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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118356/

Published online 2011 May 4. doi: 10.1186/2041-2223-2-12
PMCID: PMC3118356

Copyright ©2011 A Babiker et al; licensee BioMed Central Ltd.

Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat {STR} loci

Hiba MA Babiker,1,2 Carina M Schlebusch,1 Hisham Y Hassan,3 and Mattias Jakobsson1
1Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
2Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, D-24306 Plön, Germany
3University of Science and Technology, College of Medical Laboratory Sciences, Khartoum, Sudan
Corresponding author.
Hiba MA Babiker: hibababiker@gmail.com; Carina M Schlebusch: cschlebu@gmail.com; Hisham Y Hassan: hishamalwazer@hotmail.com; Mattias Jakobsson: mattias.jakobsson@ebc.uu.se
Received January 2, 2011; Accepted May 4, 2011.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License {http://creativecommons.org/licenses/by/2.0}, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Other Sections▼
Abstract
Background
There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.
Result
We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion {PE} was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.
Conclusion
We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.
Other Sections▼
Background
Sudan is located in northeastern Africa, with a total of 133 living languages listed by Ethnologue [1]. Local languages belong to three of the major African linguistic families proposed by Greenberg [2]: the Niger-Congo, Nilo-Saharan and Afro-Asiatic language families. The considerable ethnic and cultural diversity within Sudan make the study of existing genetic diversity of human populations an attractive effort. The Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, which remain to be fully examined on a genetic level. These groups include people with an established history in the area, {for example, Nuba and Nilotic} and groups that migrated to the area in relatively recent times {for example, Hausa, Copt and Arab}. Furthermore, population samples from Sudan are important for studies concerning human migration and the exodus from Africa 60,000 to 80,000 years ago, because the Nile Valley runs through Sudan, which is part of the traditionally favored model of the migratory route out of Africa for anatomically modern humans [3]. Previous genetic studies in Sudan have mainly focused on mitochondrial {mt}DNA, the Y chromosome [4-8], and a small number of autosomal markers [9-12]. Recently, Tishkoff et al. [13], conducted a large survey of 121 African populations using more than 800 microsatellites that included six populations from Sudan. Three of these populations were Nilotic populations, and one was a Nuba population, and these four populations speak Nilo-Saharan languages. The remaining two populations are Beja, who speak Afro-Asiatic languages. The study by Tishkoff et al. [13] showed that eastern Africa harbors substantial amounts of genetic diversity, only superseded by the amount of genetic diversity in southern Africa, but it is difficult to rank these regions, because of the very different sample density across Africa.
Since the introduction of a standardized set of forensic microsatellite markers [14], over 1000 populations across the world have been studied using these genetic markers [15]. The main results from these studies have been used to generate relevant reference data for a large number of populations, and to demonstrate that the set of microsatellite markers were sufficiently diverse to result in high PE {or low match probability} for particular populations. One of the more common commercial sequence-tagged repeat {STR} kits available for human identity testing is the AmpFlSTR® Identifiler™ PCR Amplification Kit {Applied Biosystems, Foster City, CA, USA}, which includes the 13 core STR loci from the FBI Combined DNA Index System {CODIS}, and two additional markers commonly used for forensic investigations in Europe. The marker panel has also been used in population structure and admixture studies of humans [16-21], and knowledge about population structure has contributed to our understanding of human origins [22]. Admixture or ancestry analysis is also important in forensics; for instance, to pinpoint an appropriate reference population for a particular case from which to compute match and exclusion probabilities, or to potentially get an indication of the perpetrator's ethnicity [23]. However, recent studies investigating the informativeness for ancestry inference of the CODIS markers have suggested that these markers are less informative about ancestry than are many other marker sets of similar size [16,23,24].
In this study, we report the genotypes of 15 autosomal STR markers {the markers in the AmpFlSTR Identifiler PCR Amplification Kit} for different populations in Sudan, and compute commonly used forensic summary statistics. We infer population structure for the Sudanese population and for an expanded set of populations {compiled from previous studies} from Uganda [25], Egypt [26] and Somalia [27]. Lastly, we characterize the informativeness of the 15 forensic STR markers for assignment for the populations from northeast Africa and compare the result to another set of microsatellites.
Other Sections▼
Results and discussion
The geographic locations of the sampled populations are indicated on a map of Sudan {Figure {Figure1},1}, and sample sizes for the populations are given in Table Table1.1. For the population-genetics analyses, we also combined the genotype data from our Sudanese sample {454 individuals} with previously published genotype data from Uganda [25], Egypt [26] and Somalia [27].
For the combination of the 18 Sudanese populations, allele frequencies for the 15 STR loci are shown in Table Table2.2. Commonly used forensic summary statistics and deviations from Hardy-Weinberg equilibrium {HWE} for each locus are shown in Table Table3.3. The D18S51 locus was found to have the greatest value of expected heterozygosity and it was also the locus with the lowest match probability, and the greatest powers of exclusion and discrimination {Table {Table3}.3}. The combined PE for the 15 loci was 99.99981%, and the combined match probability was 1.35 × 10-18. Five of the 15 loci {D13S317, D2S1338, D7S820, D8S1179, vWA; P = 0.021, 0.022, 0.015, 0.005 and 0.018, respectively, Fisher's exact test [28]} had deviation from HWE at the 5% level, suggesting a systematic, non-locus-specific deviation from HWE, potentially caused by population structure {see below}. However, no individual locus deviated significantly from HWE after applying Bonferroni correction for 15 tests {adjusted P = 0.003}.
Informativeness for assignment
Rosenberg et al. [29] developed a statistic, the informativeness for assignment {Ιn}, which describes the information content of a particular genetic marker for ancestry inference {it ranges from zero {no information} to the natural logarithm of the number of populations {maximum information}}. We computed Ιn values for the 15 Identifiler STRs {all tetranucleotide microsatellites} from the present study. The mean, across markers, {and standard deviation} Ιn was 0.167 {0.070} for the Sudanese populations, and 0.154 {0.066} for the Sudanese populations and the populations from Egypt, Somalia and Uganda {the Karamoja}. To determine the relative informativeness of the 15 Identifier microsatellites, we computed In for 377 microsatellites {of which 274 were tetranucleotide microsatellites} for two groups of African populations from Rosenberg et al. [29]; six sub-Saharan African populations {Kenyan Bantu speakers, Mandenka, Yoruba, San, Mbuti Pygmy, Biaka Pygmy} from the Human Genome Diversity Panel {HGDP}; the 'HGDP sub-Saharan group'; and a subgroup of three populations from the HGDP, who all speak Niger-Congo languages {Kenyan Bantu speakers, Mandenka, Yoruba}, termed the 'HGDP Niger-Congo group'. Based on the 377 microsatellites from Rosenberg et al. [29], the mean In {across markers} was 0.234 {0.098} for the HGDP sub-Saharan group and 0.106 {0.054} for the HGDP Niger-Congo group, which was a significant difference {P < 0.001, Wilcoxon signed-rank test}. The In statistic depends on both marker information about ancestry and the level of differentiation between the investigated populations. Because the same markers were used for both the HGDP sub-Saharan group and the HGDP Niger-Congo group, the difference in In between the two groups was due to the greater level of differentiation between populations in the HGDP sub-Saharan group. The In values for the Sudanese populations and the larger group of northeast African populations {from Sudan, Egypt, Somalia and Uganda} were found to lie between the values for the HGDP Niger-Congo group and the HGDP sub-Saharan group. This result is not surprising, considering that the sampled populations from Sudan belonged to different linguistic groups, although the groups are not as differentiated as the Pygmy, the San and the Niger-Congo-speaking populations in the HGDP sub-Saharan group. We concluded that the CODIS STRs contain information on population structure in the same range as many other microsatellites. However, it is possible to select more informative STR loci for population structure inference; for example, the top 15 most informative loci of the 377 microsatellites [29] {for the HGDP sub-Saharan group and for the HGDP Niger-Congo group} had mean In values of 0.489 {0.062} and 0.249 {0.041} respectively. This observation can be explained by the fact that the Identifiler STRs have been selected to have high levels of variation, because of the potentially high mutation rates of these STRs, in order to be powerful tools for identifying individuals, but the high level of variation also makes it challenging to separate alleles that are identical by state from those identical by descent [15].
Population diversity and sub-structure in Sudanese and neighboring populations
The greatest number of distinct alleles [30], considering a sample size of 58 chromosomes {29 individuals} from each of the Sudanese populations, the Somali population, the Egyptian population- and the Karamoja population from Uganda, was found in the Karamoja {mean ± SE 8.37 ± 0.63} followed by the Zagawa {8.27 ± 0.74}, the Nuba {8.04 ± 0.67} and the Nilotic {8.01 ± 0.67} {Figure {Figure2A}2A} populations. The mean number of private alleles was greatest in the Somali {0.400 ± 0.171}, followed by the Nilotic {0.292 ± 0.093}, the Zagawa {0.273 ± 0.122} and the Karamoja {0.250 ± 0.066} groups {Figure {Figure2B}.2B}. This observation of greater levels of diversity for the Nilo-Saharan populations from southern and western Sudan and for the Karamoja population from Uganda indicates larger effective population sizes of Nilo-Saharan populations compared with Afro-Asiatic populations. The low number of private alleles found for the Beja {0.031 ± 0.012} and the Nubian {0.129 ± 0.040} {Figure {Figure2B}2B} groups could be the result of high migration rate and greater gene flow from Eurasian populations, because these populations traditionally occupy the entry ports to Sudan, that is, the Beja at Red Sea and the Nubian at the Nile River Valley. A similar result was found previously [4], based on Y-chromosome data. The low number of private alleles in the Coptic groups {0.075 ± 0.053} may be a result of the recent migration of this population from Egypt, where they may have been influenced by gene flow from Asia and Europe. The Nuba also contained few private alleles {0.123 ± 0.065}, which may be a consequence of the population being an amalgamation of many groups with high levels of diversity {Hassan et al., unpublished data}.
For pairs of Sudanese populations, the greatest mean number of alleles that are private to pairs of populations was found for the Zagawa-Nuba pair {0.131 ± 0.064}, followed by the Zagawa-Nilotic pair {0.080 ± 0.051} and the Zagawa-Copt pair {0.076 ± 0.063; Figure Figure3}.3}. The lowest number of private alleles for pairs of populations were typically found when we compared a western group {for example, the Zagawa} with a northern {for example, the Nubian} or a central {for example, the Arab} group. When the Sudanese populations were compared with their neighboring populations {sample size of 58 chromosomes}, three of the four highest numbers of private alleles for population pairs were seen between the Karamoja population {from Uganda} and either the Zagawa {0.055 ± 0.026}, the Nilotic {0.034 ± 0.012} or the Nubian {0.029 ± 0.021} populations {Figure {Figure4},4}, indicating gene flow and/or shared ancestry between the Karamoja population and Nilo-Saharan populations. For smaller sample sizes {10-44 chromosomes}, the Zagawa-Nuba pair also has a high number of private alleles. A similar result was found in a previous Y-chromosome study [6], in which all Nilo-Saharan populations {which included the Zagawa, the Nilotic and the Nubian} had little evidence of gene flow with other Sudanese populations. The second largest value for the number of private alleles for population pairs in our study was for the Arab-Somali pair {0.036 ± 0.029; Figure Figure4},4}, which may be a result of the influence of Arab groups in east Africa as the product of continuous migrations from the Arabian Peninsula across the Gate of Tears over the past three millennia [31]. Among pairs of populations that included the Egyptian population, the Egyptian-Copt pair had the greatest number of private alleles {0.012 ± 0.008} indicating a connection between the Coptic and the Egyptian population {Figure {Figure44}.
We estimated population structure for the Sudanese populations together with the previously published data from the Somali, Egyptian and Karamoja populations using the software program Structure {version 2.3.3; http://pritch.bsd.uchicago.edu/software/structure2_2.html} [32]. Although most individuals had substantial parts of their genomes assigned to more than one cluster, three main patterns could be distinguished {Figure {Figure5}.5}. Individuals from northern Sudan and Egypt were {generally} more likely to fall within the 'green' cluster {P < 0.001, Mann-Whitney U-test}, these from southern Sudan and Uganda into the 'red' cluster {P < 0.001, Mann-Whitney U-test}, and those from Somalia into a {partly} separate 'yellow' cluster {P < 0.001, Mann-Whitney U-test}. The mixed ancestry of basically all individuals is probably a consequence of the limited number of markers {and of the set of markers not being particularly informative about ancestry} rather than an indication of recent admixture, a behavior of admixture analyses that has been reported previously {see Figure 4 in Rosenberg et al. [29]}. Using principal component analysis {PCA}, based on pairwise genetic distance between populations, the first principal component explained 25.5% of the genetic variation, and distinguished the Coptic, Egyptian, Somali and Nubian populations from the others {Figure {Figure6A}.6A}. The second component {10.6%} distinguished the Egyptian, and to some extent, the Somali and the Nubian population from most of the others {Figure {Figure6A},6A}, and the third component {9.9%} distinguished the Somali population from all others {Figure {Figure6B}.6B}. PCA indicated that the Egyptian, Coptic, Somali, and to some extent the Nubian groups form genetically distinct populations. The Nuba, Zagawa, Nilotic and Gemar groups clustered with the Karamoja group from Uganda, as was also indicated by the clustering using Structure {Figure {Figure55}.
We estimated population structure for the Sudanese populations together with the previously published data from the Somali, Egyptian and Karamoja populations using the software program Structure {version 2.3.3; http://pritch.bsd.uchicago.edu/software/structure2_2.html} [32]. Although most individuals had substantial parts of their genomes assigned to more than one cluster, three main patterns could be distinguished {Figure {Figure5}.5}. Individuals from northern Sudan and Egypt were {generally} more likely to fall within the 'green' cluster {P < 0.001, Mann-Whitney U-test}, these from southern Sudan and Uganda into the 'red' cluster {P < 0.001, Mann-Whitney U-test}, and those from Somalia into a {partly} separate 'yellow' cluster {P < 0.001, Mann-Whitney U-test}. The mixed ancestry of basically all individuals is probably a consequence of the limited number of markers {and of the set of markers not being particularly informative about ancestry} rather than an indication of recent admixture, a behavior of admixture analyses that has been reported previously {see Figure 4 in Rosenberg et al. [29]}. Using principal component analysis {PCA}, based on pairwise genetic distance between populations, the first principal component explained 25.5% of the genetic variation, and distinguished the Coptic, Egyptian, Somali and Nubian populations from the others {Figure {Figure6A}.6A}. The second component {10.6%} distinguished the Egyptian, and to some extent, the Somali and the Nubian population from most of the others {Figure {Figure6A},6A}, and the third component {9.9%} distinguished the Somali population from all others {Figure {Figure6B}.6B}. PCA indicated that the Egyptian, Coptic, Somali, and to some extent the Nubian groups form genetically distinct populations. The Nuba, Zagawa, Nilotic and Gemar groups clustered with the Karamoja group from Uganda, as was also indicated by the clustering using Structure {Figure {Figure55}.
Conclusion
Even though the 15 Identifiler microsatellites are not the most informative markers for inference of ancestry, these markers contain sufficient information to differentiate {to some degree} between distinct geographic and linguistic groups within Sudan and within a larger collection of northeast African populations. We conclude that geography, language and culture have played an important role in shaping patterns and structure of genetic variation in Sudan, and that these patterns may have been shaped by long-term occupation by Nilo-Saharan groups and more recent migration from North Africa and Eurasia to the Nile Valley, but a larger number of markers would be needed for fine-scale population structure inference. This study confirms that the set of 15 Identifiler microsatellites is a suitable tool for personal identification and parentage analysis in Sudan, despite the levels of population structure.
Other Sections▼
Methods
The study was described to each participant before sampling, and informed consent was obtained from each participant.
Samples
In total, 498 unrelated subjects {366 men, 132 women} were recruited from different geographic regions of Sudan. For each individual, we collected blood and {self-reported} information about the gender and ethnic background of the participant and their parents and grandparents. For the calculation of forensic summary statistics, we excluded seven people because of a potential first-degree relationship, which was inferred using Relpair v2.0.1 [36,37], leaving 491 subjects. For the population-genetics analyses, we excluded {i} the same 7 subjects because of a potential first-degree relationship, {ii} 29 for whom the sample size of the particular population was <6, and {iii} eight who failed genotyping for at least one marker, resulting in a final subject group size of 454 from 18 Sudanese populations. The geographic locations of the sampled populations are indicated on a map of Sudan {Figure {Figure1},1}, and sample sizes for the populations are given in Table Table1.1. For the population-genetics analyses, we also combined the genotype data from our Sudanese sample {n = 454} with previously published genotype data from Uganda [25], Egypt [26] and Somalia [27].
Genetic markers
Genomic DNA was extracted from DNA storage cards {FTA Classic Cards; Whatman, Maidstone, Kent, UK}, following the manufacturer's instructions. Fifteen STR loci {D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D16S539, TH01, TPOX, CSF1PO, D7S820, D2S1338 and D19S433} were co-amplified for each of the 498 subjects {AmpFlSTR® Identifiler™ PCR Amplification Kit; Applied Biosystems} following the manufacturer's recommendations [38]. The amplified PCR products were genotyped using an automatic analyzer {ABI PRISM 3730 XL Genetic Analyzer; Applied Biosystems}. For each run on the analyzer, an allelic ladder, positive and negative controls, and an internal lane standard {GeneScan-600 LIZ; Applied Biosystems} were included. Allele calling was performed {GeneMapper ID software, version 4.0; Applied Biosystems}. We followed the International Society for Forensic Genetics {ISFG} recommendations on the analysis of DNA polymorphisms. The recommended nomenclature was used, and we followed the guidelines on quality control [39].
Analysis of genotype data
Standard summary statistics for forensic applications, including allele frequencies, PE, power of discrimination, and polymorphism information content, were computed {PowerStats, version 12.0; Promega Corp., Madison, WI, USA; http://www.promega.com/geneticidtools/powerstats/}. Testing for deviations from Hardy-Weinberg equilibrium was performed using Arlequin, version 3.11; {http://cmpg.unibe.ch/software/arlequin3/} [28]. To assess the power of the 15 Identifiler microsatellite loci for population structure inference, we calculated the informativeness for assignment, In, [29] for each locus. The In statistic is based on information theory, and evaluates the efficiency of a marker for assigning individuals to one of K populations. Following Rosenberg et al. [29] for a particular locus,

where N is the number of alleles for the locus, K is the number of populations, pijis the {parametric} frequency of allele j in population i, pjis the mean frequency of allele j across populations and 'log' denotes the natural logarithm. The minimal In value is 0 {when all alleles have equal frequencies in all populations}, and the maximal value is log K {which occurs when no allele is found in more than one population}. In was computed for the combined dataset of northeast African populations from Sudan, Egypt, Somalia and Uganda. For comparison of the level of informativeness for the 15 Identifiler microsatellites, we computed In values for 377 microsatellites genotyped in the HGDP [29]. Average In values were computed for two groups of populations from the HGDP: six African populations {Kenyan Bantu speakers, Mandenka, Yoruba, San, Mbuti Pygmy, Biaka Pygmy}, referred to as the 'HGDP sub-Saharan group', and a subgroup of three populations from the HGDP who all speak Niger-Congo languages {Kenyan Bantu speakers, Mandenka, Yoruba}, referred to as the 'HGDP Niger-Congo group'.
Based on the genotype data from the 15 microsatellites, we inferred population structure for northeast African populations using the clustering software Structure [32,40]. We used the admixture model, using the F model of correlated allele frequencies across clusters. Each replicate Structure run used a burn-in period of 100,000 iterations, followed by 10,000 iterations from which estimates were obtained. We replicated the Structure analysis 10 times for each choice, based on the number of assumed clusters {K}, from K = 2 to K = 10. The 10 replicates for each choice of K was summarized {CLUMPP software; http://rosenberglab.bioinformatics.med.umich.edu/clumpp.html[41]}, with the Large K Greedy algorithm {10,000 random permutations} to identify common modes of replicates, and to combine the clustering-results across replicates. The combined clustering result was visualized {distruct package; http://rosenberglab.bioinformatics.med.umich.edu/distruct.html[42]}. Population structure was also assessed through calculating the mean squared distance for microsatellite loci [43] between pairs of populations {Populations version 1.2.30; http://bioinformatics.org/project/?group_id = 84}. The distance matrix was visualized using PCA.
We computed the mean number of distinct alleles, the mean number of private alleles and the mean number of private alleles for pairs of populations {ADZE; http://rosenberglab.bioinformatics.med.umich.edu/adze.html[44]} for the Sudanese populations {Table {Table1}.1}. For this analysis, we merged populations into larger 'ethnic groups' to avoid small sample sizes, and we also excluded the Gemar because of the small sample size {n = 6}, and because they could not be grouped with any of the other populations. This analysis was repeated for the Sudanese ethnic groups, including the populations from Egypt, Somalia and Uganda {the Karamoja}. The sample from Egypt was collected from five populations, but because no structure could be detected in these five populations [26], we treated them as one population. Analysis of molecular variance {AMOVA} [45] was used to partition genetic variation for predefined linguistic and geographic groups {Arlequin version 3.11 [28]} and the Nuba population was excluded because the group encompassed individuals speaking different languages belonging to the Niger-Congo and Nilo-Saharan linguistic divisions.
Competing interests
The authors declare that they have no competing interests.
Authors' contributions
HB and MJ conceived of the study; HB collected samples with help from HH; HB conducted the genotyping; HB, CS and MJ analyzed the data; and HB, CS and MJ wrote the paper with input from HH. All authors read and approved the final manuscript.
 
Posted by astenb (Member # 14524) on :
 
Do you know what any of that means?
 
Posted by the lioness (Member # 17353) on :
 
quote:
Originally posted by astenb:
Do you know what any of that means?

none of it, fill me in
 
Posted by zarahan- aka Enrique Cardova (Member # 15718) on :
 
^^lol..
-----------------------------------------------------------------------------------------

THE "STRUCTURE" COMPUTER PROGRAM HAS SEVERAL
WEAKNESSES WHEN USED FOR "RACIAL" CLASSIFICATION
BY ITS OPERATORS. BARBUJANI BELOW RUNS STRUCTURE
ANALYSIS AND FINDS THAT IT CONTRADICTS THE RACE
CATEGORIZERS, EXPOSING WEAKNESSES IN THEIR
APPROACH. GENETIC DIFFERENTIATION OR GEOGRAPHIC
DIFFERENCES DO NOT AUTOMATICALLY TRANSLATE INTO "RACE".


BUT WE'LL WAIT AND SEE IF OUR FRIEND ABOVE CAN
EXPLAIN..


EXCERPT FROM:
Human Races: Classifying People vs Understanding Diversity.
Current Genomics, 2005, 6, 000-000. Guido Barbujani*

--STRUCTURE software's mixed results in classifying "races

--Weaknesses of FOrensic Scientists claim to identifying "races"

--Dubious nature of US racial classification pigeonholes

etc..
..

 -
"Structured" tropical diversity... [Smile]

quote:

EXCERPT FROM:
Human Races: Classifying People vs Understanding Diversity.
Current Genomics, 2005, 6, 000-000 Guido Barbujani*


ARE RACES A BIOLOGICAL REALITY? INFERRING
POPULATION STRUCTURE
STRUCTURE PROGRAM

This approach differs from the previous one, in that
groups or races are not assumed from the start, but inferred
from the pattern of genetic variation in the data. A likelihood-
based approach, implemented in the software package
Structure, was used in several recent studies [67]. No particular
mutational model is assumed. Each individual’s
genotype is regarded as a mixture of contributions originating
in k population clusters (I shall use the term ‘clusters’ for
the sake of clarity, although in the original paper these clusters
are referred to as populations), and q(i) is the fraction of
the genes of that individual that come from the i-th cluster.

The analysis is run for different values of k, whose likelihood
is eventually compared. Once k has been estimated or somehow
defined, each individual’s genotype is supposed to have
been generated by drawing alleles, in different proportions,
from the k clusters. Under the assumption that each of the
populations is in Hardy-Weinberg equilibrium, allele frequencies
are estimated for each cluster by a Monte Carlo-
Markov Chain algorithm, and the vector q(1), q(2)…q(k) is
then evaluated for each individual, regardless of her/his geographical
provenance. In this way, ultimately one can estimate
the probability of every individual genotype to belong
to each of the inferred clusters.

Analysing by Structure two datasets of Alu insertions,
Romualdi et al. found evidence for three (two worldwide
distributed, one Eurasian) and four (African-Oceanian,
Asian-American, European, Eurasian) non-overlapping
clusters, respectively [48]...

In two other studies [49, 68] apparently the most
likely k was not estimated from the data, but rather
given arbitrary values between 2 and 6. With k=6 Rosenberg
et al. [49] found genetic clusters corresponding
to (1) Africa, (2) Europe, Western Asia and part of
Central Asia; (3) the Kalash of Pakistan; (4) East Asia and
part of Central Asia; (5) Oceania; and (6) South America.
Bamshad et al. [68] observed a separation between Africa
and Eurasia with k=2, a split between Asia and Europe with
k=3, and two African clusters with k=4, confirming that
variation within Africa exceeds that among other continents
[57, 69, 70].

To summarize, almost each of the studies mentioned in
this section was based on a different collection of populations
and individuals, and hence it is difficult to jointly interPRET
their results. All of these studies identified a geographical
structure, but each time a different structure, with different
genetic datasets suggesting different clusterings of the
individuals [48, 68]. The results of Ref. 49 have been interpreted
as showing that there are six major genetic groups in
humankind corresponding to common notions of races [71]
and hence that self-reported ancestry can facilitate the assessment
of epidemiological risk, but that does not seem the
case, for three reasons.

Firstly, the studied subjects were not
asked to self-report their ancestry, and there is no guarantee
that they regard themselves as external researchers do.

Secondly, the six clusters do not correspond to any previously
proposed racial classification (Table 1).

Thirdly, the clusters found in other studies are different [30, 48, 60].
Neither the studies apportioning diversity nor those describing population
structure have made it possible: (a) to agree on a race
list; (b) to place races on the world’s map, and (c) to associate
each race with diagnostic alleles or haplotypes.

Despite extensive use of the race concept in various fields of medicine
(see e.g. Refs. 72-74), the claim that clusters inferred
from genetic data coincide closely with groups defined by
self-identified racial or continental ancestry [29] is in open
contradiction with the available evidence.



SUBDIVISION AND ISOLATION BY DISTANCE

The above conclusions may seem at odds with the fact
that large differences are consistently observed among ethnic
groups in the US, or comparing samples coming both from
the US and from other locations in Africa and Eurasia [3, 8,
37, 68, 71]. However, the US ethnic groups cannot possibly
be regarded as representative samples of the populations
from the five continents. Indeed, their relationships with
their European, African, Asian and native American ancestors
are often unclear, and the way people are classified in
the US gives little consideration to admixture, so that, just to
mention an example, children of a Norwegian and of a Nigerian
are classified as African-Americans [10]. In addition,
many US studies include Hispanics [8], a problematic category
that does not fit any traditional or common definition of
race [26], comprising people whose mother tongue is Spanish
or Portuguese. Hispanics are individuals with extremely
variable physical aspect and skin colour, whose genomes are
often mosaics of contributions originating in two or three
continents, who are identified as Hispanics only in the country
where they immigrated in the last decades, and who
would never define themselves as such in their place of origin.

In short, no serious conclusion about human biodiversity
can be drawn from studies including Hispanics [8, 37], and
other samples of recent immigrants can be considered only if
there is evidence that they represent one specific community,
and not a heterogeneous assemblage of many. Of course, in
some contexts it makes sense to compare the genetic features
of groups labelled on the basis of their language or of other
non-biological features of theirs, for instance for forensic
identification purposes. However, these data provide no information
on the global structure of the human population.

The second reason why differences among US groups do
not suggest the existence of deep subdivision among the
main human groups is that, as we saw in the section on genetic
variances, allele-frequency differences exist between
all populations, including communities separated by short
geographic distances, or by cultural barriers at geographical
distance zero [66]. With large sample sizes, these differences
reach statistical significance. Clearly, recent immigrating
groups coming together from different continents are going
to have different allele frequencies, and there is no doubt
about that. The question is not whether human group A can
somehow be shown to differ from group B, because the answer
is invariably positive. The question is whether these
differences are distributed continuously or discontinuously
or, in other words, whether humans show the biological subdivision
that would justify clustering of its members into
discrete races.

To find a convincing answer, one must study population
samples from all over the world. In the broadest metaanalysis
so far, multilocus allele frequencies, summarised by
means of synthetic components and plotted on the map,
showed continuous, gradual change in all continents [75].
Recently, Serre and Pääbo [76] addressed the same question
at the DNA level by reanalysing the 377 loci typed in Ref.
49. They resampled random individuals from that dataset, so
as to eliminate as far as possible the effect of the clustering
of genotypes in populations that is likely to result from the
sampling of geographically discrete populations. They confirmed
that the direct analysis of discrete samples tends to
suggest the existence of clusters, roughly corresponding to
continents. However, these clusters disappeared when the
unit of analysis became the randomly-sampled individual,
indicating that discontinuities are probably an artefact due to
the discontinuous design of that and other studies.

Therefore, assigning individual genotypes to groups apparently conceals
the continuous nature of human diversity and entails a high
degree of arbitrariness, although local differences exist and
may be of evolutionary or medical significance.
Continuous genetic variation in the geographic space,
such as observed in Refs. 73, 74, and in several papers cited
therein, is the expected product of isolation by distance [15],
loosely defined as the process whereby gene flow between
communities is inversely related with their geographic distance.
Because drift affects populations independently, but
spatially close populations tend to exchange more genes than
distant populations, the overall effect of isolation by distance
is a decline of genetic similarity at increasing spatial distances.

On the contrary, if there are reproductive barriers,
genetic differences will not be simply proportional to geographic
distances, and patterns of genetic variation will not
fit models of isolation by distance. In other words, population
subdivision and isolation by distance are alternative
models, only the former causing the onset of genetic boundaries
between populations [16]. John Relethford applied a
formal model of isolation by distance for the analysis of
classical protein polymorphisms, microsatellite DNA markers
and craniometric measures taken from worldwidedistributed
samples. An excellent fit was observed for the
three classes of data, suggesting that patterns of human diversity
can largely be accounted for by the simple interaction
of drift and geographically-structured gene flow [76]. Jointly
taken, these results confirm the existence of geographic
structuring in the human genome, and the absence of clear
boundaries suggests that, as a rule, migrational networks
were more important than reproductive barriers in determining
the observed patterns of human biodiversity.
------------------
8 Current Genomics, 2005, Vol. 6, No. 4 Guido Barbujani


IS RACIAL CLASSIFICATION USEFUL?

Our species is comparatively young, and its current diversity
can be traced back to one or a few founder populations
that expanded from Africa not long ago [78, 79]. Under
that scenario, and given the evidence for extensive gene flow
[80, 81] it is unsurprising that, as we saw in the previous
sections, genetic differences between continents be small,
geographic variation be continuous, and populations that appear
to form a cluster when studied for certain markers do
not cluster together when analyzed for other markers. Human
population had too little time, and too intense migrational
exchanges, to develop racial differences. Therefore, we can
define groups based on the physical aspect of people, but the
alleles found in these groups are not reliable predictors of
variation at other independently-transmitted loci [see especially
Ref. 60]. By studying genotypes we can identify with
good approximation the geographic origin of most individuals,
but humans do not come in neat racial packages. If races
are defined as entities separated by boundaries [11], characterized
by common gene pools [12] and fixed allelic differences
[13], there is no such thing in humans.

Perhaps things will change when we have more data on
genome diversity. However, increases in our knowledge of
variation will result in a greater discriminating power only if
there is something to discriminate. At present, the labels used
to classify people do not appear to reflect a recognizable
biological subdivision of our species. Should these results be
confirmed, no technical progress will be able to provide us
with a biologically stable classification of human groups.
Is there any practical reason to maintain some kind of racial
classification, then, even though its biological meaning
is, at best, unclear? There seem to be three arguments in favour
of this view.

One is that races are important for gene
hunting because alleles that cause monogenic disorders are
enriched in, for example, Mexicans in Texas, Ashkenazi
Jews and the inhabitants of Tristan da Cunha [1].

However, none of these populations can possibly enjoy the status of a
race, according to any of the definitions listed at the beginning
of this manuscript. They are populations, a concept of
population is all we need to study their pathologic alleles,
and the presence of these alleles cannot dictate medical
treatment for an entire continent, whose inhabitants will
mostly carry the common alleles [82]. Few multigenic diseases
are well understood at the genetic level, but some
populations can conceivably carry certain combinations of
predisposing alleles in linkage disequilibrium. However,
once again, we have no evidence that these combinations
characterise broad groups which could possibly be called
races, whereas there is reason to believe they tend to occur in
specific genetic isolates [83]. The same seems the case for
allele frequencies at loci of pharmacogenomic interest,
whose extreme values are observed in groups such as “Japanese”
or “Mediterranean people” [84] that were never proposed
as races, to the best of my knowledge.

However, the clearest demonstration of the ambiguous relationships between
racial classification and disease comes from Ioannidis
et al.’s [85] meta-analysis of studies of association between
disease and genes in different groups that the authors of the
original papers defined as ‘racial’. More than half, 43 of the
83 studies considered, showed overall significant differences
for at least one of the continental groups considered, but the
relative risks, expressed as odds ratios, differed significantly
among continents in a much smaller fraction of cases, 14%.
Ioannidis and collaborators interpret this finding as a consequence
of the fact that not only genetic variation is greater
within than between groups, but so are additional factors of
risk, such as those related with lifestyle and environment
[85]. In summary, it seems that the word race is and has been
used loosely by authors who really meant populations.

In this case the problem is only semantic and can easily be fixed,
perhaps resorting to the expression “genetically differentiated
populations” when necessary.

The second argument is that, by and large, commonly
used racial labels reflect the underlying genetic structure of
humankind [75]. Therefore, skin color and body measures
would allow inferences on the likely allelic state at untyped
genes [2, 8, 71]. Clearly,10% difference between continents
(Table 1), less than 5% continent-specific polymorphisms in
Asia or Europe [56, 57], lack of correlation between skin
color and African ancestry [39] and inconsistent clusterings
of populations inferred from different genes [48, 49, 60, 68]
leave little hope of accuracy. Predicting allelic state at a locus
based on variation at other genotypic or phenotypic traits
seems more complicated and error-prone than actually typing
the locus of interest. But an additional, and so far irresolvable,
problem is that no “commonly used racial labels” exist,
because scientists never agreed on those labels (Table 1), and
because people are classified differently in different cultures
[86]. Whereas in the USA Japanese and Chinese people
would be considered to be “Asian”, in apartheid South Africa
the former were considered to be white and the latter
Asian [87]. In Japan, the majority of the population considers
the ethnic group burakumin as biologically distinct from
them, but in the USA both the Japanese majority and minority
groups would be considered part of the same race. [88].
The Bribri of Costa Rica refer to themselves as bribri, which
means “the people”, whereas all others are ña, which has a
very negative connotation (L. Madrigal, pers. comm.). That
classification is subjective, of course, but not necessarily
more so are than the many and conflicting Western classifications.

If races don’t exist, why are forensic scientists so good at
finding them?, asked Sauer [89], and this is the third argument
in favour of a racial classification. By considering
separate databases for different ethnic groups, forensic scientists
minimize the probability of unfair decisions against
members of minorities [90]. However, this seems yet another
case in which people say race but mean something else. If
races are biological realities, i.e., if they are subspecies, they
must be the same everywhere, whereas forensic race catalogs
differ across countries. In the UK we find White-skinned
European, Afro-Caribbean, Indian Subcontinent, South East
Asian and Middle Eastern: (www.forensic.gov.uk/forensic/
foi/ foi_docs/43L_Commonplace_characteristics.pdf), only
two of which (the 1st and the 4th) correspond to races in the
USA (Table 1). Which list is right?

My answer is that neither gives a sensible, all-purpose description of human diversity,
but both can work if one is to categorize people in specific
urban areas, where boundaries between groups are sharper
than at the world scale and certain groups are underrepresented
or absent altogether. Once again, a concept of population
diversity seems all that is needed for forensic identification.
Contrary to the claim that racial stereotypes capture some
meaningful aspects of biological variation, the available data
suggest that a good way to predict whether certain individuals
will have certain health risks or will benefit from pharmaceutical
treatment is to study their genes.

For example, Fig. 2 shows the distribution of the genotypes of CYP2D6, a
locus coding for one of the main drug-metabolizing enzymes
of the cytochrome, in two large samples of Asians and Europeans
[91]. Depending on the genotype, people benefit from
standard treatment (normal metabolizers), have side-effects
(slow metabolizers), or eliminate the drug before it has exerted
its action (fast metabolizers). Genotype frequencies are
almost identical in the two groups, but this not the main
point here. Even if allele frequencies differed, it is clear that
both samples contain the whole spectrum of genotypes, and
hence in both populations there will be fast, normal and slow
metabolizers. That leaves little hope to develop different
drugs, or drug dosages, specific for the Asian or the European
market. Much more productive, and now technically
conceivable, is concentrating the efforts on genetic typing of
individuals, which in turn may lead to tailoring specific
pharmacological treatment for different classes of metabolizers
[92], no matter where in the world they live."
--------------------------

Human Races Current Genomics, 2005, Vol. 6, No. 4 7

------------- ENDQUOTE--------


SOMALI RECAP:

 -


 -


 -
 
Posted by the lioness (Member # 17353) on :
 
zarahan has no class attaching photos of no relation objectifying black women to scientific articles
 
Posted by africurious (Member # 19611) on :
 
Methinks the lady doth protest too much.

Great visual example of structured tropical diversity Zarahan, especially the structured part, hahahaaa!
 
Posted by Djehuti (Member # 6698) on :
 
^ And you know she's got problems when she protests about things she doesn't know anything about!
quote:
Originally posted by the lyinass:

quote:
Originally posted by astenb:
Do you know what any of that means?

none of it, fill me in
ROTFLMAO
 -
 
Posted by the lioness (Member # 17353) on :
 
All have to do to discredit any study is to be the first one to post it and associate it with my name, ha ha

you guys are that predictable
 
Posted by xyyman (Member # 13597) on :
 
Give him/her credit for making an effort at posting anything else but pictures.

quote:
Originally posted by Djehuti:
^ And you know she's got problems when she protests about things she doesn't know anything about!
quote:
Originally posted by the lyinass:

quote:
Originally posted by astenb:
Do you know what any of that means?

none of it, fill me in
ROTFLMAO
 -


 
Posted by astenb (Member # 14524) on :
 
^ He-she is a troll. You have not noticed he/she practice of derailing threads with good content? One post of something this fool doesn't even have the knowledge to interpret cannot fix that incessant trolling.
 
Posted by the lioness (Member # 17353) on :
 
quote:
Originally posted by astenb:
^ He-she is a troll. You have not noticed he/she practice of derailing threads with good content? One post of something this fool doesn't even have the knowledge to interpret cannot fix that incessant trolling.

when I put up good informationlike this I don't get rewarded for good behavior.

so I resort to bad behavior
apparently that's what the people want. the bad girl
 
Posted by astenb (Member # 14524) on :
 
quote:
Originally posted by the lioness:
quote:
Originally posted by astenb:
^ He-she is a troll. You have not noticed he/she practice of derailing threads with good content? One post of something this fool doesn't even have the knowledge to interpret cannot fix that incessant trolling.

when I put up good informationlike this I don't get rewarded for good behavior.

so I resort to bad behavior
apparently that's what the people want. the bad girl

No we want the absent girl. Why post a block of text and not ask question on it. You seen to ask millions of questions about every one piece of nonsense.
 
Posted by zarahan- aka Enrique Cardova (Member # 15718) on :
 
No we want the absent girl. Why post a block of text and not ask question on it.

^^The purpose is to disrupt the forum with inane, multiple
troll posts, often on the same thing again & again
trying to make ES less usable to casual visitors and serious students,
and in this way, seek to bury, obscure or distort the information.

But what the pathetic fools don't seem to realize is
that good content will CONTINUE to be posted across
the board, which will be in turn picked up by other
students of the field and used around not only the web,
but in schools and other media as well. This
content is based on the hard data of credible
mainstream scholars, exposing bogus claims and distortions.

A shrewd racist would do everything possible to NOT
have more content posted, but the idiots face a
cruel dilemma. If they try to ignore the
data, they stand debunked here as well as in the
"amen corner" of Dodona, zetaboards etc. If they
try to disrupt, they spark a chain reaction that results
in STILL MORE data being posted and distributed.
The buffoonish "volume" tactics fall flat. Either way, they lose...


 -
 
Posted by the lioness (Member # 17353) on :
 
quote:
Originally posted by astenb:
quote:
Originally posted by the lioness:
quote:
Originally posted by astenb:
^ He-she is a troll. You have not noticed he/she practice of derailing threads with good content? One post of something this fool doesn't even have the knowledge to interpret cannot fix that incessant trolling.

when I put up good informationlike this I don't get rewarded for good behavior.

so I resort to bad behavior
apparently that's what the people want. the bad girl

No we want the absent girl. Why post a block of text and not ask question on it. You seen to ask millions of questions about every one piece of nonsense.
the post was fyi
not all posts are required to have a question

quote:
Originally posted by zarahan- aka Enrique Cardova:
[QB] No we want the absent girl. Why post a block of text and not ask question on it.

^^The purpose is to disrupt the forum with inane, multiple
troll posts, often on the same thing again & again

But what the pathetic fools don't seem to realize is
that good content will CONTINUE to be posted across
the board,

that's crap. this is a legitimate recent study on Sudan, good content.

You are a propagandist like none other on this forum. This is a public forum you are not a moderator.
What you do no one else in this forum does.
You have premade narrow blocks of text that are 3 feet long. You copy and paste them as replies if you happen not to like the thread. These are blocks of text that may have nothing to do with the thread and you use the same information over and over again. You are a bigger spammer than anybody.
Even poster sympathetic to your points of view have noted this.
So just because certain people might like your content it doesn't mean you are using a respectable tactic.
A lot of it stems from jealousy. A lot of your threads get few replies. You don't have new ideas. You don't even make that many new threads. Your are a broken record in your replies.
All posters who get a lot of replies are legitimate do to the fact that people have chosen to interact with them.
Who are you to judge who people choose to interact with on a public forum?
I have issues with Mike. MK, cassertides posts all the time but I don't and they don't, nobody uses the infantile text block attacks that you do.
If everybody did what you did it would destroy the forum.
This forum is about freedom of speech not freedom to disrupt the format. This is meeting place for black sumprmacists, white supremacists and everybody in between to converse.
If you want something more in line with your point of view there is a website created for that exact purpose. It's called Reloaded.
And the fact that people keep coming here, spending time writiong threads interacting with white supremacists and psuedo scientists attests to the hypocrisy and lack of support and investment of time to that site.
 
Posted by astenb (Member # 14524) on :
 
^ All that nonsense and you still have not asked questions on the study you have decided to post.
 
Posted by .Charlie Bass. (Member # 10328) on :
 
quote:
Originally posted by astenb:
^ He-she is a troll. You have not noticed he/she practice of derailing threads with good content? One post of something this fool doesn't even have the knowledge to interpret cannot fix that incessant trolling.

She is a troll and thinks she rules this board.
 
Posted by Djehuti (Member # 6698) on :
 
^ Yet her rule depends on other members of this board.
 
Posted by zarahan- aka Enrique Cardova (Member # 15718) on :
 
This forum is about freedom of speech not freedom to disrupt the format. This is meeting place for black sumprmacists, white supremacists and everybody in between to converse.

^^My, my, arent you the pious one? The starter of multiple
threads on the same topic already ongoing in an existing one,
to avoid continual debunking and exposure of your ignorance..
and to continue your denials of reality?
Whatsa matta? Panties in a wad? Can't take the heat?

 -
 
Posted by The Explorer (Member # 14778) on :
 
The second largest value for the number of private alleles for population pairs in our study was for the Arab-Somali pair (0.036 ± 0.029; Figure ​Figure4),4), which may be a result of the influence of Arab groups in east Africa as the product of continuous migrations from the Arabian Peninsula across the Gate of Tears over the past three millennia [31].....


Because the Somali population is separated both geographically and linguistically from the other populations included in our study, it is not surprising that it is also genetically distinct.

It is possible that the Bantu expansion from West Africa had a stronger effect on the region of the Horn of Africa, where Somalia is located, compared with the region where Sudan is located. For example, the languages in Somalia belong to two major linguistic families, the Afro-Asiatic and Niger-Congo, whereas Nilo-Saharan is absent and the Bantu Swahili language is one of the major languages in Somalia (Ethnologue [1]).

Another explanation could be that the Somali population is of both Eurasian and sub-Saharan origin, as suggested by a recent study [33], potentially explaining the differentiation of this population from some east African groups, although many of the Sudanese populations, such as Arabs and the Beja, may also have mixed Eurasian and sub-Saharan origin.


I like the very last segment of the above extracts from the study. [Smile]

And besides, with regards to "Bantu expansion from West Africa", Uganda has a larger Bantu speaking population than Somalia. That would in effect reduce the number of unique "private" markers of the Somali sample and push it closer to the Ugandan sample, just going off on the rationale of geographic proximity between distinct major African language phylum speaking populations; I did not get the impression that that crossed the minds of these authors.
 
Posted by Sundjata (Member # 13096) on :
 
The authors are being irresponsible with what they attribute to their sources.

quote:
From the study:

Another explanation could be that the Somali population is of both Eurasian and sub-Saharan origin, as suggested by a recent study [33]

Oh, really? You guys mean this study here that corresponds to citation #33?

quote:
High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males.


We genotyped 45 biallelic markers and 11 STR systems on the Y chromosome in 201 male Somalis. In addition, 65 sub-Saharan Western Africans, 59 Turks and 64 Iraqis were typed for the biallelic Y chromosome markers. In Somalis, 14 Y chromosome haplogroups were identified including E3b1 (77.6%) and K2 (10.4%). The haplogroup E3b1 with the rare DYS19-11 allele (also called the E3b1 cluster gamma) was found in 75.1% of male Somalis, and 70.6% of Somali Y chromosomes were E3b1, DYS19-11, DYS392-12, DYS437-14, DYS438-11 and DYS393-13. The haplotype diversity of eight Y-STRs ('minimal haplotype') was 0.9575 compared to an average of 0.9974 and 0.9996 in European and Asian populations. In sub-Saharan Western Africans, only four haplogroups were identified. The West African clade E3a was found in 89.2% of the samples and the haplogroup E3b1 was not observed. In Turks, 12 haplogroups were found including J2*(xJ2f2) (27.1%), R1b3*(xR1b3d, R1b3f) (20.3%), E3b3 and R1a1*(xR1a1b) (both 11.9%). In Iraqis, 12 haplogroups were identified including J2*(xJ2f2) (29.7%) and J*(xJ2) (26.6%). **The data suggest that the male Somali population is a branch of the East African population** - closely related to the Oromos in Ethiopia and North Kenya - with predominant E3b1 cluster gamma lineages that were introduced into the Somali population 4000-5000 years ago, and that the Somali male population has approximately 15% Y chromosomes from Eurasia and approximately 5% from sub-Saharan Africa.

http://www.ncbi.nlm.nih.gov/pubmed/15756297?dopt=Abstract

Umm, ok. [Confused] I wonder who else came to the same interpretation that the authors came to after reading the conclusion and data from this study? That the latter authors ignorantly exclude Ethiopia and Kenya from "sub-Saharan" Africa has no bearing on the facts here either. I really don't see how the former authors can use the above to make that kind of argument.
 
Posted by Djehuti (Member # 6698) on :
 
^ Indeed, it is nothing but more obfuscation of not only the indigenous nature of eastern Africa but that these indigenous lineages spilled out into Southwest Asia which is why the presence of E derived clades in both the Levant and Arabia as well. As such the authors play the game of claiming an African lineage as 'Eurasian' just like they do with entire African peoples from the Egyptians to the Beja and even the Somali! LOL This is the type of game that Euronuts like Racial Fantasy and his master Dienekes likes to play.

On a serious note, what do you guys make of paragroup F* in Sudan? From all the sources I've read, the authors attribute it to a back-migration yet I'm under suspicion that it is indigenous based not only on what Keita wrote in regards to the ambiguous nature of the African/Southwest Asian divide but also because derived groups like J1 have the highest frequency in Socotra and Yemen real close to Africa as well as what Explorer and Rasol told me about derived K in east Africa as well.
 
Posted by The Explorer (Member # 14778) on :
 
We can make either of two things of the paragroup F*:

It is very likely a newly detected F downstream clade that is independent of preexisting known F sub-clades, assuming that the nucleotide screening of the given study, regardless of its published date, was comprehensive by the very latest standard.

And/Or...

They could be relatively more basal remnants of the original F clade that did not have a chance to give way to the more established F downstream markers, due to persistence of small effective population size of the populations carrying them.

Either way, the results would point to a very intriguing presence of F clades in Sudan, that cannot easily be explained away by back migration. Any back-migration, at most, would point to an essentially fledgling or fairly newly-emerged F clade back to the African mainland...meaning that using the clade to make some sort of statement about "Eurasian" physiological influence on Africans is essentially a futile undertaking.
 
Posted by the lioness (Member # 17353) on :
 
Sweetnet gave us the Nubian hair samples, that ties in with the F clades in Sudan
 
Posted by Perahu (Member # 18548) on :
 
 -

Nubians are ~50% Caucasoid.
 
Posted by Djehuti (Member # 6698) on :
 
^ Not this bullsh|t again. [Roll Eyes] Hey, Paironuts give us a valid definition of "caucasoid" or GTFOH!
quote:
Originally posted by the lyinass:

Sweetnet gave us the Nubian hair samples, that ties in with the F clades in Sudan

What da f*ck does my mention of F clades have to do with hair, you twit! I suppose you'll attribute F clades to similar hair texture in Uganda and Tanzania as well? Sorry lyinass but it ain't happening!
 
Posted by Djehuti (Member # 6698) on :
 
quote:
Originally posted by The Explorer:

We can make either of two things of the paragroup F*:

It is very likely a newly detected F downstream clade that is independent of preexisting known F sub-clades, assuming that the nucleotide screening of the given study, regardless of its published date, was comprehensive by the very latest standard.

And/Or...

They could be relatively more basal remnants of the original F clade that did not have a chance to give way to the more established F downstream markers, due to persistence of small effective population size of the populations carrying them.

Either way, the results would point to a very intriguing presence of F clades in Sudan, that cannot easily be explained away by back migration. Any back-migration, at most, would point to an essentially fledgling or fairly newly-emerged F clade back to the African mainland...meaning that using the clade to make some sort of statement about "Eurasian" physiological influence on Africans is essentially a futile undertaking.

Interesting. I was guessing these would be the scenarios. IF it was a back-migration it would have to come from southwest Asia (Arabia) among a population of recently derived Africans. So the whole label of 'Eurasian' would be invalid. I'll have to hunt down the studies again.
 
Posted by the lioness (Member # 17353) on :
 
quote:
Originally posted by Djehuti:
I suppose you'll attribute F clades to similar hair texture in Uganda and Tanzania as well? Sorry lyinass but it ain't happening! [/QB]

learn my last lesson, anecdotal rare individuals (and who we don't even know the entire ancestral background of) do not even represent a whole tribe of persons with a given trait
 
Posted by Perahu (Member # 18548) on :
 
quote:
Originally posted by Djehuti:
^ Not this bullsh|t again. [Roll Eyes] Hey, Paironuts give us a valid definition of "caucasoid" or GTFOH!

Clearly Nubians are racially admixed. They carry high levels of Caucasoid admixture.
 
Posted by Djehuti (Member # 6698) on :
 
^ And until you define what "caucasoid" is let alone any genetic components thereof your claims remain nothing but that-- claims! Then again, you are the same idiot who claims "caucasoid" admixture for Rwandan Tutsi! LMAO [Big Grin]

quote:
Originally posted by the lyinass:

learn my last lesson, anecdotal rare individuals (and who we don't even know the entire ancestral background of) do not even represent a whole tribe of persons with a given trait

Whose talking about anecdotal rare individuals, you dumb twit?! I'm talking about entire peoples who display such traits, and the genetics shows they are entirely African which means your dumbass is debunked!
 
Posted by The Explorer (Member # 14778) on :
 
quote:
Originally posted by Djehuti:
Interesting. I was guessing these would be the scenarios. IF it was a back-migration it would have to come from southwest Asia (Arabia) among a population of recently derived Africans. So the whole label of 'Eurasian' would be invalid. I'll have to hunt down the studies again.

The back-migration scenario is by no means an unequivocal, given or established theory. It is thrown out there as a possibility, and under such a possibility, what would the Sudanese paraphyletic F markers mean.

It remains to be seen if any of the paraphyletic Sudanese F markers even exist in the so-called "Southwest Asia" for starters.
 
Posted by zarahan- aka Enrique Cardova (Member # 15718) on :
 
quote:
Originally posted by Djehuti:
^ Not this bullsh|t again. [Roll Eyes] Hey, Paironuts give us a valid definition of "caucasoid" or GTFOH!

PEr the writer N. Krieger below:

 -

QUOTE:

"On what basis, however, has Caucasian entered
the scientific lexicon? Is it truly an objective
factual term? A review of its actual etymology
quickly reveals it is anything but.

In brief, the term Caucasian was coined in the
18th century by Johann Friedrich Blumenbach
(1752–1840), for what became one of the world’s
most influential racial typologies.33–36 In his
1775 opus On the Natural Variety of Mankind, 33(
pp65–145) Blumenbach reported data on skeletal
traits and bodily characteristics of people
worldwide to answer the question: “Are men, and
have the men of all times and of every race been
of one and the same, or clearly of more than one
species [italics in original]?”3 6(pp 97,98)

Framing his work was the then-prevalent
pre-Darwinian assumption that “variation” in
humans, as in other animals, represented
“degeneration” from a basic “type,” as brought
about by climate and other external
influences.2 8,35,36(pp196–200)
On the basis of his analyses, Blumenbach arrived
at 4 major conclusions:


* All humans belong to 1 species, with equal
human capacities to think, feel, and act.

* “Caucasians” constitute the “primeval”
human type from which all other varieties have
diverged.

* The “[i]nnumerable varieties of mankind run
into each other by insensible degrees [italics
in original].”33(p264)

* While any division of these varieties is
“arbitrary,” humankind “may best, according to
natural truth, be divided into the five following
varieties; which may be designated and
distinguished from each other by the names
Caucasian, Mongolian, Ethiopian, American, and
the Malay.”33(p264)


These varieties arose, he hypothesized, because
Caucasians, the original humans, “degenerated,”
in his words, into “Mongolian,” by way of the
intermediate “American” variety, and also into
“Ethiopian,” by way of the “Malay” variety
33(pp264–266)—a hypothesis that notably is the
complete reverse of contemporary scientific
research indicating that Homo sapiens originated
in the African continent.2,4

Why, however, the term Caucasian? As cogently
argued by several contemporary scholars, but
rarely noted in the public health or biomedical
literature, answers lie at the crossroads of
national politics, religious beliefs, racial
aesthetics, and sexual desire.37,38 In brief, the
region of the Caucasus (located between the Black
Sea and the Caspian Sea, abutting Europe, Asia,
and the Middle East) provided a “safe” place on
which to project back a common European ancestry
without getting embroiled in volatile nationalist
politics.37 In the late 18th century, the
Caucasus region, then under Russian rule, was
relatively unknown to Western Europeans.

At the same time, it was literally legendary. In
Greek myths, it was where Zeus seduced Europa,
Jason sought the Golden Fleece, the Amazons
roamed, and the Greek gods chained Prometheus to
a mountain peak as punishment for giving
humanity fire.37,39 From a Judeo-Christian
perspective, it was home to Mount Ararat—of
biblical fame for being the peak on which Noah’s
ark rested to survive the Deluge.37 Hence the
appeal of the term Caucasian: a politically
palatable name with a rich legacy, free of the
stamp of “nationality,” and with all of the
allure of a new scientific taxonomic term."


Equally revealing is the reason Blumenbach
himself gave for his choice: “beauty.” He wrote:
“I have taken the name of this variety from Mount
Caucasus, both because its neighbourhood, and
especially its southern slope, produce the most
beautiful race of men, I mean the Georgian. ”33( p269)

On this basis, Caucasian became a scientific term.

Of note, Blumenbach’s terminology was quickly
taken up by his scientific peers..
By the time the British Anthropological Society
published a special edition of Blumenbach’s
collected writings in 1865,33 which commemorated
his role as a key founder of the discipline of
anthropology, the more malleable term varieties
was replaced by more rigid term race, which in
turn was tightly bound to concepts of inequality.
In the preface to this volume, the editor posed
what he deemed the key question regarding “the
five races of Blumenbach”: “Is it proper to place
them in the same rank, and allow them all the
same zoological value?”42(x,xi) To this question,
he said, there could only be one scientific
answer: no. “Thus it has happened that these
races, after having been once introduced into
science by Blumenbach, have been retained there,”
he continued, predicting that “we may assert
that they will always be retained, with some
rectifications in their characteristics and
their several boundaries.”42(x,xi)"
[ ENDQUOTE]

 
Posted by The Explorer (Member # 14778) on :
 
quote:
Originally posted by Perahu:

 -

Nubians are ~50% Caucasoid.

It's a mystery why you are posting a map that doesn't reflect your ideological remark below.
 
Posted by Perahu (Member # 18548) on :
 
quote:
Originally posted by The Explorer:
It's a mystery why you are posting a map that doesn't reflect your ideological remark below.

Nubians are clearly intermediate between true Nilotes and Caucasoid Copts.

Their highly admixed nature is quite evident. There's no point in denying it.
 
Posted by The Explorer (Member # 14778) on :
 
quote:
Originally posted by Perahu:

Nubians are clearly intermediate between true Nilotes and Caucasoid Copts.

Their highly admixed nature is quite evident. There's no point in denying it.

I see; what does the study, where you got that map from, say makes Copts representative of "caucasoids"?

Does that then leave Egyptians and Somalis, as seen on the map, as the extreme opposites of "caucasoid"?
 
Posted by Perahu (Member # 18548) on :
 
quote:
Originally posted by The Explorer:
I see; what does the study, where you got that map from, say makes Copts representative of "caucasoids"?

Yes, Copts are very Caucasoid.

quote:
Originally posted by The Explorer:
Does that then leave Egyptians and Somalis, as seen on the map, as the extreme opposites of "caucasoid"?

PCA1 is the most important component, showing strong racial differences (Nuba vs Copts). PCA2 and PCA3 show far less variance.
 
Posted by The Explorer (Member # 14778) on :
 
quote:
Originally posted by Perahu:
quote:
Originally posted by The Explorer:

I see; what does the study, where you got that map from, say makes Copts representative of "caucasoids"?

Yes, Copts are very Caucasoid.
Dodging the question. Take another, good, look at what is being asked of you.

quote:
PCA1 is the most important component, showing strong racial differences (Nuba vs Copts). PCA2 and PCA3 show far less variance.
You must be blind to say that there isn't clear and strong variation along the PC2.

And given your mindset, should it then be said that the Hausa, the Karamoja and the Nubian samples, which all appear in between the Copt and the Nuba samples, are all ~50% "caucasoid"?
 
Posted by Perahu (Member # 18548) on :
 
quote:
Originally posted by The Explorer:
Dodging the question. Take another, good, look at what is being asked of you.

Of course it isn't mentioned. But anyone familiar with population genetics knows a strong divergence exists between Caucasoids and Negroids. This is represented by PCA component 1 (showing the greatest variance in the data).

quote:
Originally posted by The Explorer:
And given your mindset, should it then be said that the Hausa, the Karamoja and the Nubian samples, which all appear in between the Copt and the Nuba samples, are all ~50% "caucasoid"?

No, those appear to have a strong Negroid dominance.

Only the Nubians, Somalis, Egyptians, and Copts appear to have a strong Caucasoid component.

Although, I am baffled by the position of the Beja, you would expect them to be more Caucasoid. Perhaps unrepresentative sampling.
 
Posted by the lioness (Member # 17353) on :
 
quote:
Originally posted by Perahu:

Only the Nubians, Somalis, Egytpaisn, and Copts appear to have a strong Caucasoid component.

what is the geographic origin of their Caucasoid component?
 
Posted by Perahu (Member # 18548) on :
 
quote:
Originally posted by the lioness:
what is the geographic origin of their Caucasoid component?

Middle East and North Africa.
 
Posted by the lioness (Member # 17353) on :
 
quote:
Originally posted by Perahu:
quote:
Originally posted by the lioness:
what is the geographic origin of their Caucasoid component?

Middle East and North Africa.
You include North Africa, does this mean straight hair and light skin are indigenous to Africa?
 
Posted by Perahu (Member # 18548) on :
 
quote:
Originally posted by the lioness:
You include North Africa, does this mean straight hair and light skin are indigenous to Africa?

Possibly, but it originated in biologically Caucasoid Africans not Negroids.
 
Posted by The Explorer (Member # 14778) on :
 
quote:
Originally posted by Perahu:
Of course it isn't mentioned. But anyone familiar with population genetics knows a strong divergence exists between Caucasoids and Negroids. This is represented by PCA component 1 (showing the greatest variance in the data).

Bingo! It isn't mentioned anywhere in that study, that the Sudanese Copts are the quintessential "caucasoids" of the study. Now do you see what is flawed about your remark, as if the map reflected it? Or are you still steeped in ideology?

quote:
No, those appear to have a strong Negroid dominance.

Only the Nubians, Somalis, Egyptians, and Copts appear to have a strong Caucasoid component.

Although, I am baffled by the position of the Beja, you would expect them to be more Caucasoid. Perhaps unrepresentative sampling.

Your earlier qualifier of "intermediacy" should render all those I mentioned "caucasoid". Are you then retracting that qualifier now?
 
Posted by Perahu (Member # 18548) on :
 
quote:
Originally posted by The Explorer:
Bingo! It isn't mentioned anywhere in that study, that the Sudanese Copts are the quintessential "caucasoids" of the study. Now do you see what is flawed about your remark, as if the map reflected it? Or are you still steeped in ideology?

Copts are predominantly Caucasoid.

quote:
Originally posted by The Explorer:
Your earlier qualifier of "intermediacy" should render all those I mentioned "caucasoid". Are you then retracting that qualifier now?

No.
 
Posted by The Explorer (Member # 14778) on :
 
Man, you have no credibility; just opinions.
 
Posted by the lioness (Member # 17353) on :
 
quote:
Originally posted by Perahu:
quote:
Originally posted by the lioness:
You include North Africa, does this mean straight hair and light skin are indigenous to Africa?

Possibly, but it originated in biologically Caucasoid Africans not Negroids.
If there is such a thing as completely indigneous cucasoid Africans
how and why would they have come about? What would have caused there to be two different "races" in Africa?
 
Posted by Perahu (Member # 18548) on :
 
^ Africa is a big place. Egypt is far closer to the Caucasus mountain range than to Nigeria.
 
Posted by Whatbox (Member # 10819) on :
 
But it's also much closer to Darfur than is it even to the Georgians and Armenians of the Caucasus.

Closer to the Dinka than to South Western Russia (tha Caucasus).
 
Posted by zarahan- aka Enrique Cardova (Member # 15718) on :
 
Indeed.. Vogel mentions the Sudan below..

 -


 -
 
Posted by Perahu (Member # 18548) on :
 
quote:
Originally posted by Whatbox:
But it's also much closer to Darfur than is it even to the Georgians and Armenians of the Caucasus.

Closer to the Dinka than to South Western Russia (tha Caucasus).

Closer to Israel than all of these!
 
Posted by zarahan- aka Enrique Cardova (Member # 15718) on :
 
Egypt is closer to the Sudan genetically and historically.
CLosest people ethnically to Ancient Egyptians are Nubians
as credible scholarship shows.

 -


 -
 
Posted by Perahu (Member # 18548) on :
 
Egyptians are genetically closer to Arab Near Easterners.
 
Posted by zarahan- aka Enrique Cardova (Member # 15718) on :
 
 -
 
Posted by Djehuti (Member # 6698) on :
 
^ Of course. This is no doubt the reason why Paironuts never cites studies comparing Nubians and Egyptians to Israelis, let alone Circassians of the Caucasus! LOL This guy is so disingenuous it's quite funny. [Big Grin]
quote:
Originally posted by The Explorer:

The back-migration scenario is by no means an unequivocal, given or established theory. It is thrown out there as a possibility, and under such a possibility, what would the Sudanese paraphyletic F markers mean.

It remains to be seen if any of the paraphyletic Sudanese F markers even exist in the so-called "Southwest Asia" for starters.

Point taken.
 
Posted by Troll Patrol (Member # 18264) on :
 
quote:
Originally posted by Perahu:
quote:
Originally posted by the lioness:
You include North Africa, does this mean straight hair and light skin are indigenous to Africa?

Possibly, but it originated in biologically Caucasoid Africans not Negroids.
And what is the basal clade in indignious North Africans? lol
 
Posted by Whatbox (Member # 10819) on :
 
quote:
Originally posted by Perahu:
^ Africa is a big place. Egypt is far closer to the Caucasus mountain range than to Nigeria.

quote:
Originally posted by Whatbox:
But it's also much closer to Darfur than is it even to the Georgians and Armenians of the Caucasus.

Closer to the Dinka than to South Western Russia (tha Caucasus).

quote:
Originally posted by Perahu:
Closer to Israel than all of these!

But it's closer to Nubia than it is to Israel! Nubia is a region within Sudan but aswell Egypt.

I guess I win. You cannot get any closer than that. Inside a Country.
 
Posted by Troll Patrol (Member # 18264) on :
 
quote:
Originally posted by Perahu:
Egyptians are genetically closer to Arab Near Easterners.

DNA analysis shows that Egyptians group with African peoples from the Sudan, Ethiopia, East Africa and parts of Cameroon, not with Europe or the Middle East.

Notes on E-M78 and Rosa DNA study linking Egyptians with East and Central Africans. DNA study (Rosa et al. 2007) groups Egyptians with East and Central Africans. Other DNA studies link these peoples together. Quote:“the majority of Y chromosomes found in populations in Egypt, Sudan, Ethiopia and Oromos in Somalia and North Kenya (Boranas) belong to haplogroup E3b1 defined by the Y chromosome marker M78“(Sanchez 2005). Codes: Egy=Egypt. Or= Oromo, Ethiopia. Am=Amahara, Ethiopia. Sud=Sudan.

FCA=Cameroon. Maa= Massai, Kenya. Note: Eighty (80)% or more of the haplotypes in Cameroon are of West African origin (Rosa et al. 2007, Cerny et al. 2006). Ethiopia, Cameroon and most of the Sudan is located below the Sahara, and thus sub-Saharan.-- Rosa, et al.(2007) Y-chromosomal diversity in the population of Guinea-Bissau. BMC Evolutionary Biology. 7:124
 


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