Saturday, August 6, 2011

Proto-Greek homeland.

The following map represents the 'Proto-Greek' homeland, ie where the earliest form of Greek speech was located, thus where the earliest Greek peoples were located.


Indo-European linguist
V. I. Georgiev.
"The Proto-Greek region included Epirus, approximately up to Αυλών in the north including Paravaia, Tymphaia, Athamania, Dolopia, Amphilochia, and Acarnania), west and north Thessaly (Hestiaiotis,, Perrhaibia, Tripolis, and Pieria), i.e. more or less the territory of contemporary northwestern Greece)"
SOURCE : Georgiev, Vladimir Ivanov (1981). Introduction to the history of the Indo-European languages. Pub. House of the Bulgarian Academy of Sciences. pp. 156.


EDIT : What a coincidence Epirus (my ancestral homeland) is at the center of where the likely original Greeks were from, not trying to brag of course. : )

Proto-Greek was probably spoken in North/Northwestern Greece at latest in the late 3rd millennium BC. Why? Because Mycenaean Greek which is documented to be have been spoken at around 1600 BC is already fully recognizable Greek, so it must have been Greek for quite a while before. Not to mention Mycenaean Greek was also dialectal Greek, so its divergence from Proto-Greek must be pushed into the past, certainly in the 3rd millennium BC at the latest.

It should be noted that this linguistic timescale and Proto-Greek homeland map is going by the still somewhat speculative Kurgan hypothesis for the breakdown of Indo-European.

Wednesday, June 8, 2011

Northern Italians are biologically SOUTHERN European.

Above : Pictures of Venice Italy

It is often stated that Northern Italians are "Germanic" (don't know why they single out Northern Italians as Germanic 'barbarians' also invaded and controlled the south of Italy and Sicily in historic times), or more related to Germans and Northern Europeans than to the Southern Italians or other Southern Europeans; this notion however is completely incorrect. More recent genome wide association studies generally show Northern Italians clustering with Southern Europeans, pulling further south and distant from Northern Europeans than Spaniards. Here are several genetic studies demonstrating this fact.

European Population Substructure: Clustering of Northern and Southern Populations. Seldin et al (2006).
"Using a genome-wide single nucleotide polymorphism (SNP) panel, we observed population structure in a diverse group of Europeans and European Americans. Under a variety of conditions and tests, there is a consistent and reproducible distinction between “northern” and “southern” European population groups: most individual participants with southern European ancestry (Italian, Spanish, Portuguese, and Greek) have >85% membership in the “southern” population; and most northern, western, eastern, and central Europeans have >90% in the “northern” population group. Ashkenazi Jewish as well as Sephardic Jewish origin also showed >85% membership in the “southern” population, consistent with a later Mediterranean origin of these ethnic groups. Based on this work, we have developed a core set of informative SNP markers that can control for this partition in European population structure in a variety of clinical and genetic studies."

The recent development of methodologies for defining population structure has provided the ability to identify the major ethnic contributions in individual participants in diverse populations. These statistical approaches utilize non-hierarchical clustering algorithms in which Markov chain Monte Carlo methods are used to infer ancestry, based solely on genotyping information. Furthermore, related algorithms provide methods for controlling for population stratification in genetic studies. These methods are important in assessing the results of case-control and other non–family-based association tests. In addition, defining population structure is potentially useful both in clinical outcome studies and in the examination of pharmacologic response and toxicity. Previous studies of human population structure have primarily considered different continental populations or admixed populations between two or more different continental populations. However, some of these studies have also suggested that sub-continental differences in population structure can be discerned. The examination of population differences within Europe using mitochondrial or Y chromosome haplogroups has been particularly useful in tracing part of the routes of migration and populating of Europe, but these haplogroups do not provide strong inferences on population genetic structure. Autosomal studies using small numbers of classical genetic markers (nuclear protein polymorphisms) have suggested broad genetic gradients across Europe, leading to the proposal of demic diffusion models. These include a principal component analysis of small numbers of classic genetic markers that suggested three clines accounting for a proportion of the genetic variation in the continent.

A total of 1,094 participants were genotyped with more than 5,700 SNPs distributed over the entire genome. After excluding participants with > 10% estimated non-European ancestry (see Methods), 928 participants were selected for further analysis.

Populations studied: First sample set.

European Americans of different regional European origins (681 participants), East Asian Americans (13), African Americans (22), South Asian Americans (48), Amerindians (48), and Swedish (92), Finnish (13), Italian (91), Portuguese (3), southern France (1), and Spanish participants (82) were included in this study. None of the individuals were first-degree relatives of other participants in the study. These populations were based on self-identified ethnic affiliation. The European Americans, African Americans, and East Asian Americans were recruited from across the United States, and the majority of the participants, including all of the European Americans, were RA probands identified as part of the North American Rheumatoid Arthritis Consortium (NARAC) as previously described (61). The South Asian American participants were recruited from Houston, Texas, and Amerindian participants were self-identified as Mayan (Kachiquel language group) and were recruited in Chimaltenango, Guatemala, as previously described. The Italian participants were normal healthy volunteers recruited from throughout Italy: 38 from northern Italy, 23 from central Italy, and 30 from southern Italy. The Swedish and Finnish participants were healthy normal controls collected in these countries. The other participants recruited in southwestern Europe included 86 from Spain, three from Portugal, and one from southern France. Of the Spanish participants, there were 43 from northern Spain, 12 from central Spain, and 19 from southern Spain. Of these participants from Spain and Portugal, 61 were probands for a multiple sclerosis study. Blood cell samples were obtained from all individuals, according to protocols and informed-consent procedures approved by institutional review boards, and were labeled with an anonymous code number linked only to demographic information.

For the European Americans, grandparental information was available for the majority of the participants. These included the following self-identifier classifications of grandparents: western European (United Kingdom, northern France, Holland, Belgium, and Switzerland), eastern European (Russia, Poland, Romania, Ukraine, Lithuania, Latvia, Estonia, and Czech Republic), central European (Germany, Austria, and Hungary), southern European (Spain, Portugal, Italy, and southern France), Scandinavian (Denmark, Norway, Sweden, and Finland), and eastern Mediterranean (Greece, Turkey, Croatia, Bosnia, Yugoslavia, and Albania), Sephardic Jewish American, and White French Canadian. All participants with any reported mixed-continental origins (e.g., African) were excluded".

"Grouping of individuals with different north–south contributions from the k = 2 analysis further illustrates this division of individual participants from different European population sets and some of the variability observed (Figure 2). Italy (84 of 86 individuals), Spain (66 of 74), Portugal (3 of 3), and Sephardic Jewish Americans (3 of 3) had majority contributions from the “southern” population group as defined by this population structure analysis. In addition, a large fraction of southern European Americans (7 of 11) without other reported European heritage had majority “southern” contribution. Those Americans with self-identified mixed “southern” and “northern” heritage showed a substantial but less impressive “southern” population component (8 of 23 with majority “southern”). Those American participants with mixed eastern Mediterranean–reported heritage also had two of ten individuals with a majority “southern” population component. All other groups showed only a few isolated participants with more than a limited “southern” population component.
Trends in both the Italian and Spanish participants were also consistent with this north–south pattern: ten of 32 participants from northern Italy had greater than a 10% “northern” component compared with two of 28 from southern Italy; and 23 of 43 from northern Spain had greater than a 10% “northern” contribution compared to five of 19 from southern Spain."Analyses were performed with 2,657 SNPs under the condition of two population (Pop) groups (k = 2)."
FIGURE 1 Analysis of Population Structure in Participants of European Ancestry"Analysis was performed without any prior population assignment using STRUCTURE. The European ancestry groups, western European American (WEURA), central European American (CEURA), eastern European American (EEURA), Finland (FND), Italy (ITN), Spain (SPN), Sweden (SWD), and other European American (OEURA) are indicated by color code. The latter group consisted of individuals with mixed European ancestry from several regions and additional smaller groups (see Methods)....In (D), the proportion of each cluster (ordinate) is shown for each individual."

As we see above, each little line represents 1 Italian. As we can see, the Italians are scorching red here, even the Northern Italians; it looks like 1 (possibly although not certainly Northern) Italian is half blue.

FIGURE 2 - Distribution of “Southern” Population Components among Participants with Various Self-Identified Ethnic or Regional European Origins
"For each self-identified group, the fraction of individual participants in each group with the color-coded frequency “southern” contribution is shown. For southern European American I (SEA1), only southern European grandparents were identified. For southern European American II (SEA2), grandparents were self-reported as being of both southern European decent and western, central, or eastern European decent. For the eastern Mediterranean American (EMEDA) group, four of ten were of mixed-European decent with one or more grandparents of western, central, or eastern European decent.

CEURA, central European American; EEURA, eastern European American; FND, Finland; ITN, Italy; PTG, Portugal; SCNA, Scandinavian; SJA, Sephardic Jewish American; SPN, Spain; SWD, Sweden; WEURA, western European American; WFC, White French Canadian."
As we can see above, the Italians (38 of 87 of whom are Northern Italians) are scorching red (90%+ 'Southern'), only a minority are orange (60-90% 'southern'), while none are entirely or predominately in the blue (Northern) cluster. There are more Swedes (1 outlier) who are in predominately 'Southern' cluster than Italians who are predominantly in the 'Northern' cluster.

So yes, virtually every Northern Italian clustered predominantly in the 'Southern' cluster, while only 10 of 32 Northern Italians showed less than a 90% contribution to the 'Southern' cluster (compared to 23 of 43 from Northern Spain, and 5 of 19 from Southern Spain), and only 2 of 28 participants from Southern Italy had less than a 90% contribution to the 'Southern' cluster. The remaining Italians were between 60% and 90% in the Southern cluster. Northern Italians are overwelmingly 'Southern' in biological affinity when speaking in a European wide context; Southern Italians more-so, but Spaniards slightly less. 

SOURCE : Seldin MF, Shigeta R, Villoslada P, Selmi C, Tuomilehto J, et al. (2006) European Population Substructure: Clustering of Northern and Southern Populations. PLoS Genet 2(9): e143. doi:10.1371/journal.pgen.0020143

Refinement of ancestry informative markers in Europeans. Tian et al (2009).
"The definition of European population genetic substructure and its application to understanding complex phenotypes is becoming increasingly important. In the current study using over 4,000 subjects genotyped for 300,000 single-nucleotide polymorphisms (SNPs), we provide further insight into relationships among European population groups and identify sets of SNP ancestry informative markers (AIMs) for application in genetic studies. In general, the graphical description of these principal components analyses (PCA) of diverse European subjects showed a strong correspondence to the geographical relationships of specific countries or regions of origin. Clearer separation of different ethnic and regional populations was observed when northern and southern European groups were considered separately and the PCA results were influenced by the inclusion or exclusion of different self-identified population groups including Ashkenazi Jewish, Sardinian, and Orcadian ethnic groups. SNP AIM sets were identified that could distinguish the regional and ethnic population groups. Moreover, the studies demonstrated that most allele frequency differences between different European groups could be controlled effectively in analyses using these AIM sets. The European substructure AIMs should be widely applicable to ongoing studies to confirm and delineate specific disease susceptibility candidate regions without the necessity of performing additional genome-wide SNP studies in additional subject sets."
"Figure 1. Principal component analyses of substructure in a diverse set of subjects of European descent. Graphic representation of the first two PCs based on analysis with >250K SNPs are shown. Color code shows subgroup of subjects for each population group.
The subjects included Adygei (ADY, 12 subjects), Ashkenazi Jewish American (AJA, 40 subjects), Basque (BAS, 12 subjects), Bedouin (BDN, 23 subjects), CEPH European American (CEU, 48), Druze (20 subjects), Eastern European American (EEUR, 11 subjects), German American (GERM, 17 subjects), Greek American (GRK, 7), Hungarian American (HUN, 4 ), IRISH (84 subjects), Italian American (ITN, 20 subjects), northern Italian (ITN_N, 13 subjects), Dutch American (NETH, 3 subjects), Orcadian (ORC, 14 subjects), Palestinian (PAL, 22 subjects), Russian (RUS, 13 subjects), Sardinian (SARD, 28 subjects), Scandinavian American (SCAN, 6 subjects ), Spanish (SPAIN, 12 subjects), Swedish (SWED, 591 subjects), Tuscany (TUSC, 8 subjects), and United Kingdom American (UK, 5 subjects). Each of the specific country or ethnic color coded origins had consistent 4 grandparent origin information. The total number of individuals in this analysis was 4446. In panel A European Americans (EURA) without 4 grandparental information are shown (contains both NYCP and CHOP). Panels B and C illustrate the distribution of the EURA from NYCP (1873 subjects) and CHOP (1488 subjects), respectively."

As we can see by PCA analysis, Tuscans (TUSC) and Northern Italians (ITL N) group well within the Southern European cluster, far away from the Northern/Central/East European cluster. Italian Americans (ITN) with 4 Italian grandparents of Southern Italian/Sicilian origin overlap with the Greeks, while Northern Italians (ITL N) seem to be smack dab in the middle of the Southern European cluster, between Spaniards and Tuscans. Tuscans also pull even further south than the Northern Italians, between Southern Italians/Greeks and Northern Italians.

The lack of important European groups like the French and Swiss does seem to make the gap between Southern Europe and Northern/Central/Eastern Europe very large and not just gradual or clinal, but if those two populations were to be included the gap from Southern Europe to Central Europe would appear less significant with the alps showing a large (but not massive) barrier. Anyway, this study also irrefutably proves the Southern European biological affinities of Northern Italians and that is what is important.

Also, here is an interesting Fst genetic distance table from the study, although it unfortunately doesn't include Northern Italians it does include Tuscans (ie where the Renaissance first sprung up).


The results as seen in Table 1.

Tuscany to Southern Italy - 0.0004
Tuscany to Greece - 0.0005
Tuscany to Germany - 0.0032
Tuscany to Ireland - 0.0055
Tuscany to Sweden - 0.0061
Tuscany to Russia - 0.0108

SOURCE : Tian et al. (2009). European Population Genetic Substructure: Further Definition of Ancestry Informative Markers for Distinguishing Among Diverse European Ethnic Groups. Mol Med; doi: 10.2119

Link PDF

Genetic Structure of Europeans: A View from the North–East. Nelis et al (2009).
"Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (λ) (ranging from 1.00 to 4.21), fixation index (Fst) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS)."

Yet again, as we can see by PCA analysis, Northern Italians blend perfectly in the Southern European area, and are the second most "southerly" population sampled here after the Southern Italians. Northern Italians pull further south than Spaniards from Madrid, and while they seem to be a little closer to the Spanish and some Swiss (who are partly Italian) than to Southern Italians, they are equidistant between Southern Italians and the French, and they're much closer to the Southern Italians than to Southern Germans. The Northern Italians also surprisingly pull quite a bit further to the south end of Europe than Bulgarians do, which might mean Bulgarians have substantial medieval Slavic admixture (Bulgarians are southern Slavs after all) which would have brought more "northerly" gene-flow into Bulgaria; there's no telling really regarding them. 

One more thing of note, unlike the other previous two studies, in this study the samples that represented Northern and Southern Italy only came from 2 different locations; here are the sample set locations as representative of "Northern Italy" and "Southern Italy".
Northern Italy:
"The Northern Italian samples have been randomly collected from the Borbera Valley. The Borbera Valley is located in Northern Italy, namely the northern part of the Apennines mountains, between Liguria and Piedmont, about 80 km south of Milan. For the current analysis, 96 individuals were selected from the database where all the samples have complete phenotypic data."

Southern Italy:
"The Italian samples were randomly chosen from those enrolled in a population study named Carlantino Project, which is focused on inhabitants arising from an isolated village at the border between Central and Southern Italy (Province of Foggia, Region of Apulia with 1200 inhabitants)."

Also, it is important to note that while genetic distance is often heavily correlated to geographical distance, genetic barriers can be created by substantial geographical barriers which limit gene flow and cause breeding isolation. In Europe the Alps represent such a genetic barrier and it is not surprising that this study confirms that.
"Barrier analysis revealed genetic barriers between Finland, Italy and other countries, as has been described before [12]. Interestingly, barriers could be demonstrated within Finland (between Helsinki and Kuusamo) and Italy (between northern and southern part). Another barrier emerged between the Eastern Baltic region and Sweden, but not between the Eastern Baltic region and Poland (Figure S4). The barrier between Bulgaria and Western Russia, Poland and Lithuania may have arisen due to the fact that several populations are missing in between those countries"

As stated above there is a noticeable difference between Northern and Southern Italians, according to PC analysis the medians of North and South Germans seem to be roughly 0.005 apart, while those of North and South Italians seem to be 0.005 apart. So no big difference among the ethnic stratification between the two countries. The biological difference between Northern and Southern Italians though rather noticeable, does seem to have been somewhat exaggerated by laymen 'racialists' of past and present.
"Interestingly, PC analysis was also capable of highlighting intra-population differences, such as between the two Finnish and the two Italian samples, respectively. A low level of intra-population differentiation in Germany has been reported previously, and was confirmed here. In addition, we detected intra-population differences within the Czech and Estonian samples."

SOURCE : Nelis M, Esko T, Mägi R, Zimprich F, Zimprich A, et al. (2009) Genetic Structure of Europeans: A View from the North–East. PLoS ONE 4(5): e5472. doi:10.1371/journal.pone.0005472

Also, other than the Greeks in Southern Italy, historical admixture seems to be quite minimal in Italians.
"An analysis of the genetic makeup of Italy's modern population argues that the various distinctive genetic combinations currently found in different regions within the peninsula by and large track the linguistic distribution that resulted from the migrations of the Iron Age. No data indicate the subsequent large-scale infusion of new genetic material into the populations of these regions except in the case of southern Italy and eastern Sicily, which is explained by the well-documented Greek migrations there."
SOURCE : Rosenstein, Nathan. Rome at War: Farms, Families, and Death in the Middle Republic. Chapel Hill: University of North Carolina Press, 2004.


The genetic article which that book used as a source for that statement is Piazza's "A Genetic History of Italy", and although unfortunately I don't have access to the entire study, the abstract is available online. It's conclusions are clear that the biological stratification seen in today's Italy is reflective of pre Roman times.

"Statistical techniques for displaying the geographical distribution of many genes in few synthetic images have been used to represent the various patterns of gene frequencies in Europe and in the world (Menozzi et al. 1978; Piazza et al. 1981a). It has also been shown that such synthetic displays are particularly useful in detecting clines of genetic differentiation associated with movements of populations like those accompanying the Neolithic expansion of farmers from the Near East or, in more recent times, the putative diffusion of Indo-European-speaking populations (Ammerman & Cavalli-Sforza, 1984; Gimbutas, 1973).

In this paper we use the same combination of statistical and graphical techniques to study the genetic structure of Italy, a European country whose unity of people and cultures was quite a recent event. The possibility of studying genetic differentiation in a small geographical area is tested and trends of genetic differences are tentatively interpreted in terms of historic and linguistic knowledge. The few demographic pieces of information taken from historical sources and compared with linguistic records support the hypothesis that the genetic structure of Italy still reflects the ethnic stratification of pre-Roman times."
SOURCE : Piazza, A., N. Cappello, E. Olivetti, and S. Rendine. 1988. A genetic history of Italy. Ann. Hum. Genet. 52:203-213.


(EDIT 2015) Admixture ratios in modern populations based on prehistoric genomes

All populations in Europe can be modeled as being a mixture of 3 major and distinct ancestral strains from prehistoric migrations. These are 

1. Paleolithic West European Hunter Gatherers

2. Early European Farmers of the Neolithic revolution who had most their genetic origin in Mesolithic and Neolithic Anatolia and brought the earliest agricultural practices to Europe.

3. Yamnaya steppe pastoralists who likely domesticated the horse. The Yamnaya steppe pastoralists are believed by most linguists to have been the speakers of the late stage proto Indo-European language (see Kurgan hypothesis). 

As we can see in Figure 3 below, all Europeans can basically be modeled as a composite of the same 3 ancestral mixtures, it's just that the ratios are different. We can also see that that the biggest differences in Europe are between the North of Europe, and the South of Europe. As we can see in their admixture ratios, the Northern Italians (here represented by a sample set from Bergamo Lombardy) are unsurprisingly most similar to other Southern Europeans (ie Northern Spanish, Greeks, Albanians, Bulgarians, etc) in their admixture ratios, and that is being of heavy Early Neolithic Farmer ancestry. Tuscans as anyone can see also come out very heavily Neolithic.

SOURCE : Haak, et al. (2015). "Massive migration from the steppe was a source for Indo-European languages in Europe". Nature. doi:10.1038/nature14317.edit


And lastly, for the most part irrelevant, I found some old hair and eye pigmentation data from Livi on Italian conscripts. Interesting stuff but for the most it's not that important.

SOURCE : Antropometria Militare. Ridolfo Livi. Two volumes, 4°, with atlas. Rome: Preso il Giornale Medico del Regio E Sercito, 1896, 1905..

Summary and conclusions
1. Northern and Central Italians are biologically SOUTHERN European...broadly speaking. In so far that they share their overall closest genetic relationships with other Southern Europeans, and that they are more distinct from Northern European groups than the Spanish.

2. Northern-Central Italians may be a bit closer to North/Central/East Europeans than Southern Italians are (just as Southern Germans are a bit closer to Southern Europeans than Northern Germans are), but Northern-Central Italians still biologically pull to Southern Europe quite strongly as seen that they ALWAYS pull further south than Spaniards, and also one study showed them a bit below Balkan Southern Slavs like Bulgarians. They also always structure with Southern Europeans in European exclusive STRUCTURE analysis studies. And their admixture ratios based on actual ancient genomes using ADMIXTURE is much more similar to the ratios present in other Southern Europeans than in Northern Europeans.

3. Slight Germanic admixture is possible for all Italian populations, not just the Northern Italians. I would venture that actual Germanic ancestry is larger in Northern Italy and that the Lombards in Northern Italy had a bigger impact than the Goths or Normans in Southern Italy. However one thing is for certain, and that is that large scale Germanic admixture in any Italian groups is certainly not the case and easily refuted by the data.

4. There is a noticeable difference between the Northern Italians and Southern Italians, and I don't want people to think that Northern Italians cannot be argued to be a genetically distinct (Southern European) ethnos. The Southern Italians are actually closer to the Greeks than they are to actual Northern Italians. However, I want to point out that the differences between Northern Italians and Southern Italians seems to be mostly due to an ethnogenisis prior to Germanic or non European invasions because geneticists agree that no migrations other than the Greek migrations in Southern Italy and Sicily had any substantial biological impact on Italians. Also, the genetic distance between Northern and Southern Italians, although pretty large from a single European 'nationality' point of view, is only roughly equal [marginally greater] to that of the genetic distance between Northern Germans and Southern Germans.

Sunday, June 5, 2011

Craniometrics show ancient Etruscans group with modern Italians (Sardinians) before any group of modern Europeans.

The origin of the Etruscans is somewhat unclear still to this date. It's been shown that a good chunk of their mitochondrial lineages were from the East Mediterranean including what was likely Anatolia. Regardless of the still somewhat cloudy picture of their origins and ethnogenisis, craniometric data shows them to be related to contemporary Sardinians, and not to more Northerly European populations.

SOURCE : Brace CL and Tracer DP. 1992. Craniofacial continuity and change: A comparison of Late Pleistocene and recent Europe and Asia

Thursday, June 2, 2011

Caucasoid racial affinities of the ancient Egyptians.


The origin of the Nile valley civilization has been one of speculation for centuries. Broadly speaking they were a 'Caucasoid' population, related primarily to fellow Northern Africans, and secondly related to Middle Easterners and Europeans. They were not however related to Sub-Saharan Africans of Central, West, and South Africa (ie 'Negroids').

Cranio-facial patterns

1. Craniometric

"The biological affinities of the ancient Egyptians were tested against their neighbors and selected prehistoric groups as well as against samples representing the major geographic population clusters of the world. Two dozen craniofacial measurements were taken on each individual used. The raw measurements were converted into C scores and used to produce Euclidean distance dendrograms. The measurements were principally of adaptively trivial traits that display patterns of regional similarities based solely on genetic relationships. The Predynastic of Upper Egypt and the Late Dynastic of Lower Egypt are more closely related to each other than to any other population. As a whole, they show ties with the European Neolithic, North Africa, modern Europe, and, more remotely, India, but not at all with sub-Saharan Africa, eastern Asia, Oceania, or the New World. Adjacent people in the Nile valley show similarities in trivial traits in an unbroken series from the delta in the north southward through Nubia and all the way to Somalia at the equator. At the same time, the gradient in skin color and body proportions suggests long-term adaptive response to selective forces appropriate to the latitude where they occur. An assessment of “race” is as useless as it is impossible. Neither clines nor clusters alone suffice to deal with the biological nature of a widely distributed population. Both must be used. We conclude that the Egyptians have been in place since back in the Pleistocene and have been largely unaffected by either invasions or migrations. As others have noted, Egyptians are Egyptians, and they were so in the past as well."

SOURCE : Brace, C. L., D. P. Tracer, L. A. Yaroch, J. Robb, K. Brandt, and A. R. Nelson. 1993. Clines and Clusters Versus "Race": A Test in Ancient Egypt and the Case of a Death on the Nile. Yearbook of Physical Anthropology 36:1-31.


2. Cranial Non-metric

Pre-Dynastic Southern Egyptians from Naqada (#59), 26th-30th Dynasty Northern Egyptians from Gizeh (#60) cluster with Northwest Indians from Punjab and Kashmir (#44), Ancient and Modern Greeks (#48), Scandinavians from Finland, Sweden and Norway (#51, #52), and Modern Germans (#53).

Sample Set

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)

"Roughly three major constellations are evident. The Subsaharan African, Southeast Asian, and Oceanian samples form a cluster in one quadrant of Figure 2a. However, the Subsaharan African samples form a distinct grouping, well removed from the Southeast Asian and Oceanian samples on the third and fourth principal coordinates. In Figures 1 and 2, the Subsaharan African samples show significant separation from other regions, as well as diversity among themselves. The East/Northeast Asian and European samples form two additional discernable clusters. The New World and Arctic samples are peripheral subgroups in the large East/Northeast Asian cluster, and the two Ainu samples are outliers to other East Asians. The Central Asian samples are located between the Eastern Asian and European clusters. In the bottom half of Figure 2a, the South Asian samples are nearest to the center of all groups, the North African samples are a bit further removed, and the European samples are more separated, having the lowest scores on principal axis 2. Applying the neighbor-joining method to the MMD distances results in the dendrogram illustrated in Figure 3. The initial split, suggesting the greatest dissimilarity, is between Subsaharan Africans and the rest of the world. The Europeans, North Africans, and South Asians are then separated from the remaining groups. Oceania and the Southeast Asian groups form a separate branch that is separated from a large grouping of Central andEast/Northeast Asian, Arctic, and New World series clusters. The Arctic cluster, which includes groups from northeasternmost Siberia, is deep in a branch containing all New World groups. The Ainu samples are more similar to mainland groups from the Amur River basin and Lake Baikal than to the Japanese."
SOURCE : HANIHARA, TSUNEHIKO, HAJIME ISHIDA, AND YUKIO DODO. 2003. Characterization of biological diversity through analysis of discrete cranial traits. American Journal of Physical Anthropology 121:241-251.


3. Cranial Non-metric

Pre-Dynastic Southern Egyptians from Naqada and late dynastic 26th-30th Dynasty Northern Egyptians from Gizeh cluster with Caucasoids [modern Europeans, ancient Byzantine Greeks, and modern Turks]. Note ancient Nubians from Kerma also cluster with Caucasoids and show strong ties with ancient pre dynastic Southern Egyptians. Also not modern sub-Saharan Africans including these East African Somalis do not.
"The dendrogram produced by Ward's clustering procedure for the global data set is shown in Figure 3 and provides a relatively similar representation of the MMD^sub st^ distance matrix than that provide by the MDS analysis. The populations clearly fall into two groups. The first main group can be broken down into two subgroups: (1) all the recent sub-Saharan populations and (2) mainly Central, East, and Northeast Eurasians. West Eurasians form the second main group, which is also subdivided into two subgroups. One of these subgroups includes all the eastern Mediterranean populations (three ancient Egyptian/Sudanese populations from Naqada, Gizeh, and Kerma as well as the Cypriot/Turkish, Greek, and Sagalassian populations) and the Scandinavian sample; the second subgroup includes the other West Eurasian populations."

SOURCE : Ricaut, F. X. and Waelkens, M (2008) "Cranial Discrete Traits in a Byzantine Population and Eastern Mediterranean Population Movements," Human Biology: Vol. 80: Iss. 5, Article 5.


Dental affinities

1. Dental Metric

Pre-Dynastic and 12th-29th Dynasty Egyptians cluster with modern Afghans and modern North Indians on the edge of a larger cluster of modern Europeans and modern West Asians.

It has been argued by Afrocentrists that dental data is insufficient because of  "tooth sized reduction" which indeed can undergo high change do to selective forces which have to do the diet of a population and other things, thus creating results that don't have much to do with genetic admixture or relatedness [for example see here]. However, in this study tooth size and it's effects were controlled and these relationships do indeed broadly match both cranio-facial and genetic data.
"It was asserted that tooth size has been exposed to strong natural selective force (Brace et al., 1991). It is true that overall tooth size plays a major role in odontometric variation, but when the effects of overall tooth size are eliminated with standardized data, several independent vectors with eigenvalues greater than 1.0 remain."
"Mesiodistal and buccolingual crown diameters of all teeth recorded in 72 major human population groups and seven geographic groups were analyzed. The results obtained are fivefold. First, the largest teeth are found among Australians, followed by Melanesians, Micronesians, sub-Saharan Africans, and Native Americans. Philippine Negritos, Jomon/Ainu, and Western Eurasians have small teeth, while East/Southeast Asians and Polynesians are intermediate in overall tooth size. Second, in terms of odontometric shape factors, world extremes are Europeans, aboriginal New World populations, and to a lesser extent, Australians. Third, East/Southeast Asians share similar dental features with sub-Saharan Africans, and fall in the center of the phenetic space occupied by a wide array of samples. Fourth, the patterning of dental variation among major geographic populations is more or less consistent with those obtained from genetic and craniometric data. Fifth, once differences in population size between sub-Saharan Africa, Europe, South/West Asia, Australia, and Far East, and genetic drift are taken into consideration, the pattern of sub-Saharan African distinctiveness becomes more or less comparable to that based on genetic and craniometric data. As such, worldwide patterning of odontometric variation provides an additional avenue in the ongoing investigation of the origin(s) of anatomically modern humans."

SOURCE : Hanihara T and Ishida H, (2005) Metric dental variation of major human populations American Journal of Physical Anthropology, Volume 128 Issue 2, Pages 287 - 298.


2. Dental Non-metric

12th Dynasty Northern (Lisht), Roman/Byzantine (El Hesa), and Byzantine (Kharga) Egyptians cluster with other North Africans and Europeans (Poundbury, England).

"In several previous studies (e.g. IRISH 1993a, 1994, 1995, 1996, 1997) the biological affinities of Sub-Saharan and North African dental samples were estimated based on comparative analyses of morphological traits. A significant dichotomy between samples from the two geographic regions was revealed. However, intra-region trait homogeneity was observed, particularly within North Africa. Further analyses of the North Africans resulted in two additional findings. First, this homogeneity spans both space - from the Canary Islands to Egypt, and time - from recent Arabs and Berbers to West Asian-derived Carthaginians (751?-146 BC), 18th Dynasty (1575-1380 BC) Pharonic Nubians, and 12th Dynasty (1991-1783 BC) Egyptians. A small Capsian sample (ca. 8,500-5,000 BP) from Algeria and Tunisia also exhibits many trait similarities. Late Pleistocene Nubians (14,500-12,500 BP), however, are significantly different. Second, the post-Pleistocene North Africans are similar to Europeans in that they possess numerous dental features involving morphological simplification. Any North African deviations away from this pattern are in the direction of mass-additive Sub-Saharan traits. This finding supports the results of prior genetic-based studies that link North Africans to Europeans and western Asians, yet record several Sub-Saharan tendencies. Together, the two findings suggest that a morphologically simple dental pattern is shared by the indigenous peoples of North Africa, as well as Europe and perhaps western Asia, and this pattern has existed for the past 4,000 to perhaps 8,500+/- years."

SOURCE : Irish J.D. 1998b. Diachronic and synchronic dental trait affinities of late and post-pleistocene peoples from North Africa. Homo. 49(2) 138-155


Ancient Egyptians had simple, mass-reduced teeth like Caucasoids.
"However, all 15 samples exhibit morphologically simple, mass reduced dentitions that are similar to those in populations from greater North Africa (Irish, 1993, 1998a–c, 2000) and, to a lesser extent, western Asia and Europe (Turner, 1985a; Turner and Markowitz, 1990; Roler, 1992; Lipschultz, 1996; Irish, 1998a).Similar craniofacial measurements among samples from these regions were reported as well (Brace et al., 1993)"
SOURCE : Joel D. Irish (2006). Who Were the Ancient Egyptians? Dental Affinities Among Neolithic Through Postdynastic Peoples. Am J Phys Anthropol. 2006 Apr;129(4):529-43.


This contrasts with the dental pattern of Sub-Saharan Africans who had massive complex teeth.
"Dentitions of Late Pleistocene Jebel Sahaba Nubians have extremely high frequencies of complex, mass-additive (and other) traits, including UI1 labial curvature, UI1 shoveling, Bushman Canine, UC distal accessory ridge, midline diastema, sixcusped LM1, LM2 Y-5, and LP1 Tome’s root. Furthermore, they exhibit low frequencies of typical North African features.This trait combination is ubiquitous in sub-Saharan Africans;(Irish & Turner, 1990; Irish, 1993, 1997, 1998a,b, for details)."
SOURCE : Irish, J.D., 2000. The Iberomaurusian enigma: North African progenitor or dead end? Journal of Human Evolution, 39(4), pp.393–410.


Forensic reconstruction of King Tut

Forensic anthropologists classify King Tut as being "Caucasian". 

May 10, 2005 
''Is this the true face of Tut? This silicone-skinned bust is billed as the most accurate forensic reconstruction ever of ancient Egypt's Pharaoh Tutankhamun. It was based on recent 3-D CT scans of the mummy of the "boy king," who is believed to have been about 19 when he died some 3,300 years ago. 
Led by Zahi Hawass, head of Egypt's Supreme Council of Antiquities, a National Geographic Society team commissioned French experts to create the lifelike bust. Using the CT scans (see "King Tut Mummy Scanned"), French forensic anthropologist Jean-Noël Vignal determined the basic measurements and features of Tutankhamun's face. Vignal deduced that Tutankhamun had a narrow nose, buck teeth, a receding chin, and Caucasian features. Such features are typical of European, North African, Middle Eastern, and Indian peoples. 
Paris-based forensic sculptor Elisabeth Daynès then created the bust shown above. She used Vignal's estimates of skin thickness and other data, plus wooden sculptures of Tut made in his youth. Soft-tissue features, such as the nose and ears, had to be guessed at, though within a scientifically determined range. Daynès based the skin tone on an average shade of Egyptians today and added the eyeliner that the king would have worn in life. 
Finally, National Geographic gave the CT data to a U.S. forensic team, who were to work "blind"—not knowing who the subject was. Their findings validated the French team's conclusions. And their plaster cast (see photo) turned out remarkably similar to the silicon bust. The reconstruction will be featured in the June issue of National Geographic, in the touring exhibit "Tutankhamun and the Golden Age of the Pharaohs," and on the National Geographic Channel's King Tut's Final Secrets, airing Sunday night." 
For the full story, see "King Tut's New Face: Behind the Forensic Reconstruction." 
See more pictures of the reconstruction.
—Ted Chamberlain

EDIT 2017 - First Genome wide studies of Ancient Egyptian mummies!

"Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level."
PCA plot in Figure a below reveals Ancient Egyptian clustering on a global scale. The magnified rectangle gives a detailed analysis of how the Ancient Egyptians cluster in a modern West Eurasian and North African context. 

Also ADMIXTURE analysis in Figure b reveals ancestral components that peak in Natufians, Neolithic Anatolians, and Neolithic Iranians..but do not exist in modern Sub-Saharan West Africans. Most modern North African samples, including modern Egyptians have a small but noticeable increase in Sub-Saharan ancestry [red] that ancient Egyptians and ancient Middle Easterners lacked during the Neolithic to Bronze age.

I thought I would edit the PCA and remove the magnified rectangle in Figure a for clarity. This gives us an idea how homogeneous the West Eurasian genetic cluster is, which includes present North Africans. It also demonstrates just how vast the differences are between the Ancient Egyptians and Modern Sub-Saharan groups. Even East Africans from the Horn such as Somalis show no strong ties to Ancient Egyptians.

SOURCE : Schuenemann et al. "Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods". Nature Communications, 2017.


Wednesday, May 18, 2011

Relationship between skull patterns and genes.

Here are 4 peer reviewed studies which show how cranio-facial patterns indicate genetic ancestry and similarity.

Race and global patterns of phenotypic variation

Relethford et al (2009).

"Phenotypic traits have been used for centuries for the purpose of racial classification. Developments in quantitative population genetics have allowed global comparison of patterns of phenotypic variation with patterns of variation in classical genetic markers and DNA markers. Human skin color shows a high degree of variation among geographic regions, typical of traits that show extensive natural selection. Even given this high level of geographic differentiation, skin color variation is clinal and is not well described by discrete racial categories. Craniometric traits show a level of among-region differentiation comparable to genetic markers, with high levels of variation within populations as well as a correlation between phenotypic and geographic distance. Craniometric variation is geographically structured, allowing high levels of classification accuracy when comparing crania from different parts of the world. Nonetheless, the boundaries in global variation are not abrupt and do not fit a strict view of the race concept; the number of races and the cutoffs used to define them are arbitrary. The race concept is at best a crude first-order approximation to the geographically structured phenotypic variation in the human species."
SOURCE : Relethford, J. H. (2009), Race and global patterns of phenotypic variation. American Journal of Physical Anthropology, 139: 16–22. doi: 10.1002/ajpa.20900


Congruence of individual cranial bone morphology and neutral molecular affinity patterns in modern humans

Noreen von Cramon-Taubadel et al (2009).


"Recent studies have demonstrated that the shape of the human temporal bone is particularly strongly correlated with neutral genetic expectation, when compared against other cranial regions, such as the vault, face, and basicranium. In turn, this has led to suggestions that the temporal bone is particularly reliable in analyses of primate phylogeny and human population history. While several reasons have been suggested to explain the temporal bone's strong fit with neutral expectation, the temporal bone has never systematically been compared against other individual cranial bones defined using the same biological criteria. Therefore, it is currently unknown whether the shapes of all cranial bones possess reliable information regarding neutral genetic evolution, or whether the temporal bone is unique in this respect. This study tests the hypothesis that the human temporal bone is more congruent with neutral expectation than six other individual cranial bones by correlating population affinity matrices generated using neutral genetic and 3D craniometric data. The results demonstrate that while the temporal bone shows the absolute strongest correlation with neutral genetic data compared with all other bones, it is not statistically differentiated from the sphenoid, frontal, and parietal bones in this regard. Potential reasons for the temporal bone's consistently strong fit with neutral expectation, such as its overall anatomical complexity and/or its contribution to the architecture of the basicranium, are examined. The results suggest that future phylogenetic and taxonomic studies would benefit from considering the shape of the entire cranium minus those regions that deviate most from neutrality."
SOURCE : Von Cramon-Taubadel N (in press) Congruence of individual cranial bone morphology and neutral molecular affinity patterns in modern humans. Am J Phys Anthropol. doi 10.1002/ajpa.21041.


The questionable contribution of the Neolithic and the Bronze Age to European craniofacial form

C. Loring Brace et al (2005).

"Many human craniofacial dimensions are largely of neutral adaptive significance, and an analysis of their variation can serve as an indication of the extent to which any given population is genetically related to or differs from any other. When 24 craniofacial measurements of a series of human populations are used to generate neighbor-joining dendrograms, it is no surprise that all modern European groups, ranging all of the way from Scandinavia to eastern Europe and throughout the Mediterranean to the Middle East, show that they are closely related to each other."
SOURCE : C. Loring Brace et al. The questionable contribution of the Neolithic and the Bronze Age to European craniofacial formProc Natl Acad Sci U S A. 2006 January 3; 103(1): 242–247. Published online 2005 December 21. doi: 10.1073/pnas.0509801102

Link PDF

Characterization of biological diversity through analysis of discrete cranial traits

Hanihara et al. (2003)

"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. Copyright 2003 Wiley-Liss, Inc."
SOURCE : HANIHARA, TSUNEHIKO, HAJIME ISHIDA, AND YUKIO DODO. 2003. Characterization of biological diversity through analysis of discrete cranial traits. American Journal of Physical Anthropology 121:241-251.

Link PDF