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Author Topic: Mahra Yemeni populations, 86% Arabian
the lioness,
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The 85th Annual Meeting of the American Association of Physical Anthropologists (2016)
Neanderthal ancestry in Yemeni populations

DEVEN N. VYAS1,2, ALI AL-MEERI3 and CONNIE J. MULLIGAN1,2.
1Department of Anthropology, University of Florida, Gainesville, 2Genetics Institute, University of Florida, Gainesville, 3Department of Clinical Biochemistry, Faculty of Medicine and Health Sciences, University of Sana’a, Sana’a, Yemen

April 16, 2016 , Atrium Ballroom A/B

Analyses of the Neanderthal genomes are strongly consistent with the idea that early modern human populations interbred with Neanderthals in the Near East soon after their successful dispersal out of Africa. However, it is unclear which part of the Near East this dispersal first crossed through, and few studies have assessed Neanderthal ancestry in Near Eastern populations,

We assayed 90 Yemenis sampled from across the country using the Affymetrix Human Origins array. We merged our data with previously published datasets from around the world as well as data from Neanderthal and Denisovan genomes in order to estimate archaic ancestry in modern populations. We also conducted ADMIXTURE analyses on a more regionalized dataset in order to infer ancestral components in Near Eastern populations.

Consistent with other studies, we found that North African and Near Eastern populations (including the Yemeni) generally have less Neanderthal ancestry than other western Eurasian populations. However, our ADMIXTURE results indicate that a subset of Yemeni samples from the Mahra governate share a very high level of ancestry (~85%) with a single Near Eastern component. Interestingly, these individuals have Neanderthal ancestry estimates that are greater than estimates from almost all Near Eastern and North African populations and are more consistent with estimates from European and South/Central Asian populations, suggesting that eastern Yemen may be an area of elevated Neanderthal introgression in the Near East. Greater sampling of Near Eastern populations is needed to better understand variation in Neanderthal ancestry and the site(s) where modern humans and Neanderthals interbred.

Samples used in the study were collected with support of NSF grant BCS-0518530 and genotyped with support of NSF grant BCS-1258965

_______________________________________

http://onlinelibrary.wiley.com/doi/10.1002/ajpa.23312/full

Testing support for the northern and southern dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations

Authors
Deven N. Vyas,
Ali Al-Meeri,
Connie J. Mulligan
First published: 15 September 2017Full publication history
DOI: 10.1002/ajpa.23312


Abstract

Objectives

The Northern Dispersal Route (NDR) and Southern Dispersal Route (SDR) are hypothesized to have been used by modern humans in the dispersal out of Africa. The NDR follows the Nile into Northeast Africa and crosses the Red Sea into the Levant. The SDR emerges from the Horn of Africa and crosses the Bab el-Mandeb into southern Arabia. In this study, we analyze genetic data from populations living along the NDR and SDR to test support for each dispersal route.

Materials and methods

We genotyped 90 Yemeni samples on the Affymetrix Human Origins array. We analyzed these data with published data from Levantine and other southern Arabian populations as well as 157 comparative populations for a total sample size of >550,000 genetic variants from >2,000 individuals in >160 populations. We calculated outgroup f3 statistics to test how Levantine and southern Arabian populations relate to African populations living along the NDR and SDR and to other non-African populations.
Results

We find that Levantine and southern Arabian populations bear similar genetic relationships to both African and non-African populations, thus providing no support for the use of one dispersal route over the other.
Discussion

Our results are consistent with a history of gene flow between the Levant and southern Arabia. Consideration of genetic, archaeological, and paleoclimate data provide a slight edge for the SDR but, ultimately, more data are needed to definitively identify which dispersal route out of Africa was used.


We find that most of the Levantine and southern Arabian populations have low levels of the four sub-Saharan African IACs (1%–6% total)It is also notable that the Yemen Desert population has more West African ancestry than East African ancestry, unlike most of the Levan- tine and other southern Arabian populations

Mahra are minimally or non-admixed as they have >85.9% Arabian ancestry proportions (which exceed most other southern Arabians)


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Elite Diasporan
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Good read.
Posts: 1136 | From: NY | Registered: Sep 2014  |  IP: Logged | Report this post to a Moderator
Swenet
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This deserves repeating here:

quote:
Originally posted by Swenet:
^This is true. But bioanthropology research requires talent. Anyone can be a SJW. No credentials or talent needed. But being competent in this area requires investigative talent and intellectual honesty. Most aDNA research teams are only good at producing the data. They can't draw a coherent analysis from the data because their talent may lie in statistics or computer science. If a lot of these PhDs can't do it, I'm definitely not looking to blogs or message boards for leadership in this area.

There is no such thing as "86% Arabian ancestry". When you break down that 86% you will see it's partly Eurasian and partly African.

In 2013 another research team tried that "pure Arabian" approach, and tried to sweep the African mtDNAs under the rug.

But I can see why this type of research appeals to Lioness. [Wink]

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the lioness,
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quote:
Originally posted by capra:


The vast majority of non-Africans belong to haplogroup L3, specifically the M and N branches [some sub-branches of those are also found in Africa). There are 5 other L3 branches which are primarily African.

quote:
Originally posted by Swenet:


In 2013 another research team tried that "pure Arabian" approach, and tried to sweep the African mtDNAs under the rug.

The Saudi Arabian Genome Reveals a Two Step Out-of-Africa Migration

The two most frequent mitochondria haplogroups [30% each) were the Middle Eastern U7a and the African L. The presence of the L haplogroup common in Africa was unexpected given the clustering of the Saudis with Europeans in the phylogenetic tree and suggests some recent African admixture. To examine this further, we performed formal tests for a history of admixture and found no evidence of African admixture in the Saudi after the split. Taken together, these analyses suggest that the L3 haplogroup found in the Saudi were present before the bottleneck 50,000 YBP. Given the TMRCA estimates for the L3 haplogroup of approximately 70,000 YBP and the timing of the Out-of-Africa split, these analyses suggest that L3 haplogroup arose in the Middle East with a subsequent back migration and expansion into Africa over the Horn-of-Africa during the lower sea levels found during the glacial period bottleneck.



Sorry for my Arabcentiricty but we are dealing with the Mahra [Mehri) not the L3s of the Saudi genome
R0a is the most common mtDNA of the Mahra (Mehri)
Their YDNA largely J* considered and Arab marker
Their L's area a modest 4.6% ( L2a1)

According to Y-DNA analysis by Černý et al. [2009), most inhabitants of Socotra are Mehri descendants, belong to the basal haplogroup J*. Around 71.4% of them carry J*[xJ1,J2), which is the highest reported frequency of the paternal clade

Maternally, basal haplogroup N* likewise occurs at its highest frequencies on the island [24.3%).Mitochondrial analysis by Non [2010) found that the haplogroup R0a [27.7%) is the most common mtDNA clade among the Mehri within the Mahra Governorate. The next most frequent maternal lineages borne by the Mehri are the haplogroups H [13.9%), R2 [13.9%), L2a1 [4.6%), and K [1.5%), as well as various subclades of the macro-haplogroup L[xM,N) [21.5%).

____________________________________


Mol Biol Evol. 2011 Jan;28[1):71-8. doi: 10.1093/molbev/msq178. Epub 2010 Jul 19.

Internal diversification of mitochondrial haplogroup R0a reveals post-last glacial maximum demographic expansions in South Arabia.

Cerný V1, Mulligan CJ, Fernandes V, Silva NM, Alshamali F, Non A, Harich N, Cherni L, El Gaaied AB, Al-Meeri A, Pereira L.
Author information

Abstract
Widespread interest in the first successful Out of Africa dispersal of modern humans ∼60-80 thousand years ago via a southern migration route has overshadowed the study of later periods of South Arabian prehistory. In this work, we show that the post-Last Glacial Maximum period of the past 20,000 years, during which climatic conditions were becoming more hospitable, has been a significant time in the formation of the extant genetic composition and population structure of this region. This conclusion is supported by the internal diversification displayed in the highly resolved phylogenetic tree of 89 whole mitochondrial genomes [71 being newly presented here) for haplogroup R0a-the most frequent and widespread haplogroup in Arabia. Additionally, two geographically specific clades [R0a1a1a and R0a2f1) have been identified in non-Arabic speaking peoples such as the Soqotri and Mahri living in the southern part of the Arabian Peninsula where a past refugium was identified by independent archaeological studies. Estimates of time to the most recent common ancestor of these lineages match the earliest archaeological evidence for seafaring activity in the peninsula in the sixth millennium BC.

______________________


https://en.wikipedia.org/wiki/Haplogroup_R0_[mtDNA)

Haplogroup R0 has been found in around 55% of osteological remains belonging to the Eneolithic Trypillia culture [ Ukraine and northeastern Romania)

The R0 clade has also been found among Iberomaurusian specimens dating from the Epipaleolithic at the Taforalt and Afalou prehistoric sites. Among the Taforalt individuals, around 17% of the observed haplotypes belonged to various R0 subclades, including R0a1a [3/24; 13%) and R0a2c [1/24; 4%). Among the Afalou individuals, one R0a1a haplotype was detected [1/9; 11%).[Additionally, the 3rd century AD Catholic Church Saint, Fortunato of Serracapriola, was found to carry the R0a'b subclade

R0 has likewise been observed among ancient Egyptian mummies excavated at the Abusir el-Meleq archaeological site in Middle Egypt, which date from the Pre-Ptolemaic/late New Kingdom, Ptolemaic, and Roman periods.

R0 today occurs commonly in the Arabian peninsula, with its highest frequency observed nearby among the Soqotri [40.7%).[9] The Soqotri also have the greatest R0 subclade diversity.[10] The clade is likewise found at high frequencies among the Kalash in South Asia [23%).[11] Additionally, moderate frequencies of R0 occur in Northeast Africa, Anatolia, the Iranian Plateau and Dalmatia. The haplogroup has been observed among Chad Arabs [19%),[12] Copts [13.8%),[13] Tigrais [13.6%),[9] Somalis [13.3%),[9] Oromos [13.3%),[9] Afar [12.5%),[9] Amhara [11.5%),[9] Gurage [10%),[9] Reguibate Sahrawi [9.26%; 0.93% R0a and 8.33% R0a1a),[14] Gaalien [9%),[13] Beja [8.3%),[13] Nubians [8%),[9] Arakien [5.9%),[13] Yemenis [5.1–27.7%),[9] Iraqis [4.8%),[9] Druze [4.3%),[9] Palestinians [4%),[9] Algerians [1.67%),[14] and Saudis [0–25%).[9]


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Swenet
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You can use haplogroups to infer the ancestry that must be in a population. But you can't use haplogroups to say certain forms of ancestry are not in a population. The failure of haplogroups to pick up on certain types of ancestry was proven a long time ago, when several ghost populations were not detected in haplogroup profiles.

Anyway, the paper's Fst data indicates that the Arabian ADMIXTURE component itself (that is, excluding any recent SSA ancestry in the Middle East), is closer to Africans than all other Eurasian components. And of course, the authors never mentioned this. Attentive readers have to dig in their data and see what "86% Arabian" really means because the authors were too busy pushing their own narrative.

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the lioness,
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quote:
Originally posted by Swenet:


Anyway, the paper's Fst data indicates that the Arabian ADMIXTURE component itself (that is, excluding any recent SSA ancestry in the Middle East), is closer to Africans than all other Eurasian components

which figure or chart are you referring to ?
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Swenet
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I believe it's table s3. Download the xls file. It's in one of the tabs of that document.
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the lioness,
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quote:
Originally posted by Swenet:
I believe it's table s3. Download the xls file. It's in one of the tabs of that document.

http://onlinelibrary.wiley.com/doi/10.1002/ajpa.23312/full

that is the 4th item in Supporting Information

Supporting Information Tables

and then s3 in the PDF

can you do a screen shot of that I have a glitch in the tabs

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