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apophis99942
08-30-2012, 05:42 AM
See: http://halshs.archives-ouvertes.fr/docs/00/33/49/92/PDF/Population_Genetic_Dynamics_Mazieres.pdf


A curious finding reported by Mazieres et al (2008) was the presence of the L2d2 mtDNA sequence in two Kali'na subjects. Since this is a very rare haplotype we surveyed all the literature on African or African-derived persons to ascertain its detailed frequency ... In Africa only 21 instances of it in 1951 individuals from 47 samples were found (1.1%), all of them in West Africa. A similar prevalence (1.0%) was found in African-derived American people. The most probable source of this haplotype in the Kali'na are the Buchinengue (Noir-Marron) ... (Price and Price 2004). It is possible that this sequence may have an unsually high frequency among the Buchinengue, a study worth pursuing.

mtDNA L2d2 among different populations:
Cameroon (Hide) [1/23]
Cameroon (Fali) [1/41]
Cameroon (Mandar) [2/37]
Cameroon (Podokwo) [1/20]
Cabo Verde [1/292]
Guinea-Bissau (Balanta) [2/62]
Guinea-Bissau (Mandenka) [1/30]
Senegal (Mandenka) [1/119]
Sao Tome and Principe (Tongas) [1/38]
Sierra Leone (Mende) [3/59]
Sierra Leone (Tenme) [4/121]
Sierra Leone (Loko) [1/29]
Sierra Leone (Limba) [1/67]
Nigeria/Niger (Kanuri) [1/14]
USA [26/1943]
Brazil [1/120]

Spark
08-30-2012, 05:53 AM
I have never seen L2d2 (it is now called L2e) before in any of the 23andme members with whom I am sharing. My mtDNA haplotype, which is also relatively rare, is considerably more common than this one. In fact, there is only one public 23andme member with mtDNA L2e I can find using the search engine!

apophis99942
08-30-2012, 06:27 AM
High divergence was also noted between L2d1 and L2d2 as well, which IMO likely explains the new nomenclature: http://mbe.oxfordjournals.org/content/21/10/1843.full


Salas et al. (2002), who used the HVS1 segment of the control region to construct African haplogroup L phylogenetic trees, found that the L2d1 and L2d2 subclades branch from a common L2d ancestor (see their fig. 2). In contrast, our coding region network shows that these two subclades are separate branches off the L2 ancestral node. A similar branching pattern was noted in the quartet puzzling trees (data not shown) and these results suggest that they are distinct L2 subclades.

Angoliga
03-28-2016, 04:55 PM
My paternal-grandmother is L2e (L2d2); she's from a Central-Sudanic speaking tribe called Aringa (https://en.wikipedia.org/wiki/Aringa_people) in North-Western Uganda.

This frequency map of L2e seems to be inline with Uganda's Central-Sudanic speakers migration from the West (illustrated in orange on the bottom map below). Many speakers of this Nilo-Saharan branch reside in south/central Chad and extreme-northern Cameroon.


Frequency distribution maps for mtDNA haplogroup L2 -- L2e found on map e)

http://www.nature.com/article-assets/npg/srep/2015/150727/srep12526/images_hires/w926/srep12526-f2.jpg



Map of Central-Sudanic Speakers

https://upload.wikimedia.org/wikipedia/commons/7/77/Central_Sudanic_Languages.png



...
mtDNA L2d2 among different populations:
Cameroon (Hide) [1/23]
Cameroon (Fali) [1/41]
Cameroon (Mandar) [2/37]
Cameroon (Podokwo) [1/20]...


Interesting enough, all the aforementioned Cameroonian ethnic groups are from northern Cameroon; some more specifically in the extreme north. Perhaps there's more L2e affinity with Nilo Saharan or Chadic speakers in and around the Chad basin -- that would explain L2e showing up among the small sample of Kanuri (Nigeria/Niger). "Kanuri (https://en.wikipedia.org/wiki/Kanuri_people#cite_note-Decalo1997-5) groups have traditionally been sedentary, engaging in farming, fishing the Chad Basin, and engaged in trade and salt processing".

Angoliga
03-29-2016, 03:36 PM
B) I did a little more digging and found the publication below; it affirms the Chad Basin connection -- proportionately, the Buduma/Yedina (https://en.wikipedia.org/wiki/Buduma_people) have the highest detection of any population so far, I believe their sample size was n=30 (5/30, 17%)...

"L2e (~47 ka) shows high frequencies in around Lake Chad: Buduma/Yedina, currently Chadic speakers (17% L2e and 30% L2a, b and c) and lesser among Fulani and Fali, North Cameroon, currently Niger-Congo speakers (3-5% L2e)."
The 200,000-Year Evolution of Homo sapiens sapiens Language and Myth Families based on the mtDNA Phylotree, Fossil mtDNA and Archaeology: A Thought Experiment (2014) (https://www.researchgate.net/publication/296058918_The_200000-Year_Evolution_of_Homo_sapiens_sapiens_Language_an d_Myth_Families_based_on_the_mtDNA_Phylotree_Fossi l_mtDNA_and_Archaeology_A_Thought_Experiment_2014) - James B. Harrod.

Angoliga
03-24-2019, 06:04 PM
I uploaded my paternal grandmother's FASTA file on Yfull's new Mtree (https://www.yfull.com/mtree/L2e2/) (id:YF09620); she's the elderly lady in white on my avatar -- she's still alive and kickin' it in her 90s :)

Following the upload and analysis, below is a breakdown of the new subclades (L2e2*, L2e2a):

https://i.imgur.com/t3Acv9u.png


id:EU092724.1 is a Mandenka sample from Guinea Bissaeu, I'll ask the Yfull team to update the country of origin
id:KT819255.1 is from a Moroccan Berber




I would've expected a lower TMRCA for trans-saharan SSA mtdna entering a North-African pop; these dates surprisingly stretch further back than the green Sahara period and camel travel. The Sahara would've been impassible during these suggested TMRCA dates, could this be a coastal migration?

Maybe a closer TMRCA to the Moroccan Berber will be detected once we get more West-Central African samples from Sahelian pops (Mali, Chad, Niger, northern Cameroon/Nigeria etc..). This would seem like a more reasonable explanation since the Mtree is still in it's infancy and the CI is too broad.

Шад
03-31-2019, 05:46 PM
See: http://halshs.archives-ouvertes.fr/docs/00/33/49/92/PDF/Population_Genetic_Dynamics_Mazieres.pdf



mtDNA L2d2 among different populations:
Cameroon (Hide) [1/23]
Cameroon (Fali) [1/41]
Cameroon (Mandar) [2/37]
Cameroon (Podokwo) [1/20]
Cabo Verde [1/292]
Guinea-Bissau (Balanta) [2/62]
Guinea-Bissau (Mandenka) [1/30]
Senegal (Mandenka) [1/119]
Sao Tome and Principe (Tongas) [1/38]
Sierra Leone (Mende) [3/59]
Sierra Leone (Tenme) [4/121]
Sierra Leone (Loko) [1/29]
Sierra Leone (Limba) [1/67]
Nigeria/Niger (Kanuri) [1/14]
USA [26/1943]
Brazil [1/120]

https://yfull.com/mtree/L2e/

Angoliga
04-15-2019, 03:04 AM
Dr. Ian Logan is skeptical about yfull's mtree formation date for L2e2 but saw relevance in yfull's inclusion of the L2e2 subclade, so he added it on his page (http://www.ianlogan.co.uk/sequences_by_group/l2e_genbank_sequences.htm).

From our last correspondence, he noted the actual formation date should be a lot younger:


"The subgroup 'L2e2' is certainly old, but surely not as old as 15,000 years ! More like 5,000 years I would think." (Either upper paleolithic or neolithic dates could work I suppose.)


After uploading the FATSA file on Genebank (MK732938), I ran a BLAST database comparison. Interestingly, none of the closest database matches were the fellow afmd L2e2 samples (Mandenka, Moroccan Berber) but were instead a Sudanese L2e1 (KR135861) followed by a Tunisian L2e1a (FJ460523):

https://i.imgur.com/ICfTVs5.png

I'm not sure how this BLAST run could show a closer similarity to samples of a different subclade? Hopefully we'll have more clarity when more L2e samples are taken into account,

Angoliga
04-26-2019, 04:37 AM
Formation and TMRCA dates have decreased by over 7 thousand years on this last update (MTree 1.01.6657):

https://i.imgur.com/b9O45qf.png




Previous updates:

https://i.imgur.com/t3Acv9u.png

Angoliga
09-09-2019, 04:24 PM
An L2e sample was found in a modern Polish survey, perhaps also ascribed to Ashkenazi Jewish influences. These would probably be closer related to North-African subclades detected in Morocco and Tunisia than SSA.


Interestingly, the frequency of L haplogroup, one of the rarest in Europe, observed in the current study and the study of Mielnik-Sikorska et al. [11] was similar for Podhale region (1% vs. 3%). L1b is the most common African clade in Europe; [42] in the studies of Mielnik-Sikorska et al. [11], L1b1a8a and L2a subclusters were identified among Polish individuals, with the presence of L2a1 haplotype ascribed to Ashkenazi Jewish influences. In this study, both haplotypes (L1b1 and L2a1) were found in individuals from different regions of Poland: 4 individuals with L1b1 from Upper Silesia and 3 individuals with L2a1 haplotype from Gorlice and Częstochowa counties. We additionally identified L2e and L3e subclades: 1 individual with L2e from Nowy Tomyśl county and 2 individuals with L3e from Poznań. Interestingly, L0 is the most common haplotype in East Africa, the Near East and Arabian Peninsula [43].
Mitochondrial DNA variability of the Polish population, (Jarczak et. al, 2019) (https://www.nature.com/articles/s41431-019-0381-x#Sec2)


I made a Yfull request to upload the sample (id:3091, EGAD00001004483)