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Resolved: Allele 12f2.1/12f2.2 - Present>Absent
Semino et al. 2002 : Out of/Sample : 15/48 = 31.3% J(xJ2) and 1/48 = 2.1% J2 for a total of 16/48 = 33.3% haplogroup J among Amhara (Semitic) and 3/78 = 3.8% J(xJ2) and 1/78 = 1.3% J2 for a total of 4/78 = 5.1% haplogroup J among Oromo (Cushitic). Underhill et al. 2000 : 3/88 = 3.4% haplogroup J(xJ2) among a sample of Ethiopians, which were reported as haplogroup 71 (i.e. haplogroup F-M89(xM170, M172, M52/M69, M62)) in the original study.

Based on the 2007 Census conducted by the Central Statistical Agency of Ethiopia (CSA), the Amhara Region has a population of 17,214,056 of whom 8,636,875 were men and 8,577,181 women; urban inhabitants number 2,112,220 or 12.27% of the population.

Yet, the genetic studies do not give the impression that 33% 8,636,875 Amhara males are haplogroup J. Why do people speak about the significant J?


Resolved: Allele 12f2.1/12f2.2 - Present>Absent
Divergent outcomes of intrachromosomal recombination on the human Y chromosome: male infertility and recurrent polymorphism.
by P Blanco, M Shlumukova, C Sargent, M Jobling, N Affara, M Hurles
http://www.mendeley.com/research/divergent-outcomes-intrachromosomal-recombination-human-y-chromosome-male-infertility-recurrent-polymorphism/

The Y chromosome provides a unique opportunity to study mutational processes within the human genome, decoupled from the confounding effects of interchromosomal recombination. It has been suggested that the increased density of certain dispersed repeats on the Y could account for the high frequency of causative microdeletions relative to single nucleotide mutations in infertile males. Previously we localised breakpoints of an AZFa microdeletion close to two highly homologous complete human endogenous retroviral sequences (HERV), separated by 700kb. Here we show, by sequencing across the breakpoint, that the microdeletion occurs in register within a highly homologous segment between the HERVs. Furthermore, we show that recurrent double crossovers have occurred between the HERVs, resulting in the loss of a 1.5kb insertion from one HERV, an event underlying the first ever Y chromosomal polymorphism described, the 12f2 deletion. This event produces a substantially longer segment of absolute homology and as such may result in increased predisposition to further intrachromosomal recombination. Intrachromosomal crosstalk between these two HERV sequences can thus result in either homogenising sequence conversion or a microdeletion causing male infertility. This represents a major subclass of AZFa deletions.Keywords: HERV; AZFa; infertility; Y chromosome

Resolved: Allele 12f2.1/12f2.2 - Present>Absent
A human Y-linked DNA polymorphism and its potential for estimating genetic and evolutionary distance.
by M Casanova, P Leroy, C Boucekkine, J Weissenbach, C Bishop,
http://www.mendeley.com/research/human-ylinked-dna-polymorphism-potential-estimating-genetic-evolutionary-distance/

Abstract

A human DNA sequence (p12f2), derived from a partial Y-chromosome genomic library and showing homology with the X and Y chromosomes and with an undetermined number of autosomes, detected two Y-specific restriction fragment length variants on male DNA that had been digested with Taq I and Eco RI. These variants may have been generated through a deletion-insertion mechanism and their pattern of holoandric transmission indicates that they represent a two-allele Y-linked polymorphism (RFLP). By means of DNA from patients with inborn deletions in chromosome Y, this polymorphic DNA site was mapped to the interval Yq11.1-Yq11.22. The frequency of the rarest allele was about 35 percent in Algerian and Sardinian human males, whereas it was only 4 percent among Northern Europeans. The p12f2 probe also detected Y-specific DNA fragments in the gorilla and chimpanzee. In view of the monosomy of the Y chromosome in mammalian species, Y-linked RFLP's may prove to be more useful than autosomal or X-linked markers in estimating genetic distances within and between species.

The Final Degrees - Ten to Eleven
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The Final Degrees - Ten to Eleven
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Pan-africanism In South Asia
The earliest settlers' antiquity and evolutionary history of Indian populations: evidence from M2 mtDNA lineage

Satish Kumar email, PBSV Padmanabham email, Rajasekhara R Ravuri email, Kiran Uttaravalli email, Padmaja Koneru email, P Aditi Mukherjee email, B Das email, M Kotal email, D Xaviour email, SY Saheb email and VR Rao email

Anthropological Survey of India, 27 Jawaharlal Nehru Road, Kolkata 700 016, India

BMC Evolutionary Biology 2008, 8:230doi:10.1186/1471-2148-8-230

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2148/8/230
Received: 6 March 2008
Accepted: 11 August 2008
Published: 11 August 2008

© 2008 Kumar et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. http://www.biomedcentral.com/1471-2148/8/230

"Unlike M2a, M2b instead of early branching represented by a single deep root defined by the motif 152-182-195-522,523d-1453-2831T-3630-5744-6647-9899-13254-14766-16183C-16189-16193+C-16320 which, of late shows branching pattern similar to the sub-branches of M2a. The M2b1 defined by the transition at np 6260-5420 harbour population of eastern region. Whereas, M2b2 defined by transition at np 16295, harbours Dravidians. Other branches within M2b are more or less population specific. In this study, spread of M2b by and large restricted to Dravidians and tribes of eastern region. The root of M2b in our tree differs in two positions to the earlier definition of Sun et al. [7] i.e. transition at np 182 is present in all of our M2b samples so we treated this as basal mutation and lack of this in one sample of Sun et al. [7] could be better explained by reversion event, second our all M2b samples has poly 'A' at np 16180–16182 and twelve 'C's thereafter. Hence in our tree an additional 'C' at np 16184–16193 has been treated as insertion at np 16193, than transversion (A16182C) reported by Sun et al. [7]."

Haplogroup M2 - found in South Asia, with highest concentrations in SE India and Bangladesh; oldest haplogroup M lineage on the Indian sub-continent. M2a - most common in Bangladesh. M2b - most common in SE India.




Track back mutation : http://www.familytreedna.com/mtDNA-Haplogroup-Mutations.aspx


16295T : L31f1b, M2b2, M7c1, M7c2, N1e, R21.
16259C : M7c2a.
16259G : R12.
CRS : 16295C.

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M7c2a : found in East Asia, especially in Japan.

Resolved: Allele 12f2.1/12f2.2 - Present>Absent
Draft of A Detailed Y-DNA Categorization Scheme SNPs Groups and Their STR Marker Value Oddity Subgroups and Additional Distinct Clusters of Men with Shared Ancestor. Compiled by Ray Banks.


If this is your first visit, it is strongly recommended that you visit the separate section on Criteria and Explanations Otherwise this chart probably will not make sense. The categories listed in red italics have no official status. They were added to make the tree structure clearer. http://www.members.cox.net/generalbanks/completecategorieshapj.html


J (12f2.1+, M304+, P209+, S6+/L60+, S34+, S35+, L60+, L134+) but negative for subgroups .....

In (A-5) a small % of Saudi Arabia men were M304+ but neg for J1 and J2 subgrps.

In (A-6) among 12f2.1+ men neg. for M172, small % (aver. 1%) such 12f2.1+ men found throughout Iberia, but aver. 17% in n.w Africa & 22% among Sephardic Jews.

In (B-2) tho testing only for J2 (M172), small % 12f2.1 found in Albanian-speaking Arbereshe of Calabria, Italy.

In (B-5) among M267+ men neg for M365, found in small % in Balkans countries, in 1% of Poles & 3% of Georgians, but none found in most of nations just north of the Balkans, in n.e. Italy or among Ukranians or among Balkarians of the n.w. Caucasus.

In (B-6) among 1525 samples from the w., central and n.e. Caucasus 354 were M267+ but P58-, or abt a fourth of the total. Among the Kubachi and Kaitak of the n.e., a high % is this type M267. More than half the Avars and half the Lezghins of the n.e. are the same. Abt a fourth of Chechens of the n.e. are in this category, and the % drops to single digits elsewhere.

In (B-8) those haplo J men neg for J2 are 3% of Adyghes, 11% of Armenia, 22% of Ashkenazi Jews, 14% of Azerbaijani Jews,
67% of Bedouins, less than 1% of Belorussians & Chuvash, 0% of Cochini Jews, 17% of Druze, 12% of Egypt, 0% of Ethiopian
Jews, less than 1% in France, 2% of Georgian Jews, % in south India, 19% in Iran, 16% of Iranian Jews, 16% of Iraqi Jews, 58% of Lezgins, 19% of Mumbai Jews, 36% of Palestinians, 3% in Romania, 23% among Sephardic Jews, 2% in Uzbekistan, 7% of Uzbek Jews, 34% of Yemeni Jews. In (G-4) all 12f2.1+ Portuguese Gypsies belong to 12f2.1 subgrps.

In (B-9) tho not checking for M267 subgrps, M257 found in fewer than half of populations in European Russia & was 1-4% when present.

In (B-10) those men 12f2.1+ but neg for M172 subgrp are 3% of Albanians, 1% in Romania, & 3% among Aromuns in Dukasi, Albania. But no such 12f2.1 found among Greeks and Macedonians or among other Aromuns of the region.

In (C-6) checking only for M62, M365, M390 & P58 subdivs of M267, found abt 70% of each of 5 ethnic groups of highland n.e. Caucasus Mtns. were M267+.

In (C-7) among the following there were no M267+ men who did not belong to a M267 subgrp: Sednaya Syriac Catholics, Catholics at Damascus, Syria, Syrian Alawites, Syrian Assyrians, Syrian Ismailis, Jordanians, Palestinians, Saudis. Also in (C-7) tho testing only P58 sub-subgrp, a small % of M267 men were M267 not P58 among Druze, Sunni Hann of n. Syria, Ma'loula Aramaeans, Iraqi Kurds. Though small sample sizes, the % was 10-20 among Assyrians from Iraq, Iran & Turkey. In (A-5) 40% of Saudi Arabia men were M267+ but neg. for M365.

In (C-10) tho not checking for M267 subgrps, M267 found in 14% of men on Soqotra Isl. off Yemen. In (C-10) 71% of men on Soqotra Isl. off Yemen found to be M304+ & neg for both M304 subgrps.

In (C-11) tho not testing for M267 subgrps, M267 found in 3% of Hungarians, and 10% of Romanian Szeklers.

In (C-12) tho not testing for M267 subgrps, M267 found at 2% in Sardinia, but none found in northern part of island.

In (C-14) 2f2.1+ men neg for M172 subgrp are 0-7% of men in parts of peninsular Italy, with half the locations not reporting any. No such 12f2.1 found in island of Elba or far n.e. corner of Italy.

In (C-17) those men 12f2+ but neg for subgrp M172 were 7% in east Sicily, 0% in s.w. Sicily, 7% in n.w. Sicily, 4% in south Italy, 5% in Sardinia, 8% in Malta, 23% in Tunisia, 32% among Djerba Jews, 31% in Muslim Lebanese, 9% in Christian Lebanese & 6% of Cyprus J1 (M267+, L255+, L321+) for negative for subgroups .....

In (D-6) tho not checking 12f2.1 subgrps, 12f2.1 found at 2% of Russians, and 2% in Altaians-Kizhi & Teleuts of south Siberia, but no 12f2.1 found in other south Siberian ethnic grps or in Mongolians or Koreans.

In (D-4) tho not checking for subgrps, 4% of 236 Sicilians were M267+.

In (G-3) tho not testing for M267 subgrps, M267 found in 1% of N. Sardinian males.

In (G-5) no M267 found in Nepal & Tibet. In (M-9) tho not checking for M410 subgrps, M410 found in range of 0 to 2% are sites in Crete.

In (F-4) tho not checking M267 subgrps, M267 found in abt 1% of Albanians. In (K-5) tho not testing for M267 subgrps. 1% of men in Bali, Indonesia were M267+. But no M267 found in rest of Indoneia, s.e. Asia, China, Philippines, Melanesia, other Oceania and aboriginals of Taiwan.

In (F-6) those men 12f2.1+ but neg for subgrps M267 & M172 were 3% in Pakistan, 0% in Greece.

In (F-7) tho not checking for M267 subgrps, M267 found at 41 among Jordanians in Amman, but at 9% among Jordanians at the Dead Sea.

In (H-4) tho not testing subgrps, found in a fifth of Lebanese of varied religions & also in less than a 10th of east and west Iranians. No (H-4) samples have double DYS19, but both Iran and Lebanon have a divide between men DYS388=13 and those several higher.

In (H-5) tho not testing for I2f2.1 subgrps, I2f2.1+ men found in the majority among multiple n.e. Sudan groups, is small % in Central Sudan & absent elsewhere in Sudan.

In (J-4) seemingly a small group neg. for all subgroups but better testing needed.

In (K-3) tho not tested for subgrps, small % found in Bali. No confirmed samples from the projects.

In (K-6) tho not testing M267 subgrps, a third of men tested in Egypt's western desert were M267+. In (T-4) among M267+ samples from variety of locations in Asia, s. Europe and northern Africa, only a few could be assigned to M62, M365, M390, M367, M368, M369 subgroups or sub-subgroups except for substantial M267 DYS388=13 subgrp in n.e. Caucasus Mtns. (see below) In

(K-7) tho not testing for M267 subgrps, M267 ranges from 3-10% in many parts of Turkey, in mainland Greece, but 2% in s. e. France.

In (K-9) tho not testing for M267 subgrps, M267 found at 11% in north Greece, 4% in central Greece, 2% in south Greece & 8% in Crete.

In (K-11) tho not checking for 12f2.1 subgrps, 12f2.1 found at 4% in Swedish males, but none found in s.w. Finland or among nomadic Swedish Saami.

In (L-3) tho not testing for J1 subgrps, found tiny % M267 in Belgium & in N. Brabant Netherlands.

In (L-5) two 12f2a+ men found who were neg for sub-subgrps M62 and M172. One French, one Spanish.

In (L-8) tho not testing for M172 subgrps, M172 found at 2% in Estonia and Lithuania, but not found in Latvia, Finland, Sweden or among Karelians. In (E-9) among men M304+ but neg for M172, such M304 men found at 1% among Muslim Shia of north India, 10% among Muslim Dawoodi Bohras of west India. But no such M304 men found among Muslim Sunnis of north India, Dawoodi Bohras of south India, Iranian Shia of south India or Muslim Mapplas of south India.

In (L-9) 12f2.1+ men neg for M267 & M172 subgrps were 1% of men in Czech Republic. In (L-9) no M267+ men found in Czech Republic. In (F-6) tho not checking for M267 subgrps, M267 found 1% in Greece, 2% in Pakistan. But no M267 found among Pakistani Burushos & Kalash, 1% among Pathans.

In (L-10) no 12f2.1 men found in Finland.

In (N-8) tho not checking for M267 subgrps, M267 found in 12% of Portuguese Jews.

In (O-3) tho not testing for M267 subgrps, M267 found in 20% of Morocco men and 35% in Tunisia.

In (P-3) tho not testing for I2f2.1 subgrps, I2f2.1 found in 4% of Mansi and 0% of Khanty of n.w. Siberia.

In (R-1) tho not tested for subgrps, abt 10% in north and south Iran.

In (R-28) tho not checking for subgrps, J1 found in 23% of Arabs of n.w. Algeria. In (Y-2) abt 600 confirmed M267+ men listed but no info as to whether tested for subgrps. In (J-4) also large number of M267+ men listed, but only six tested for all subgrps
and found neg for each. These are fom Armenia, Turkey, Greece and a man with a British Isles surname.

In (S-4) tho not testing subgrps, a small to significant amt M267 found in all major grps in Israel except Palestinians & Ethiopian Jews. In (S-4) 1 J only sample found among Ashkenazi Jews from Poland in Israel, but not in other Israeli grps. In (M-3) tiny % of men in Comoros off east Africa found M304+ and unassignable to J1 or partially tested J2 subgrps.

In (S-5) tho testing only for J2 (M172), very small % of M304 found among some of the ethnic grps of n.w. China. In (V-2) tho not checking for J subgrps, tiny % J found in s.e. Nigeria, but none in Cameroon or Ghana. In (K-5) tiny % of men in Bali, Indonesia are M304+ not neg for subgrps. But no men in this category found in rest of Indonesia, s.e. Asia, China, Philippines, Melanesia, other Oceania and among aboriginals of Taiwan.

In (T-6) no 12f2.1+ men found on Sao Tome e Principe off west central Africa.

In (U-1) tho not tested for subgrps, found 5 samples in S. Pakistan and 2 in India among 904 samples. [latter study may have tested 1a and 1b].

In (V-3) found 1% of Gauguz of Moldova originating in n.e. Bulgaria were 12f2.1+ but neg for M267 & M172. In (V-3) tho not testing for M267 subgrps, M267 found in 1% of Gauguz of Moldova originating in n.e. Bulgaria.

In (V-4) small % of Hungarians & Malaysian Indians were M304+ but neg for M72. In (R-30) tho not checking for haplo J subgrps, haplo J found at 3% in Finistrere dept., tip of Brittany, n. w. France. All of this concentrated in port cities.

In (Y-2) (J-4) no confirmed J only men listed, as all seem confirmed to belong to a J subgroup.

In (Z-3) tho not tested for J1 subgrps, (7) M267+ men found among ethnic grps of n.w. China. In (M-3) tho not testing for J1 subgrps, found 5% of men in Comoros off east Africa were M267+.

In (Z-6) tho not testing for 12f2.1 subgrps, 12f2.1 found at 18% among Uygurs of n.w. China, 10% of Han Chinese of n. centratl China, 5% of Tibetans in China, average 3% of Yugurs of n. Central China and 0% in Mongolians.

In (Z-7) 20% of Lebanese men 12f2.1+ but neg for M172 subrgp.

Resolved: Allele 12f2.1/12f2.2 - Present>Absent
RESOLVED: 12f2a deletion

http://hmg.oxfordjournals.org/content/9/17/2563.full

“…Based on these alignment data, the molecular origin of the 12f2 STS polymorphism is assumed to be linked to the deletion of the L1PA4 element in the HERV15yq2 sequence block. The polymorphic 12f2 Y-DNA marker was first described as a restriction fragment length polymorphism (RFLP) for EcoRI and TaqI in human male DNA (12). In genomic DNA blots of human MALES and FEMALES, the probe 12f2 (Fig. 1a) crosshybridized to a polymorphic male-specific EcoRI fragment of 5.2 and 3.2 kb, whose presence was mutually exclusive.

“…It seems likely that the presence of the L1PA4 element in the HERV15yq2 sequence block represents the ancestral state in humans since POPULATIONS WITH ONLY THE ‘LONG’ 12f2 ALLELES (5.1 kb EcoRI/10 kb TaqI) were FOUND IN AFRICAN BLACKS, in ORIENTALS and in NATIVE AMERICANS and a FREQUENCY GRADIENT OF ITS DELETION was observed in EUROPEAN populations (34). We assume that a gene conversion event between the two HERV15yq sequence blocks in proximal Yq11 most likely caused the precise deletion of this L1PA4 element.”

http://docs.google.com/viewer?a=v&q=cache:H4w_tkJUJS0J:www.ncbi.nlm.nih.gov/pmc/articles/PMC1757162/pdf/v037p00752.pdf+12f2+deletion+%2B+Ethiopia&hl=en&gl=us&pid=bl&srcid=ADGEESiJBKwzi5wG4Iz_fB78DbiVS5fylAYAk6ufu2RHJ68VxxeDb_YelwWSCLsV1NV1bC9XkT-PC6OgoibMllfKHmEq04fvRIY7FvJ7M71mAXNUJsRe3RWcaOrvzR1yWEy0RB0YnbwI&sig=AHIEtbRwiuZ60SAo0ZwmwDtTduH3rEi0FA

“…The assumption that markers such as the 12f2 deletion are neutral is required for their use in reconstructing human prehistory. This assumption may be violated if these markers represent permutations, though only if negative selection outweighs drift.”

CN (European Times : http://www.eutimes.net/2010/06/king-tuts-dna-is-western-european/),

You are incorrect the derived 12f2.2 deletion is found only in Europeans advent of Hg D2-J12f2.1-8kb.

You are incorrect in that the ancestral 12f2.1-10kb (Undeleted) is found in African Blacks, Orientals, i.e., Near Easteners, and Native Americans.

L1PA4 deletion:

The deletion of the L1PA4 element was recognized as the molecular origin of the DYS11 12f2 restriction fragment length polymorphism.

http://docs.google.com/viewer?a=v&q=cache:nBYGCDu-6mUJ:www.pasteur.edu.uy/publico/bonilla/Genetica%2520Humana/Fathers%2520and%2520sons%2520The%2520Ychromosome%2520and%2520Human%2520Evolution.pdf+Ann+Hum+Genet+54.287-296&hl=en&gl=us&pid=bl&srcid=ADGEESi9A5pSglrYzCGUBaMt5xxXIbrf7ckuq0Ek3ErT-pB0yGclDYhjSJ3bIz1npB50n15rtXgrNPQoBnpBugjxYIqszXIoKE_lHWmACCymrjuAwbKcim0FYfJCYm_nyy-illqexQI2&sig=AHIEtbTpdaSJjaDNuOHhRh9LcEoS4U4s0w

“The geographical distribution of loci, such as YAP, focuses attention on specific novel questions about population origins. Although the Alu insertion is found at highest frequency in Africa, it is found a moderate frequency in Japan and at low frequency in some other areas, such as Europe. Its presence outside Africa is often not due to recent admixture, but does it represent, for example, admixture a few centuries ago or the presence of YAP* chromosomes in founding populations? These questions cannot be answered yet, but more detailed analysis of the Y chromosomes should allow such possibilities to be distinguished.”

AZF DELETIONS AND Y CHROMOSOMAL HAPLOGROUPS : HISTORY AND UPDATE BASED ON SEQUENCE, PETER H. VOGHT, Section of Molecular Genetics & Infertility, Department of Gynecological Endocrinology & Reproductive Medicine, University of Heidelberg, Heidelberg, Germany

http://humupd.oxfordjournals.org/content/11/4/319.full.pdf

“…However, the two variable fragment lengths (8, 10.4kb) observed after TaqI restriction were only present in genomic male DNA, indicating their Y chromosomal origin (Figure 2). Analysis of the frequency of this 2.4kb deletion polymorphism (here designated as DYS11 12f2-2.4kb allele) in different populations from Europe, Africa and Asia revealed it specificity for Caucasian populations because it is absent in African Blacks, in Orientals and in Native Americans (Semino et al., 1996). Most interesting, the frequency of the 12f2-2.4kb deletion decreased from the Near East to northwestern Europe populations, reflecting the neolithic demic diffusion of the ancient farming cultures. Today we know that the 12f2-2.4kb deletion is the derived state (12f2.2/12f2-B allele) of the undeleted ancient DYS11 sequence (12f2.1/12f2-A allele) and that this deletion must have occurred at least two times during the evolution of the human population history (Blanco et al., 2000).”

17 New Pyramids Unearthed in Egypt - 2011

17 New Pyramids Unearthed in Egypt - 2011
The Fall of the Old Kingdom
http://www.bbc.co.uk/history/ancient/egyptians/apocalypse_egypt_01.shtml

End of a dynasty

Nothing prepared Egypt for the eclipse of royal power and poverty that came after Pepy II (Neferkare). He had ruled for more than 90 years (2246 - 2152 BC) as the fourth king of the 6th Dynasty of the Old Kingdom. Within the span of 20 years, fragmentary records indicate that no less than 18 kings and possibly one queen ascended the throne with nominal control over the country. This was the entire length of the 7th and 8th Dynasties (2150 - 2134 BC). In the last few years of the 6th Dynasty, the erosion of power of the centralized state was offset by that of provincial governors and officials who became hereditary holders of their posts and treated their regions as their own property.

Egypt, to be sure, survived the disastrous collapse of the monarchy. Within a century, Egyptians had re-invented centralized government. They refurbished the image of kings so that they were not merely rulers by virtue of their divine descent but more importantly had to uphold order and justice, care for the dispossessed and show mercy and compassion. The crisis that shook Egyptian society thus heralded the most dramatic transformation in the royal institution, which was destined never to be separated from this social function.

The crisis not only reformed the monarchy but also instilled the spirit of social justice and laid the foundation for mercy and compassion as fundamental virtues. It was these concepts that were later to infuse Christianity and Islam. It was these same concepts that eventually led to the overthrowing of monarchs who repeatedly usurped their powers and denied people their religious rights.

Some Egyptologists attribute the sudden collapse of the Old Kingdom to the long reign of Pepy II. However, a reign which lasted for more than 90 years suggests, if anything, stability and strength. Even if the collapse was due to Pepy II's long reign, the struggle for power among the sons of Pepy II at the end of his rule is not a reason for the dissolution of the monarchy. Moreover, it is misleading to speak of his successors as being 'weak' kings without giving any reasons as to how such divine rulers of absolute power could have become so. Under such conditions, even imbeciles and children could rule with no threat to the royal institution.

Historically, this has always been the case because kingship is less about the king in person than the institution whose beneficiaries - the royal court, nobles, regional governors and priests - gain from its presence. They suffer to lose everything if the intuition is compromised or handed over to another royal personage. For this reason, the principle of divine kingship was maintained even when the king was replaced by rulers drawn from outside the family of the enthroned king.

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Image showing an inscription found in the tomb of local Governor, Ankhtifi Inscription in the tomb of local Governor, Ankhtifi, who lived during the time of the collapse of the Old Kingdom. © We have no indication at the end of the 6th Dynasty that there was a bid for power by the local governors. It is only after the initial breakdown that power was wielded by the kings of a province in Middle Egypt, later called Herakleopolis. The capital was approximately 15 km west of Beni Suef on the right bank of Bahr Yusuf. According to Manetho, Herakleopolis became the capital of Egypt during the 9th and 10th Dynasties and the town played a major role after the end of the Old Kingdom. Evidence for this account comes from inscriptions in the tombs of a vassal prince at Asyut. These reveal that war broke out between the kings of Herakleopolis and Theban kings. The war lasted for several years and ended when the Theban king Mentuhotep II Nebhepetre (2061 - 2010 BC) defeated Herakleopolis before re-unifying the country.

Contrary to what some Egyptologists claim, the stability of the long reign of Pepy II was most likely due to the decentralization of the government. This is one of the most successful strategies in managing complex organizations. The ambitions of local governors in such a system are primarily curtailed by the economic and defence rewards of being a vassal. In addition, there is the strong likelihood of failure in staging an uprising because the king can count on many more loyalists. Only when the monarchy is undermined by some unforeseen cause, would charismatic and ambitious provincial governors seek to become kings. In this situation, they stand to gain from restoring the monarchy in their name, thus counting on the support of others who, in the absence of a powerful king, would rally behind them.

17 New Pyramids Unearthed in Egypt - 2011
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Pyramid of Djoser: Many more are thought to be buried underground. The cameras on the satellites are so powerful that they can precisely image objects on Earth that are less than one metre in diameter

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The amazing satellite images have revealed pyramids and ancient homes
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Ancient streetmap: A satellite image shows Tanis to be a city littered with underground tombs. Buildings in ancient Egypt were constructed out of mud brick - the material is dense, allowing satellites orbiting above Earth to photograph the outlines of structures invisible to the human eye
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Hidden history: This image of Tanis shows the difference between what the naked eye can see and the underground details that the high-powered satellite camera can pick up
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Only the beginning: Archaeologist Dr Sarah Parcak points out the site of a buried pyramid on a satellite image

The camera's high level of accuracy has impressed the Egyptian government, which now plans to use the technology to identify and protect its colossal heritage in the future.

Dr Parcak, whose work will feature in the BBC documentary Egypt’s Lost Cities on Monday, believes that there are many more buildings buried deeper than those already spotted, the most likely location being under the banks of the River Nile.

She said: 'These are just the sites close to the surface. There are many thousands of additional sites that the Nile has covered over with silt.

'This is just the beginning of this kind of work.'
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Digging deep: The archaeologists' most promising excavations are taking place in the ancient city of Tanis

She told the BBC: ‘It just shows us how easy it is to underestimate both the size and scale of past human settlements.

‘These are just the sites [close to] the surface. There are many thousands of additional sites that the Nile has covered over with silt. This is just the beginning of this kind of work.’

She said the technology could be used to monitor the looting of antiquities, as well as to engage young people around the world in science and help archaeologists in their quest to uncover the secrets of the past.

The archaeologist said, ‘We have to think bigger and that’s what the satellites allow us to do. Indiana Jones is old school. We’ve moved on from Indy, sorry Harrison Ford.’

• A hidden chamber unseen for 4,500 years may have been discovered inside the Great Pyramid of Giza. A robotic probe designed by British engineers found hieroglyphs inside a tunnel that leads from the pyramid’s Queen’s chamber, New Scientist magazine reports. Cameras have also sent back images of a stone door which it is thought could lead to a hidden chamber.


Read more: http://www.dailymail.co.uk/sciencetech/article-1390667/Seventeen-lost-pyramids-thousands-buried-Egyptian-settlements-pinpointed-infrared-satellite-images.html#ixzz1XgQIKsVx





17 New Pyramids Unearthed in Egypt - 2011
http://www.youtube.com/redirect?q=http%3A%2F%2Fwww.dailymail.co.uk%2Fsciencetech%2Farticle-1390667%2FSeventeen-lost-pyramids-thousands-buried-Egyptian-settlements-pinpointed-infrared-satellite-images.html&session_token=IifWIVq3G2NR5djZvpu1zbDsUTh8MTMxNTg2MzQzM0AxMzE1Nzc3MDMz

17 New Pyramids Unearthed in Egypt - 2011

Lack of Specific Mutations Deiiferentiates Hg H
“…In this study, we type the hypervariable region I (HVRI) of the mitochondrial genome (360 bp) from the bones of two early anotomically modern humans of the Cro-Magnon type from Southern Italy. We validated the sequences obtained through a number of biochemical tests, and we compared them with those of four Neandertal (8, 16-18) specimens and with a large data set of modern human sequences (19, 20). (P.1)

The sequences reported in this paper have been deposited in the GenBank database; accession no. AY283027 and AY283028).

Paglicci-12, shows a single difference (a C>T transition at nt 16223)

Track back 16223:

16223C : L0b, L0d1a, L0k2, L1c1a1, L2d, L3x2a, M1a3b, N21, Q1a, R, R2a, X2h, Y, D4c1a, D4g2a1, D5c2.
16223T : L3e2b, U4a2b, B5b1b.

It is particulaly curious that the mt/dna haplogroup of Paglicci is predicted to be either N or U. This means the C>T transition was L3e2b directly to U4a2b which according to the mtDNA Mutations Table http://www.familytreedna.com/mtDNA-Haplogroup-Mutations.aspx is defined only by 16233T.

Distribution

Haplogroup U is subdivided into Haplogroups U1-U8. Haplogroup K is a subclade of U8.[2] The old age has led to a wide distribution of the descendant subgroups that harbor specific European, Berber, Indian, African, Arab, northern Caucasus Mountains and the Near East clades.[3]

If, on the other hand, the Ooa progression is L3x2a > Mia3b > N21 > R > R2a > C> U4a2bT, then what is the time of L3x2a?

L3x - East Africa. Ethiopian Oromos,[10] Somalis[16] and Egyptians[Note 1][17]

Note: GUR46 on table 1. is a mtDNA haplogroup L3x2a.
17 : Stevanovitch, A.; Gilles, A.; Bouzaid, E.; Kefi, R.; Paris, F.; Gayraud, R. P.; Spadoni, J. L.; El-Chenawi, F. et al. (2004). "Mitochondrial DNA Sequence Diversity in a Sedentary Population from Egypt". Annals of Human Genetics 68 (Pt 1): 23–39. doi:10.1046/j.1529-8817.2003.00057.x. PMID 14748828 ; http://dx.doi.org/10.1046%2Fj.1529-8817.2003.00057.x ; http://www.ncbi.nlm.nih.gov/pubmed/14748828

Quote:
 
Mitochondrial DNA Sequence Diversity in a Sedentary Population from Egypt

A. Stevanovitch1,*,
A. Gilles2,
E. Bouzaid1,
R. Kefi1,
F. Paris3,
R. P. Gayraud4,
J. L. Spadoni1,
F. El-Chenawi5,
E. Béraud-Colomb1,*

Article first published online: 29 JAN 2004

DOI: 10.1046/j.1529-8817.2003.00057.x
http://onlinelibrary.wiley.com/doi/10.1046/j.1529-8817.2003.00057.x/full


Summary

The mitochondrial DNA (mtDNA) diversity of 58 individuals from Upper Egypt, more than half (34 individuals) from Gurna, whose population has an ancient cultural history, were studied by sequencing the control-region and screening diagnostic RFLP markers.

This sedentary population presented similarities to the Ethiopian population by the L1 and L2 macrohaplogroup frequency (20.6%), by the West Eurasian component (defined by haplogroups H to K and T to X) and particularly by a high frequency (17.6%) of haplogroup M1. We statistically and phylogenetically analysed and compared the Gurna population with other Egyptian, Near East and sub-Saharan Africa populations; AMOVA and Minimum Spanning Network analysis showed that the Gurna population was not isolated from neighbouring populations.

Our results suggest that the Gurna population has conserved the trace of an ancestral genetic structure from an ancestral East African population, characterized by a high M1 haplogroup frequency. The current structure of the Egyptian population may be the result of further influence of neighbouring populations on this ancestral population.

Lack of Specific Mutations Deiiferentiates Hg H
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Lack of Specific Mutations Deiiferentiates Hg H
Quote:
 
Haplogroup R0, formerly known as pre-HV [1], is defined by the absence of transitions A73G and G11719A relative to haplogroup R. There is one main sub-branch of R0 defined by the lack of C14766T (haplogroup HV) and a minor branch known as R0a [2]. HV embraces the most frequent haplogroup in Europe (~40%), namely, haplogroup H, which is defined by the lack of the characteristic transitions A2706G and C7028T. HV also contains some other less frequent clades, such as HV1, HV2, and specially HV0, where haplogroup V is nested. Most of the haplogroup H sub-lineages are most likely of Middle Eastern origin (as it is the case of the majority of the typical West European clades). Overall, R0 shows frequency patterns declining from West towards East and South Europe and Middle East [1], [3], [4].


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Track back mutations: mtDNA L3 : 73, 7028, 10873, 11719, 12705, 14766, 16223.
http://familypedia.wikia.com/wiki/Haplogroup_L3_%28mtDNA%29

73A : L0abf, N1c, R0, rCRS.
A73G : L3e2b, H1a, H3d, H4a1a1.

11719G : R0, rCRS.
G11719A : L3, L3e2b, R0a2a, HV0d.

A2706G :
2706A : L0d1, U2b, H, J1c3c, D4f, rCRS.

C7028T : L3, L3e2b.
7028C : H, rCRS.

C14766T : L3, L3e2b.
14766C : M2b, B2a1a, HV, rCRS.

mtDNA branch structure : L>M>N> R>U.

Quote:
 
A 2003 study was published reporting on the mtDNA sequencing of the bones of two 24,000-year-old anatomically modern humans of the Cro-Magnon type from Southern Italy. The study showed one was of either haplogroup HV or R0.[1 : B. Malyarchuk et al 2008, Mitochondrial DNA phylogeny in Eastern and Western Slavs MBE Advance Access published May 13, 2008 ; http://www.pnas.org/cgi/reprint/100/11/6593.pdf]

Evidence for genetic discontinuity between Neandertals and 24,00 year-old anatomically modern Europeans



Lack of Specific Mutations Deiiferentiates Hg H
Mitochondrial Haplogroup H1 in North Africa: An Early Holocene Arrival from Iberia
http://www.plosone.org/article/slideshow.action?uri=info:doi/10.1371/journal.pone.0013378&imageURI=info:doi/10.1371/journal.pone.0013378.g001

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Lack of Specific Mutations Deiiferentiates Hg H
New Population and Phylogenetic Features of the Internal Variation within Mitochondrial DNA Macro-Haplogroup R0
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0005112

Quote:
 
Age Correction of Hg H2a5 : http://www.plosone.org/annotation/listThread.action?inReplyTo=info:doi/10.1371/annotation/25b9ed74-e963-496e-84bb-526bd6867221&root=info:doi/10.1371/annotation/25b9ed74-e963-496e-84bb-526bd6867221

Haplogroup R0, formerly known as pre-HV [1], is defined by the absence of transitions A73G and G11719A relative to haplogroup R. There is one main sub-branch of R0 defined by the lack of C14766T (haplogroup HV) and a minor branch known as R0a [2]. HV embraces the most frequent haplogroup in Europe (~40%), namely, haplogroup H, which is defined by the lack of the characteristic transitions A2706G and C7028T. HV also contains some other less frequent clades, such as HV1, HV2, and specially HV0, where haplogroup V is nested. Most of the haplogroup H sub-lineages are most likely of Middle Eastern origin (as it is the case of the majority of the typical West European clades). Overall, R0 shows frequency patterns declining from West towards East and South Europe and Middle East [1], [3], [4].


Mitochondrial Haplogroup H1 in North Africa: An Early Holocene Arrival from Iberia
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013378

Quote:
 
The Tuareg of the Fezzan region (Libya) are characterized by an extremely high frequency (61%) of haplogroup H1, a mitochondrial DNA (mtDNA) haplogroup that is common in all Western European populations. To define how and when H1 spread from Europe to North Africa up to the Central Sahara, in Fezzan, we investigated the complete mitochondrial genomes of eleven Libyan Tuareg belonging to H1. Coalescence time estimates suggest an arrival of the European H1 mtDNAs at about 8,000–9,000 years ago, while phylogenetic analyses reveal three novel H1 branches, termed H1v, H1w and H1x, which appear to be specific for North African populations, but whose frequencies can be extremely different even in relatively close Tuareg villages. Overall, these findings support the scenario of an arrival of haplogroup H1 in North Africa from Iberia at the beginning of the Holocene, as a consequence of the improvement in climate conditions after the Younger Dryas cold snap, followed by in situ formation of local H1 sub-haplogroups. This process of autochthonous differentiation continues in the Libyan Tuareg who, probably due to isolation and recent founder events, are characterized by village-specific maternal mtDNA lineages.


Evidence of trans-Mediterranean contacts between Northern Africa and Western Europe has been assessed at the level of different genetic markers (e.g. [21], [22], [23], [24]). With regards to the mtDNA, the high incidence of H1 and H3 in Northwest Africa, together with some other West European lineages (i.e. V and U5b), reveals a possible link with the postglacial expansion from the Iberian Peninsula, which not only directed north-eastward into the European continent [17], [18], [25], but also southward, beyond the Strait of Gibraltar, into North Africa [26], [27]. So, besides the ‘autochthonous’ South-Saharan component, the maternal pool of Northern Africa appears to be characterized by at least two other major components: (i) a Levantine contribution (i.e. haplogroups U6 and M1, [11]), associated with the return to Africa around 45 kya, and (ii) a more recent West European input associated with the postglacial expansion.

Within the West-European component in North Africa, H1 is the most represented haplogroup with frequencies ranging from 21% in some Tunisian Berber groups to 1% in Egypt [28]. Recently, an extremely high incidence of H1 (61%) has been reported in a Tuareg population from the Central Sahara, in Libya [29]. Tuareg are a semi-nomadic pastoralist people of Northwest Africa, who speak a Berber language. MtDNA analyses performed on the Libyan Tuareg have highlighted their genetic relatedness with some Berber groups and other North African populations, mainly resulting from the sharing of a common West-Eurasian component. A high degree of homogeneity in the Libyan H1 lineages was observed, suggesting that the high frequency of H1 in the Tuareg may be the result of genetic drift and recent founder events.

To better define the nature and extent of H1 variation in the Tuareg from Libya we have now determined the complete sequence of eleven of their mtDNAs belonging to H1. The comparison of these H1 sequences with those already available from Europe and North Africa provides new clues on how and when H1 spread in Northern Africa up to the Central Sahara.

Quote:
 
Results Top

The most parsimonious tree encompassing eleven complete H1 mtDNAs from the Tuareg together with four previously published sequences from Tunisia [35], one Berber from Egypt [17] and two Jewish Moroccans [36] is illustrated in Figure 1. All Tuareg sequences clustered into three clades that had not been previously reported and thus were termed H1v, H1w and H1x. Five sequences grouped into the sub-clade H1v1 defined by the transition at np 4313. One Tunisian sequence (# 8) did not cluster into H1v1 but was closely related, since it harbored the mutation at 10314 that defines the clade H1v (Figure 1). The sub-clade H1v1 splits into two branches defined by the transitions at np 9148 (clade H1v1a) and 14560 (clade H1v1b). Three Tuareg mtDNAs formed the novel clade H1w that is defined by the transition at np 8966, while the last three Tuareg mtDNAs, apart from the HVS-I transitions at 16037 and 16256, were found to harbor mutations at nps 7765 and 10410 in the coding region (clade H1x). The Tuareg complete mtDNAs have been deposited in GenBank, under the accession numbers reported in Table S1.


Divergence values (rho statistics and ML estimates) and the age in years of the most recent common ancestor of the main clusters are reported in Table 1, according to the evolutionary rate estimates described in Soares et al. [32] and Loogväli et al. [33]. The two evolutionary rates provide a coalescence time of about 8–9 kya for the whole H1 haplogroup in North Africa. As expected, the North African-specific clades are characterized by younger ages ranging from about 3.8 to 6.7 kya for H1v, and from 2.1 to 7.9 kya for H1v1. The youngest clades were found to be H1w and H1x, with an age of about 0.8–1.1 kya.

The H1 phylogeny based on complete North African sequences reveals a degree of branch diversification that is almost undetectable when using only control region data. Moreover, when compared to the H1 phylogeny built using complete sequences from Europe [17], [19], [38], [39], it appears that the novel branches H1v, H1w and H1x identified during the course of this study are all African-specific. This finding suggests that these H1 sub-clades most likely arose in North Africa after the arrival of the H1 European founder sequence, corresponding to the H1 node in Figure 1. The issue of the North African specificity of H1v, H1w and H1x needs to be corroborated by additional survey of H1 variation in Western Europe, especially in Iberia, but for the moment none of the European complete mtDNA sequences belonging to H1 were found to belong to these clades. This scenario is further supported by the overall age of haplogroup H1 in North Africa. Using the evolution rates recently proposed by Soares et al. [32] and Loogväli et al. [33], haplogroup H1 shows a coalescence time of approximately 8–9 ky (Table 1), in agreement with the hypothesis of an early arrival and radiation of H1 in the African continent in the first half of the Holocene, as a consequence of the postglacial expansion from the Iberian Peninsula. An arrival from Iberia explains the extent of H1 variation observed in North African populations (Table 2). Indeed, Moroccans and Tunisians, the populations geographically closest to Europe, harbor the highest diversity values for all considered indices. Thus, the coastal areas of northwestern Africa, after the arrival of the Iberian founder H1 mtDNAs, probably acted as centers for the subsequent diffusion of H1 in the internal regions of North Africa. The rather high frequency of H1 in the Tuareg from Sahel (23.3%), in association with intermediate diversity values, is in agreement with the proposal that drift played a major role in shaping the genetic structure of inland populations after they were entrapped in the Sahel belt by the desertification of the Sahara [37]. As for the Libyan Tuareg, the extremely low values of the diversity indices confirm that the outstanding high frequency of H1 in this population is the result of even more recent founder events.

The H1 phylogeny shows a link between the Tuareg of Libya and one Tunisian at the level of clade H1v (Figure 1). Therefore, the H1v coalescence time of about 4–7 ky (Table 1) might correspond to an ancestral split within a nomadic population of Northwest Africa, which led also to the formation of a derived Central Saharan population. The H1v1 sub-clade most likely arose in this population of Central Sahara, which, in turn, contributed extensively to the mtDNA pool of the modern villages of Tahala and Al Awaynat. However, the distribution of the H1v1 lineages in the two Tuareg villages, with H1v1b found only in Al Awaynat and 80% of H1v1a in Tahala and only 7% in Al Awaynat, indicates a rather sharp distinction and a village-specificity of the modern mtDNA gene pool. This is probably the result of peculiar long lasting cultural practices in the Tuareg, who define the affiliation to tribes by matrilineal descent [40], and points to a high degree of isolation between the two villages, at least at the maternal level, regardless of their geographic proximity.

Quote:
 
The migratory dynamics which took place over the last 2 ky in the hyperarid Central Sahara, and which possibly led small Tuareg groups with different maternal ancestries to mix and separate from one another [29], [41], [42], could explain the presence of the other two clades, H1w and H1x (respectively 53% and 9% of the total H1 mtDNAs analyzed), in the Libyan Tuareg sample. It should be noted that historically this phase coincides with the decline of the Garamantes, whom the Tuareg consider as their ancestors according to oral traditions [43], [44], [45]. These people inhabited the Fezzan between 2.7 and 1.8 kya and established state-entities based on sedentary settlements and the trans-Saharan caravan trade system. It is plausible that the dismantling of the Garamantian society led small groups to separate as distinct tribes, or alternatively to blend into larger groups.

Overall, the results of this study support the hypothesis that most of the West Eurasian maternal contribution detectable in Northwest African populations is likely linked to prehistoric (i.e. the post-glacial expansion from the Iberian Peninsula) rather than more recent historic events [26], [27], [37]. Furthermore, the data presented confirm that the analysis of complete mtDNA sequences represents a valuable tool to reveal not only the spatial patterns beneath large-scale colonization events, but also those of smaller-scale dispersals which may have contributed to the origin of modern populations. In this regard, additional efforts in the full mtDNA analyses of nomad Northern African populations might resolve the debate concerning their origin and their mutual relationship.





Genetic evidence for a Paleolithic human population expansion in Africa
Genetic evidence for a Paleolithic human population expansion in Africa
PDF file : http://www.broad.mit.edu/mpg/popgen/pubs/1998_PNAS_PaleolithicExpansion.pdf

Quote:
 
Human populations have undergone dramatic expansions in size, but other than the growth associated with agriculture, the dates and magnitudes of those expansions have never been resolved. Here, we introduce two new statistical tests for population expansion, which use variation at a number of unlinked genetic markers to study the demographic histories of natural populations. By analyzing genetic variation in various aboriginal populations from throughout the world, we show highly significant evidence for a major human population expansion in Africa, but no evidence of expansion outside of Africa. The inferred African expansion is estimated to have occurred between 49,000 and 640,000 years ago, certainly before the Neolithic expansions, and probably before the splitting of African and non-African populations. In showing a significant difference between African and non-African populations, our analysis supports the unique role of Africa in human evolutionary history, as has been suggested by most other genetic work. In addition, the missing signal in non-African populations may be the result of a population bottleneck associated with the emergence of these populations from Africa, as postulated in the "Out of Africa" model of modern human origins.


Charting the Ancestry of African Americans
http://docs.google.com/viewer?a=v&q=cache:QT8Yw6GvSQEJ:www.africandna.com/ScienPapers%255CCharting_the_Ancestry_of_African_Americans.pdf+States+where+African+admixture+components+in+European+Americans+are+up+to+about+one+third+%28Kittles+et+al.,+2003&hl=en&gl=us&pid=bl&srcid=ADGEESjTIVUmzaO5IgUcfRq9vULRJIZcGg4IsWqTyvSQiHWtMj_UEcjyFBg9pleLUr_eLFmq9eUWEqet8hi0NNk40eLgOJ3zYCOc72joROsD9XShModd3_cth85Qi9u6iCLtmtsFtbBa&sig=AHIEtbQvK5A8QS6cxhnDh3PUdhc8Z6sHhQ

…More significantly, we are now able to substantially revise and update the estimates for the main contributing regions. We performed the analysis in several ways. In the first, low resolution analysis, for which we used the 15 haplogroups that are illustrated in figure 1a and were used for the PCA, West Africa contributed 56.0+/- 4.2%, Southwestern Africa 27.8%+/-6.6%, and West-Central Africa 13.5%+/-8.3% (table 2). Although the last is not significantly different than zero, the admixture values for the west-central and southwestern samples are highly negatively correlated (Pearson correlation coefficient of –0.9), indicating that the large SD of the posterior distribution is most plausibly explained by the similarity of haplogroup frequency profiles of our west-central and southwestern subdivisions. A reanalysis that combined these two similar regions (and also excluded the other uninformative regions of Africa) yielded values of 52.5%+/-4.1% for West Africa and 47.5%+/-4.1% for west-central Africa.”