Intra African Genome-Wide Analysis, V2

See Also : Intra African Genome-Wide Analysis, V1


Population References and First Pass K10 Analysis

Finally got some more badly needed genome-wide data from East Africa. 12 sets of populations were added, 9 Afroasiatic (3 Omotic, 4 Cushitc, 2 Semitic) and 3 Nilo Saharan.

I updated my Africa reference map and table below where the newer populations are to be found indexed from 46-57,

 

In addition the data was merged with the older dataset, the bad news is that the genotyping rate for all the 26,129 SNPs dropped by about 7% to 92.4%, the good news off-course is that the data I was eagerly anticipating, especially Nilotic from South Sudan and Omotics from Ethiopia are now available.

When I re-run the model-based analysis with the same settings, i.e ADMIXTURE K10, the major shifts in the cluster allocations were that the Mbuti and Biaka Pygmy clusters combined and formed one Pygmy cluster, the West-Central African cluster disappeared, and in their place a Nilotic and an Omotic cluster were formed. There were quite major shifts in the ADMIXTURE proportions for all the populations except South AFRICA, including the FST distances where the previous major East African cluster (East Africa 2) is shifted much closer to the North African cluster:

 

This is also seen in the ADMIXTURE proportions where the East African proportion in North Africans is sgnificantly higher. I will look to update this post with more analysis but for now:

K2 - K10 Analysis

UPDATE:

Had a chance to rerun the exact same intra-African dataset as above, but this time for K=2-10, while at the same time checking for the Cross Validation Error values:

K, CV Error

1 0.58753

2 0.56519

3 0.55874

4 0.55554

5 0.55379

6 0.55315

7 0.55269

8 0.55239

9 0.55215

10 0.55201

As can be seen, the CV Error is still decreasing, meaning I still have some room to go in my K selection beyond K=10 for this Dataset.

I have uploaded the full set of results and processed output (mean, median, standard deviation) for anybody that may be interested here, but since I do not have time to plot out each K's results like I did for K10 earlier, I will post the peaking population breakdowns for each K run as my program tells me, as well as the Median Values for 3 selected populations: EtA-P (26), ARI-B (17) and South-Sudan (24):

A Supervised Global ADMIXTURE Run

A supervised ADMIXTURE run, assumes that certain populations within a given dataset are 100% of a certain ancestry, so for instance, given one wants to run ADMIXTURE at K=10 in supervised mode, then 10 different populations that are assumed to come from the 10 putative ancestral clusters that the software will infer, or rather will be forced to infer, must be manually selected.

I wanted to explore this type of a run on a global basis and purposefully select populations that not only may form their own clusters in an unsupervised run, but are also thought to be within the 'trunk', bifurcation 'nodes' and end 'branches' of the ancestral 'tree' of all people.

  

The basis of this run is the global dataset than can be downloaded in PLINK format from here. The dataset, a superset of the African dataset that I have been thus far utilizing, contains 3,970 individuals from around the world typed at 27,022 genome-wide SNPs.

A 3 dimensional, as well as a dim1 vs dim2, MDS plot labelled according to the median coordinates of the population groups for this dataset can be seen below:

The general structure of a globally spread PCA/MDS plot is well known and understood, the first principal component, describing the highest variation of all the components, separates Africans from non-Africans, while the second principal component separates West Asians/Europeans from East Asians, Oceanians and Native Americans. The 3^rd principal component can be however shaky, in the plot above it separates Native Americans from the rest, however other sources have shown that the 3^rd principal component in a global PCA separates divergent hunter gatherers (like the Hadza, Sandawe, San and Pygmies) from every body else, perhaps a 3-D PCA generated from full genome scans will put this to rest once and for all.

Analyzing the North African cluster

Continuing with  the Intra-African genome-wide analysis, I wanted to further explore the 'North African' Cluster that appeared to be wide spread from East to North and West Africa, 408 individuals out of the 1065 total samples carried the North African cluster at a frequency greater than 5%. With some of these populations showing a relatively high Standard deviation (Normalized with N-1) for that particular cluster. 

The table below shows the Standard Deviation for each of the 10 clusters found in the Intra-African Genome-Wide Analysis.

Yellow; Moderate Standard Deviation, 5-10%

Green; High Standard Deviation, 10-20%

Red; Very High Standard Deviation, >20%

 

The North African cluster had a high standard deviation in the Sahara-OCC, Morrocans, SAN, Mozabite and Morroco-S populations. All of these populations however, excluding the SAN, carried the North African cluster, on Median, in very high proportions (> 69%), while the SAN had it on Median only at ~4%. 18 out of the 36 SAN samples did however carry the North African cluster anywhere between 5-56%. Therefore, I excluded these 18 samples from the 408 individuals who carried the North African cluster at greater than 5% and proceeded to create a Dataset with PLINK.

The North African Cluster Dataset thus included 390 individuals (plus a few private samples) typed at 26,129 SNPs (all other specifications held constant with the previous Dataset).

  

MDS Analysis

Here below are the MDS plots for the Dataset, the plots include a 3 Dimensional plot, C1 Vs. C2 plot and C1 vs. C3 Plot respectively.

 

The 1^St component separates North Africans from the rest, with Ethiopians and Fulanis located at an intermediate position in this separation. The  2^nd component separates West Africans from the rest, with Bantus (Kenya and South Africa) located at an intermediate position in this separation. The Last and 3^rd component separates the Sandawe from everybody else.

Model Based Analysis.

5 clusters were generated from this dataset using ADMIXTURE, K=5, Unsupervised. A cluster that peaked in the Fulani, one cluster that peaked in the Mozabites, another cluster that peaked in the Sandawe, a fourth cluster that peaked in the Maasai, which I named East African, and a Last cluster that peaked in the Egyptians, which I named North East African, were observed. A PCA for the Fst distances that were generated by ADMIXTURE for these clusters can be seen below.

  

The largest vectorized Fst distance is seen for the Fulani, both for components 1&2, while the East African and Sandawe clusters appear to be close, similar to how the Mozabite and North East African clusters are close.

A standard deviation table (Normalized with N-1) for the 5 clusters generated can be seen below.

The Highest Average Standard Deviation across populations for the five clusters was among the Southern Morrocans and Mozabites (10.61 and 11.7% respectively).

Above are the Median proportions for all five clusters in the dataset.

The Mozabite cluster tapers off in a direction going east from the Northwest of Africa, where it is found at moderate frequencies in Egypt (~10%), the same can be said of the Fulani cluster, i.e tapering off in an eastward direction from Western Africa and found at a moderate (~6%) frequency in the Sandawe. The Sandawe cluster seems to be restricted to East Africa, although relatively high frequencies of it can also be seen in Southern Africa. The East African cluster, which peaks in the Maasai, is observed throughout East, West and Southern Africa. Finally, the North East African cluster merges North Africa with East Africa, for which a major portion can be accounted for with bi-directional Nile Corridor migrations, in addition to populations that used to live in the Sahara at a time when the desert was habitable. Minor, but gradiently significant Extra African input in the formation of the Mozabite and North East African clusters can also not be ruled out.

Updates on the Human Journey Project: Spencer Wells

Notes:

• Estimates YDNA TMRCA to 60 KYA, this is in conflict with Cruciani et. al (2011) :"A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa", where the root of the MSY was estimated to 142 KYA, although Dr. Wells may be talking about CT-M168, it is not clear enough from the video.
• So far the project has sampled over 1000 different populations around the world, with about 75,000 samples collected from 'indigenous' people, and an additional 415,000 samples from the public who purchased kits.
• Climate appearing to be a 'key motivator' of migrations.
• Europe colonized from the south at the end of the ice age from two different directions/sources that acted as a 'Refugium' during the ice age, a Franco-Cantabrian refugium in the southwest of Europe and another refugium in the Southeast (around the Balkans).
• 'Middle Easterners' from the 'northern area of the Fertile crescent' literally replaced Mesolithic Europeans during the Neolithic revolution, he points to ancient DNA evidence for this.

The Mother of Mothers !

It has been well known for about 20 years now that the mother of all Non-Africans, and indeed a lot of Africans, was an East African woman, in more recent nomenclature this woman has been called L3, so what do geneticists recently say about this woman, mother to greater than six and a half billion people on Earth, including many who still inhabit her original homeland?

The most recent study conducted to uncover the story behind L3 and her compatriots was one from the end of last year entitled “The Expansion of mtDNA Haplogroup L3 within and out of Africa”. 

This important study capped the timing of the out of Africa migrations, which all contemporary men and women outside of Africa are descended from, to no earlier than Seventy Thousand Years Ago.

The basis for this reasoning can be found in this paragraph from the text:

“The time window for the out-of-Africa migration on the basis of mtDNA lies between the emergence of haplogroup L3 in Eastern Africa and its derivative non-African haplogroups M and N, which most likely arose during the departure or outside Africa (Richards et al. 2006).”

Meaning, since all Non-Africans are descended from this woman, the timing of the out of Africa migration can not be any older than when she lived and can not be any younger than when here descendant daughters M and N lived, although there still remains a possibility that M and N emerged in Africa, albeit increasingly unlikely.

The expansion of L3 however has been linked in the past to not only the Out of Africa expansion but also Expansions within Africa, generally in association with two different episodes:

1. With the spread of Pastoralism in the Sahara of the early Holocene
2.  With the Bantu Expansion/s

To this end, the samples for this study were said to come from:

“We collected a total of 102 Sudanese, 77 Ethiopian (both emigrants in Dubai), and 148 Somali (refugees in Yemen) samples, belonging to unrelated individuals, who gave appropriate informed consent for their biological samples to be used for mtDNA characterization.”

Where a set of identified L3 lineages from above (plus other previous papers) were then selected for complete mtDNA sequencing:

“We selected for complete mtDNA sequencing a total of 21 Sudanese, 16 Ethiopian, and 20 Somali samples chosen from the sequences characterized in this work, and 11 from Chad and 2 from Soqotra belonging to haplogroup L3 from data sets published previously (Cerny´ et al. 2007; Cerny´, Pereira, et al. 2009).”

So what were the main results of the extensive statistical analysis done on this lineage?

A) Complete mtDNA phylogeny for Haplogroup L3:

 

Schematic tree of haplogroup L3. Age estimates are respectively rho estimates from the complete mtDNA genome (black font), rho estimates using the synonymous clock (gray font), and ML estimates using the complete mtDNA genome (black font underlined). Color scheme for each clade indicates the probable geographic origin. Haplogroups M and N are indicated and age estimates are according to Soares et al. (2009). MSA refers to Middle Stone Age and LSA to Late Stone Age.

B) Reaffirmation of what was known in the past with respect to the origins of L3:

“L3 most likely had an origin in Eastern Africa (Torroni et al. 2006). This is supported by the presence of all major branches, with L3a and L3h virtually specific to the region and L3eikx and the L3f haplogroups having a probable origin there as well, whereas for L3bcd, the region of origin is less clear and will be discussed in more detail below. The other two main branches of L3, M and N, exist only outside Africa, except for some back-migrations into Africa around 50–30 ka in the form of haplogroups U6 and M1 (Olivieri et al. 2006; Pereira et al. 2010) and some more recent intrusions (Cherni et al. 2009; Ottoni et al. 2010). Since there is strong evidence that the dispersal out of Africa was via the Horn, soon after L3 arose (Macaulay et al. 2005), the distribution of M and N also points to Eastern Africa as the center of gravity for L3.”

C) Temporal analysis of the sampled L3 lineages with origins bracketed within 60 – 70 thousand years ago:

 

"It seems likely that L3 dates somewhere between 60 and 70 ka, as the TMRCA estimates vary between 58.9 ka (using rho and the complete genome) and 70.2 (using ML), with the synonymous clock providing a value between the two (63.1 ka). We checked if the L3 tree rejected a strict molecular clock by running the ML analysis without stipulating a molecular clock and performing a likelihood ratio test that clearly did not reject the clock hypothesis (P 5 0.9899). These results led us to consider an age of 65 ka (varying between 60 and 70 ka in the 95% percentile) in the internal calibration of BEAST, as there was no other reliable calibration point we could use. The ages using the complete genome and the synonymous clock were 1.04 and 0.97 times the BEAST estimates, respectively, indicating that the BSPs were calculated using a similar rate to the other analyses, as we intended.”

D) Identification of 3 main episodes of population growth/expansion within Africa:

i) Approximately 40 thousand years ago corresponding with the emergence of the various intra-African subclades of L3.

ii) Around the Holocene, associated mainly with L3bd and L3e (Central Africa)

iii) The largest increase of the expansions detected around four thousand years ago and most pronounced in the Central African Bayesian Skyline Plots.

E) L3f and L3eikx both implied to have an origin in Eastern Africa. Where L3f was carried into the Sahel and Central Africa, with L3f3 specifically expanding into the Sahel 8 to 9 thousand years ago.

F) The most frequent clade of L3, i.e. L3e implied to have an origin in Central/Western Africa. With Eastern African L3e discounted as more recent introgression from there.

 

G) An ambiguous interpretation for the origin of L3bcd, a tentative east African origin is however suggested:

“L3bcd has three main subclades, with L3b and L3d tentatively united by a transition at control region position 16124 to form the putative subclade L3bd. The great age of L3bcd and its wide distribution across Africa makes phylogeographic inferences difficult. Furthermore, L3c is extremely rare: Only two samples have been detected so far, one in Eastern Africa and the other in the Near East. This might echo an early origin of L3bcd in Eastern Africa, before moving west, but its rarity makes this conclusion extremely tentative. In a scenario of an early origin of L3bcd in Eastern Africa, M and N would be the only subclades of L3 to have most likely originated outside of Eastern Africa (although an origin in Eastern Africa remains possible: Richards et al. 2006).

H) A virtual exclusion of a scenario in which the ancestors of contemporary people outside of Africa migrated out of Africa before the eruption of Toba.

I) And finally the most interesting part of this paper's conclusion, a unified demographic process that led to both the out-of-Africa and within Africa primary expansion of L3:

“Furthermore, since the age of the M and N Eurasian founders of ;50 to 65 ka (Soares et al. 2009) is close to the age of their ancestral L3 clade in Africa, the out of-Africa dispersal may have been of a piece with the initial diversification and expansion of L3, so that the L3 expansions in Eastern Africa and the exit of modern humans from Africa;60 ka were all part of a single demographic process.

It seems likely that the moister climate after;70 ka in Eastern Africa allowed dramatic human population growth (Scholz et al. 2007), perhaps associated with improved hunting, marine exploitation, exchange networks, and possibly even plant food management strategies as suggested by Mellars (2006). This generated the oldest major signal of expansion in the human mtDNA tree, the radiation of L3, leading rapidly to the spread of H. sapiens toward the rest of the world. It is worth stressing that this signal is not reflected in other mtDNA lineages at this time (Behar et al. 2008). Within Africa, the Pleistocene migrations detected in the L3 pool were responsible for the introduction of L3bd and L3e into Central Africa in the period between 60 and 35 ka (fig. 5A), but none reached Southern Africa at that time.”

Interestingly, the previous explanations that the Out of Africa expansion of modern humans being linked with behavioral modern thinking is largely dismissed by these authors for the sole explanation of Environmental factors, their main reasoning being that there is evidence for behavioral modernity of humans in Africa (Both in South and North Africa) long before their proposed timing of the OOA migrations.

“Thus, as suggested by Basell (2008), the demographic expansions that led to the first successful dispersal out of Africa seem better explained by the play of palaeoenvironmental forces than by recourse to the advantages of ‘‘modernity." 

More interesting figures from the paper:

“Frequency maps based on HVS-I data for haplogroups L3a, L3i, L3h, and L3x combined (A), L3f (B), L3e (C), L3b (D), and L3d (E).”

“Outline of the main dispersals detected in this work during the Pleistocene (A) and the Holocene (B).”

 ** Sketches on top of page depicting contemporary women that still live in the putative land of  L3's origin. Credit goes to Ethiopian Artist Adis Gebru and taken from this blog.