Phylogenetic and phylogeographic analysis of African mitochondrial DNA variation

Phylogenetic and phylogeographic analysis of African mitochondrial DNA variation
Sadie Anderson-Mann, March 2006

With mitochondrial DNA lineages tracing back more than 100,000 years, the genetic diversity
present throughout Africa is unparalleled. Within this continent, a wide array of different
mitochondrial haplotypes are found; as a result of the numerous demographic movements
that this region has witnessed, these have been differentially dispersed, some being
geographically localised whilst others are found over a large proportion of the continent.
Along with the Atlantic slave trade, the Bantu dispersals are the most recent of population
movements to have had significant effect on the genetic landscape of Africa, and are
associated with the distribution of several different haplogroups. Here, phylogenetic and
phylogeographic analysis of over 2,000 predominantly sub-Saharan African mtDNA
sequences has been carried out, through construction of reduced median and, where
necessary, median joining networks, based on mtDNA hypervariable segment 1 (HVS-I)
variation.

A big article that I will read sometime I don’t have food poisoning. It contains a lot of info about the Bantu expansion in it.

Hanihara: Characterization of Biological Diversity Through Analysis of Discrete Cranial Traits

This is a 2003 publication showing the relationship of the worlds populations by studying the crania. This paper says that both multiregional and the out of Africa scenario are possible from these results. As can be seen on the dendrogram, the Egyptian samples (Gizeh and Naqada) are on the North African twig along with the Nubians, which are themselves very close to the European cluster, which supports the Loring Brace study showing ancient Egyptians as being non-similar to Sub Saharan Africans. In fact a look at all the diagrams shows Hanihara grouping the ancient North Africans closer to west Eyurasian groups.

The only downer is that modern North Africans aren’t included on this.

 

I’ve added colour to the diagrams as they are a little hard to make out if you have poor sight. Sub Saharan is red (Somalis have a black dot inside) and Europeans are blue, North African samples are bright green, and South Asian are violet.

Characterization of Biological Diversity Through Analysis of Discrete Cranial Traits
Tsunehiko Hanihara,1* Hajime Ishida,2 and Yukio Dodo3, 2003

ABSTRACT In the present study, the frequency distributions of 20 discrete cranial traits in 70 major human
populations from around the world were analyzed. The principal-coordinate and neighbor-joining analyses of Smith’s mean measure of divergence (MMD), based on trait frequencies, indicate that 1) the clustering pattern is similar to those based on classic genetic markers, DNA polymorphisms, and craniometrics; 2) significant interregional separation and intraregional diversity are present in Subsaharan Africans; 3) clinal relationships exist among regional groups; 4) intraregional discontinuity exists in some populations inhabiting peripheral or isolated areas. For example, the Ainu are the most distinct outliers of the East Asian populations. These patterns suggest that founder effects, genetic drift, isolation, and population structure are the primary causes of regional variation in discrete cranial traits. Our results are compatible with a single origin for modern humans as well as the multiregional model, similar to the results of Relethford and Harpending ([1994] Am. J. Phys. Anthropol. 95:249– 270). The results presented here provide additional measures of the morphological variation and diversification of modern human populations.

East Asians
1. Japanese 98–108 (94) 62–64 (59) Tokyo and Tohoku (Northern Japan) regions (UT, TU)
2. Hokkaido Ainu 122–151 (113) 84–108 (76) Recent Ainu people (SMU, UT)
3. Sakhalin in Ainu 62–65 (54) 28–29 (32) Southern Sakhalin (MAE, MSU, KU, MH)
4. North Chinese 132–139 (75) 26–27 (14) Mainly from Liaoning Prefecture (UT, KU) Southeast Asians
5. Myanmar 132–135 (48) 47–49 (3) Recent Burmese (NHM, UC)
6. Mainland SE Asians 125–141 (105) 41–43 (30) Thai, Vietnam, Laos, Cambodia, and Malay (NHM, UC, MH)
7. Javanese 94–97 (83) 32–26 (32) Greater Sunda islands (NHM, UC, MH, AMNH)
8. Philippines 135–144 (49) 62–66 (31) Non-Negrito Filipinos (NHM, UC, MH)
9. Borneans 78–109 (74) 37–40 (21) Mainly land Dayaks (NHM, UC, MH)
10. Lesser Sunda 52–54 (39) 11–12 (6) Timor, Bali, Sumbawa, Flores, and Celebes Islands (NHM, UC, MH, AMNH)
11. Andamanese/Nicobarese 65–71 (43) 40–43 (30) Andaman Negritos and Nicobar Islands (NHM, UC, MH)
Northeast Asians
12. Mongolians 116–121 (69) 53–59 (38) Ulan Bator (Urga) and other regions (MH, NMNH, AMNH)
13. Buryats 76–81 (65) 64–69 (58) From Northeast Siberia (MAE, MH, NMNH)
14. Amur Basin 85–92 (57) 67–74 (48) Ulchs, Nanaians, Negidals, Nivkhs, and Orochs (MAE, MSU, MH)
15. Neolithic Baikalians 40–59 (45) 14–22 (19) From around Lake Baikal (MAE, MSU, ISU)
16. Yakuts 43–45 (38) 19–20 (18) From Northeast Siberia (MAE, MSU, MH) Arctic
17. Ekvens 45–55 (48) 49–56 (44) Iron-Age people from Ekven site, Chukot Peninsula (MSU)
18. Chukchis 43–48 (17) 22–26 (10) From Arctic region of Northeast Siberia (MAE, MSU, MH, NMNH, AMNH)
19. Aleuts 63–67 (48) 30–43 (17) Mainly from Unalaska Island (NMNH, AMNH)
20. Asian Eskimos 66–73 (48) 53–59 (16) From Arctic region of Northeast Siberia (MAE, MSU)
21. Greenland Eskimos 82–85 (47) 70–76 (25) West Coast of Greenland (NHM, UC, MH, AMNH, NMNH)
New World
22. Northwest Coast 53–59 (15) 29–35 (12) Northwest Coast of Canada (NHM, UC)
23. Northwest America 48–61 (40) 19–24 (16) Plateau, Great Basin, California, and Southwest Cultural
areas (NHM, UC, MH)
24. Northeast America 42–50 (20) 21–29 (8) Great Plains, Northeast, and Southeast Cultural areas
(NHM, UC)
25. Central America 45–58 (21) 24–30 (12) Mexico, Colombia, Ecuador, Carib, Venezuela, and Guyana
(NHM, UC)
26. Peruvians 115–123 (60) 55–60 (33) Cerro del Oro, Huacho, Pisagua, etc. (NHM)
27. Fuegians/Patagonians 39–44 (24) 20–23 (7) Terra del Fuego and Patagonia region (NHM, UC, MH)
Micronesians
28. Mariana 91–120 (82) 70–93 (75) Guam, Saipan, and Tinian (BM, MH) Polynesians
29. Hawaii 82 (58) 63–64 (42) Mainly from Oahu Island (NHM, UC)
30. Easter 63–79 (41) 59–71 (31) Easter Islanders (NHM, UC, MH, AM, US, SAM)
31. Marquesas 55–61 (24) 39–42 (9) Mainly from Uahuka Island (NHM, MH)
32. Maori 109–140 (58) 37–49 (23) New Zealand (NHM, UC, AM, US, SAM)
33. Moriori 66–78 (24) 18–20 (6) Chatham Islands (NHM, UC, AM, US) Melanesians
34. Papua New Guinea 54–175 (84) 51–154 (83) Purari River delta, Fly River delta, Sepik River Delta, etc.
(NHM, AM, US, SAM)
35. Torres Strait 59–65 (37) 35–38 (37) Island of Torres Strait (NHM, UC, MH)
36. North Melanesians 64–196 (119) 41–103 (72) New Ireland, New Britain, Solomon, and Santa Cruz (NHM,
UC, AM, US, SAM)
37. South Melanesians 58–137 (67) 27–57 (33) Loyalty, New Caledonia, Vanuatu, and Fiji (NHM, UC, AM,
US, SAM)
Australians
38. East Australians 53–88 (55) 33–46 (36) New South Wales, Queensland, and Victoria (AM, NHM, UC, MH, AMNH)
39. South/West Australians 86–260 (159) 34–128 (77) South Australia and Western Australia (SAM, NHM, UC, MH, AMNH)
Tibet/Nepal/Northeast India
40. Tibetans/Nepalese 91–94 (58) 23–25 (4) Tibetan Soldiers (19th Century), lowland of Nepal (NHM,
UC)
41. Assam/Sikkim 40–41 (30) 23–24 (19) Darjeeling, Assam, and Sikkim districts (NHM)
South Asians
42. Northeast India 90–93 (61) 23–24 (14) Bengal and Bihar districts (NHM)
43. South India 123–127 (65) 45–46 (30) Madras, Tamil Natu, Malabar Coast, and Karnataka (NHM)
44. Northwest India 125–131 (71) 32–35 (16) Punjab and Kashmir districts (NHM)
Central Asians
45. Tagars 62–72 (44) 60–76 (50) Iron-Age Tagar culture (MAE, MSU)
46. Kazakhs 75–77 (75) 42–43 (42) From Central Asia, Kazakh (MAE)
Europeans
47. Russians 72–74 (74) 45–47 (41) Recent Russians (NHM, UC, MAE, MSU)
48. Greece 46–54 (20) 12–16 (4) Ancient and recent Greece (NHM)
49. Eastern Europeans 80–98 (52) 18–24 (16) Slav group: Poland, Czecho, Hergegovina, Bulgaria, and
Yugoslavia (NHM)
50. Italy 131–146 (82) 42–47 (31) Recent Italians (NHM)
51. Finland/Ural 72–75 (35) 5–6 (2) Including a few samples of Ural-language people (NHM, MH)
52. Scandinavia 57–60 (30) 5 (3) Norwegians and Swedish (NHM, UC)
53. Germany 58–61 (44) 9–10 (7) Recent German (NHM, UC)
54. France 74–86 (23) 18–21 (0) Recent French (NHM, UC, MH)
UK series
55. Ensay 64–68 (58) 29–30 (30) Late Medieval to post-Medieval periods, Scotland (NHM)
56. Poundbury 97–109 (106) 46–52 (47) Late Roman period, Southwest England (NHM)
57. Spitalfields-1 122–135 (121) 104–113 (106) Mid-Victorian, London (NHM)
58. Spitalfields-2 73–74 (75) 17–19 (35) Pre-17th century, London (UC)
North Africans
59. Naqada 82–87 (57) 89–93 (39) Predynastic Egypt, ca. 5,000–4,000 BP (UC)
60. Gizeh 122–125 (91) 46–51 (32) 26th–30th Dynasty, Egypt, 664–343 BC (UC)
61. Kerma 114–132 (58) 79–92 (51) 12th–13th Dynasty of Nubia (UC)
62. Nubia 86–92 (39) 42–47 (9) Early Christian or Christian date Nubia (UC)
Subsaharan Africans
63. Somalia 58–64 (53) 10–12 (5) Erigavo District, Ogaden Somali (US)
64. Nigeria-1 74–83 (72) 65–76 (53) Ibo tribe (NHM, UC)
65. Nigeria-2 73–80 (17) 46–53 (7) Ashanti tribe (NHM, UC)
66. Gabon 82–86 (47) 55–57 (36) Fernand Vaz River (NHM, NMNH)
67. Tanzania 69–75 (54) 20–25 (17) Haya tribe, Musira Island, Lake Victoria (UC, NHM)
68. Kenya 71–82 (31) 55–63 (10) Bantu-speaking people from Kenya (UC, NHM)
69. South Africa 100–109 (53) 21–25 (8) Zulu and once called Kaffir tribes (UC, NHM, AMNH)
70. Khoisans 43–36 (28) 17–22 (13) Bushmans and Hottentots (NHM, UC, AMNH)

Fig. 2. Two-dimensional scattergrams drawn by using first-second (a), second-third (b), and third-fourth (c) principal coordinates. Numbers correspond to sample numbers in Table 1

Useful info for reference!

Mitochondrial DNA structure in the Arabian Peninsula

Mitochondrial DNA structure in the Arabian Peninsula

Background
Two potential migratory routes followed by modern humans to colonize Eurasia from Africa have been proposed. These are the two natural passageways that connect both continents: the northern route through the Sinai Peninsula and the southern route across the Bab al Mandab strait. Recent archaeological and genetic evidence have favored a unique southern coastal route. Under this scenario, the study of the population genetic structure of the Arabian Peninsula, the first step out of Africa, to search for primary genetic links between Africa and Eurasia, is crucial. The haploid and maternally inherited mitochondrial DNA (mtDNA) molecule has been the most used genetic marker to identify and to relate lineages with clear geographic origins, as the African Ls and the Eurasian M and N that have a common root with the Africans L3.

Results
To assess the role of the Arabian Peninsula in the southern route, we genetically analyzed 553 Saudi Arabs using partial (546) and complete mtDNA (7) sequencing, and compared the lineages obtained with those present in Africa, the Near East, central, east and southeast Asia and Australasia. The results showed that the Arabian Peninsula has received substantial gene flow from Africa (20%), detected by the presence of L, M1 and U6 lineages; that an 18% of the Arabian Peninsula lineages have a clear eastern provenance, mainly represented by U lineages; but also by Indian M lineages and rare M links with Central Asia, Indonesia and even Australia. However, the bulk (62%) of the Arabian lineages has a Northern source.

Conclusion
Although there is evidence of Neolithic and more recent expansions in the Arabian Peninsula, mainly detected by (preHV)1 and J1b lineages, the lack of primitive autochthonous M and N sequences, suggests that this area has been more a receptor of human migrations, including historic ones, from Africa, India, Indonesia and even Australia, than a demographic expansion center along the proposed southern coastal

Odd that the authors refer to M1 as African, as they themselves point out it’s Eurasian in origin in another paper. However, they do radiate out of North Africa, so possibly that was what it meant.. see below.

I’m guessing that a lot of the M1’s you find across North Africa and the near East were brought up from upper Egypt with the expansion of the Halfan culture into the Levant and Maghreb, and got into Ethiopia via the Southern expansion of the same population, following the M78 Y chromosome. Although I expect quite a few in the near East were due to the slave trade on the East African coast too. This paper also describes M1b as North African, not Ethiopian (although they haven’t standardised the naming yet, so M1b is differently named in various papers).

 

Also interesting was the appearance of some ‘Australian’ Mt DNA.

 However, the link found between the M Saudi 201 sequence and an M14 Australian sequence is puzzling. Although at first sight it could be taken as a signal of the connection between the two utmost ends of the southern route, it seems not to be the case. First, both lineages share three basal positions and this hypothetical link would considerably delay the arrival age of M in comparison to that of East Asia. It would be improbable that similar Australian links with other M lineages mainly from India were not found. Third, if the Arab lineage had such an old implantation in the Arabian Peninsula some detectable autochthonous radiation should be expected. Most probably, the M42 sequence belongs to an Australian clade and its related lineage found in Saudi Arabia is also of Australian origin. Historical links as those invoked to explain the presence of Indian and Indonesian sequences in the Arabian Peninsula pool should also be valid for this case. In our opinion, the camel trade between Saudi Arabia and Australia [54] could be a probable historic cause of this link. Future detection in Aboriginal Australians of other M42 lineages will confirm the Australian origin of this clade and its radiation age in that Continent. However, the link between the East Asia M10 clade [40] and the Australian M42 clade, if not due to convergence, seems to be more interesting as it would confirm, once more, the rapid expansion of macrohaplogroup M all along the Asian coasts [6,13]. The lack of autochthonous M and N lineages in the present day Arabian Peninsula populations confirms that this area was not a place of demographic expansion in the dispersal out of Africa [55].

 

Otzi the Iceman’s mitochondrial DNA

The Iceman reconstruction and mummy

For anyone not familiar with the Ice mummy, he’s a copper age man from the Alps, about 5,300 years old. He’s too well documented on for me to bother with a full biography of him. But the more interesting points are in brief..

He had tattoos of dots and spirals, that are possibly related to the arthritis in his knee as a form of acupuncture. He also had the blood of several people on him and his gear, so he seems to have been in some kind of conflict, possibly a tribal raid. He had an arrow head lodged in him (probably the cause of death) and his position suggests that he may have been turned over so the arrow could be removed. This suggests he wasn’t alone when he died.

Close examination of his mitochondrial DNA showed mutations associated with low sperm mobility, so it’s possible he was infertile. The more interesting thing about his mt DNA is that it is a previously unseen variant of K1, and it’s quite possibly extinct in the modern European population. What’s that? Banging on about how mt DNA types can be lost? How out of character.

 

Complete Mitochondrial Genome Sequence of the Tyrolean Iceman

Luca Ermini et al.

Abstract

The Tyrolean Iceman was a witness to the Neolithic–Copper Age transition in Central Europe 5350–5100 years ago, and his mummified corpse was recovered from an Alpine glacier on the Austro-Italian border in 1991 [1]. Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations.This is the oldest complete Homo sapiens mtDNA genome generated to date. The results point to the potential significance of complete-ancient-mtDNA studies in addressing questions concerning the genetic history of human populations that the phylogeography of modern lineages is unable to tackle.

Mitochondrial DNA haplogroups influence AIDS progression

Mitochondrial DNA haplogroups influence AIDS progression.

Hendrickson SL, Hutcheson HB, Ruiz-Pesini E, Poole JC, Lautenberger J, Sezgin E, Kingsley L, Goedert JJ, Vlahov D, Donfield S, Wallace DC, O’brien SJ.

OBJECTIVE:: Mitochondrial function plays a role in both AIDS progression and HAART toxicity; therefore, we sought to determine whether mitochondrial DNA variation revealed novel AIDS restriction genes, particularly as mitochondrial DNA single-nucleotide polymorphisms are known to influence regulation of oxidative phosphorylation, reactive oxygen species production, and apoptosis. DESIGN:: This is a retrospective cohort study. METHODS:: We performed an association study of mitochondrial DNA haplogroups among 1833 European American HIV-1 patients from five US cohorts: the Multicenter AIDS Cohort Study, the San Francisco City Clinic Study, Hemophilia Growth and Development Study, the Multicenter Hemophilia Cohort Study, and the AIDS Linked to Intravenous Experiences cohort to determine whether the mitochondrial DNA haplogroup correlated with AIDS progression rate. RESULTS:: Mitochondrial DNA haplogroups J and U5a were elevated among HIV-1 infected people who display accelerated progression to AIDS and death. Haplogroups Uk, H3, and IWX appeared to be highly protective against AIDS progression.

CONCLUSION:: The associations found in our study appear to support a functional explanation by which mitochondrial DNA variation among haplogroups, influencing ATP production, reactive oxygen species generation, and apoptosis, is correlated to AIDS disease progression; however, repeating these results in cohorts with different ethnic backgrounds would be informative. These data suggest that mitochondrial genes are important indicators of AIDS disease progression in HIV-1 infected persons.

Yet again, mt DNA not a neutral marker.

Genes, peoples, and languages, a paper by Cavalli Sforza.

Genes, peoples, and languages
L. LUCA CAVALLI-SFORZA
Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305-5120

Abstract
The genetic history of a group of populations is usually analyzed by reconstructing a tree of their origins. Reliability of the reconstruction depends on the validity of the hypothesis that genetic differentiation of the populations is mostly due to population fissions followed by independent evolution. If necessary, adjustment for major population admixtures can be made. Dating the fissions requires comparisons with paleoanthropological and paleontological dates, which are few and uncertain. A method of absolute genetic dating recently introduced uses mutation rates as molecular clocks; it was applied to human evolution using microsatellites, which have a sufficiently high mutation rate. Results are comparable with those of other methods and agree with a recent expansion of modern humans from Africa. An alternative method of analysis, useful when there is adequate geographic coverage of regions, is the geographic study of frequencies of alleles or haplotypes. As in the case of trees, it is necessary to summarize data from many loci for conclusions to be acceptable. Results must be independent from the loci used. Multivariate analyses like principal components or multidimensional scaling reveal a number of hidden patterns and evaluate their relative importance. Most patterns found in the analysis of human living populations are likely to be consequences of demographic expansions, determined by technological developments affecting food availability, transportation, or military power. During such expansions, both genes and languages are spread to potentially vast areas. In principle, this tends to create a correlation between the respective evolutionary trees. The correlation is usually positive and often remarkably high. It can be decreased or hidden by phenomena of language replacement and also of gene replacement, usually partial, due to gene flow.

Which contains the

One reasonable hypothesis is that the genetic distance between Asia and Africa is shorter than that between Africa and the other continents in Table 1 because both Africans and Asians contributed to the settlement of Europe, which began about 40,000 years ago. It seems very reasonable to assume that both continents nearest to Europe contributed to its settlement, even if perhaps at different times and maybe repeatedly. It is reassuring that the analysis of other markers also consistently gives the same results in this case. Moreover, a specific evolutionary model tested, i.e., that Europe is formed by contributions from Asia and Africa, fits the distance matrix perfectly (6). In this simplified model, the migrations postulated to have populated Europe are estimated to have occurred at an early date (30,000 years ago), but it is impossible to distinguish, on the basis of these data, this model from that of several migrations at different times. The overall contributions from Asia and Africa were estimated to be around two-thirds and one-third, respectively.

Which doesn’t seem to fit the mt/Y DNA patterns, although to be fair L mt types don’t seem to thrive in a cold climate. Since he gives a 146,000 ya date for the first migration out of Africa, this second wave of expansion could have been a very long time ago. Possibly a double OOA might explain the total failure of Y chr dates to tally with the mt DNA expansion dates.

The first estimate gave a separation time of the first migrants out of Africa of 146,000 years ago, very close to the date obtained with the mtDNA full sequence. This was based on results with 30 microsatellites (5). More recent results (L. Jin, unpublished work) with 100 microsatellites gave an earlier date.

Also more humourously, but unlikely..

The Ethiopians genotype is more than 50% African. It is difficult to say if they originated in Arabia and are therefore Caucasoids who, like Lapps, had substantial gene flow after they migrated to East Africa, or if they originated in Africa and had substantial gene flow from Arabia, but not enough to pass the 50% mark.

I think the ‘ mixed expansion south from Egypt with some later Neolithic Arabian farmer’ is a more likely scenario.

I’ll admit to not reading the whole thing before posting it. I have a rotten headache and the kids are playing up. I’ll read it tomorrow.

And having had another look..

There’s this interesting map showing patterns of variation in Europe.

FIG. 2. Hidden patterns in the geography of Europe shown by the first five principal components, explaining respectively 28%, 22%, 11%, 7%, and 5% of the total genetic variation for 95 classical polymorphisms (1, 13, 14).

 

The first component is almost superimposable to the archaeological dates of the spread of farming from the Middle East between 10,000 and 6,000 years ago.

 

 

 

 The second principal component parallels a probable spread of Uralic people and/or languages to the northeast of Europe.

 

 

 

The third is very similar to the spread of pastoral nomads (and their successors) who domesticated the horse in the steppe towards the end of the farming expansion, and are believed by some archaeologists and linguists to have spread most Indo-European languages to Europe.

 

 

The fourth is strongly reminiscent of Greek colonization in the first millennium B.C.

 

 

 The fifth corresponds to the progressive retreat of the boundary of the Basque language. Basques have retained, in addition to their language, believed to be descended from an original language spoken in Europe, some of their original genetic characteristics. (From ref. 1, with permission of Princeton University Press, modified.)

Algerian Y chromosomes

Analysis of Y-chromosomal SNP haplogroups and STR haplotypes in an Algerian population sample.

Robino C, Crobu F, Di Gaetano C, Bekada A, Benhamamouch S, Cerutti N, Piazza A, Inturri S, Torre C.

The distribution of Y-chromosomal single nucleotide polymorphism (SNP) haplogroups and short tandem repeat (STR) haplotypes was determined in a sample of 102 unrelated men of Arab origin from northwestern Algeria (Oran area). A total of nine different haplogroups were identified by a panel of 22 binary markers. The most common haplogroups observed in the Algerian population were E3b2 (45.1%) and J1 (22.5%). Y-STR typing by a 17-loci multiplex system allowed 93 haplotypes to be defined (88 were unique). Striking differences in the allele distribution and gene diversity of Y-STR markers between haplogroups could be found. In particular, intermediate alleles at locus DYS458 specifically characterized the haplotypes of individuals carrying haplogroup J1. All the intermediate alleles shared a common repeat sequence structure, supporting the hypothesis that the variant originated from a single mutational event.

I’ve been over at Dienekes and found this. I  can’t access the full text 

• 22   J1                 22.5%
• 8    E3a-M2         8.6%
• 6    E3b1-M78     6.12%
• 40  E3b2-M81     45.1%
• 5    J2f-M67         5.1%
• 1    R1-M173       1% 
• 11  R1b3-M269   11.2%
• 1    Q-M242         1%

I noticed the R1’s there. It’s unlikely to be from Europeans, probably the ancient Y chr’s from the back migration from Eurasia, plus some variants of it. R1 is also seen in the Sudan, Cameroon and the Ouldeme, in surprisinly high amounts.

Studies of Ancient Crania From Northern Africa

Normally I’m a bit averse to Keita, who waffles on like he’s being paid by the word. I was also initially rather put off by the iffy paper on the Badarians, which had a couple of glaring problems with it, as does this one. But, you can’t really look at North Africa without reading his publications.

He takes a viewpoint that the partially Eurasian derived Berbers and Egyptians are mainly ‘indigenous Africans’. Once you get your head around that ‘indigenous African’ doesn’t mean black or sub Saharan African but also refers to Egyptians and modern Berbers, his work makes a lot more sense. He’s massively misquoted by the muppets on Egyptsearch, who always manage to ignore that Keita explicitly states in one paper that modern Egyptians are mainly the same as the pre-Neolithic Egyptians, with some immigration due to the Neolithic and later invasions, which is exactly what everyone else sane says. He’s also on the record as saying Egyptians look pretty much the same. He also rambles on a bit. But then, Brace is irritatingly self contradictory at times. So I guess no author is without their faults

Keita on Egyptians.

..current inhabitants of the Nile valley should be understood as being in the main, although not wholly, descendants of the pre-neolithic regional inhabitants 

Studies of Ancient Crania From Northern Africa

S.O.Y. KEITA AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 83:35-48 (1990)

ABSTRACT Historical sources and archaeological data predict significant population variability in mid-Holocene northern Africa. Multivariate analyses of crania demonstrate wide variation but also suggest an indigenous cranio- metric pattern common to both late dynastic northern Egypt and the coastal Maghreb region. Both tropical African and European metric phenotypes, as well intermediate patterns, are found in mid-Holocene Maghreb sites. Early southern predynastic Egyptian crania show tropical African affinities, displaying craniometric trends that differ notably from the coastal northern African pattern. The various craniofacial patterns discernible in northern Africa are attributable to the agents of microevolution and migration.

That both phenotypes are found, not really a shocker as the DNA studies show continuity in North Africa since the 12,000 BP Taforalt site.

Conclusion

The analyses demonstrate the metric heterogeneity of pre-Roman mid-Holocene Maghreban crania. The range of variation in the restricted area described extends from a tropical African metric pattern to a European one and supports the phenotypic variability observed in and near Carthage by ancient writers and in morphological studies. Thus the population emerges as a composite entity, no doubt also containing hybrid individuals. However, the centroid value of the combined Maghreb series indicates that the major craniometric pattern is most similar to that of northern dynastic Egyptians, not northwest Europeans. Furthermore, the series from the coastal Maghreb and northern (Lower) Egypt are more similar to one another than they are to any other series by centroid values and unknown analyses.

The upper Nile Valley series show close affinities to one another and to tropical African series. Thus variation is also present in the Egyptian Nile Valley, as the northern pattern trend is distinguishable from the southern one. The Badari and Nagada I cranial patterns emerge as tropical African variants (with Kerma). Badari remains show little affinity to the mass of Maghreban crania. Notable Nagada/Kerma metric overlapis observed with the first dynasty series,which shares the pattern to a lesser degree, as indicated by its centroid values.

In summary, canonical variate analysis demonstrates the impressive variation suggested previously for early northern Africa. It also suggests that there was a modal craniometric phenotype common to northern-Egypt and the coastal Maghreb in the mid Holocene, intermediate to European and southern Egyptian Nile Valley/tropical series.

A few comments on this paper. He points out that NW Europeans have absolutely no resemblance to these North Africans (fair enough) but neglects to mention how similar or dissimilar they are to SE Europeans. Which is particularly odd, since a moderate Neolithic inflow from SE Europe/near East is accepted by him in another publication. So, you’d think a comparison to SE Europeans or Levantine populations would be more appropriate. Then, another paper uses NW Europeans as the base line for all Europeans when comparing them to the Badarians, instead if groups like Greeks or Levantine people or modern North Africans, or heaven forbid, modern Egyptians. Which makes no sense. And he had the cheek to criticise Brace and other authors on their choice of sample populations.

Just for once I’d like to see a direct comparison of ancient to modern Egyptians, for hair, limb length and crania with the few DNA samples taken chucked in for good measure.

Also, my long running bugbear is his quote from Strouhal.

Strouhal(1971) also analyzed hair in his study of 117 Badari crania, in which he concluded that >80% were Negroid; most of these were interpreted as being hybrids

I’ve seen material from Strouhal; it doesn’t say the hair was greater than 80% negroid. I’ve seen ’sterotypically mulatto’ and a detailed description that was anything other than >80% negroid. Strouhal also describes the Badari crania as a ‘mix of races’, slightly overweighted to the European. Which is pretty standard for the older crania studies. So I’m baffled as to the exact reference for this. However, points he and I agree on are that there was a 24k or so old expansion from upper Egypt so I know he’s not an idiot.

Continuity in the Epipaleolithic of Northern Africa with Emphasis on the Maghreb

Another bookmarked item for my reference.

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Continuity in the Epipaleolithic of Northern Africa with Emphasis on the Maghreb

This article is primarily a review and reinterpretation of the Epipaleolithic pre-history of the Maghreb. However, in view of the similarities to other parts of North Africa, we include some discussion of areas outside the Maghreb proper, specifically Cyrenaica and the Nile Valley. Research on Maghreb prehistory hasbeen undertaken for close to a century. The vast majority of published information is in French and is not always familiar to or well understood by Anglophone scholars. Archaeology in the Maghreb has been dominated by a typological approach, both in terms of artifacts and human skeletal remains. This approach has provided most of the data from which our re-interpretations are derived. It has also, inevitably perhaps, fostered the division of prehistory into segments that, while they may have some reality for the archaeologist trying to under-stand the geographic and chronological patterning of remains, do not necessarily tell one very much about the cultural interrelationships of the people those remains represent. It is our basic contention in this essay that one should never propose direct correspondences between archaeological industries and ethnic groups, or “races,” without clear and indisputable evidence. Such correspondences have been made many times for the Maghreb and it is this, if nothing else, that we hope to show to be unlikely. Our basic premise throughout this essay is that differences have been emphasized over similarities and that theidentification of distinctions has been the preferred method of describing variability in the prehistoric record.

It’s got a lot of information on North African blade industries on it.

Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland

Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland

27 June 2008

The Paleo-Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World’s northern extremes. However, their origin and genetic relationship to later cultures are unknown. We sequenced a mitochondrial genome from a Paleo-Eskimo human by using 3400-to 4500-year-old frozen hair excavated from an early Greenlandic Saqqaq settlement. The sample is distinct from modern Native Americans and Neo-Eskimos, falling within haplogroup D2a1, a group previously observed among modern Aleuts and Siberian Sireniki Yuit. This result suggests that the earliest migrants into the New World’s northern extremes derived from populations in the Bering Sea area and were not directly related to Native Americans or the later Neo-Eskimos that replaced them.

Oh look, a lost mt DNA lineage. People will think I’m getting repetetive.