The Study of Racialism

William · Posted: Tue 01 Nov 2005 21:49 Post subject: Various admixture studies

The following are various admixture studies. This page is updated frequently. Where a link to only an abstract is given, often a link to a full-text version is available on the abstract page, sometimes for a fee. Note that studies using blood group markers, such as proteins and antigens, are perfectly valid, despite fraudulent claims to the contrary on various Internet message boards and sites with agendas. The use of blood proteins has decreased substantially (but has not been abandoned by any stretch of the imagination) simply because the decoding of the human genone has permitted researchers to look directly at the DNA, which provides detail and depth unavailable at the protein level. But the various blood group markers used for determining population relationships have been the subject of study for decades, and consequently, researchers know their origins, or at least where they are found in their greatest frequencies. This is why they are valid for determining if admixture occurred.

Scandinavians (including Greenland)

Evidence for mtDNA admixture between the Finns and the Saami (2001). Uses mtDNA. Abstract only.
Population studies in northern Sweden. XVII. Estimates of Finnish and Saamish influence (1991). Uses blood proteins. Abstract only.
A population genetic study in Finland: comparison of the Finnish- and Swedish-speaking populations (1991). Uses blood proteins. Abstract only.
High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosomal analysis (2003). Uses Y. Complete article.
Origin and population structure of the Icelanders (1993). Uses blood proteins. Abstract only.

South African "Whites"

Definition of the HLA-Aw43 antigen (1989). Uses MHC/HLA. Abstract only.

Jews, Arabs, North Africans, and other Middle Easterners

The Duffy blood group system in Israeli Jews and Arabs (1979). Uses Fy. Abstract only.
HLA DR and DQ polymorphism in Ashkenazi and non-Ashkenazi Jews: comparison with other Mediterraneans (1996). Uses MHC/HLA. Abstract only.
Jewish and Middle Eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes (2000). Uses Y. Abstract only.
High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews (2000). Uses Y. Abstract only.
The Y chromosome pool of Jews as part of the genetic landscape of the Middle East (2001). Uses Y. Abstract only.
Gm and Inv [Km] allotypes among Libyan and Ashkenazi jews, and Armenians living in Israel (1980). Uses blood proteins. Abstract only.
Gm and Inv studies on eight Iranian populations with distance measures among the six from the Caspian Littoral (1980). Uses blood proteins. Abstract only.
Lebanese population: prevalence of the erythrocyte phenotypes (2001). Uses blood proteins. Abstract only.
Human mitochondrial DNA sequence variation in the Moroccan population of the Souss area (2001). Uses mtDNA Abstract only.
Extensive Female-Mediated Gene Flow from Sub-Saharan Africa into Near Eastern Arab Populations (2003). Uses mtDNA and Y. Full article.
Consistent Long-Range Linkage Disequilibrium Generated by Admixture in a Bantu-Semitic Hybrid Population (2000). Uses autosomal markers. Complete Article. Measures historical gene flow between Bantu and Arab populations in Africa.
A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes (2002). Uses Y. Complete Article.
HLA genes in Southern Tunisians (Ghannouch area) and their relationship with other Mediterraneans (2006). Abstract only. Also confirms relatedness of Greeks to sub-Saharans.
The origin of Palestinians and their genetic relatedness with other Mediterranean populations (2001). Uses HLA. Abstract only. || Note: Study passed peer review, was published, and then was retracted purely for political reasons. It is clear, judging from the above statement, from Arnaiz-Villena's excellent track record, from the information in the abstract, and from the fact that other studies have obtained similar results, that nothing is scientifically wrong with it. Furthermore, the study's results are the study's results, and there isn't much that can be said against hard scientific data. See posting for detailed explanation. Unfortunately, the entire study is no longer available in electronic form.||

Italy (including Sicily and Sardinia) and France (including Corsica) & General Mediterranean (For more on Italy, click here. The below Italian studies are included there, as well as a few others.)

Blood group phenotypes and the origin of sickle cell hemoglobin in Sicilians (1978). Uses blood proteins. Shows sub-Saharan origin of sickle-cell in Sicily, and shows sickle-cell to be only one of several sub-Saharan genetic markers in Sicilians. Abstract only.
Presence of hemoglobinopathies in Sicily: a historic perspective (1997). Abstract only. Shows various globin gene clusters in the Sicilian population, and mentions how the "presence of many different alterations in the globin gene clusters can surely be considered testimony of past colonizations."
Clinical, hematological, and molecular features in Sicilians with sickle cell disease (1992). Abstract only. Mentions that all HbS patients studied were homozygous for haplotype #19 (Benin).
Sickle cell disease in Sicily (1980). Abstract only. Shows that HbS in Sicily is identical to that of U.S. Blacks.
Beta S gene in Sicily is in linkage disequilibrium with the Benin haplotype: implications for gene flow (1988). Shows the Central West African origin for sickle cell in Sicily. Abstract only. The article The Geography of Sickle Cell Disease also contains a wealth of information, showing the strain of sickle cell in Sicily and Greece originated in Benin.
Molecular characterization of hemoglobin C in Sicily (1992). Shows HbC in Sicily is derived from African black chromosomes and is not an independent mutation. Abstract only. The study Evidence of Negro Origin of HbC in Sicily (1987) supports this, but unfortunately not even an abstract is available. (Incidentally, the study 'African' Genetic Markers in Sicilians (1980) shows that markers of African origin exist in Sicilians, but again, not even an abstract is available online. Evidence of the African origin of sickle cell hemoglobin in western Sicily is self explanatory but again no abstract is available.)
Presence of an African beta-globin gene cluster haplotype in normal chromosomes in Sicily (1992). Uses blood proteins. Abstract only.

Mitochondrial DNA polymorphisms in Italy. III. Population data from Sicily: a possible quantitation of maternal African ancestry (1989). Uses mtDNA. Abstract only. This study, headed by Dr. Ornella Semino, finds a 4.4% sub-Saharan mtDNA contribution to its sample of 90 diverse Sicilians (4 L sequences in the 90 subjects). The HpaI-3 {equivalent to the +3592HpaI} AvaII-3 association corresponds to haplogroups L1/L2, as learned by corresponding with Dr. Semino.

||Note: There is a fraudulent and patently ridiculous claim (by those with idealogical investments in the topic) on the Internet that the above 1989 Semino study has been "refuted" or "discredited" or some such nonsense by a passage from Vona, et al. (2001). Sometimes this bogus "refutation" is accompanied by the title "0% Black DNA in Sicilians: erratum" which is a fabrication and appears nowhere in the Vona study ("errata" are not ussued 12 years later by scientists not involved in the study, and the word "erratum" isn't used by those attempting to refute data or conclusions, anyway; it is used when a bit of data is incorrect or was misprinted, and the corrigendum is published soon after). The Vona passage cites this study for comparison purposes only, and doesn't attempt to refute it:

Quote:

In work carried out with restriction enzymes on mt DNA in a sample of Sicilians, Semino et al. (1989) indicated the presence (4.4%) of the African complex HpaI-3/AvaII-3 (40% in Senegal and in the Bantu of South Africa). The authors hypothesized a migration of genes from Africa to Sicily, estimated at about 10%, which was introduced into the Sicilian gene pool by Black slaves brought by the Phoenicians and the Romans and/or by Arab migrations. Results at the mtDNA sequencing level, however, show no Black African influence in the Sicilian population.

As anyone can easily see, what this passage is saying is that while Semino (1989) found sub-Saharan sequences in their sample of Sicilians at a rate of 4.4% by using the (perfectly acceptable and very popular) RFLP method, they (Vona) did not find such sequences by sequencing the HVR1 in their sample. To reiterate, it is strictly a comparison, not an attempt at a "refutation" (which would be impossible, anyway). The quote has been brazenly misrepresented by those with an axe to grind. The Vona study goes on to say:

Quote:

The haplotypes that emerge from the sequences, some of which [are] common to both Sicilians and Berbers, suggest the possibility of a certain amount of contact with the populations of North Africa. Results of the analysis of mtDNA sequences indicate that it is difficult to identify in the characteristics of the present-day population of Sicily genetic influences that could be attributed to any single group that invaded the island and settled there for shorter or longer periods. Further study of mtDNA by applying the restriction enzymes to the present and earlier (from the time of the 1837 cholera outbreak) populations could shed light on the interactions between the Sicilian population and other populations of the Mediterranean area which needs to be examined more thoroughly.

There is no possible way Vona (2001) can refute or discredit Semino (1989), since each study uses different samples. One cannot "refute" the other. In fact, no study that comes up with definite results with regard to its sample (e.g., 4 sub-Saharan lineages out of 90 people tested) can be "refuted" at all, period. The 1989 Semino study tests 90 Sicilians from different parts of the island, and consequently clearly finds four L1/L2 lineages in subjects from Messina, Enna, and Palermo. The 2001 Vona study only tests the HVR1 of 49 subjects from a single Sicilian village, so it is not odd that no L sequences were observed. Fact is, most mtDNA studies on Sicily do indeed find L sequences, even those that test single villages: Plaza, 2003, Romano, 2003, Cali, 2001, Richards, 2000, Forster, 2002). The finding of sub-Saharan sequences in Sicily agrees with history (as well as geography). Rest assured that the 1989 Semino study and its findings are perfectly valid, and are not open to question or challenge by any method. Just to cover all angles, the study's validity has also been confirmed with Dr. Semino in private correspondence (even though this clearly wasn't necessary). This may seem like an inordinately long explanation for something that is so obvious that it doesn't need explanation, but the drivel about the study being "refuted" still exists on old Internet message boards and needed to be cleared up here.

Incidentally, the use of restriction enzymes is just as valid as sequencing the section of DNA in question; it is not "outdated" or "invalid" or "unreliable" or any such drivel, and is still frequently used because it is relatively inexpensive and accurate. (Even the Vona study cited above recommends this method for further studying the relationship between Sicilians and other peoples.) Indels (insertion/deletion polymorphisms) are easy to spot using this method, and the method saves the cost of sequencing the section in question. In fact, when sequencing the HVR does not give satisfactory results, or if the two HVR's don't match, often restriction enzymes will be applied to the coding region to determine the mutation, and then haplotype can be ascertained.||

Restriction fragment length polymorphism of human mitochondrial DNA in a sample population from Apulia (southern Italy) (1989). Abstract only. Shows 3 sub-Saharan haplogroup L1/L2 markers (HpaI-3 {equivalent to the +3592HpaI} AvaII-3 association, as in Semino study above) in a sample of 87 Apulians (3.4%). Data not available in abstract, and full study not available online, but data supplied by Dr. Ornella Semino.
MtDNA control region and RFLP data for Sicily and France (2001). Abstract only. Study's data table shows one sub-Saharan haplogroup L in a sample of 106 Sicilians.
Genetic analysis of a Sicilian population using 15 short tandem repeats (2003). Uses mtDNA. Complete article. Shows introgression of African genes into Sicily by demonstrating an affinity between Egyptians and Sicilians. Shows the Sicilian population is a heterogeneous one.
New data on the genetic structure of the population of Sicily: analysis of the Alia population (Palermo, Italy) (2002). Abstract only. Uses classical markers (blood proteins). Shows heterogeneity in the Sicilian population.
Y-Chromosomal Diversity in Europe Is Clinal and Influenced Primarily by Geography, Rather than by Language (2000). Uses Y. Full article and chart show sub-Saharan haplogroup 8 present in Sardinians (1/10) and French (1/40).
Y-chromosome 10 locus short tandem repeat haplotypes in a population sample from Sicily Italy (2004). Abstract only. Mentions there is a significant African component to the paternal Sicilian gene pool. In the study itself, a figure of 5% is given for this component, which is Northwest African.
Y-chromosome haplotypes in Corsica (2002). Uses Y. Abstract only. Full-text (in French) not available online, and the following information isn't available in the abstract, but through correspondence with Dr. Lucotte, it has been learned that 11 out of the 328 Y-chromosomes tested in Corsica were of sub-Saharan origin.
Autosomal Microsatellite and mtDNA Genetic Analysis in Sicily (Italy) (2003). Full article. Finds sub-Saharan L sequences at a rate of 2% in Sciacca & less than 1% in Castellammare, and finds haplogroup M (which is, according to this study, usually the East African M1 in the Mediterranean area) at a rate of 8% in Sciacca, 3% in Castellammare, and 2% and Ragusa.
Population Structure in the Mediterranean Basin: A Y Chromosome Perspective (2006). Abstract only. Extensive and involved study. Full study shows sub-Saharan haplogroup A in Sardinians and Cypriots, sub-Saharan E3a in Maltese, and sub-Saharan E*(xE3b E3a) in Maltese. Also shows various forms of E3b, which ultimatedly traces its way back to eastern sub-Saharan Africa (since it originated there), in many different Mediterraneans, including Sicilians, Sardinians, Maltese, Italians, etc.
Joining the Pillars of Hercules: mtDNA Sequences Show Multidirectional Gene Flow in the Western Mediterranean (2003). Uses mtDNA. Complete article. This includes information on sub-Saharan admixture in Italy, Iberia, and North Africa. The central Portuguese sample has sub-Saharan L sequences at a rate of around 6%, and the south Italian sample has these sequences at a rate of about 8%.
Sequence diversity of the control region of mitochondrial DNA in Tuscany and its implications for the peopling of Europe (1996). Abstract only. Full study (not available through Pubmed) shows that out of 49 Tuscanese tested, 2 have haplotype L3b.
Continental and subcontinental distributions of mtDNA control region types (2002). Abstract only. Full study (not available through Pubmed) shows that out of 80 Sicilians from Sciacca, three have L2a, one has L3*, two have L3e, and five have M1 (13.8% maternal sub-Saharan contribution to the sample from this region of Sicily).

Iberia (including Balearics, Canaries, Madeira, Azores, etc.)

Mitochondrial DNA HVRI variation in Balearic populations (2005). Uses mtDNA. Abstract only.
Genetic variation in the population of Ibiza (Spain): genetic structure, geography, and language (1996). Uses blood proteins. Abstract only.
HLA in the Azores Archipelago: possible presence of Mongoloid genes (1999). Uses MHC/HLA. Abstract only.
The Y-chromosomal heritage of the Azores Islands population (2005). Uses Y. Abstract only.
Genetic structure and origin of peopling in the Azores islands (Portugal): the view from mtDNA (2005). Uses mtDNA. Abstract only.
Y-chromosome lineages from Portugal, Madeira and Acores record elements of Sephardim and Berber ancestry (2005). Uses Y. Abstract only.
HLA genes in Portugal inferred from sequence-based typing: in the crossroad between Europe and Africa (2005). Uses MHC/HLA. Abstract only.
Distribution of HLA alleles in Portugal and Cabo Verde. Relationships with the slave trade route (2002). Uses MHC/HLA. Complete Article. Afro-European admixture in Portugal and the Cape Verdes.
Clinal variation of YAP+ Y-chromosome frequencies in Western Iberia (2000). Uses Y. Abstract only.
Mitochondrial portraits of the Madeira and Acores archipelagos witness different genetic pools of its settlers (2003). Uses mtDNA. Abstract only.
Genetic structure and origin of peopling in the Azores islands (Portugal): the view from mtDNA (2003). Uses mtDNA. Abstract only.
Mitochondrial DNA affinities at the Atlantic fringe of Europe (2002). Uses mtDNA. Full text. Includes a chart showing sub-Saharan admixture in various European countries, inclucing England, Scotland, France, Portugal, etc.
Diversity of mtDNA lineages in Portugal: not a genetic edge of European variation. Uses mtDNA. Complete article. || Note: Mentions that some lineages in their L3* "default group" may not be of recent sub-Saharan origin. In actuality, all true L3* lineages are of sub-Saharan origin. However, in some cases, as in this study, L3* is not distinguished properly from haplogroups M (possibly of sub-Saharan origin) or N (not sub-Saharan in origin), and is thus considered a "default category" (in another study this same thing is described as "N/M/L3"). In studies where L3* is mentioned without qualification, it is indeed true L3*, which is sub-Saharan. According to this study, sub-Saharan L3* is distinguished from M and N at nucleotide positions 10400 and 10873, respectively. Incidentally, Plaza, 2003 used the Pereira sample; they re-examined the motifs, and made some adjustments. Some of the Portuguese motifs assigned to L3* that may not have actually been so were not listed as L3's in the Plaza study. ||

United States of America

Who Are the Americans?. Regional variation of autosomal SNP admixture for White and Black Americans (August, 2008).
Human Population Genetic Structure and Inference of Group Membership (2003). Uses Alu. Complete article. Shows that Alu insertion polymorphisms identify ancestry better than do traditional methods like ethnic self-identify or skin tone.
Admixture in Hispanics: Distribution of Ancestral Population Contributions in the Continental United States (2003). Uses autosomal markers. Complete article. Shows that eastern U.S. Hispanics (Cubans, Puerto Ricans, Dominicans) are genetically distinct from western U.S. Hispanics (Mexicans).
Ethnic-Difference Markers for Use in Mapping by Admixture Linkage Disequilibrium (2002). Uses autosomal markers. Complete Article. Afro-European linkage disequilibrium.
Markers informative for ancestry demonstrate consistent megabase-length linkage disequilibrium in the African American population (2003). Uses autosomal markers. Complete Article. Afro-European linkage disequilibrium.
Markers that discriminate between European and African ancestry show limited variation within Africa (2002). Uses autosomal markers. Complete Article. Afro-European admixture.
Association of African Genetic Admixture with Resting Metabolic Rate and Obesity Among Women (2003). Uses autosomal markers. Complete Article. Afro-European admixture.
Race-specific HIV-1 disease-modifying effects associated with CCR5 haplotypes (1999). Uses questionnaire. Complete Article. Deeply flawed study claiming to show correlation between HIV prognosis and patients' “race,” but measures “race” via a questionnaire. Mike Bamshad signed it; he should have known better.
Using Genetic Admixture to Explain Racial Differences in Insulin-Related Phenotypes (2003). Uses autosomal markers. Complete Article.
Control of Confounding of Genetic Associations in Stratified Populations (2003). Uses autosomal markers. Complete Article.
Y Chromosome STR Haplotypes and the Genetic Structure of U.S. Populations of African, European, and Hispanic Ancestry (2003). Uses autosomal markers, but very coarse resolution. Complete Article. Measures Euro admixture in U.S. Blacks.
Influence of genetic admixture on polymorphisms of alchohol metabolyzing enzymes: Analyses of mutations on the CYP2E1, ADH2, ADH3, and ALDH2 genes in a Mexican-American population living in the Los Angeles Area (2002). Uses specific genes for alchoholism. Complete Article. Chicanos differ genetically among themselves.
HLA Class II and TNF Genes in African Americans From the Southeastern United States: Regional Differences in Allele Frequencies (2003). Uses MHC/HLA. Complete Article. Regional differences in A-A admixture.
Estimating African American Admixture Proportions by Use of Population-Specific Alleles (1998). Uses autosomal markers. Complete Article. European admixture in Black Americans.
Ancestral Proportions and Admixture Dynamics in Geographically Defined African Americans Living in South Carolina (2001). Uses autosomal markers. Complete Article. European admixture in Black Americans.
Implications of correlations between skin color and genetic ancestry for biomedical research (2004). Uses autosomal markers. Complete Article. Refutes the idea that skin color reveals admixture.
Using estimates of individual admixture to study the genetics of phenotypic traits: skin pigmentation in African Americans (2001). Uses autosomal markers. Abstract only. European admixture in Black Americans.
Population Structure in Admixed Populations: Effect of Admixture Dynamics on the Pattern of Linkage Disequilibrium (2001). Uses autosomal markers. Complete article. Linkage disequilibrium suggests rate of gene flow.
Skin pigmentation, biogeographical ancestry and admixture mapping (2003). Uses autosomal markers. Complete Article. Groundbreaking study; Afro-European admixture in U.S. population.
Genetic ancestry and the search for personalized genetic histories (2004). Uses autosomal markers. Complete Article. Surveys use of genetics in genealogy.
Implications of biogeography of human populations for “race” and medicine (2004). Uses various markers. Complete Article. Shows that classification by the traditional “races” fails to describe the actual patterns of human genetic diversity.
Maximum-Likelihood Estimation of Admixture Proportions From Genetic Data (2004). Uses various markers. Complete Article. Explains methodology. Shows Afro-European admixture in U.S. population as example.
Mitochondrial Versus Nuclear Admixture Estimates Demonstrate a Past History of Directional Mating (1997). Uses mtDNA and blood proteins. Complete Article. Hispanic males mated with Amerind females, but Anglo/Amerind mating was more male/female symmetrical.
Effects of cis and trans Genetic Ancestry on Genetic Expression in African Americans (2008). Uses the degree of gene expression, rather than specific markers, to show Euro-Afro admixture rates in A-As. Complete Article.
The Role of Self-Defined Race/Ethnicity in Population Structure Control (2005). Measures the intra-group genetic homogeneity of southern California subjects who self-identify as "Black," "White," and "Hispanic" (actually Chicano). Finds that southern California Chicanos are relatively homogeneous genetically, in contrast to Hispanics nationwide who vary greatly. Oddly worded abstract has been mis-interpreted by some to suggest that self-identity was matched against measured admixture percentages. Not so. What was measured was the intra-group genetic homogeneity of three ethno-political groups in southern California. Complete Article.

India

Ethnic India: A Genomic View, With Special Reference to Peopling and Structure (2003). Uses mtDNA, Y, and autosomal markers. Complete article. Traces India’s ethnic, caste, and tribal divisions using 58 markers.
Genetic Evidence on the Origins of Indian Caste Populations Genome Research Vol. 11, Issue 6, 994-1004, June 2001.Complete article.

Central, Eastern, and Southeastern Europe

Probable ancestors of Hungarian ethnic groups: an admixture analysis. Abstract only.
Genetic structure in relation to the history of Hungarian ethnic groups. Abstract only.
Uralic genes in Europe. Abstract only.
Gm and Km(Inv) frequencies in two Roumanian populations. Abstract only. Detects Asiatic and sub-Saharan genetic material in Romanians.
Mitochondrial DNA variation in Russian populations of Stavropol krai, Orel and Saratov oblasts. Uses mtDNA. Abstract only. Detects Asiatic admixture in European Russians.
Variability in mitochondrial DNA in Russian inhabitants from Krasnodar Krai, Belgorod and the lower Novgorod region. Uses mtDNA. Abstract only. Detects Asiatic admixture in European Russians.
HLA genes in Macedonians and the sub-Saharan origin of the Greeks (2001). Uses HLA. Abstract only. Full study cached at this link. ||Note: There is a fraudulent claim (by those with idealogical investments in the topic) on the Internet that this study has been "retracted" or "refuted." The study is perfectly valid. Sub-Saharan-specific and quasi-sub-Saharan-specific alleles were definitely detected in the Greek population at the DRB1 locus, and this is not open to question. See posting for detailed explanation. The retraction (which was purely for political reasons) applies to another Arnaiz-Villena study that concerned itself with Palestineans, Jews, and other Mediterraneans, and cross-referenced some of the Greek data.|| Shows a sub-Saharan contribution to the Greek genepool.
The origin of the sickle mutation in Greece; evidence from beta S globin gene cluster polymorphisms (1991). Abstract only. Shows that HbS in Greece is mostly haplotype #19 (the one that originated in Benin).
Sickle cell anemia, sickle cell beta-thalassemia, and thalassemia major in Albania: characterization of mutations (1994). Abstract only. Mentions that the HbS in their sample is the Benin-originating haplotype #19.
Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects (2003). Abstract only. Full study shows sub-Saharan haplogroup A in a sample of Greeks from the island of Mitilini (1/27).
Excavating Y-chromosome haplotype strata in Anatolia (2003). Full PDF article. Finds sub-Saharan and Asiatic DNA in Anatolian Turks.
Phylogeographic Analysis of Mitochondrial DNA in the Nogays: A Strong Mixture of Maternal Lineages from Eastern and Western Eurasia (2004). Full study. Finds sub-Saharan and Asiatic mtDNA in Turks and others speaking a Turkic language.

General European and Northern and Northwestern Europe

Tracing European Founder Lineages in the Near Eastern mtDNA Pool (2000). Uses mtDNA. Full article. Supplementary data here.. Very interesting and involved study. An examination by a geneticist acquaintance reveals haplogroup M (East African M1) in Greeks. Also found are one sub-Saharan L3e and one sub-Saharan M1 in a sample of 90 Sicilians from Troina (n.=42) and Trapani (n.=48 ). In 69 Sardinians, there are one L1a and one L2a. In 48 Romans there are one L2a and one L3b sequences.

Phylogeography of mitochondrial DNA in western Europe (1998). Uses mtDNA. Abstract only. Finds sub-Saharan markers in various European populations. The following quote from the full PDF article (available online) is noteworthy:

Quote:

Two sequences, from Sardinia and Portugal, are members of RFLP haplogroup L2 (confirmed by testing for the HpaI site at position 3592 characterizing L1 and L2 in Africans: Chen et al. 1995). One, from Iberia, is a one-step derivative of the most frequent and widespread member of L3b. An individual from North Germany, one from Britain and one from Sardinia are members of L1, and the 6209±16223±16311 sequence is a member of an African subcluster of L3a, and ndeed is found in a Portuguese subject with Angolan ancestry.

The correlation between languages and genes: the Usko-Mediterranean peoples (2001). Uses HLA. Abstract only. Shows genetic relatedness between many Mediterranean populations. Mentions that Greeks are outliers due to a "significant genetic input from sub-Saharan Ethiopians and Blacks."
Population genetic relationships between Mediterranean populations determined by HLA allele distribution and a historic perspective (2002). Uses HLA. Abstract only. Points out several facts, including the introgression of sub-Saharan genes to the Greek genepool, in the form of HLA alleles and Chromosome 7 markers.
Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area (2004). Full study. Self explanatory, but includes charts which shows sub-Saharan E-M33 in Italian Calabrians (1.3%) and also in Albanians in Calabria (2.9%); shows sub-Saharan E-M35* in Italian Calabrians (1.3%), Albanians in Calabria (1.5%), Sardinians (0.7%) and Sicilians (5.5%). This study and this one show E-M35* to reach its highest frequencies in sub-Saharans (Ethiopians and southern Africans), with only sporadic occurrences at low levels in North Africa and Europe; this proves it is useful as a marker of sub-Saharan admixture.
The molecular spectrum of beta-thalassemia and abnormal hemoglobins in the allochthonous and autochthonous dutch population (1998). Abstract only. Discusses hemoglobin defects, but is also of interest because it mentions that 1-2 million 'autochthonous' (i.e., native, "White") Dutch have Asian, southern European, or African ancestors.

Latin America

African-derived South American Populations: A History of Symmetrical and Asymmetrical Matings According to Sex Revealed by Bi- and Uni-parental Genetic Markers (1999). Uses mtDNA and Y. Complete Article. Sexual asymmetry.
Spanish genetic admixture is associated with larger V˙ O2 max decrement from sea level to 4,338 m in Peruvian Quechua (2003). Uses autosomal markers. Complete Article.
Genetic Structure of Seven Mexican Indigenous Populations Based on Five Polymarker Loci (2003). Uses autosomal markers. Complete Article.
Genetic Admixture in Three Mexican Mestizo Populations Based on D1S80 and HLA-DQA1 Loci (2002). Uses MHC/HLA. Complete Article.
Ethnic Admixture Composition of Two Western Amazonian Populations (2002). Uses blood proteins. Complete Article.
Mitochondrial DNA Analysis Reveals Substantial Native American Ancestry in Puerto Rico (2001). Uses mtDNA. Complete Article. Puerto Ricans have native ancestry.
The Phylogeography of Brazilian Y-Chromosome Lineages (2001). Full study. Table also shows one sub-Saharan Y-haplogroup 8 in a sample of 93 Portuguese.
Relation of risk of systemic lupus erythematosus to west African admixture in a Caribbean population (2002). Uses autosomal markers. Complete Article. Trinidadian correlation between lupus and African admixture.
Mitochondrial DNA Studies Show Asymmetrical Amerindian Admixture in Afro-Colombian and Mestizo Populations (2003). Uses mtDNA and Y. Complete Article. African males mated with Amerind females.
Unequal Contributions of Male and Female Gene Pools From Parental Populations in the African Descendants of the City of Melo, Uruguay (2002). Uses mtDNA and Y. Complete Article. African males mated with Amerind females.
Admixture Studies in Latin America: From the 20th to the 21st Century (2000). Summary. Complete Article. Survey of numerous Latin American admixture studies. (Spanish Translation of English original.)
Admixture Studies in Latin America: From the 20th to the 21st Century (2000). Summary. Complete Article. Survey of numerous Latin American admixture studies. (English original of the above item.)
Beta-Globin Gene Cluster Haplotypes as Evidence of African Gene Flow to the Northeastern Coast of Venezuela (2003). Uses MHC/HLA. Complete Article. Afro-European admixture in Venezuela.
Abnormal Hemoglobins and Racial Admixture in Villa Clara Province (Cuba) (1999). Complete PDF article.. Shows mixing of Africans and Europeans in Cuba.
Maximum likelihood estimates of admixture in Northeastern Mexico using 13 short tandem repeat loci (2002). Uses autosomal markers. Abstract only.
Admixture in Mexico City: implications for admixture mapping of Type 2 diabetes genetic risk factors (2007). Uses 69 autosomal markers as well as mtDNA and Y. Full Text. Very up-to-date and comprehensive DNA admixture analysis for Mexico City shows a Native American contribution of 65%, European contribution of 30%, and West African contribution of 5%.
Genetic composition of rural Chilean communities inhabiting Elqui, Limari and Choapa valleys (2002). Uses blood proteins. Full Text (in Spanish). The three populations studied show 5-to-10 percent subSaharan admixture. "Las frecuencias estimadas para el haplotipo cDe del sistema Rh en los valles de Elqui y Limarí sugiere la presencia de genes negros en estos valles, hecho que se reafirma por la presencia del alelo 2M en el valle de Elqui. Cuando se considera como población ancestral la negra, además de las poblaciones española y aborigen, el porcentaje de mezcla negra promedio estimado para ambos valles varía de 5% a 10%."

Origins of Native Americans

Mitochondrial DNA Analysis of Mongolian Populations and Implications for the Origin of New World Founders (1996). Uses mtDNA. Complete Article. Shows that Amerinds originally came from Mongolia.

Paleolithic Europe

Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans (2003). Uses mtDNA. Complete Article. Neandertals were a different species.
The Neandertal type site revisited: Interdisciplinary investigations of skeletal remains from the Neander Valley, Germany (2000). Uses mtDNA. Complete Article. Neandertals were a different species.
DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen (1999). Uses mtDNA. Complete Article. Shows that Neandertals were a different species.

Paleolithic Africa

Ethiopians and Khoisan Share the Deepest Clades of the Human Y-Chromosome Phylogeny (2002). Uses Y. Complete Article. Ethiopians and Khoisan are the oldest living H. sapiens sapiens.
Y chromosome sequence variation and the history of human populations (2000). Uses Y. Complete Article. Out-of-Africa.
Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms (2003). Uses autosomal markers. Complete Article. Out-of-Africa.
The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations (2001). Uses Y. Complete Article. Out-of-Africa.

Africa (general); Africa and its Relationship to Other Areas

Phylogeographic Analysis of Haplogroup E3b (E-M215) Y Chromosomes Reveals Multiple Migratory Events Within and Out of Africa
(2004). Full study. Discussess E3b and its derivatives. It is of interest when studying sub-Saharan admixture in Europeans because it has a chart showing sub-Saharan E(xE3b) in Northern Portuguese (4.0%), Southern Portuguese (2.0%), and Sardinians (1.6%); shows sub-Saharan E-M35* in Northern Portuguese (2.0%), Pasiegos from Cantabria (1.8%), Southern Spaniards (1.6%), Corsicans (0.7%), Sardinians (1.1%), and Estonians (1.4%).
Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa (1999). Full study. Shows (in addition to what's stated in the title) that most of the mtDNA haplogroup M types found sporadically in the Mediterranean are the East African version (M1).

fwsweet · Posted: Tue 01 Nov 2005 22:00 Post subject:

Outstanding! I shall be adding to it over the next few days. Glad to hear you are feeling better. Mary Lee and I caught a bug from our latest grandchild (who just started daycare) and we have been coughing with sore throats. I guess it is the season.

William · Posted: Thu 03 Nov 2005 16:53 Post subject: Frank

I've been adding to this index using your format exactly, which is great. I wonder if you and I are the only ones at ODR interested in these studies.

William · Posted: Thu 03 Nov 2005 20:52 Post subject: Articles of interest...

One in one hundred white Britons directly descended from an African or Asian

May 20 2001

DNA reveals black genes in white Britons

Jonathan Leake, Science Editor

punjabtrini · Mentor Joined: 04 Sep 2007 {Posts: 253 } Location: USA

William,

Fantastic! Thank you.
I came across a few of them before but it is great to have them in one location.

fwsweet · Posted: Wed 10 Dec 2008 16:34 Post subject:

I have just posted two additional full-text studies to the bottom of the "United States" section. They are: Effects of cis and trans Genetic Ancestry on Genetic Expression in African Americans (2008) and The Role of Self-Defined Race/Ethnicity in Population Structure Control (2005).