Natufians -Origin of Basal Eurasian Farmers - Lazaridis 6-16

[djoser-xyyman]

Quote from FTDNA poster

“20 of the R1b-P297 (XL51) ancients have been placed on the R1b-M269 (P312- U106-) DNA Project (aka ht35 Project) aDNA chart. www.familytreedna.com/groups...out/background PDF download is available. Very cool. “


Quote:
The goal of the R1b-M269 (P312- U106-) DNA Project is to investigate the history and distribution of the most upstream (or basal) clades of haplogroup R1b-M269/R1b1a2. The project is open to anyone tested to be M269+ P312- U106-. You may join our project by clicking this link.

This project is sometimes called the ht35 project, a legacy of its early history. The original goal of this project, when it was formed in 2007, was to facilitate the discovery of SNP markers that would help differentiate the old "ht15" type of R1b1a2 found primarily in western Europe from the "ht35" type of R1b1a2 found primarily in southeastern Europe and southwestern Asia.

The list of SNPs discovered in members of this project since then and especially since late 2013 is quite long. These discoveries have kept us busy, not least in a need to continually update the names we use.

The data in our project demonstrate that haplogroup R1b1a2 is relatively young, with its most recent common ancestor having lived less than 7,000 years ago somewhere in southwestern Asia

[djoser-xyyman]

Originally posted by xyyman:
[QB] Y-chromosomal sequencing and screening reveal both stability and migrations in North Eurasian populations. - O. Balanovsky


Abstract:
Y-chromosomal markers exhibit the highest interpopulation diversity in the genome and thus form one of the most informative tools for tracing population history. However, their information value depends on discovering SNPs which subdivide haplogroups with broad geographic distribution into branches revealing fine population structure. Progress in such discoveries has recently moved from a slow linear phase to a rapid exponential phase due to NGS.
We applied this approach to the Y-chromosomal pool of North Eurasian populations and concentrated on haplogroups C, G1, G2, N1b, N1c, and R1b. We sequenced 181 Y-chromosomes (capturing 11 Mb from each sample), developed the NGSConv software for calling Y-chromosomal SNPs, and identified roughly 2,500 SNPs, most of which were new. Then we constructed phylogenetic trees and dated dozens of their branches using our estimates of the mutation rate. The last – but not the least – step included screening branch-defining SNPs in the entire Biobank of indigenous North Eurasian populations (led by prof. Elena Balanovska), which includes 26,000 samples from 260 populations. This screening resulted in frequency distribution maps of 29 branches of haplogroups R1b and C, thus increasing the phylogenetic resolution by an order of magnitude compared to the two initial haplogroups.
For haplogroup R1b, we identified a previously unstudied “eastern” branch, R1b-GG400, found in East Europeans and West Asians and forming a brother clade to the “western” branch R1b-L51 found in West Europeans. The ancient samples from the Yamnaya archaeological culture are located on this eastern branch, showing that the paternal descendants of the Yamnaya population –***** in contrast to the published autosomal findings**** - still live in the Pontic steppe and were not an important source of paternal lineages in present-day West Europeans. For haplogroup C-M217 - the predominant paternal component in Central Asians - we found signals of simultaneous expansion in two independent branches. Both expansion times and gene geographic maps of the expanded lineages indicated the emergence of the Mongol Empire as the likely trigger. We conclude that simply discovering new SNP is not enough, but in combination with screening for the branch-defining SNPs in large biobanks of indigenous populations, it allows comprehensive reconstruction of male population history. [/QB]

[djoser-xyyman]

Originally posted by xyyman:
[QB] ASHG 2016 Abstracts - -

Abstract:
The area of southeastern Europe known as the Balkans has always been a crossroads between Europe and Asia: a conduit for people, culture and language. Beginning around 6,500 BCE, the Balkans was the first place in Europe to become transformed by farming, brought by a new wave of migrants from Anatolia. From this staging point, farming and people spread to all corners of Europe. However, the dynamics of the interaction between farmers and indigenous European hunter-gatherers in the first place that they encountered each other remains poorly understood because of the near complete absence of genetic data from prehistoric specimens from this region.

We generated new genome-wide ancient DNA data from 65 farmers from the Balkans and adjacent regions dating as far back as 6,400 BCE. We document how the dynamics of admixture between the regions first farmers and its indigenous hunter-gatherers was complex, with evidence of local admixture from hunter-gatherers related to those from Scandinavia and Eastern Europe. The population admixture was patchy across both space and time, varying in magnitude between 0% and 30% for different early Balkan farming populations. The hunter-gatherer admixture in the early farmers of the Balkans is ****not ***** closely related to the hunter-gatherer admixture that is predominant in present-day Europeans. This suggests that the waves of farmers that contributed most of the migrants to northern and western Europe were ****not**** ones that mixed substantially with local Balkan hunter-gatherers.

We also analyze the data to generate new insights about natural selection. The first farmers of the Balkans were in the initial stages of adaptation to environments that were dramatically different from those that their ancestors had encountered. We show that many of the adaptations related to diet and immunity that later become common in Europe were already present in early Balkan farmer populations, but not at high frequency. Thus, the adaptation of the first European farmers to their local environment was driven to a substantial extent by pre-existing variation.


Sardinia is off the coast of North Africa------

Abstract:
Genetic studies of complex traits using individuals from the island of Sardinia have been fruitful for decades. Understanding the population history of Sardinia may provide insights to how risk alleles arise in Sardinia and the expected degree of sharing with mainland populations. Current models for the peopling of Europe consider extant Europeans as having varying ancestral contributions from Paleolithic hunter-gatherers, Neolithic farmers, and Steppe pastoralists. In these analyses, extant Sardinians are inferred with the largest amount of Neolithic farmer ancestry among Europeans. However, previous studies of uniparental markers have highlighted the high frequency of the Y-chromosome haplotype I2a1a1 in Sardinia, which has been associated with Paleolithic ancestry in Europe. Here we aim to elucidate finer details of the population history of Sardinia. We study >3,500 whole-genome sequenced individuals across Sardinia together with reference European datasets and recently published ancient humans. We confirm that compared to mainland Europeans, Sardinians exhibit the greatest amount of shared drift with Neolithic farmers. Within the island of Sardinia, there is a demarcation of individuals from the Lanusei Valley in the geographically isolated province of Ogliastra and individuals from other provinces. In ****unsupervised analyses****, a Sardinian-specific ancestry component correlates with shared drift parameters with both the Neolithic farmers and Paleolithic hunter-gatherers, and is consistent with supervised estimates of ancestry proportions in which the Ogliastra individuals have higher Neolithic farmer and Paleolithic hunter-gatherer ancestries, while individuals from the rest of the island show an infusion of the pastoralist ancestry. Finally, we find that the Sardinian people exhibit increased sharing of alleles with the Neolithic farmers on the X chromosome compared to the autosome (P < 1x10-4), suggesting a sex-biased demographic history in Sardinia. Together, our results indicate that in addition to the strong Neolithic farmer component of ancestry, isolated regions of Sardinia also harbors significant ancestry components from Paleolithic Europe and that the Neolithic transition in Sardinia may have involved sex-biased demographic change. These results help provide more insight into the history of Sardinians and the frequency distribution of variants they carry.


Abstract:
The sequencing of complete Neanderthal and Denisovan genomes has provided several insights into human history. One important insight stems from the observation that modern non-Africans and archaic populations share more derived alleles than they should if there was no admixture between them. We now know that the ancestors of modern non-Africans met, and introgressed with, Neanderthals and Denisovans. The estimate of the quantity of shared derived alleles, the mixture proportion, rests on ***an assumption ***of no archaic admixture in African populations, and so African populations have been used as the “non-admixed” outgroup in prior analyses. We find that the story is likely more complex, that the history within Africa involves admixture with population(s) related to Neanderthal and Denisova, and that the mixture proportion estimates for non-African populations have been biased, particularly in Melanesia. Here, we present results from a composite likelihood estimator of archaic admixture, which allows multiple sources of archaic admixture. We apply the method to archaic introgression, but it can be used to estimate ancient admixture among any four populations where the modeled assumptions are met. This joint estimate of Neanderthal and Denisovan admixture avoids the biases of previous estimators in populations with admixture from both Neanderthal and Denisova. To correct for dependence in our data, we use a moving blocks bootstrap to calculate confidence intervals. With assumptions about population size and more recent population separation dates taken from the literature, we estimate the archaic-modern separation date at ~440,000 ± 300 years ago for all modern human populations. We also estimate the archaic-modern mixture proportion in the 1000 genomes, and the modern genomes sequenced with the high coverage Neanderthal and Denisovan genomes. We report those estimates here, support several prior findings, and provide evidence for a lower level of Denisovan admixture (0.0191 [0.0184, 0.0197]), relative to Neanderthal (0.0256 [0.0247, 0.0265]), in Melanesia. On the basis of an excess of shared derived alleles between San, Neanderthal, and Denisova we suggest that a third archaic population related more closely to Neanderthal and Denisova than to modern humans introgressed into the San genomes studied here. [/QB]

[djoser-xyyman]

Don't blow a fuse reading the above. I know you may not understand it and have no clue what was posted above. But we have new and more reliable technology to help us elucidate past human history. really! lol! it is called genetics. lol! What does the above all mean

Originally posted by xyyman:
[QB] What does it all mean?

1. Sardinia NOT the Levant was the stepping stone from Africa to Europe. That also applies to ancient Hunter- gatherers and not only Neolithics
2. The Yammanya are NOT ancestral to Western Europeans
3. Africans carry archaic ancestry related to Neanderthal and Denisovan. Khoi-San being the oldest population will be expected to have this archaic "admixture". Meaning there was not fugking between AMH and Neanderthals/Denisovan [/QB]

I know if you have the slightest clue on what I posted you would shut up. Seriously. If you come back with more Caucasoid and Negroid nonsense. I will know you are a clown. You know more than all these researchers(sarcasm). lol. SMH.

[djoser-xyyman]

BTW. Europeans are from 3 sources. Yes.

1. Neolithics(Basal Eurasian/Natufians)( who were bringing in light skin genes)
2. Ancient North East Hunter gatherers Related to East Asians
3. Western Huntergatherers - La Brana and Loshcbour ( who are black skinned)

Both 2 and 3 are related to blacks of Asia like Makrani and Onge pictured above. So sorry don't delude yourself. loL!

[jethro]

Sept 17, 2016 6:14:26 GMT -5 djoser-xyyman said:

BTW. Europeans are from 3 sources. Yes.

1. Neolithics(Basal Eurasian/Natufians)( who were bringing in light skin genes)
2. Ancient North East Hunter gatherers Related to East Asians
3. Western Huntergatherers - La Brana and Loshcbour ( who are black skinned)

Both 2 and 3 are related to blacks of Asia like Makrani and Onge pictured above. So sorry don't delude yourself. loL!

LABRANA  MAN WAS  NOT BLACK SKINNED,  but had brown  skin,  BLUE EYES, CAUCASIAN  FEATURES AND STRAIGHT HAIR!!!!!

[jethro]

LOLOLOLOLOL THE ANDAMANESE ARE CLOSELY RELATED TO ASIANS NOT BLACK AFRICANS!

[jethro]

Sept 18, 2016 5:53:06 GMT -5 jethro said:

LOLOLOLOLOL THE ANDAMANESE ARE CLOSELY RELATED TO ASIANS NOT BLACK AFRICANS!

EUROPEANS  ORIGINATED  FROM THREE SOURCES!

1   THE  VERY  CAUCASIAN  CRO-MAGNON   whose SKULL AND  DNA   is  found  throughout the world INCLUDING SOUTH AFRICA  and  EGYPT!

    FIRST  MODERN MAN  ABSOLUTELY EVERYWHERE:




2    THEN  EUROPEANS   ORIGINATED  FROM THE  VERY  WHITE  MIDDLE EASTERN FARMERS  8000  YEARS AGO:





3    THEN  LASTLY<  EUROPEANS  ORIGINATED  FROM THE   YAMNAYA   CULTURE  of  EAST EUROPE   WHO  WAS ALSO  RELATED TO  NATIVE AMERICANS!   Native Americans  carry  1/3 ANCIENT  EUROPEAN DNA:
www.bbc.com/news/science-environment-25020958

[djoser-xyyman]

Yes. Lollololol. Strawman argument. Lol! Who said Andamanese are NOT Asians. Ancient "Negros" who Asians. Sigh!

Have YOU looked at the genetic profile of LA Brana. Pssst , LA a Brana was Onge /Australian. Read the study and don't listen to wiki or youtube. SMH.

[djoser-xyyman]

If you don't read the research papers and citing youtube as a source we cannot continue this discussion. You are only interested in dogma and not the actual research.

[jethro]

EUROPEANS LIKE MIDDLE EASTERN PEOPLE carry E-M78 as their majority E-HAPLOGROUP!!! Haplogroup E-M78 ORIGINATED IN ANCIENT CAUCASIAN EGYPT!

www.transpacificproject.com/wp-content/uploads/2011/06/Y-Haplogroups-World-Map.jpg

[jethro]

Sept 18, 2016 6:01:21 GMT -5 djoser-xyyman said:

Yes. Lollololol. Strawman argument. Lol! Who said Andamanese are NOT Asians. Ancient "Negros" who Asians. Sigh!

Have YOU looked at the genetic profile of LA Brana. Pssst , LA a Brana was Onge /Australian. Read the study and don't listen to wiki or youtube. SMH.

PSSSSSSSSSSSST   he  carried  C-6  INDIGENOUS TO  EUROPE 



C  originated  from  CF   which is MIDDLE EASTERN IN ORIGIN!   

en.wikipedia.org/wiki/Haplogroup_CF_(Y-DNA)

One  lot of  C  went into   ASIA,  the  other into EUROPE!!!

THAT  IS WHY  LABRANA  MAN  IS A  CAUCASIAN!!!

AS  FOR WIKI,   IT IS THE  6th  most  popular  site on the WEB  used  by millions of students
listabuzz.com/top-10-most-visited-websites-in-the-world/


IT  HAS ALSO  BEEN ENDORSED   BY TWO  RESPECTED  SCIENTIFIC  INSTITUTES   STATING IT IS ACCURATE
FROM  NATURE:
www.livescience.com/32950-how-accurate-is-wikipedia.html

I WILL BE USING  WIKI ALL THE TIME!

[jethro]

Sept 18, 2016 6:03:45 GMT -5 djoser-xyyman said:

If you don't read the research papers and citing youtube as a source we cannot continue this discussion. You are only interested in dogma and not the actual research.

Youtube  often  is  used  by scientists!

NATIVE AMERICANS  are 1/3   ANCIENT EUROPEAN:

www.nature.com/news/americas-natives-have-european-roots-1.14213

24 000  year old  SIBERIAN,   MAL'TA   BOY   was a EUROPEAN/WEST ASIAN

[jethro]

Sept 18, 2016 6:01:21 GMT -5 djoser-xyyman said:

Yes. Lollololol. Strawman argument. Lol! Who said Andamanese are NOT Asians. Ancient "Negros" who Asians. Sigh!

Have YOU looked at the genetic profile of LA Brana. Pssst , LA a Brana was Onge /Australian. Read the study and don't listen to wiki or youtube. SMH.

THE ANDAMANESE  ISLANDERS  DO  NOT CARRY  Y-DNA  C   BUT   D-M174   and  MTDNA  M  specific to themselves!

en.wikipedia.org/wiki/Andamanese_people

[djoser-xyyman]

Quote

Figure 2 | Ancestral variants around the SLC45A2 (rs16891982, above) and SLC24A5 (rs1426654, below) pigmentation genes in the Mesolithic genome.



The SNPs around the two diagnostic variants (red arrows) in these two genes were analysed. The resulting haplotype comprises neighbouring SNPs that are also absent in modern Europeans (CEU) (n = 112) but present in Yorubans (YRI) (n = 113). This pattern confirms that the La Braña 1 sample is older than the positive-selection event in these regions. Blue, ancestral; red, derived.

--Carles Lalueza-Fox

Nature 507, 225–228 (13 March 2014) doi:10.1038/nature12960

Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers

Lalueza-Fox states: "However, the biggest surprise was to discover that this individual possessed African versions in the genes that determine the light pigmentation of the current Europeans, which indicates that he had dark skin, although we can not know the exact shade."

www.sciencedaily.com/releases/2014/01/140126134643.htm

comparing craniometric and neutral genetic affinity matrices have concluded that, on average, human cranial variation fits a model of neutral expectation. While human craniometric and genetic data fit a model of isolation by geographic distance, it is not yet clear whether this is due to geographically mediated gene flow or human dispersal events. Recently, human genetic data have been shown to fit an iterative founder effect model of dispersal with an African origin, in line with the out-of-Africa replacement model for modern human origins, and Manica et al. (Nature 448 (2007) 346-349) have demonstrated that human craniometric data also fit this model. However, in contrast with the neutral model of cranial evolution suggested by previous studies, Manica et al. (2007) made the a priori assumption that cranial form has been subject to climatically driven natural selection and therefore correct for climate prior to conducting their analyses. Here we employ a modified theoretical and methodological approach to test whether human cranial variability fits the iterative founder effect model. In contrast with Manica et al. (2007) we employ size-adjusted craniometric variables, since climatic factors such as temperature have been shown to correlate with aspects of cranial size.


Despite these differences, we obtain similar results to those of Manica et al. (2007), with up to 26% of global within-population craniometric variation being explained by geographic distance from sub-Saharan Africa. Comparative analyses using non-African origins do not yield significant results. The implications of these results are discussed in the light of the modern human origins debate.

--von Cramon-Taubadel N1, Lycett SJ.

Am J Phys Anthropol. 2008 May;136(1):108-13.

Brief communication: human cranial variation fits iterative founder effect model with African origin.