Post by anansi on Jan 29, 2017 20:35:17 GMT -5
Mapping Post-Glacial expansions: The Peopling of Southwest Asia
Results
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www.nature.com/articles/srep40338
Samples and Genotyping
A total of 8,515 samples were analyzed (Supplementary Table S1) for their Y-chromosome genetics. All participants recruited and genotyped by our team had at least three generations of paternal ancestry in their country of birth and provided details of their geographical origin. A written informed consent was signed and obtained by each participant prior to recruitment for this study. The study protocol and the informed consent form were approved by the IRB of the Lebanese American University. The study methods were carried out in accordance with the principles of the Declaration of Helsinki. DNA was extracted from blood or buccal swabs using a standard phenol–chloroform protocol. Samples were genotyped for binary Y chromosome polymorphisms as reported previously23.
Our previously described samples (n = 2047)23,28,29 were further subtyped to achieve the same Haplogroup (Hg) differentiation as the new samples analyzed here23,28,29, with the additional 6 SNPs (J1e-P58, J2a-M410, J2b-M12, E1b1b1a-M78, E1b1b1b-M81 and E1b1b1c-M123). DNA samples were also typed for 11 microsatellite loci (DYS 388, 389I, 390, 391, 393, 19′, 437, 439, 389II, 392 and 438).
A total of 8,515 samples were analyzed (Supplementary Table S1) for their Y-chromosome genetics. All participants recruited and genotyped by our team had at least three generations of paternal ancestry in their country of birth and provided details of their geographical origin. A written informed consent was signed and obtained by each participant prior to recruitment for this study. The study protocol and the informed consent form were approved by the IRB of the Lebanese American University. The study methods were carried out in accordance with the principles of the Declaration of Helsinki. DNA was extracted from blood or buccal swabs using a standard phenol–chloroform protocol. Samples were genotyped for binary Y chromosome polymorphisms as reported previously23.
Our previously described samples (n = 2047)23,28,29 were further subtyped to achieve the same Haplogroup (Hg) differentiation as the new samples analyzed here23,28,29, with the additional 6 SNPs (J1e-P58, J2a-M410, J2b-M12, E1b1b1a-M78, E1b1b1b-M81 and E1b1b1c-M123). DNA samples were also typed for 11 microsatellite loci (DYS 388, 389I, 390, 391, 393, 19′, 437, 439, 389II, 392 and 438).
Results
Y-chromosome haplogroups J1 and J2 and E1b1b are the major paternal lineages, accounting for 50.9% in Southwest Asia and North Africa. The Y haplogroup frequency pie-chart map (Supplementary Figure S1), and PCA (Supplementary Figure S4) both show broad geographic differentiation. Similarly, an MDS plot based on Y-STR across all haplogroups (Fig. 1a) reveals similar geographic organization, reflecting correlation between STR haplotypes and haplogroups. However, the MDS shows weak geographical organization among J2 and J*(xJ2) haplogroup Y-STR RST distances analyses compared to RST distances analyses applied to all haplogroups (Fig. 1b and c). Likewise, a reduced median NETWORK analysis of STR haplotypes within J haplogroups, namely J2d, J1e and J1xJ1e, also reveals less geographical organization (Supplementary Figure S5). Since Y-chromosomal lineages generally show strong geographical structure, the lack of such structure within J is unexpected.
Figure 1
Figure 1
MDS analyses of RST distances based on STR haplogroup variances (a) across all haplogroups, for (b) J*(xJ2), and (c) J2.
Full size image
Maximal diversities, indicative of possible origins, are observed for J*(xJ2) in the Caucasus and for J2 in Armenia, decreasing south and east, although high diversities do not entirely correlate with high relative frequencies (frequency contour Supplementary Figure S2 and variance contour Supplementary Figure S3). BATWING TMRCA (Supplementary information) estimates for J*, J1, J1e, J2, and E1b1b are shown in Table 1. These results indicate slightly greater time depth information of J, J1, and J2 in Turkey and populations from the Caucasus, in agreement with their higher diversity in this area. They also show greater differentiation of the E1b1b1 haplogroups between North Africa and the rest of Asia. The great time depth of J2 and E in Iberia are consistent with a longer period of isolated evolution. Haplogroup J* is the least differentiated in time, but shows maximum values in Turkey Iran as well as North Africa, with decreasing values progressively further away from these geographical locations. Due to the phylogenetic relationship between J1 and J2 markers, the TMRCAs for these are identical. The J1 and J2 split shows deepest time in the Caucasus, Syria and Turkey at 8.9 ka and 8.4 ka, respectively.
The population split estimates (Fig. 2) show divergences largely reflecting the trend in TMRCAs with older dates closer to the Caucasus, but with differentiation times roughly 1/3 of the TMRCAs, suggesting that 2/3 of STR diversity evolution occurred prior to the earliest population differentiations that followed the Late Glacial Period expansions. Expansions therefore distributed a broad spectrum of shared STR haplotypes that had already evolved within their isolated populations. This broadly shared diversity explains the weak geographical discrimination observed in the phylogenetic networks (Supplementary Figure S5) and the lack of organization found in the MDS analysis for haplogroup specific J*(xJ2) and J2 Y STR FSTs (Fig. 1b and c).
Figure 1
Figure 1
MDS analyses of RST distances based on STR haplogroup variances (a) across all haplogroups, for (b) J*(xJ2), and (c) J2.
Full size image
Maximal diversities, indicative of possible origins, are observed for J*(xJ2) in the Caucasus and for J2 in Armenia, decreasing south and east, although high diversities do not entirely correlate with high relative frequencies (frequency contour Supplementary Figure S2 and variance contour Supplementary Figure S3). BATWING TMRCA (Supplementary information) estimates for J*, J1, J1e, J2, and E1b1b are shown in Table 1. These results indicate slightly greater time depth information of J, J1, and J2 in Turkey and populations from the Caucasus, in agreement with their higher diversity in this area. They also show greater differentiation of the E1b1b1 haplogroups between North Africa and the rest of Asia. The great time depth of J2 and E in Iberia are consistent with a longer period of isolated evolution. Haplogroup J* is the least differentiated in time, but shows maximum values in Turkey Iran as well as North Africa, with decreasing values progressively further away from these geographical locations. Due to the phylogenetic relationship between J1 and J2 markers, the TMRCAs for these are identical. The J1 and J2 split shows deepest time in the Caucasus, Syria and Turkey at 8.9 ka and 8.4 ka, respectively.
The population split estimates (Fig. 2) show divergences largely reflecting the trend in TMRCAs with older dates closer to the Caucasus, but with differentiation times roughly 1/3 of the TMRCAs, suggesting that 2/3 of STR diversity evolution occurred prior to the earliest population differentiations that followed the Late Glacial Period expansions. Expansions therefore distributed a broad spectrum of shared STR haplotypes that had already evolved within their isolated populations. This broadly shared diversity explains the weak geographical discrimination observed in the phylogenetic networks (Supplementary Figure S5) and the lack of organization found in the MDS analysis for haplogroup specific J*(xJ2) and J2 Y STR FSTs (Fig. 1b and c).
This is just a sample I cut and paste pls klik for full info
www.nature.com/articles/srep40338