alone. I only count circles one step from center circle. So I didn't count 264 355 189 304.
quote:Originally posted by xyyman: I got 16 African and 9 for Arabian
quote:Originally posted by capra: okay, there are 9 basal branches containing only Africans (North or East/West). then there are 9 which contain both Africans and Eurasians. now i expect you to count shared branches as African because circular reasoning, but why only 7 of them?
posted
^^ Dinkum That model is against Occam's razor You can go to African and see all four looks in one tribe if not one family. Posts: 1254 | From: howdy | Registered: Mar 2014
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