Tag Archives: DNA studies

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).

cruciani's 2004 J tables jfreq

From Giacomo 2004 and Battaglia 2008

jneo2 jneo


greekj  cintj  etj

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

jiran  mulj  omegar

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.

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.


  • 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.


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.

Chenchu men

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

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

Genes, peoples, and languages
Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305-5120

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.)

Egyptians are not Arabs, they are Egyptians.

Modern Upper Egyptians


A strange title for a blog entry I know. But this is a result of a little nosing through the DNA studies available of modern Egypt, and some irritation at modern Egyptians being incessantly called ‘thieving Arabs’ by on-line Afrocentrists.

This is more focussed on the Egyptians around Luxor, where old upper Egypt was located. A recent DNA study by Cruciani that focused on the Y chromosome E-M78 revealed that it was ‘born’ in North East Africa , not East Africa as previously thought. This means, that an Egyptian with an m78 Y chromosome has had a male line ancestry reaching back to the Pleistocene inhabitants of Egypt; as far back as the Halfan culture about 24,000 years ago.

Southern Egyptians Y Chromomses are mainly native to Africa, both sub and supra Saharan. This makes a grand total of 80.3% definitively African non-Arab ancestry in the upper Egypt region. Y chromosomes possibly attributable to Arab males are very much in the minority in this area. A rough estimate (since no women invaded Egypt) is that about 5% or less of this population are from non dynastic Egyptian peoples, and not all of these would be Arabs.

Northern Egyptians are a bit more cosmopolitan in their ancestry  64.8% indigenous African. About 20% of the Y chrom0somes are near Eastern in origin, and 10.5 % are R Y chromosomes. However, some of these near eastern and European Y chromosomes show an ancient entry to Africa (G, K2, R1, R1b are 8,000 BP and older) and any historical contribution from foreign men is more likely to be in the 15% area. Divided by two (no recent female contribution to speak of). This makes non-dynastic Egyptian population around the 7% mark in Lower Egypt; and only some of this is Arab.

As for the maternal inheritance; this is more varied. From a study at Gurna (of modern upper Egyptians):

H 14.7%, I  5.9%, J   5.9%, L1a   11.7%, L1e   5.9%, L2a   2.9%, M1   17.6%, N1b   8.8%, T   5.9%, U   8.8%  U3   2.9%, U4   5.9% ,L3*(a)  5.9%, L3*(b)  2.9%, Other   2.9%.

Of these, the L haplotypes are typically sub Saharan (23.7%), M1 and U are ancient Eurasian, present at least 30,000 years and many of the other Eurasian haplotypes have been found in 12,000 year old bones in Morocco. The N an I  are possibly attributable to Arab ancestry, about 15% non-Arab in upper Egypt. But still, most of that would easily be attributable to the Neolithic input from Asia- and very little of this would be attributable to Arabs

To sum up, there doesn’t seem to be majority ‘Arab’ genetic component to the Egyptian DNA pool,  20% absolute maximum. And a lot of the non African DNA is traceable to the Neolithic farming expansion that swept across North Africa, so it would be a lot lower in reality.

In upper Egypt a maximum of 20% of the Y chromosomes are non African (the Mt DNA has been shown to be the same since dynastic times from Nubian mummy studies).. so how these people are supposed to have magically changed appearance in the past few thousand years with so little foreign input I’d like to know.

Egyptians are Egyptian, not Arab.


Very simplified Y chromosome information from Lucotte 2003.

The Origin of the Baltic-Finns

Paparazzi Model Management - Mia Frilander, Suvi Jokinen, Anette Montin

Volume XLIII Number 2, Winter 2002
The Origin of the Baltic-Finns from the Physical Anthropological Point of View

Markku Niskanen1
University of Oulu, Finland
The author provides a comprehensive analysis of the physical anthropology of the Finns and Saami, comparing them with other Scandinavian peoples and contrasting them genetically with the Mongoloid peoples of Asia, notwithstanding the affinities which  link the Finnish language with the Uralic and to a lesser extent the Altaic languages. He concludes that both the Finns and the Saami are genetically Caucasoid or European, and that the Finns especially are closely akin to the other North European peoples of Scandinavia.

It is impossible to reconstruct the origins of ethnic groups without information about their genetic relationships. This information provides knowledge about inter-population contacts, assists in determining the geographic areas of origins of the populations in question, and sometimes even reveals how long these populations have lived in their present territories. Therefore, these reconstructed genetic relationships can be used to test hypotheses and theories of ethnic origins based on linguistic and/or archeological evidence. In this article, craniometric and nuclear DNA data, as well as the findings of recent studies of mitochondrial DNA and Y-chromosomal DNA variation are used to determine whether the origin of the Baltic- Finns is better explained by the traditional migration theory or by the more recent settlement continuity theory. These two competing theories are reviewed briefly below.

This publication describes the Finns as typically European, and attributes their ‘Mongoloid characteristsics’ to retaining features from Upper Paleolithic Europeans. This really an ‘all you ever wanted to know about Finns’ paper.

Strong cheekbones and flaring zygomatic arches of many Finno- Ugrians, commonly and erroneously assumed to be Mongoloid features, are actually inherited from European Cro-Magnons (Coon 1939, Niskanen 1994b). These two “Paleo-European” features have survived especially well among the Finno-Ugrians of northern Europe because, as the archeological evidence presented by Zvelebil (1986) indicates, the subsistence transition from foraging to farming occurred more recently and with a lesser influx of immigrants in these marginal regions for agriculture than further south. Most other Europeans have been farmers for so many generations (eating soft bread, porridge, etc.) that their cheek bones (which provide attachments for the masseter muscle) have reduced in size in comparison to other parts of their facial anatomy.

Figure 2. Plot of sample means of the first (CAN1) and the second (CAN2) canonical discriminant function scores computed from c-scores of 42 craniofacial measurements. These two scores explain 70.04% of the total variance. CRO = Cro-Magnons, IRI = Irish, SCO = Scottish, ENG = English, SWE = Swedish, FIN = Finnish, SAA = Saami, GER = German, FRE = French, CZE = Czech, and RUS = Russian. This is the same set of variables than the one used to calculate Mahalanobis distances of Table 3 except that none of the raw measurements were used to compute indices.

Figure 1. A mirror image of dimension coefficient plot extracted from Mahalanobis distances between the European samples of Table 3 using the MDS-procedure. BRI = British (pooled English, Scottish, and Irish), NOR = Norwegian, SWE = Swedish, FIN = Finnish, SAA = Saami, GER = German, FRE = French, CZE = Czech, and RUS = Russian. Modified from Niskanen (1994a).

He also says..

These craniometric analyses demonstrate that the Finns (and presumably other Baltic-Finns) and Saami (although they form their own subset within the European set) possess North European craniofacial configuration with more than average amount of Paleo-European (Cro-Magnoid) features. This finding indicates that the Baltic-Finns and Saami (as well as their Scandinavian neighbors) are indigenous people of northern Europe and not recent immigrants from elsewhere (Niskanen 1998).

As it can be seen on fig 2, the Cro Magnons are an outlier to Northern European populations, but not wildly so. There being less distance between them and the Finns than there is between the Finns and the Russians.

It suggests that Finns and Saami’s don’t share a common origin, from DNA evidence.

The mtDNA studies (Sajantila et al. 1995, Lahermo et al. 1996) reveal that the non-Saami Finno-Ugrians of Europe (the Finns, Karelians, Estonians, Volga-Finns) have the same genetic origin as the non-Uralic-speaking Europeans, and that the Saami represent a unique and ancient sub-group of Europeans that had separated from the other Europeans over 10,000 years ago. Therefore, the Baltic-Finns (the Finns, Karelians, and Estonians) and the Saami do not appear to descend from a common ancestral population that lived as recently as a few thousand years ago. The genetic admixture between the Baltic-Finns and the Saami is also rather recent, but adequate enough to make the Finns and the Karelians the closest genetic relatives of the Saami.

Studies on the MC1R site for skin and hair colour.


Evidence for Variable Selective Pressures at MC1R

Both African and non-African data suggest that the time to the most recent common ancestor is ª1 million years and that the age of the global 314 variant is 650,000 years. On this time scale, ages for the Eurasian distributed Val60Leu, Val92Met, and Arg163Gln variants are 250,000–100,000 years; the ages for African silent variants—Leu106Leu, Cys273Cys, and Phe300Phe—are 110,000–40,000 years. For the European red hair–associated Arg151Cys and Arg160Trp variants, we estimate an age of ª80,000 years; for Asp294His, and Ser316Ser, we estimate an age of <30,000 years. SDs are approximately half these expectations.

These ages are entirely compatible with age distributions estimated for African and non-African mutations in other nuclear genes (Harding et al. 1997; Zietkiewicz et al. 1998). The ages estimated for the Arg151Cys and Arg160Trp red hair–associated variants are consistent with a widespread European distribution, as we also observed.

Red hair associated MC1R variants are Arg151Cys, Asp294His and Arg160Trp  (two are 80,000 years old, one 30,000). Val60Leu is associated with fair or light brown hair and is estimated at 250,000 ot 100,000 years.

More MC1R studies..

Melanocortin 1 receptor (MC1R) gene variants are associated with an increased risk for cutaneous melanoma which is largely independent of skin type and hair color

Individuals carrying melanocortin 1 receptor gene variants have an increased risk for the development of cutaneous melanoma. Melanocortin 1 receptor gene variants are also associated with other risk factors for melanoma such as fair skin and red hair. We evaluated the relationship of melanocortin 1 receptor gene variants, fair skin, red hair and the development of melanoma in 123 patients with cutaneous melanoma and 385 control subjects. To analyze the association between melanocortin 1 receptor gene variants and skin type or hair color we also made use of 453 patients with nonmelanoma skin cancer. We analyzed the coding sequence of the melanocortin 1 receptor gene region by single-stranded conformation polymorphism analysis, followed by DNA sequence analysis. Risk of melanoma dependent on the various melanocortin 1 receptor variant alleles was estimated by exposure odds ratios. The analyses of all different melanocortin 1 receptor gene variants combined, showed that the presence of melanocortin 1 receptor gene variants amounted to a higher melanoma risk, which, in stratified analyses, was independent of skin type and hair color. The odds ratios after adjusting for skin type were 3.6 (95% CI 1.7-7.2) for two variants and 2.7 (95% CI 1.5-5.1) for one variant, respectively. Compound heterozygotes and homozygotes for the Val60Leu, Val92Met, Arg142His, Arg151Cys, Arg160Trp, Arg163Gln, and His260Pro variants had odds ratios of about 4 to develop melanoma, whereas heterozygotes for these variants had half the risk. The presence of the melanocortin 1 receptor gene variant Asp84Glu appeared to impose the highest risk for cutaneous melanoma with odds ratios of 16.1 (95% CI 2.3-139.0) and 8.1 (95% CI 1.2-55.9) in compound heterozygotes and heterozygotes, respectively. The broad confidence intervals, when the different variants were analyzed separately, however, do not allow drawing definite conclusions about the magnitude of these risks. Of the more frequently occurring melanocortin 1 receptor variant alleles the Asp84Glu, Arg142His, Arg151Cys, Arg160Trp, His260Pro, and Asp294His variants were strongly associated with both fair skin and red hair. The Val60Leu, Val92Met, and Arg163Gln variant alleles, however, were only weakly or not associated with fair skin type and/or red hair, which further illustrates the finding that skin type, hair color, and melanoma are independent outcomes of the presence of melanocortin 1 receptor gene variants. We conclude that numerous melanocortin 1 receptor variants predispose to cutaneous melanoma and that possibly the Asp84Glu variant confers the highest risk. This predisposition is largely independent of skin type and hair color.

Melanocortin-1 receptor gene variants in four Chinese ethnic populations

There is strong relationship between melanocortin-1 receptor (MC1R) gene variants and human hair color and skin type. Based on a sequencing study of MC1R gene in 50 individuals from the Uygur, Tibetan, Wa and Dai ethnic populations, we discuss the occurrence of 7 mc1r variants consisting of 5 nonsynonymous sites (Val60Leu, Arg67Gln, Val92Met, Arg163Gln and Ala299Val) and 2 synonymous sites (C414T and A942G), among which C414T and Ala299Val were reported for the first time. Confirmation and analysis were also made of 122 individuals at three common point mutations (Val92Met, Arg163Gln, A942G) using PCR-SSCP. The frequency of Arg163Gln variant varies in the four ethnic populations, with percentage of 40%, 85.0%, 66.2% and 72.7%, respectively, while those of Val92Met and A942G are roughly similar in these four populations. The different environments, migration and admixture of various ethnic groups in China might have impact on the observed frequency of Arg163Gln.

The variation in human hair and skin color in different geographic regions of the world is the result of differences in two principal forms of melanin, the red-yellow phaeomelanins and the black-brown eumelanins, which are present in the epidermal layer of human skin and hair1,2. The type of melanin produced is under the control of two genes, identified initially by the mouse mutation, extension and agouti. The extension gene is expressed in melanocytes, producing the melanocyte stimulating hormone receptor (MSHR) or melanocortin-1 receptor ( MC1R)3,4. The human MC1R gene, homologous to the mouse extension locus, was cloned3,5,6, located to chromosome 16q247 and shown to encode the MC1R protein. Expressed on cutaneous melanocytes3, MC1R is a seven transmembrane domain G protein-coupled receptor of 317 amino acids belonging to the melanocotin receptor subfamily and has high binding affinity for MSH and ACTH8, 9. In addition, some other studies show that MC1R variants are associated with the coat colors in cattle10,11, fox12, and horse13.

Studies of MC1R polymorphism have been made in European, African and Asian populations. Valverde et al14, Box et al15 and Smith et al16 reported 18 variants of MC1R in red hair/fair skin individuals. In a recent study by Rana et al4, Africans were reported to be lack of variation while six variants were found in Asian populations. However, little is known about the variants of MC1R gene in Chinese populations, let alone data in Chinese ethnic populations. In this paper we examined the polymorphism of the human MC1R gene in four Chinese ethnic populations.

MC1R variants
The entire coding sequence of the MC1R gene was sequenced in 50 individuals from the Urgur, Tibeten, Dai, and Wa nationalities. Compared to the published sequences3, 4, 5, 6, 18, sequences of our samples differed from the human consensus sequence at five nonsynonymous sites (at codon 60, 67, 92, 163 and 299) and at two synonymous sites (at nucleotide 414 and 942) (Tab 1). In the previous study of MC1R variants, Val92Met and Val60Leu were reported to be frequent in the red hair/fair skin samples14. In this study, heterozygous Val60Leu was found only in one Uygur individual; whereas the Val92Met variant was found in Uygur, Dai, Wa ethnic populations, but no homozygote in Tibetan. Furthermore, the Val92Met variant always went with the A942G variant in our samples.

Rana et al4 reported the Arg163Gln variant to be associated with the East and Southeast Asian populations. In this study, a very common Arg163Gln variant was also found in the four ethnic groups concerned, including 21 of 35 Uygurs, 19 of 20 Tibetans, 29 of 34 Was and 27 of 33 Dais. The Arg67Gln/Arg163 variant in one Dai individual was also observed in other East and Southeast Asian populations (Rana et al, 1999), which is a combination of the Arg163Gln variant. Besides, one synonymous mutation and one nonsynonymous mutation were first found in Uygur (C414T and Ala299Val).

Gene frequency
The PCR-SSCP analysis was used to genotype the three variants, Val92Met, Arg163Gln and A942G in 122 individuals. The gene frequency of the Arg163Gln variant was found to be significantly different in the four ethnic groups, with the highest (85.0%) in Tibetan, the lowest (40%) in Uygur, and the intermediate in Dai (72.7%) and Wa (66.2%). The gene frequency of the Val92Met differed in the Dai (31. 8%), the Tibetans (10%), the Wa (11.8%) and the Uygur (11.4%). The A942G and Val92Met variant gene frequency for each of the four ethnic groups remained roughly similar, as listed in Tab 2. Hardy-Weinberg equilibrium was not rejected in all these ethnic groups (Data not shown).

Three alleles (Arg151Cys, Arg160Trp and Asp294His) that are associated with red hair/fair skin phenotype have been reported in European individuals 5,16. Recently, Franderberg et al19 found new evidence that the Arg151Cys mutation of MC1R can cause the synthesis of the red pigment. This evidence explains why the red hair person carries the Arg151Cys mutation. The Arg163Gln variant is present with relatively high frequency in the East and Southeast Asian populations 4,20. In consistent with those reports, our result shows a very common Arg163Gln variant in the four ethnic groups. It might suggest that the Arg163Gln polymorphism is associated with phaemomelanin-rich skin. But further functional study is required to confirm our expectation.

The Arg163Gln variant is found in American Indians as well as in East and Southeast Asian populations, while the allele appears at a very low frequency or even disappears in both Europeans and Africans. Rana et al4 considered that the allele has increased rapidly in frequency in East Asians by positive Darwinian selection. We suggest that the random genetic drift, migration and the admixture of various ethnic groups might have impact on the frequency of the Arg163Gln variant in different populations. Firstly, the highest frequency and the most homozygous state in Tibetans might arise from genetic drift and little possibility of gene flows among different ethnic groups. The positive Darwinian selection is also a possible explanation. Secondly, the lowest frequency in Uygurs might be the result of their genetic admixture with Caucasians. This assumption can be further supported by results from other reports17,22. On the other hand, considering the genetic admixture, it is explicable that an European specific allele, Val60Leu, is present in one Uygur individual. Lastly, the similar frequencies in the Dai and the Wa might be explained by their similar geographic locations and living environments.

High polymorphism at the human melanocortin 1 receptor locus.

Rana BK, Hewett-Emmett D, Jin L, Chang BH, Sambuughin N, Lin M, Watkins S, Bamshad M, Jorde LB, Ramsay M, Jenkins T, Li WH.

Human Genetics Center, School of Public Health and Graduate School of Biomedical Sciences, University of Texas, Houston, Texas 77030, USA.

Variation in human skin/hair pigmentation is due to varied amounts of eumelanin (brown/black melanins) and phaeomelanin (red/yellow melanins) produced by the melanocytes. The melanocortin 1 receptor (MC1R) is a regulator of eu- and phaeomelanin production in the melanocytes, and MC1R mutations causing coat color changes are known in many mammals. We have sequenced the MC1R gene in 121 individuals sampled from world populations with an emphasis on Asian populations. We found variation at five nonsynonymous sites (resulting in the variants Arg67Gln, Asp84Glu, Val92Met, Arg151Cys, and Arg163Gln), but at only one synonymous site (A942G). Interestingly, the human consensus protein sequence is observed in all 25 African individuals studied, but at lower frequencies in the other populations examined, especially in East and Southeast Asians. The Arg163Gln variant is absent in the Africans studied, almost absent in Europeans, and at a low frequency (7%) in Indians, but is at an exceptionally high frequency (70%) in East and Southeast Asians. The MC1R gene in common and pygmy chimpanzees, gorilla, orangutan, and baboon was sequenced to study the evolution of MC1R. The ancestral human MC1R sequence is identical to the human consensus protein sequence, while MC1R varies considerably among higher primates. A comparison of the rates of substitution in genes in the melanocortin receptor family indicates that MC1R has evolved the fastest. In addition, the nucleotide diversity at the MC1R locus is shown to be several times higher than the average nucleotide diversity in human populations, possibly due to diversifying selection

 Interactive effects of MC1R and OCA2 on melanoma risk phenotypes.

Duffy DL, Box NF, Chen W, Palmer JS, Montgomery GW, James MR, Hayward NK, Martin NG, Sturm RA.
Queensland Insititute of Medical Research, Brisbane, Australia.

The relationships between MC1R gene variants and red hair, skin reflectance, degree of freckling and nevus count were investigated in 2331 adolescent twins, their sibs and parents in 645 twin families. Penetrance of each MC1R variant allele was consistent with an allelic model where effects were multiplicative for red hair but additive for skin reflectance. Of nine MC1R variant alleles assayed, four common alleles were strongly associated with red hair and fair skin (Asp84Glu, Arg151Cys, Arg160Trp and Asp294His), with a further three alleles having low penetrance (Val60Leu, Val92Met and Arg163Gln). These variants were separately combined for the purposes of this analysis and designated as strong ‘R’ (OR=63.3; 95% CI 31.9-139.6) and weak ‘r ‘ (OR=5.1; 95% CI 2.5-11.3) red hair alleles. Red-haired individuals are predominantly seen in the R/R and R/r groups with 67.1 and 10.8%, respectively. To assess the interaction of the brown eye color gene OCA2 on the phenotypic effects of variant MC1R alleles we included eye color as a covariate, and also genotyped two OCA2 SNPs (Arg305Trp and Arg419Gln), which were confirmed as modifying eye color. MC1R genotype effects on constitutive skin color, freckling and mole count were modified by eye color, but not genotype for these two OCA2 SNPs. This is probably due to the association of these OCA2 SNPs with brown/green not blue eye color. Amongst individuals with a R/R genotype (but not R/r), those who also had brown eyes had a mole count twice that of those with blue eyes. This suggests that other OCA2 polymorphisms influence mole count and remain to be described.

Skin pigmentation, biogeographical ancestry and admixture mapping.

Shriver MD, Parra EJ, Dios S, Bonilla C, Norton H, Jovel C, Pfaff C, Jones C, Massac A, Cameron N, Baron A, Jackson T, Argyropoulos G, Jin L, Hoggart CJ, McKeigue PM, Kittles RA.
Department of Anthropology, Penn State University, 409 Carpenter Bld., University Park, PA 16802, USA.

Ancestry informative markers (AIMs) are genetic loci showing alleles with large frequency differences between populations. AIMs can be used to estimate biogeographical ancestry at the level of the population, subgroup (e.g. cases and controls) and individual. Ancestry estimates at both the subgroup and individual level can be directly instructive regarding the genetics of the phenotypes that differ qualitatively or in frequency between populations. These estimates can provide a compelling foundation for the use of admixture mapping (AM) methods to identify the genes underlying these traits. We present details of a panel of 34 AIMs and demonstrate how such studies can proceed, by using skin pigmentation as a model phenotype. We have genotyped these markers in two population samples with primarily African ancestry, viz. African Americans from Washington D.C. and an African Caribbean sample from Britain, and in a sample of European Americans from Pennsylvania. In the two African population samples, we observed significant correlations between estimates of individual ancestry and skin pigmentation as measured by reflectometry (R(2)=0.21, P<0.0001 for the African-American sample and R(2)=0.16, P<0.0001 for the British African-Caribbean sample). These correlations confirm the validity of the ancestry estimates and also indicate the high level of population structure related to admixture, a level that characterizes these populations and that is detectable by using other tests to identify genetic structure. We have also applied two methods of admixture mapping to test for the effects of three candidate genes (TYR, OCA2, MC1R) on pigmentation. We show that TYR and OCA2 have measurable effects on skin pigmentation differences between the west African and west European parental populations. This work indicates that it is possible to estimate the individual ancestry of a person based on DNA analysis with a reasonable number of well-defined genetic markers. The implications and applications of ancestry estimates in biomedical research are discussed.

Association of the SLC45A2 gene with physiological human hair colour variation
Wojciech Branicki, Urszula Brudnik, Jolanta Draus-Barini, Tomasz Kupiec and Anna Wojas-Pelc
Journal of Human Genetics Early online

Abstract: Pigmentation is a complex physical trait with multiple genes involved. Several genes have already been associated with natural differences in human pigmentation. The SLC45A2 gene encoding a transporter protein involved in melanin synthesis is considered to be one of the most important genes affecting human pigmentation. Here we present results of an association study conducted on a population of European origin, where the relationship between two non-synonymous polymorphisms in the SLC45A2 gene — rs26722 (E272K) and rs16891982 (L374F) — and different pigmentation traits was examined. The study revealed a significant association between both variable sites and normal variation in hair colour. Only L374F remained significantly associated with hair colour when both SNPs were included in a logistic regression model. No association with other pigmentation traits was detected in this population sample. Our results indicate that the rare allele L374 significantly increases the possibility of having black hair colour (OR = 7.05) and thus may be considered as a future marker for black hair colour prediction.

 A list of MC1R articles on pubmed (reference)

The main impression I get from this is that human colouring is a very complex process. I’m intrigued by the extremely old dates for some of the MC1R variants. If the dates are accurate, it’s an archaic human era they occurred in.