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The genetic structure of the world’s first farmers - Iosif Lazaridis
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[QUOTE]Originally posted by Ish Gebor: [QB] Here is the part were I get a bit confused: [QUOTE][b]"CT, has been interpreted as supporting an African origin for anatomically modern humans[/b],10 with Khoisan from south Africa and Ethiopians from east Africa sharing the deepest lineages of the phylogeny.15 and 16" [IMG]http://ars.els-cdn.com/content/image/1-s2.0-S0002929711001649-gr2.jpg[/IMG] These chromosomes belong to a clade (haplogroup BT) in which chromosomes C and R share a common ancestor (Figure 2). [/QUOTE]--Fulvio Cruciani et al (2011) A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa http://ac.els-cdn.com/S0002929711001649/1-s2.0-S0002929711001649-main.pdf?_tid=6ccb0c16-4e7f-11e5-b727-00000aab0f01&acdnat=1440874669_ffffe619194e1d6273f8c9b24ab42a19 http://www.sciencedirect.com/science/article/pii/S0002929711001649 [QUOTE] An independent high resolution MSY phylogeny has been recently obtained from 2,870 Y-SNPs discovered (or re- discovered) in the course of a large whole-genome re-sequencing study, but the observed variable sites all belong to the recent ‘‘out of Africa’’ CT clade [15]. Recently, in a re-sequencing study of the Y chromosome, the root of the tree moved to a new position and several changes at the basal nodes of the phylogeny were introduced [16] [..] Phylogenetic Mapping Most of the mutations here analyzed belong to the African portion of the MSY phylogeny, which is comprised of haplogroups A1b, A1a, A2, A3 and B [16]. Through phylogenetic mapping it was possible to identify 15 new African haplogroups and to resolve one basal trifurcation (Figure 1). A new deep branch within the ‘‘out of Africa’’ haplogroup C was also identified (Figure S1). Haplogroup A1b. The P114 mutation, which defines hap- logroup A1b according to Karafet et al. [14], had been detected in central-western Africa at very low frequencies (in total, three chromosomes from Cameroon) [16,19]. [...] [b]‘‘Out of Africa’’ haplogroups. All Y-clades that are not exclusively African belong to the macro-haplogroup CT, which is defined by mutations M168, M294 and P9.1 [14,31] and is subdivided into two major clades, DE and CF [1,14]. In a recent study [16], sequencing of two chromosomes belonging to haplogroups C and R, led to the identification of 25 new mutations, eleven of which were in the C-chromosome and seven in the R-chromosome. Here, the seven mutations which were found to be shared by chromosomes of haplogroups C and R [16], were also found to be present in one DE sample (sample 33 in Table S1), and positioned at the root of macro-haplogroup CT (Figure 1 and Figure S1). [/b] Six haplogroup C chromosomes (samples 34–39 in Table S1) were analyzed for the eleven haplogroup C- specific mutations [16] and for SNPs defining branches C1 to C6 in the tree by Karafet et al. [14] (Figure S1). Through this analysis we identified a chromosome from southern Europe as a new deep branch within haplogroup C (C-V20 or C7, Figure S1). Previously, only a few examples of C chromosomes (only defined by the marker RPS4Y711) had been found in southern Europe [32,33]. To improve our knowledge regarding the distribution of haplogroup C in Europe, we surveyed 1965 European subjects for the mutation RPS4Y711 and identified one additional haplogroup C chromosome from southern Europe, which has also been classified as C7 (data not shown). Further studies are needed to establish whether C7 chromosomes are the relics of an ancient European gene pool or the signal of a recent geographical spread from Asia. Two mutations, V248 and V87, which had never been previously described, were found to be specific to haplogroups C2 and C3, respectively (Figure S1). [b]Three of the seven R-specific mutations (V45, V69 and V88) were previously mapped within haplogroup R [34], whereas the remaining four mutations have been here positioned at the root of haplogroups F (V186 and V205), K (V104) and P (V231) (Figure S1) through the analysis of 12 haplogroup F samples (samples 40–51, in Table S1).[/b] [...] Supporting Information [b]Figure S1 Structure of the macro-haplogroup CT. For details on mutations see legend to Figure 1. Dashed lines indicate putative branchings (no positive control available). The position of V248 (haplogroup C2) and V87 (haplogroup C3) compared to mutations that define internal branches was not determined. Note that mutations V45, V69 and V88 have been previously mapped (Cruciani et al. 2010; Eur J Hum Genet 18:800–807).[/b] (TIF) [/QUOTE]--Fulvio Cruciani et al. (PLoS One. 2012; 7(11): e49170.) Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree [/QB][/QUOTE]
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