quote:

---

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals’ genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.

---

Haven't read it yet, but sounds like they've incorporated the Taforalt data. Hopefully the genomes have been released too.
 

---

Posted by the lioness, (Member # 17353) on :
 

 

---

Posted by Elmaestro (Member # 22566) on :
 
...So IAM are essentially show continuity from the Taforalt?

IDeK what I'm looking at anymore



KEB is Identical to IAM, IAM is just slightly less west african than taf???
EDIT: The chart is apparently shifted downwards... KEB actually lacks Hadza component, has a reduced Red-SSA component and increased anatolian.

quote:

---

West Eurasian populations can be modeled as the admixture
of four different ancestral components (2): Eastern and Western
European hunter-gatherer and Iranian and Levantine Neolithic.
We explored the placement of Moroccan and Southern Iberian
Neolithic samples in this context and compared their genetic
affinities to ancient and present-day West Eurasian and Levant
populations in the Human Origins panel, as well as to other
available aDNA population data. Interestingly, PCA revealed
that IAM individuals are similar to North African Later Stone
Age samples from the Taforalt site in Morocco, dated ∼15,000 y
ago (Fig. 2 and SI Appendix, Supplementary Note 6). When projected,
IAM samples are halfway between Taforalt and modern
North Africans, in the Levantine corner of the PCA space (Fig. 2).
Southern Iberian Neolithic individuals from TOR cluster with
Sardinians and with other Anatolian and European Neolithic
samples. Moreover, KEB samples are placed halfway between the
IAM and Anatolian/European farmer clusters, in close proximity
to Levant aDNA samples and also to Guanche samples (16) (from
the indigenous population of the Canary Islands known to have a
Berber origin; ref. 23). When compared using ADMIXTURE (SI
Appendix, Supplementary Note 7), IAM samples possess ∼100% of
a component partially shared by aDNA samples from the Levant
(Fig. 2). This IAM-like component is observed mainly in modern
North African individuals, following a west-to-east cline, and in
the Guanches. Interestingly, the Early Neolithic individuals from
Iberia form a different cluster from the Anatolian, Aegean, and
European Early Neolithic samples, sharing their main component
with Middle Neolithic/Chalcolithic samples. Lastly, KEB can be
explained as having both IAM-like and Iberian Early Neolithic
components (Fig. 2). The same admixture profile is observed in
the Guanche samples, but the amount of IAM ancestry is consistently
higher in all of the samples. Given that the Guanches
could have originated in a different area of the Maghreb, this
result might suggest that the European Neolithic impact in North
Africa was heterogeneous.

---

quote:

---

Interestingly, PCA reveals that IAM individuals are different from any aDNA sample studied to date (Figure 2; Supplementary Note 6). When projected, IAM samples are close to modern North Africans, in the Levantine corner of the PCA space (Figure 2). Southern Iberian Neolithic individuals from TOR cluster with Sardinians and with other Anatolian and European Neolithic samples. Moreover, KEB samples are placed halfway between the IAM and Anatolian/European farmer clusters, in close proximity to Levant aDNA samples and also to Guanche samples16, the indigenous population of the Canary Islands known to have a Berber origin

---

quote:

---

Originally posted by Elmaestro:

Interestingly, PCA revealed that IAM individuals are similar to North African Later Stone
Age samples from the Taforalt site in Morocco, dated ∼15,000 y
ago (Fig. 2 and SI Appendix, Supplementary Note 6). When projected,
IAM samples are halfway between Taforalt and modern
North Africans, in the Levantine corner of the PCA space (Fig. 2).
Southern Iberian Neolithic individuals from TOR cluster with
Sardinians and with other Anatolian and European Neolithic
samples. Moreover, KEB samples are placed halfway between the
IAM and Anatolian/European farmer clusters, in close proximity
to Levant aDNA samples and also to Guanche samples (16) (from
the indigenous population of the Canary Islands known to have a
Berber origin; ref. 23). When compared using ADMIXTURE (SI
Appendix, Supplementary Note 7), IAM samples possess ∼100% of
a component partially shared by aDNA samples from the Levant
(Fig. 2). This IAM-like component is observed mainly in modern
North African individuals, following a west-to-east cline, and in
the Guanches.

---

This seems to show a significant correction in a pre-print to published version, something to be aware of in this pre-print versions
 

---

Posted by Elmaestro (Member # 22566) on :
 


Anyone remember when that boy Polako(ithink thats how you spell it) Said the taf was replaced by the IAM who are incoming neolithic population from the Near east lmaooo..
 

---

Posted by the lioness, (Member # 17353) on :
 
People new to this forum are not going to be able to follow all these abbreviations that people constantly use "IAM" etc

aka "Early Neolithic Moroccans"

"IAM" is not a standard term like to an extent "EEF" has become.
It is an abbreviation of an particular arabic place name in Morocco, Ifri N'Ammar
 

---

Posted by Elmaestro (Member # 22566) on :
 
^Why don't you bring it all in with a comprehensive post.

I realized that there is a complete tonal shift in how the authors are describing the IAM. lol. No more of that "closest to the near east" bullshit.. They actually point out that Horners are the closest to the IAM. The Fst scores look like I expected them to, however I must admit I am surprised that he IAM are that close to Taforalt.

Still tryna find the link to the genomes

---

They added f4 problems to actually look for SSA correspondence this time around ..I wonder if someone got around to critiquing the preprint. Cuz now, wala, there's heavy west African signals all of a sudden.



Sidenote* Gambians seems to show the strongest signals... as opposed to YRI
 

---

Posted by the lioness, (Member # 17353) on :
 
topic artcile:
"When projected,
IAM samples are halfway between Taforalt and modern
North Africans,"


wikipedia:

Taforalt individuals belonged to mtDNA haplogroups U6a and M1b. Y-DNA analysis shows that the Taforalt males all belonged to Y-DNA haplogroup E1b1b1a1 (M78), which is closely related to the E1b1b1b (M123) subhaplogroup that has been observed in skeletal remains belonging to the Epipaleolithic Natufian and Pre-Pottery Neolithic cultures of the Levant.

______________________


E-M78 is widely distributed in North Africa, Horn of Africa, West Asia (stretching as far as Southern Asia), and Europe.[2][6]

The most basal and rare E-M78* paragroup has been found at its highest frequencies in Egyptians from the Gurna Oasis (5.88%), with lower frequencies also observed in Moroccan Arabs, Sardinians, the Balkans, and Andalusians from Huelva.[2][3][12]

The highest frequencies of all the defined E-M78 sub-clades is primarily found amongst Afroasiatic-speaking populations in the large area stretching from the haplogroup's putative place of origin in Upper Egypt to the Sudan and the Horn of Africa

________________________________________


Could the YDNA of the Taforalt originate in Egypt ????
 

---

Posted by Fourty2Tribes (Member # 21799) on :
 

quote:

---

Originally posted by Elmaestro:

I realized that there is a complete tonal shift in how the authors are describing the IAM. lol. No more of that "closest to the near east" bullshit.. They actually point out that Horners are the closest to the IAM. The Fst scores look like I expected them to, however I must admit I am surprised that he IAM are that close to Taforalt.

---

quote:

---

This suggests that most of IAM ancestry originates from an out-of-Africa source, as IAM
217 shares more alleles with Levantines than with any sub-Saharan Africans, including the
peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
bioRxiv preprint first posted online Sep. 21, 2017; doi: http://dx.doi.org/10.1101/191569. The copyright holder for this preprint (which was not
10
4,500-year-old genome from Ethiopia14

---

Serious logical fallacy to compare that many populations to MOTA.

Edit Nevamind I see it
 

---

Posted by Elmaestro (Member # 22566) on :
 
^there's one link in the op and I posted the supp above.
the study has been peer reviewed and published...
the preprint has become obsolete ..let it die.

Study OP
Supp
 

---

Posted by Fourty2Tribes (Member # 21799) on :
 

quote:

---

Originally posted by Elmaestro:
^there's one link in the op and I posted the supp above.
the study has been peer reviewed and published...
the preprint has become obsolete ..let it die.

Study OP
Supp

---

But Maestro its such a great model for ethnocentric bias.
 

---

Posted by Qward (Member # 8912) on :
 
Thanks for the links to the study.
Here's my attempt to make the first image Elmaestro posted clearer.


 

---

Posted by Clyde Winters (Member # 10129) on :
 

quote:

---

Originally posted by Fourty2Tribes:

quote:

---

Originally posted by Elmaestro:
^there's one link in the op and I posted the supp above.
the study has been peer reviewed and published...
the preprint has become obsolete ..let it die.

Study OP
Supp

---

But Maestro its such a great model for ethnocentric bias.

---

quote:

---

Originally posted by xyyman:

---

quote:

---

Originally posted by Qward:
Thanks for the links to the study.
Here's my attempt to make the first image Elmaestro posted clearer.

---

 

---

Posted by xyyman (Member # 13597) on :
 

 

---

Posted by the lioness, (Member # 17353) on :
 
^ priorites
 

---

Posted by xyyman (Member # 13597) on :
 

quote:

---

Originally posted by the lioness,:
^ priorites

---

https://s22.postimg.cc/9b9jxpzgx/U6_in_YAM-_African.jpg

IMG Resized //MOD

[ 13. June 2018, 01:53 PM: Message edited by: Elmaestro ]
 

---

Posted by xyyman (Member # 13597) on :
 
Quote from the study:
“Haplogroup T2
Samples KEB.7, TOR.6 and TOR.7 are classified as T2b3+151, with no private mutations (See Figure S4.1). T2b, dated ~10,000 years ago, is mainly distributed in Europe. T2b is considered to have dispersed within Europe in early Neolithic times53, a fact that has been confirmed by direct analysis of aDNA”

Quote from wiki…
“The basal haplogroup T* is found among Algerians in Oran (1.67%) and Reguibate Sahrawi (0.93%).[1] It is also distributed among the Soqotri (1.2%).[2]”
mtDNA T is found throughout the horn and further south in the Datoga people of Tanzania

Soqotri

 

---

Posted by Elmaestro (Member # 22566) on :
 
The genomes are being uploaded as we speak,

@Qward Thanks for the edit to the image.

@42tribes You're right, it definitely is... lol... It was super blatant... and almost disrespectful.
 

---

Posted by Swenet (Member # 17303) on :
 

quote:

---

Originally posted by the lioness,:
^ priorites

---

quote:

---

Originally posted by Swenet:

quote:

---

Originally posted by the lioness,:
^ priorites

---

Me or gramps? Don't know what you mean..

---

quote:

---

Originally posted by Elmaestro:
[Q] The genomes are being uploaded as we speak,

[/Q]

---

quote:

---

Originally posted by xyyman:
where? Link

quote:

---

Originally posted by Elmaestro:
The genomes are being uploaded as we speak,

---

---

quote:

---

Originally posted by Elmaestro:
Sidenote* Gambians seems to show the strongest signals... as opposed to YRI

---

Gambians (and to a lesser extent Mandenka) can be modelled with minor Iberomaurusian (or other North African) admixture in Global25. OTOH Skoglund et al modelled Gambians as 100% Mende with no PPNB (assuming they're the same samples), and in this study's ADMIXTURE they have almost no yellow component (Mandenka have more). Gambians have some E-M35 (including M78 and L19), plus their northern location, I'm guessing they have minor North African ancestry which Yoruba don't. The wild card is the Basal African/West African archaic thing.
 

---

Posted by xyyman (Member # 13597) on :
 
"The wild card is the Basal African/West African archaic thing."

Finally. Now you are catching on.....Took you some time but you got here. HE! HE! He!

But Skoglund had Mende as more ancient than YRI. Containing more archaic admixture.

It would be interesting to pull those archaic AIM from Mende and run it against WHG and ANE!
 

---

Posted by Tukuler (Member # 19944) on :
 
For a little African perspective on Taforalt.
Africa, south of a line from Guinea Bissau to
South Sudan to southern Kenya, was inhabitable
through time. Note yellow grasslands, purple
savanna w/trees, and various green scub and
forestry.

2600km/1600m of desert separated Taforalt from
the grasslands to its south for 10000 years. 'SSA'
'elements in Taforalt were there before the Ice Age
began. With the West African Monsoon in full retreat,
no oxen pack-asses transport beasts of burden nor
travel horses or camels, and no water storage,
crossing the vast desert = a 💀 death wish.
There were two other sites along Africa's
south Mediterranean coast though.

Below the desert line's another story. Virtually
a Grasslands Paradise throughout the Ice Ages.
Blombos and Panga ya Saidi are asterisked.
Malawi's Hora Woman lived after the mapped
Maurusian timeframe. Her 6-way African
substructure ancestry could go back to
the West African Monsoon Optimum.



 

---

Posted by Elmaestro (Member # 22566) on :
 

quote:

---

Originally posted by capra:

quote:

---

Originally posted by Elmaestro:
Sidenote* Gambians seems to show the strongest signals... as opposed to YRI

---

Gambians (and to a lesser extent Mandenka) can be modelled with minor Iberomaurusian (or other North African) admixture in Global25. OTOH Skoglund et al modelled Gambians as 100% Mende with no PPNB (assuming they're the same samples), and in this study's ADMIXTURE they have almost no yellow component (Mandenka have more). Gambians have some E-M35 (including M78 and L19), plus their northern location, I'm guessing they have minor North African ancestry which Yoruba don't. The wild card is the Basal African/West African archaic thing.

---

code:

---

                Source1;Source2                 amp (Z)                                 time in Generations (z)  
RESULT_1	Mota;Tanzania_Pemba_700BP	0.000154805 +/- 4.81939e-05 (Z=3.21213)	234.581 +/- 45.6366 (Z=5.14019)
RESULT_1	WHG;Tanzania_Pemba_700BP	0.000162835 +/- 5.16218e-05 (Z=3.15438)	234.581 +/- 45.6366 (Z=5.14019)

---

code:

---

*** Computing 2-ref weighted LD with weights WHG Tanzania_Pemba_700BP ***

analyzing chrom 1 3 2 4 8 7 6 5 12 11 10 9 16 15 20 13 14 19 17 18 21 22

==> Time to run alder: 0.406488

+6.0e-05
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|       x x                                              x                     
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|          x                 x  x      x  xxx                                  
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|                   x     xx          x x      x      x       x               x
+---------+---x---x-+---------+---------+-----x---+-----x---+---------+--------
|         1         2         3     x   4         5         6         7      cM
|              x x                                                      x      
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|            x     x    xx    x  x   x                               x      x  
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****Successful 

*** Computing 2-ref weighted LD with weights Taforalt Tanzania_Pemba_700BP ***

analyzing chrom 1 3 4 2 8 7 6 5 12 11 9 10 16 20 13 15 14 17 19 18 21 22

==> Time to run alder: 0.244233

+9.0e-05
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|                    x   x   x             x x                  x      x       
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|                         x x                            x                   x 
+---------+---------+---------+------x--+---------+----x----+------x--+--------
|         1        x2         3         4x        5         6  x      7  x xxcM
|                       x                      x                     x         
|                             x                      x                         
|             xxx                x            x     x                 x        
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|            x      x             x   x     x               x             x    
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******Failed

---

quote:

---

To follow up on my last post, some d-stats...

Mbuti/South_Africa_2000BP/Chimp Yoruba Mota Bichon
- hhuuuugelly postitive
Mbuti/South_Africa_2000BP/Chimp Mota Yoruba Bichon
- again hugely positive

These two stats suggest either Mota or Yoruba is a mix of two streams of ancestry, a basal one and one closer to the OOA node.

---

quote:

---

If A is Modern Africans B is Mena (Modern) and C is every other Modern Eurasian, can we still consider AB Eurasian??
we know B and C will undoubtedly be closer today.

Black lines are drift, red lines are admixture and X represents a single or multiple EARLY population offshoots.....

---

quote:

---

Originally posted by Elite Diasporan:
@Elmaestro

I like this graph from that anthrogenica link.
https://anthrogenica.com/attachment.php?attachmentid=24022&d=1529080224

I see you guys moved to Anthrogenica and bushed FBD.

---

It's basically a less nuanced version of what I've been trying to propose for months...if not years elsewhere.

FBD is a dubb... I'm only passing through Anthrogenica tbh. Compare results w/ other people running stats.

I'm discovering a lot of wild shit on my own.
 

---

Posted by Elmaestro (Member # 22566) on :
 
Xyyman, If you've figured out a way to genotype STR Go ahead and do IAM_5... that sample has a handful of reads viable for CODIS.
 

---

Posted by Tukuler (Member # 19944) on :
 
Please list the AmpFLSTR values.

Fregel's 18 Inner Africans with significant yellow (≥3%).


Not shown:
2 have no yellow, Biaka and Botswana Bantu Kgalagadi speakers.
All her remaining 17 Inner Africans have it, no matter how little.
 

---

Posted by Tyrannohotep (Member # 3735) on :
 
Sorry for being late to the party. I haven't been able to access the full text of the paper, so I'm thankful to everyone who has posted quotes and images in this thread.

quote:

---

Originally posted by Elmaestro:


Anyone remember when that boy Polako(ithink thats how you spell it) Said the taf was replaced by the IAM who are incoming neolithic population from the Near east lmaooo..

---

The finding that early Neolithic Moroccans (as represented by IAM) show mostly continuity with Taforalt (including the sizable SSA component) does put a damper on the Eurocentric scenario that Neolithic North Africans were primarily descended from a wave of Near Eastern back-migrants, doesn't it?

That said, I personally think it's a shame that the recent aDNA from Abusir el-Meleq hasn't been incorporated into a study like this. It would be nice to compare those samples with IAM and Taforalt, especially since the latter two seem to be the best proxies we have for ancient North African ancestry.
 

---

Posted by Elmaestro (Member # 22566) on :
 
I posted DL links for the study above, if you still need access.

Now I don’t know what this means yet but Abusir mummies Structurally looks Identical to Levant_BA samples w/ Taforalt involved... infact they’re almost indistinguishable via fst as well (Value of 0). So if you want to know how they look ahead of time just look at levant_BA w/ very slightly less green and more yellow.

Not to get too deep w/ Abusir mummies but though they appear close to levant_BA they might have different population histories... Dstats tends to favor a model where they have ancestry from Minoan Odigitria.. not to mention their anomalous SSA affinity, which makes them appear closer to EEF(especially the Aegean pops) and Levant_N when using an african(ex: mbuti) as an outgtoup.

But as far as ADMIXTURE goes they’ll probably still resemble Levant_BA with IAM involved.
 

---

Posted by Tukuler (Member # 19944) on :
 
Compare Loosdrecht's PCA, with PC1 flipped, to Fregel.

Radar ID

quote:

---

Fregel's HOD PCA S6.3 plots
• Taforalt closer to SSA than to Natufian
• Natufian overlaying Neolithic Iran
• Neolithic Iran overlayed by KEB
• Taforalt closer to Luxmanda than to Natufian
• Pemba 3X farther from Taforalt than Luxmanda is.

Consider the relative worth of PCA vs other analytic tools.

---

.

HELP, is South_Africa_12000BP a misprint?
 

---

Posted by Elmaestro (Member # 22566) on :
 
^@Tukuler yeah it is, remove one 0 the south African is only ~3,200 years old.
Also, I just realized your response to the genetic distance thing.
I want you to know that my initial concern was that YRI are closer to Natufians than they are Taforalt.
Taforalt actually are almost equidistant to YRI and Natufians (more close to YRI). just a FYI


A quick update... cuz I have no life right now.

Above I expressed how Taforalt made good curves as an ancestor to Yorubans.... To anyone who cares, Guess what?

...IAM succeeds and actually produces the best result as an ancestor to YRI against the Bantu-like Pemba individual.

RESULTS

^What's also interesting is the second admixture event (blue highlight) dated around 900ya, I couldn't confidently say how this event makes sense.

right now my best guess that some of the Yoruba have ancestry from a Nomadic Africans and Iberians have respectable YRI-like(with RHG) admixture.

aDNA from Africa is game changing.... The Fst scores from fregel et al actually makes sense.

-- -- -- --

EDIT: Iberia_EN has multiple waves of African Admixture including Mbuti/RHG and YRI seems to have an unspecified Affinity to KEB. Sadly being that these Iberians are ancient the dates for admixture aren't reliably significant... but the generations are to be calculated in respects to the age of the tested populations, the ancient Iberians are like ~7,000ya so the mean date for the earliest Admixture date is ~8380ya.

See Results here
 

---

Posted by xyyman (Member # 13597) on :
 
Come on man!!! Don’t keep us in suspense. If you have the reads..post it or send/PM me.

So you pulled STR from the BAM files of IAM_5?! NIIIICEEEE!!!!


EDIT: Props to Elmaestro!!! Excellent work! Just following up on this thread. Again. Thanks your girlfriend for giving you the time. ("you don't have a life")

quote:

---

Originally posted by Elmaestro:
Xyyman, If you've figured out a way to genotype STR Go ahead and do IAM_5... that sample has a handful of reads viable for CODIS.

---

quote:

---

Originally posted by Tukuler:
Please list the AmpFLSTR values.

---

quote:

---

Originally posted by Tukuler:
Fregel's HOD PCA S6.3 plots
• Taforalt closer to SSA than to Natufian
• Natufian overlaying Neolithic Iran
• Neolithic Iran overlayed by KEB
• Taforalt closer to Luxmanda than to Natufian
• Pemba 3X farther from Taforalt than Luxmanda is.

Consider the relative worth of PCA vs other analytic tools.

---

Thanks for drawing my attention to that.
 

---

Posted by Tukuler (Member # 19944) on :
 
Why STRS? Because they're powerful and what they
indicate is used everyday in courts everywhere.
No fancy higher math or special programs needed.

What 8 STRs can do


View image and write up @
http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=009335;p=21#001004
 

---

Posted by Tukuler (Member # 19944) on :
 

quote:

---

Originally posted by Swenet:

quote:

---

Originally posted by Tukuler:
Fregel's HOD PCA S6.3 plots
• Taforalt closer to SSA than to Natufian
• Natufian overlaying Neolithic Iran
• Neolithic Iran overlayed by KEB
• Taforalt closer to Luxmanda than to Natufian
• Pemba 3X farther from Taforalt than Luxmanda is.

Consider the relative worth of PCA vs other analytic tools.

---

Thanks for drawing my attention to that.

---

quote:

---

Originally posted by Tukuler:
Compare Loosdrecht's PCA, with PC1 flipped, to Fregel.

Radar ID

---

quote:

---

Originally posted by Tukuler:
Why STRS? Because they're powerful and what they
indicate is used everyday in courts everywhere.
No fancy higher math or special programs needed.

What 8 STRs can do
http://i66.tinypic.com/344s3l5.jpg
Write up @
http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=009335;p=21#001004

---

quote:

---

Originally posted by Swenet:
Also see the preprint supps for the missing PC3 and PC4. The latter two PCs seem to have been deleted from the paper. They show modern SSA groups as intermediate between WHG and EHG on the one hand and IAM on the other hand. As gramps likes to say.. tic toc. lol.

---

 

---

Posted by Swenet (Member # 17303) on :
 
Here is my take on PC3 and PC4.



The lower left corner is largely, or entirely correlated with African ancestry. As you can see, no Mesolithic Eurasian clusters there. Only after the Mesolithic (e.g. Neolithic, Bronze Age), West Eurasian samples start appearing in the center and in the lower left corner, where Africans are (see the transparent burgundy/bordeaux circles, the black circles and the grey circles). What this means is that some type of ancestry that wasn't common in West Europe before the Holocene, is driving these samples away from their own Mesolithic ancestors. Since Africans dominate the lower left corner, and since this corner is opposite of the relatively 'pure' Eurasians in the righthand corners, the most likely explanation is that the former corresponds to African ancestry. If you look closely, you can see that WHG, SHG and EHG themselves vary in the degree that they go in the direction of Africans. This is not expected in a single OOA scenario, with no further African input until the holocene. So some of the type(s) of African ancestry that became more common in West Eurasia after the Mesolithic, were already present during the Mesolithic, but as a relatively small component. This is where the whole conversation about WHG/Cheddar Man etc. having African ancestry comes into the picture.

What piques my interest is that SSA samples are in the center, along with modern West Eurasians (not in the lower left corner, with IAM). See the tight cluster of transparent burgundy/bordeaux circles. This could mean that SSA populations could have brought Eurasians to the center, that North African samples brought Eurasians to the center, or both (in various OOA migrations). Tic, toc, tic, toc.

Now ask yourself why PC3 and PC4 with SSA samples are rarely included in aDNA papers. Even in this paper (Fregel et al), PC3 and PC4 only seem to appear in the preprint, but not in the final paper.
 

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Posted by Tukuler (Member # 19944) on :
 
Big bite to chew. Hope I got the gist of it. (below)
Africans rarely show in Euro freq representations.
We know they have to be there. Overlooked tools
like PCA's 3'4 sets can uncover 'back-burnered'/
'hidden' African affinity.

Oh, what's your axis coordinate(s)? 0.035?
Solid math quads or looser overlapping 'ethnic' sectors.
A bit of both and knowing when to apply which.


Ah, PCA - no tool like an old tool.
Newer tool f4 comin atchas.

quote:

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Redux of post by Swenet:
Here is my take on PC3 and PC4.



The lower left corner is correlated with African ancestry.
no Mesolithic Eurasian clusters there.
after the Mesolithic W Euras appear in the center and lower left corner,
where Africans are
(the transparent burgundy/bordeaux circles, the black circles and the grey circles).

some type of ancestry uncommon in preHolocene W Europe
drives these samples away from their own Mesolithic ancestors.
Since Africans dominate the lower left corner, and
since this corner is opposite of
the righthand relatively 'pure' Eurasians corners,
the former corresponds to African ancestry.

WHG, SHG and EHG vary in their degree toward Africans.
not expected in a single OOA scenario,

with no further African input until the holocene.

some more common postMesolithic type(s) of African ancestry in W Eura
were present during the Mesolithic, as a small component.

This is where the whole conversation about WHG/Cheddar Man etc. having African ancestry comes into the picture.

What piques my interest
SSAs are in the center, along with modern West Eurasians
(not in the lower left corner, with IAM).

could mean that
SSA populations brought Eurasians to the center,
N Afric samples brought Eurasians to the center, or both (in various OOA migrations).


Now ask yourself why PC3 and PC4 with SSA samples are rarely included in aDNA papers. Even in this paper (Fregel et al), PC3 and PC4 only seem to appear in the preprint, but not in the final paper.

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quote:

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quote:

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Originally posted by Tukuler:
Big bite to chew. Hope I got the gist of it. (below)
Africans rarely show in Euro freq representations.
We know they have to be there. Overlooked tools
like PCA's 3'4 sets can uncover 'back-burnered'/
'hidden' African affinity.

Oh, what's your axis coordinate(s)? 0.035?
Solid math quads or looser overlapping 'ethnic' sectors.
A bit of both and knowing when to apply which.


Ah, PCA - no tool like an old tool.
Newer tool f4 comin atchas.

quote:

---

Redux of post by Swenet:
Here is my take on PC3 and PC4.



The lower left corner is correlated with African ancestry.
no Mesolithic Eurasian clusters there.
after the Mesolithic W Euras appear in the center and lower left corner,
where Africans are
(the transparent burgundy/bordeaux circles, the black circles and the grey circles).

some type of ancestry uncommon in preHolocene W Europe
drives these samples away from their own Mesolithic ancestors.
Since Africans dominate the lower left corner, and
since this corner is opposite of
the righthand relatively 'pure' Eurasians corners,
the former corresponds to African ancestry.

WHG, SHG and EHG vary in their degree toward Africans.
not expected in a single OOA scenario,

with no further African input until the holocene.

some more common postMesolithic type(s) of African ancestry in W Eura
were present during the Mesolithic, as a small component.

This is where the whole conversation about WHG/Cheddar Man etc. having African ancestry comes into the picture.

What piques my interest
SSAs are in the center, along with modern West Eurasians
(not in the lower left corner, with IAM).

could mean that
SSA populations brought Eurasians to the center,
N Afric samples brought Eurasians to the center, or both (in various OOA migrations).


Now ask yourself why PC3 and PC4 with SSA samples are rarely included in aDNA papers. Even in this paper (Fregel et al), PC3 and PC4 only seem to appear in the preprint, but not in the final paper.

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Originally posted by xyyman:
Indicative of TWO OOA. Last being the early Neolithic/Holocene. That’s why modern SSA and West Eurasian cluster

WHG/SHG/EHG were part of ONE/First OOA taking different routes. With Africa being the central point of dispersion. In other words the migration path was not through the Levant or Horn for all. Eg WHG dispersed through either Canary Island/Gibraltar. Holocene Africans left may be about 20years later.

Quote:
“WHG, SHG and EHG vary in their degree toward Africans.
not expected in a single OOA scenario,

with no further African input until the Holocene. SSAs are in the center, along with modern West Eurasians”

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Just two? Remember that Fst data shows YRI distance to Eurasians keeps lowering over time. It never stabilizes, nor does it ever reverse in any era. The first West Eurasian OOA migrants tend to be most distant, while modern West Eurasians tend to be the closest to YRI. All aDNA is somewhere in between, with Bronze Age West Eurasians tending to be the next in line in terms of closeness to YRI in terms of Fst. This leads to interesting comparisons where Yamnaya might be closer to YRI than they are to some eastern Asians, Fst-wise. This is very hard to explain without continuous OOA migrations.


source
 

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Posted by xyyman (Member # 13597) on :
 
You may be right. McEvoy used microsatellite DNA(STRs/IBD) and came to that conclusion. But “I” speculate two because Archeological, Anthropological supported by OTHER genetic data shows a PAUSE OOA before the Neolithic (2nd wave).

Quote
“Just two? Remember that Fst data shows YRI distance to Eurasians keeps lowering over time. It never stabilizes, nor does it ever reverse in any era. The first West Eurasian OOA migrants tend to be most distant, while modern West Eurasians tend to be the closest to YRI. All aDNA is somewhere in between, with Bronze Age West Eurasians tending to be closest to YRI in terms of Fst. This leads to interesting comparisons where Yamnaya might be closer to YRI than they are to some eastern Asians, Fst-wise. This is very hard to explain without continuous OOA migrations.”



McEvoy et al Quote:
“Both TF and TLD, two T estimators calculated by different means from the same data, ***consistently*** demonstrate a significantly MORE
RECENT relationship between Europe and Africa than between East Asia and Africa. Using simulated populations, we show that under
the single-wave ‘‘Out of Africa’’ model,
While the exact bias is difficult to estimate (Sved et al. 2008), it appears that post-divergence migration rates from Africa
to Europe would need to be approximately CONSTANT because we observe consistent ratios of TF and TLD at different genetic distances.
Thus, the observations are suggestive that** GREATER MIGRATION **TO EUROPE** FROM **SUB-SAHARAN AFRICAN HAS BEEN A **LONG-TERM** PHENOMENON.”
Y-chromosome and mtDNA lineages are generally highly differentiated between continents, making them powerful genetic”

Read more: http://egyptsearchreloaded.proboards.com/thread/2537/mevoy-ancient-connection-africa-europe?page=1#ixzz5J9XcYsFU
 

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Posted by xyyman (Member # 13597) on :
 
McEvoy used the phrase “post divergence migration rate”. I believe he is confused with how many migration or he working from the point of view of “ONE” OOA to explain his data. Because essentially he is saying East Asians and Europeans diverged then additional/more Africans migrated INTO Europe…only. That explains the close genetic relationship between Europeans and SSAfricans and the distance of SSAfricans and East Asians. To me that sounds like TWO migrations. …major? Remember Sforza came to the same conclusion. I know many of you assume 2/3 Asian for Europeans but Sforza lecture notes posted by Ish- Gebor/TP clarified that it is the reverse…ie 2/3 African and 1/3 East Asian for Europeans. May be Ish can post it again. It is here some place.
 

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Posted by Swenet (Member # 17303) on :
 
I would have to read McEvoy et al again to see if he disagrees. But I remember them saying that southern Europeans are not the only ones that have closer affinities to Africans. They said because northern Europeans are also involved in this closeness to Africans, Neolithic migrations bringing Africa ancestry are not enough to explain their results. Or am I off? I'd have to read it again.
 

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Posted by Elite Diasporan (Member # 22000) on :
 
I'm not much surprised if Southern Europeans like Iberians or even those from those Mediterranean islands have a closenesa to Africans. But Northern Europeans? I would never expect that. Not to make any bold statements but it seems Xyyman was on the money when it comes to certain topics. Who knows?
 

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Posted by xyyman (Member # 13597) on :
 
The holistic Genetic data shows , yes, there is also a connection between Northern Europeans and SSA. But it is a different and more ancient connection ie NOT RECENT as with Southern Europeans. Saami, Berber and Fula connection via mtDNA U haplotypes – Pereira et al? Remember mtDNA is close to 35,000years old which pre-dominated European hunter gatherers. West Africans dogs are genetically ancestral to ancient Scandinavian dogs, some Scandinavians carry ancestral version of SLC45A2 like West Africans and Cheddar Man etc !!! At low frequency but higher than Southern neighbors . Proving the light skin came from the south and not the North.

I believe the connection has more to do with may be Iwo-Eleru(Stone Age) than modern West Africans(Neolithic).


I remember when I looked at the SLC45A2 profile of finnish people I was shocked to see they carry as much as 5% ancestral SLC45A2. I expected it to be Zero!!! They are one of the whitest people on the planet. Why would modern Fins carry ancestral African SLC45A2 genes? Then I remembered other papers that shows African genes in Scandinavia.......even their ancient dogs are essentially African derived ....don't believe me...look it up.
 

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Posted by xyyman (Member # 13597) on :
 
As more African aDNA is unearthed we will see an stone age connection between Ancient West Africans(stone age) and WHG/ANE. Southern Europeans are primarily Neolithic so they will align more with East Africans(where the Neolithic’s originated) and Maghrebians. Keep in mind West Africans contain more archaic Admixture than East Africans but West Africans do harbor Neolithic ancestry,. So essentially we are back to TWO phases OOA. Stone Age and Neolithic. I believe people of Cape Verde and these archipelagoes off Africa have many of the clues. Their phenotypic makeup cannot solely explained by admixture with modern Europeans….Shriver et al. Cape Verdeans are essentially Cheddar Man or LA Brana. Maybe someone can load the VCF or BAM files of Cape Verdeans. That data packet will be interesting.
 

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Posted by Tukuler (Member # 19944) on :
 
I don't know about migration, large numbers moving rapidly over much land in a small amount of time.
But wanderings of bands of people, not limited to set start and stop migrations but as moved by
whatever notion, happen all the time.

No limit to the number of times Africans crossed
Gibraltar Sardinia Crete Sinai Bab em Mandeb Indian Ocean

No set dates or events.

A seeping, an oozing, sometimes a minor flow.

There was no migration per se of Levantine
Asiatic Aamw into the Lower Nile Valley. It
was a slow and steady continuous trickle.
Look how 2000 years of that altered genes
and phenes.

There's a slow and steady continuous trickle
going on now to Europe and the USA in particular.
I wouldn't classify it as a migration.


Same type of thing through out all time.


Everywhere non-African specific uniparentals that
descend from an African haplogroup exist is proof
of an African 'migration'. And a very successful
one.
 

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Posted by xyyman (Member # 13597) on :
 
Agreed! Migration is probably the wrong word.....because it was not planned or intentionally. Wondering may also be inaccurate. The fact is they expanded out and entered new lands hunting and gathering food. Food and not necessarily "space' was the motivation to "expand?" out.

To me "wondering" is equivalent to "no purpose".
 

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Posted by Tukuler (Member # 19944) on :
 
@ Swenet

I cut the quantifiers out of the summary
because I don't find it necessary since
who talks in absolutes. There's no
absolute "all". An unmeasured subset is
assumed when talking about a people.

Nigerians are the most highly educated Brits.
It doesn't mean every Nigerian in GB has
more education than every native.


But what about the questions I had about
your comments and analysis of Fregel's
Afr aDNAless preprint PCA 3'4?
 

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Posted by Tukuler (Member # 19944) on :
 
Yep, that's exactly what I mean, no purpose.

Why is the few mile hop across the BAb
3000 years ago a migration?

Why isn't the vast expanse covered by Click
speakers from NE Afr to E then to SW Afr a
migration backmigration crossmigration?

Simon Says.
Migration
Natural catastrophe refugees
Conquering hordes
Intrepid farmers (not in search of farmland?)


I'm not gonna play Simon Says.
 

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Posted by Swenet (Member # 17303) on :
 

quote:

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Originally posted by Tukuler:
@ Swenet

I cut the quantifiers out of the summary
because I don't find it necessary since
who talks in absolutes. There's no
absolute "all". An unmeasured subset is
assumed when talking about a people.

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We might be miscommunicating. This is what I meant when I said researchers are often leaving out PCA information:



In this PCA the authors clearly convey how much of the data is interpreted by both PCs. I don't see a lot of this when I browse through aDNA papers. When I read online, I see a lot of people using selective PCA information as the be-all and end-all of genetics.

quote:

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But what about the questions I had about
your comments and analysis of Fregel's
Afr aDNAless preprint PCA 3'4?

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Y-chromosome and mtDNA lineages are generally highly differentiated between continents, making them powerful genetic markers of intercontinental migration. Most of the lineages that are characteristic of sub-Saharan Africa are absent in Europe (and vice versa) (Cavalli-Sforza and Feldman 2003; Underhill and Kivisild 2007). However, the coalescent time and geographic distribution of the Y-chromosome E3b (E-M215) haplogroup points to a late Pleistocene migration from Eastern Africa to Western Eurasia via the Nile Valley and Sinai Peninsula ∼20–25 KYA (Cruciani et al. 2004, 2007; Luis et al. 2004). However, these Y chromosomes are concentrated in southern Europe (Cruciani et al. 2004), whereas the smaller average divergence times between Europe and Africa relative to East Asia and Africa are still readily apparent across each individual northern European sample population (Supplemental Table 2). This suggests that the discrepancy has, at least partially, an even earlier and more pervasive origin, being established prior to the appearance, and consequent migration tagging ability, of the current range of mtDNA and Y-chromosome haplogroups.

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The key part:

"an even earlier and pervasive origin [than E-M35 arrivals in Europe]"
--McEvoy et al 2011

They are essentially saying that modern hgs are almost worthless when it comes to quantifying ancient African admixture in Europe, because evidence of ancient migration has been overwritten by more recent haplogroup arrivals and evolutionary processes. They say evidence for this is that northern Europeans are also admixed with African ancestry, not just southern Europeans who have the hg evidence to show for it.

@Elite Diasporan
Yes, gramps can be on point when he wants to. It's just that sometimes he gets carried away with the "Euros are subsets" talk.
 

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Posted by Tukuler (Member # 19944) on :
 
Miscommunication? Yikes! Hope not.

Just trying to be sure.
Didn't know if your
center and lower left corner
was the red or blue square?
Maybe neither? Also, I had to
zoom deep to tell SSA color
from Caucasus, legend in upper left.



The Afr brown is compact.
'Radar' won't work.
Had to catch it in the crosshairs.
African PC 3 the upright bar.
African PC 4 the broad beam.


The preprint PC1'2 w/o Afr aDNA
places all Inner Africans way off
on their own. But Afr PC2 'horizon'
reveals who shares those secondary
element set precise sub-components.



The added labels make ID immediate
instead of a 3-step dance. Down and
dirty listing of tested pops sharing
African alleles that may not be in the
authored text but there nonetheless as
you have in part proposed.


PC2:
• Afr
• Ifri n'Amr/Musa
• Mid East
• Neolithic Iran
• Late Neolithic Iran
• Caucasus Hunter Gatherer
• Steppe Early Mid Bronze Age - Mid Late Bronze Age
• Europe Late Neolthic & Bronze Age
• West European Hunter Gatherer
• Eastern Europe

PC3:
• Mid East
• Anatolia Chalcolithic
• Southern Europe
• Afr
• Caucasus
• Europe Late Neolithic & Bronze Age
• Eastern Europe
• Scandinavian Hunter Gatherers

PC4:
• European Mid Neolithic & Chalcolithic
• PUL (whatever that is)
• Toro cave Malaga Spain
• Sardinia
• European Late Neolithic & Bronze Age
• Western Europe
• Southern Europe
• Afr
• Caucasus
 

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Posted by Swenet (Member # 17303) on :
 

quote:

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Originally posted by Tukuler:
Just trying to be sure.
Didn't know if your 
center and lower left corner 
was the red or blue square? 
Maybe neither? Also, I had to
zoom deep to tell SSA color 
from Caucasus, legend in upper left.

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quote:

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Originally posted by Tukuler:
The preprint PC1'2 w/o Afr aDNA
places all Inner Africans way off
on their own. But Afr PC2 'horizon'
reveals who shares those secondary
element set precise sub-components.

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“The site has been directly dated to 9650)9950 calBP (11), showing intense occupation over two to three centuries. The economy of the population has been shown to be that of pastoralists, focusing on goats (11). Archaeobotanical evidence is limited (16) but the evidence present is for two)row barley, probably wild, and no evidence for wheat, rye or other domesticates. In other words the overall economy is divergent from the classic agricultural mode of cereal agriculture found in the Levant, Anatolia and Northern Mesopotamian basin.
[...]
We compared GD13a with a number of other ancient genomes and modern populations (6, 17–29), using principal component analysis (PCA) (30), ADMIXTURE (31) and outgroup f3 statistics (32) (Fig. 1). GD13a did not cluster with any other early Neolithic individual from Eurasia in any of the analyses. ADMIXTURE and outgroup f3 identified Caucasus Hunter)Gatherers of Western Georgia, just north of the Zagros mountains, as the group genetically most similar to GD13a (Fig. 1B&C), whilst PCA also revealed some affinity with modern Central South Asian populations such as Balochi, Makrani and Brahui (Fig. 1A and Fig. S4). Also genetically close to GD13a were ancient samples from Steppe populations (Yamanya & Afanasievo) that were part of one or more Bronze age migrations into Europe, as well as early Bronze age cultures in that continent (Corded Ware) (17, 23), in line with previous relationships observed for the Caucasus Hunter)Gatherers (26).
[...]
Figure Legends:
Fig. 1. GD13a appears to be related to Caucasus Hunter Gatherers and to modern South Asian populations.
A) PCA loaded on modern populations (represented by open symbols). Ancient individuals (solid symbols) are projected onto these axes.
B) Outgroup f3(X, GD13a; Dinka), where Caucasus Hunter Gatherers (Kotias and Satsurblia) share the most drift with GD13a. Ancient samples have filled circles whereas modern populations are represented by empty symbols.
C) ADMIXTURE using K=17, where GD13a appears very similar to Caucasus Hunter Gatherers, and to a lesser extent to modern south Asian populations.
http://oi63.tinypic.com/e8r4nk.jpg (http://oi63.tinypic.com/e8r4nk.jpg)
http://oi65.tinypic.com/24zap2b.jpg (http://oi65.tinypic.com/24zap2b.jpg)
[...]
S4. Mitochondrial Haplogroup Determination
The mitochondria of GD13a (91.74X) was assigned to haplogroup X, most likely to the subhaplogroup X2. Haplogroup X2 is present in modern populations from Europe, the Near East, Western and Central Asia, North and East Africa, Siberia, and North America (7). Haplogroup X2 has been associated with an early expansion from the Near East (7, 8) and has been found in early Neolithic samples from Anatolia (9), Hungary (10) and Germany (11).”
[…]
S5. Principal component analysis shows that Southern Asian populations are the closest contemporary populations to the Iranian herder GD13a was placed close to the Southern Asian samples, specifically between the Balochi, Makrani and Brahui populations of South Asia. (Fig. S4). Of the ancient samples, GD13a falls closest to hunter-gatherers from the Caucasus (Fig. S4).
[…]
S7. Outgroup f3 statistics show that GD13a shares the most genetic drift with Caucasus Hunter-gatherers
We used outgroup f3-statistics to estimate the amount of shared drift between GD13a and contemporary populations. This was performed on the dataset described in section S6 using the qp3Pop program in the ADMIXTOOLS package (13). We computed f3(X, GD13a; Dinka), where X represents a modern population and Dinka, an African population equally related to Eurasians, acts as an outgroup (Fig. S7). We also repeated this analysis where X represents ancient individuals/populations. Among the ancient populations, Caucasus hunter-gatherers (Kotias and Satsurblia) have the closest affinity to GD13a (Table S3), followed by other ancient individuals from Steppe populations from the Bronze age and modern populations from the Caucasus.

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"For the Taforalt individuals to be considered as being Basal Eurasians, we expect that their genomes do not share significantly more alleles with the Neanderthal genome than that sub-
Saharan Africans do."

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