Y chromosome J quick reference page

My blogging lately has been slowed down by my MS flaring up and my boy discovering Lego Indiana Jones online – my  apologies to anyone I haven’t responded to in the comments.

A basic page for reference on J1 and J2 so I don’t have to root through multiple papers and blog entries every time I want to find something.

This is a homemade table and mainly from Cruciani’s 2004 figures and Hassan 2008  for a one-glace overview . The Egyptian figures are my own from several combined sources and are about as accurate as you’ll get for that country. The other countries are from single paper sources and probably aren’t as accurate overall, but it’s a decent rough guide.

The actual Cruciani table, another chart (can’t remember which paper).

 

From Giacomo 2004 and Battaglia 2008

 

 

   

Greece, From Martinez 2007. Turkey; Cinnioglu 2003 and  Semino 2002.

    

Iran, from Cadenas 2006, from Al-Zahery 2002 and Luis 2004

From Giacomo 2004

 

While not the neatest page, it should be useful for quicker referencing. A good look through the J hg’s around the near East has reinforced a Neolithic or older entry date for the J2 in North Africa as far as I’m concerned, as the ratio of J2 to J1/other hg’s is incompatible with it having a historical arrival from any of the known invading areas. I’m also wondering if upper Egypt is the switch over  area from Arab J1 to Capsian J1.

Reference list.

• Semino 2002
• Al-Zahery 2002
• Cinnioglu 2003
• Cruciani 2004
• Giacomo 2004
• Luis 2004
• Cadenas 2006
• Battaglia 2008
• Hassan 2008

If anyone else finds a Y chromosome J reference for the near East, Europe, North Africa or India/Pakistan that I haven’t included leave the name of the paper ( I expect there’s a few) in the comments, as I’ll be adding to this one as I go along. Also a decent recent tree of J would be nice – if anyone find one send me a link!

Egyptian Y DNA and mt DNA reference

All the info I could find, collected in one place from assorted studies, mainly for my own ease of reference. I’ve kept putting this off, but finally here I am.

Egyptian  Y chromosomes

From Luis et al 2004.

 Which places the African Y chromosomes (this is a lower Egyptian sample group) at about 42%. I was most interested by the expansion time for the Eurasian hg’s. Luis et al estimated an expansion time of 13.7–17.5 ky for the K2 lineages in Egypt, although it also states the K2 could have accompanied R1*-M173 back into Africa in the paleolithic along with the U and M1.

Like the R1*-M173 males, the M70 individuals could represent the relics of an early back migration to Africa from Asia, since these chromosomes are not associated with the G-M201, J-12f2, and R1-M173 derivatives, lineages that represent more-recent Eurasian genetic contributions.

It also describes J-12f2 as a marker of the Neolithic expansion. Although looking through the Sudanese Y chromosome study it Hassan puts it down as a recent Arab marker, although no expansion dates are mentioned in his paper, so I’m not sure on what basis that conclusion was drawn. The J is complicated to unravel. After a read of Cruciani 2004 it would seem about 90% of the  J-12f2 is Arabic in origin, but the M172 (J2) is rather older and probably Neolithic, although this doesn’t seem to agree with the age estimates for J-12f2 in this paper. It would seem that J has made several entrances to North Africa.

From Lucotte 2003, which needs this Keita paper to understand it. Haplotypes V, XI and IV are all Pn2 derived (E). VII and VIII are considered Arabic, so I’m assuming J1 is VIII and VII is J2.

The other study that deals with numbered and not named groups is by Franz et al. This puts Hg 1 (E) at 44% in Egypt (Cairo) and J  (Hg 9) at 35%, but unfortunately the rest of the information is a bit vague.

From Arredi 2004 which had a small study of upper and lower Egyptians as part of a North Africa overview.

Lower Egypt (0f 44 samples)

• 1 A3b2*
• 4 E3b3a
• 12 E3b1
• 2 E3b
• 5 E3b2
• 1 J2f1
• 3 J2
• 3 F
• 4 J
• 1 O
• 1 K2
• 4 R1
• 1 R1a*
• 2 P

Upper Egypt (of 29 samples)

• 2 E3b3a
• 5 E3b1
• 2 E3b2
• 1 I
• 1 J2
• 5 F
• 6 J
• 3 K2
• 4 R1

Which places AfricanY DNA at 59%, and J at 18% in Lower Egypt, which is close to the Lucotte study. Upper Egypt has a much more diverse profile (oddly) with J at 20% and African Y chromsomes at a much lower 31% with the ‘old in Africa’ R1 and K making up 24% of this (pretty small) sample. Having seen this study I’ve been obliged to dig into the origin of F, and it does look like an ‘ancient in Africa’ Y chromosome (Karafet 2008) as it turns up in the Bantu in South Africa.

From Wood et al 2005,which is in here provisionally until I can check the paper personally as I’ve borrowed it from Maju’s comments.

3/92 = 3.3% A3b2-M13
2/92 = 2.2% B2a1a-M152
1/92 = 1.1% E-SRY4064(xE1a-M33, E2-M75, E1b1-P2)
1/92 = 1.1% E1a-M33
2/92 = 2.2% E1b1a-P1(xE1b1a7-M191)
1/92 = 1.1% E1b1a7-M191
8/92 = 8.7% E1b1b1-M35(xE1b1b1a-M78, E1b1b1b-M81)
28/92 = 30.4% E1b1b1a-M78
4/92 = 4.3% E1b1b1b-M81
2/92 = 2.2% F-P14(xG-M201, H1-M52, I-P19, J-12f2, K-M9)
2/92 = 2.2% G-M201
1/92 = 1.1% I-P19
21/92 = 22.8% J-12f2
1/92 = 1.1% K-M9(xL-M20, M1-M4, N1-LLY22g, O-M175, P-P27, T-M70)
7/92 = 7.6% T-M70
1/92 = 1.1% R-M207(xR1-M173)
2/92 = 2.2% R1-M173(xR1a1-SRY10831b, R1b1-P25)
4/92 = 4.3% R1b1-P25(xR1b1b2-M269)
1/92 = 1.1% R1b1b2-M269

T formerlyK2, I believe. Finally I find a source for the R1b in the Sudan and Cameroon.

Finally a study of J (Giacomo 2004) found the Egyptian sample to be 23.4% J and with more clarity this was..

• 6 J1
• 1 J2*
• 2 J2
• 1 J2f
• 1 J2fl

I can’t help noticing there’s a fair amount of variance between these studies. But still the overall picture you get from Lower Egypt is about half native African, with most of the other Eurasian Hg’s dating back into prehistory.

Lower Egypt is about 55% African, mainly E3b, E and then A.

The next largest group is J, which is unfortunately a bit hard to separate out from Neolithic expansion, Capsian expansion, earlier historic population movements and the Arab expansion, but it averages out at 25% from all five studies, with possibly a third of it attributable to non historic expansions (J2, a little  Capsian J1).

After this comes the ‘old in Africa’ haplotypes, which make up the bulk of the remaining Y chromosomes about 19% (again averaging the studies, the HG vary in proportion but they came up near 19% overall).

Which takes Lower Egypt into the low 80% area for paternal ancestry traceable to the dynastic era and earlier. One would assume the Arab expansion didn’t bring anywhere near as much maternal DNA with it, although some tribes did settle in Egypt.

Egyptian mitochondrial DNA

From Berbers at Siwa Oasis (north west Egypt) and from Egyptians at Gurna (upper Egypt area) Detail here.

Siwa; Of 78 samples.

• Eurasian  45
• Asian (M) 1
• North African (U6 and M1) 13
• Sub Saharan 19

24% SSA, 75% Eurasian/N African.

Gurna

• H 5 14.7
• I 2 5.9
• J 2 5.9
• L1a 4 11.7
• L1e 2 5.9
• L2a 1 2.9
• M1 6 17.6
• N1b 3 8.8
• T 2 5.9
• U 3 8.8
• U3 1 2.9
• U4 2 5.9
• L3*(a) 2 5.9
• L3*(b) 1 2.9

29% SSA, 71% Eurasian/N African.

Surprisingly little difference between them. Lower Nubia came in at about 60% Eurasian an ancient mummy test– and while it’s correct that L3 also comes into the category marked out as Eurasian, it’s actually pretty close to the DNA study of modern Nubians. Unless the invading armies of history were all women there’s no plausible scenario to explain such a huge influx of Eurasian ancestry in such a relatively short space of time, as the Y chromosome presence of Arabs in the area just isn’t that massive in the modern lower Nubia area.

From Krings 1999. Which also shows that Egyptian maternal DNA is roughly 25% sub Saharan and 75% Eurasian. 

 

Ancient Egyptian DNA

To obtain the frequencies of these mtDNA types, amplification of the HVRI region and three RFLP markers was conducted. The authors succeeded in analysing RFLP markers in 34 samples and HVRI sequences in 18 of the samples. Both populations, ancient and contemporary, fit the north-south clinal distribution of “southern” and “northern” mtDNA types (Graver et al. 2001). However, significant differences were found between these populations. Based on an increased frequency of HpaI 3592 (+) haplotypes in the contemporary Dakhlehian population, the authors suggested that, since Roman times, gene flow from the Sub-Saharan region has affected gene frequencies of individuals from the oasis.

Which suggests the proportion of sub Saharan lineages is higher now than it once was at Dahkleh (SW Egypt). Bearing in mind that the Arab slave trade in African women seems to have accounted for about 10-15% of the maternal DNA in Arabia, this would seem the most likely cause in the increase of sub Saharan lineages. It would seem that post dynastic inflow maternal from sub Saharan African is passably close match to the paternal immigration from Arabs, and that these are probably the two most influential factors in immigration in post dynastic Egypt.

Not strictly speaking Egyptian but still relevant.

Copts from the Sudan, from Hassan 2008.

• 13/33 J1
• 5/33 B
• 2/33 E3b
• 5/33 E3b1
• 2/33 J2
• 1/33 K
• 5/33 R1b

Nubians from the Sudan

• 3/39 B
• 3/39 E3b
• 6/39 E3b1
• 4/39 F
• 2/49 I
• 16/39 J1
• 1/39 J2
• 4/39 R1b

The high level of J1 is quite a surprise in both of these. Particlarly since Copts aren’t supposed to marry out. A y chr study of Cairo Copts could be informative as to just how much mixing there has been between the two groups there.

One thing that became apparent after reading through these DNA studies was that there was a somewhat higher level of African male ancestry in Egyptians than in a lot of the East African groups, and that the Horn Africans and Egyptians are really made up of very similar ancestries (West Asian, North East African and East African with a little Bantu here and there) but in varying ratios.

Reference list.

1.  Luis 2004
2.  Cruciani 2004
3. Lucotte 2003
4. Wood 2005
5. Franz 2002
6. Hassan 2008
7. Krings 1999
8. Arredi 2004
9. Karafet 2008
10. Giacomo 2004

Prehistoric Iberia: Genetics, Anthropology, and Linguistics

Prehistoric Iberia: Genetics,Anthropology, and Linguistics

A pdf that does what it says. It’s a description of conference about Iberia, North Africa and the Canaries. A quick and fairly interesting read if you are interestede in this area. It mentions tha Tuareg as relative newcomers to North West Africa, being related to the Beja of the Sudan. It aslo has some HLA work by the barking mad Arnaiz-Villena in it.

The Romani; DNA, language and migration

I’m finally getting around to the Roma. Living in the South East England, I’m very familiar with people of Roma ancestry, as a lot settled here after the second world war when the new housing was built. For the most part they’ve assimilated into the rest of the population, their only real cultural footprint being their contribution to the language. Being from the SE, I’m pretty familiar with all of these, but I know the non-English will need a translation.

• Cushy = same root as Cushti
• Cushti = good, from Kusko meaing good
• Chiv = cut
• Chav = common individual from chavvie, meaning boy
• Cove = person, from cova
• Shiv = Knife-like weapon
• Nark = informant
• Hotchpotch = mixture
• Mush = face/mouth, man, from moosh meaning town-man
• Rum = strange/odd, from rrom
• Pal = friend (originally brother/comrade)
• Minge = vagina
• Minger = ugly woman
• Minging=disgusting
• Bosh = make noise
• Gaff = place of residence, from gav, meaning village
• Wonga = money, from vonga
• Lollipop= from toffee apple- cosh lollipop

These are words of an Indo-European language, and it probably had an origin in the northern India/Pakistan area, the Punjab being the most likely.

I’m friends with members of three different Rom families in Kent. While some of them still retain their dark looks here (one could easily pass for Pakistani, and one got mistaken for a local on holiday in Turkey by the locals) most don’t look any different to the rest of the population due to intermarriage. 

Their assimilation into mainstream culture is more or less a done deed here. Of the Roma I know, two are prison officers and one a teacher, so the old Nazi ideology of their being inherently criminal or less intelligent has been proven to be wrong by their recent track record in the UK.

Romany migration route.

 Romany in the UK  (a short paper on the Angloromani dialect)

 DNA articles.

 A Romani mitochondrial haplotype in England 500 years before their recorded arrival in Britain

Ana L Töpf and A. Rus Hoelzel*
Received November 9, 2004; Accepted February 27, 2005.

The nomadic Romani (gypsy) people are known for their deep-rooted traditions, but most of their history is recorded from external sources. We find evidence for a Romani genetic lineage in England long before their recorded arrival there. The most likely explanations are that either the historical record is wrong, or that early liaisons between Norse and Romani people during their coincident presence in ninth to tenth century Byzantium led to the spread of the haplotype to England.

Searching for the origin of Romanies: Slovakian Romani, Jats of Haryana and Jat Sikhs Y-STR data in comparison with different Romani populations.
 
[My paper] Melinda Nagy, Lotte Henke, Jürgen Henke, Prasanta K Chatthopadhyay, Antónia Völgyi, Andrea Zalán, Orsolya Peterman, Jarmila Bernasovská, Horolma Pamjav
J. Selye University, Komárno, Slovakia.
Haplotype frequencies for 11 Y-STR markers (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438 and DYS439) in a Romani population (n=63) from Slovakia, Jats of Haryana (n=84) and Jat Sikhs (n=80) from India were determined. The Slovakian Romani, the Haryana and Sikh populations were endogamous based on their unique haplotype ratio and haplotype diversity values, although the Sikh population appeared to be more diverse. AMOVA revealed non-significant differences between the Romanies and significant differences with non-Romani populations. The Macedonian Romani population differed from all Romani populations examined. Frequent haplotypes observed in Romani populations were sporadic in northwest Indian populations. Thirteen out of 316 populations worldwide were found to share the six most frequent haplotypes of the Slovakian Romanies when the screening conditions were narrowed based on the population size to be over 40, the occurrence of the haplotypes was more than one and the sum frequencies of the most frequent haplotypes was at least 0.02. The most common haplotypes were also observed in other Romani groups. When searching with two Indian (Malbar and Malaysian Indian) most frequent haplotypes under the same conditions matches could be detected in all Romani populations except for the Macedonian Romanies. The search with the Jat Sikhs and Jats of Haryana most frequent haplotypes resulted no matches in Romani populations.

Mitochondrial DNA Diversity in the Polish Roma.

BA Malyarchuk, T Grzybowski, MV Derenko, J Czarny, D Miścicka-Śliwka

Summary Mitochondrial DNA variability in the Polish Roma population has been studied by means of hypervariable segment I and II (HVS I and II) sequencing and restriction fragment-length polymorphism analysis of the mtDNA coding region. The mtDNA haplotypes detected in the Polish Roma fall into the common Eurasian mitochondrial haplogroups (H, U3, K, J1, X, I, W, and M*). The results of complete mtDNA sequencing clearly indicate that the Romani M*-lineage belongs to the Indian-specific haplogroup M5, which is characterized by three transitions in the coding region, at sites 12477, 3921 and 709. Molecular variance analysis inferred from mtDNA data reveals that genetic distances between the Roma groups are considerably larger than those between the surrounding European populations. Also, there are significant differences between the Bulgarian Roma (Balkan and Vlax groups) and West European Roma (Polish, Lithuanian and Spanish groups). Comparative analysis of mtDNA haplotypes in the Roma populations shows that different haplotypes appear to demonstrate impressive founder effects: M5 and H (16261-16304) in all Romani groups; U3, I and J1 in some Romani groups. Interestingly, haplogroup K (with HVS I motif 16224-16234-16311) found in the Polish Roma sample seems to be specific for Ashkenazi Jewish populations. 

Frequencies of mtDNA haplogroups in southeastern Europe–Croatians, Bosnians and Herzegovi

S Cvjetan, HV Tolk, LB Lauc, I Colak, D Dordević, L Efremovska, B Janićijević, A Kvesić, IM Klarić, E Metspalu, M Pericić, J Parik, D Popović, A Sijacki, R Terzić, R Villems, P Rudan

Mitochondrial DNA polymorphisms were analyzed in of 1,610 randomly chosen adult men from 11 different regions from southeastern Europe (Croatians, Bosnians and Herzegovinians, Serbians, Macedonians and Macedonian Romani). MtDNA HVS-I region together with RFLP sites diagnostic for main Euroasian and African mtDNA haplogroups were typed to determine haplogroup frequency distribution. The most frequent haplogroup in studied populations was H with the exception of Macedonian Romani among whom the most frequent were South Asian (Indian) specific variants of haplogroup M. The multidimensional scaling plot showed two clusters of populations and two outliers (Macedonian Romani and the most distant from mainland Croatian island of Korcula). The first cluster was formed by populations from three Croatian islands (Hvar, Krk and Brac) and the second cluster was formed by Macedonians, Serbians, Croatians from mainland and coast, Herzegovinians, Bosnians, Slovenians, Poles and Russians. The present analysis does not address a precise evaluation of phylogenetic relations of studied populations although some conclusions about historical migrations could be noticed. More extended conclusions will be possible after deeper phylogenetic and statistical analyses.

Dissecting the molecular architecture and origin of Bayash Romani patrilineages: Genetic influences from South-Asia and the Balkans

Irena Martinovi Klari et al.

The Bayash are a branch of Romanian speaking Roma living dispersedly in Central, Eastern, and Southeastern Europe. To better understand the molecular architecture and origin of the Croatian Bayash paternal gene pool, 151 Bayash Y chromosomes were analyzed for 16 SNPs and 17 STRs and compared with European Romani and non-Romani majority populations from Europe, Turkey, and South Asia. Two main layers of Bayash paternal gene pool were identified: ancestral (Indian) and recent (European). The reduced diversity and expansion signals of H1a patrilineages imply descent from closely related paternal ancestors who could have settled in the Indian subcontinent, possibly as early as between the eighth and tenth centuries AD. The recent layer of the Bayash paternal pool is dominated by a specific subset of E1b1b1a lineages that are not found in the Balkan majority populations. At least two private mutational events occurred in the Bayash during their migrations from the southern Balkans toward Romania. Additional admixture, evident in the low frequencies of typical European haplogroups, J2, R1a, I1, R1b1b2, G, and I2a, took place primarily during the early Bayash settlement in the Balkans and the Romani bondage in Romania. Our results indicate two phenomena in the Bayash and analyzed Roma: a significant preservation of ancestral H1a haplotypes as a result of considerable, but variable level of endogamy and isolation and differential distribution of less frequent, but typical European lineages due to different patterns of the early demographic history in Europe marked by differential admixture and genetic drift.

Croatian mt DNA and Y chromosomes

Review of Croatian genetic heritage as revealed by mitochondrial DNA and Y chromosomal lineages.

Pericic M, Barac Lauc L, Martinovic Klaric I, Janicijevic B, Rudan P.
Institute for Anthropological Research, Amruseva 8, 10000 Zagreb, Croatia.

The aim of this review is to summarize the existing data collected in high-resolution phylogenetic studies of mitochondrial DNA and Y chromosome variation in mainland and insular Croatian populations. Mitochondrial DNA polymorphisms were explored in 721 individuals by sequencing mtDNA HVS-1 region and screening a selection of 24 restriction fragment length polymorphisms (RFLPs), diagnostic for main Eurasian mtDNA haplogroups. Whereas Y chromosome variation was analyzed in 451 men by using 19 single nucleotide polymorphism (SNP)/indel and 8 short tandem repeat (STR) loci. The phylogeography of mtDNA and Y chromosome variants of Croatians can be adequately explained within typical European maternal and paternal genetic landscape, with the exception of mtDNA haplogroup F and Y-chromosomal haplogroup P* which indicate a connection to Asian populations. Similar to other European and Near Eastern populations, the most frequent mtDNA haplogroups in Croatians were H (41.1%), U5 (10.3%), and J (9.7%). The most frequent Y chromosomal haplogroups in Croatians, I-P37 (41.7%) and R1a-SRY1532 (25%), as well as the observed structuring of Y chromosomal variance reveal a clearly evident Slavic component in the paternal gene pool of contemporary Croatian men. Even though each population and groups of populations are well characterized by maternal and paternal haplogroup distribution, it is important to keep in mind that linking phylogeography of various haplogroups with known historic and prehistoric scenarios should be cautiously performed.

No real surprises in this paper.

 

The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations.

The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations.

2003

Two tribal groups from southern India–the Chenchus and Koyas–were analyzed for variation in mitochondrial DNA (mtDNA), the Y chromosome, and one autosomal locus and were compared with six caste groups from different parts of India, as well as with western and central Asians. In mtDNA phylogenetic analyses, the Chenchus and Koyas coalesce at Indian-specific branches of haplogroups M and N that cover populations of different social rank from all over the subcontinent. Coalescence times suggest early late Pleistocene settlement of southern Asia and suggest that there has not been total replacement of these settlers by later migrations. H, L, and R2 are the major Indian Y-chromosomal haplogroups that occur both in castes and in tribal populations and are rarely found outside the subcontinent. Haplogroup R1a, previously associated with the putative Indo-Aryan invasion, was found at its highest frequency in Punjab but also at a relatively high frequency (26%) in the Chenchu tribe. This finding, together with the higher R1a-associated short tandem repeat diversity in India and Iran compared with Europe and central Asia, suggests that southern and western Asia might be the source of this haplogroup.Haplotype frequencies of the MX1 locus of chromosome 21 distinguish Koyas and Chenchus, along with Indian caste groups, from European and eastern Asian populations. Taken together, these results show that Indian tribal and caste populations derive largely from the same genetic heritage of Pleistocene southern and western Asians and have received limited gene flow from external regions since the Holocene. The phylogeography of the primal mtDNA and Y-chromosome founders suggests that these southern Asian Pleistocene coastal settlers from Africa would have provided the inocula for the subsequent differentiation of the distinctive eastern and western Eurasian gene pools.

One for the file. Has a fairly long piece on Y chromsome R1a in it. From my POV, the interesting bits were…

Less than 10% of the maternal lineages of the caste populations had an ancestor outside India in the past 12,000 years

In contrast, the Y-chromosome genetic distance estimates showed that the chromosomes of Indian caste populations were more closely related to Europeans than to eastern Asians

The similarities with Europeans were specifically expressed in substantial frequencies of clades J and R1a

As I’m interested in the Indo-European expansion. The paper describes the Chenchu as..

Chenchus are described as an australoid population, when physical anthropological features are used as criteria…
The Chenchu language belongs to the Dravidian language family.

There’s a page on them here.

The other tribe mentioned are the Koyas, who look pretty similar.

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.)