Post by djoser-xyyman on Jan 6, 2014 20:20:02 GMT -5
Following up on an article posted by TP on ES I decided to read this and comment on it. It is much to do about nothing. There are a few issues that came up that we should be aware of
1. Estimation of the lineage should be taken with caution. It is not an exact science. We should be aware that Current mtDNA(female) age estimation is much younger than nry-DNA(male) estimation ...by about 70Ky. In other words in the strict sense...AMH male is 70ky older than AMH female!!!! Which does not make sense. Therefore age lineage estimation should treated with caution. It depends on what "clock" is used.
2. Location of the GEOGRAPHIC ORIGIN of AMH should also be looked at cautiously.
3. This new estimation by Kong et al puts A00 at 336kya. But with Cruiciani estimation puts A00 at 209kya. Which is correct?
4. The Khoi-San neither the pygmies have the most ancient lineage.
5. A higher mutational rate(Cruciani) puts AMH only about 39kya OUTSIDE of Africa. Meaning most Haplogroups are African irregardless of frequency outside Africa.
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An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree – Karafet and Hammer1
To estimate the TMRCA of the Y chromosome tree that incorporates the newly discovered root defined by A00, we developed a likelihood-based method that uses mutation rates recently estimated by Kong et al.,14 who performed high-coverage whole genome sequencing on 78 human pedigrees.
the estimated TMRCA for the tree incorporating A00 as the basal lineage would be 209 kya, which is only slightly older than current estimates of the TMRCA of mtDNA and the age of the oldest AMH fossil remains. We note, however, that the higher mutation rate produces an estimate for the common ancestor of all non-African Y chromosome haplogroups (C through T) of ~39 kya6 (i.e., versus ~63 kya for the mutation rate used here). It is difficult to reconcile the younger estimate with the timing of the out-of-Africa dispersal on the basis of the analyses of autosomal DNA21 and the fossil record outside of Africa.22–25 Regardless of which mutation rate is applied, the analysis of relative ages of nodes26 shows that the TMRCA of the A00-rooted tree is 67% older (95% CI ¼ 35%–126%) than that of the A0-rooted tree.
Upon searching a large pan-African database consisting of 5,648 samples from ten countries (Cameroon, Nigeria, Ghana, Senegal, Uganda, Tanzania, Malawi, Zimbabwe, Mozambique, and South Sudan), we identified 11 Y chromosomes that were invariant and identical to the A00 chromosome at five of the six Y-STRs (2 of the 11 chromosomes carried DYS19-16, whereas the others carried DYS19-15). These 11 chromosomes were all found in a sample of 174 (~6.3%) Mbo individuals from western Cameroon (Figure 2).
38 which show that the earliest divergence events involved the ancestors of extant traditional hunter-gatherers. 39–41 Given what we know about the coalescent process, the lack of dense sampling in sub-Saharan Africa (especially compared with Europe) has most likely contributed to the failure to identify more cases of incongruence between genealogical and population divergence. The large sample size of African Americans was critical for the discovery of the A00 lineage given its very low frequency estimate in sub-Saharan Africa
AMHs.46 Interestingly, the Mbo live less than 800 km away from a Nigerian site known as Iwo Eleru, where human skeletal remains with both archaic and modern features were found and dated to ~13 kya.47 Further
ty. Finally, the discovery of the A00 lineage demonstrates the power of public participation in the scientific process—a venture
1. Estimation of the lineage should be taken with caution. It is not an exact science. We should be aware that Current mtDNA(female) age estimation is much younger than nry-DNA(male) estimation ...by about 70Ky. In other words in the strict sense...AMH male is 70ky older than AMH female!!!! Which does not make sense. Therefore age lineage estimation should treated with caution. It depends on what "clock" is used.
2. Location of the GEOGRAPHIC ORIGIN of AMH should also be looked at cautiously.
3. This new estimation by Kong et al puts A00 at 336kya. But with Cruiciani estimation puts A00 at 209kya. Which is correct?
4. The Khoi-San neither the pygmies have the most ancient lineage.
5. A higher mutational rate(Cruciani) puts AMH only about 39kya OUTSIDE of Africa. Meaning most Haplogroups are African irregardless of frequency outside Africa.
=========
An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree – Karafet and Hammer1
To estimate the TMRCA of the Y chromosome tree that incorporates the newly discovered root defined by A00, we developed a likelihood-based method that uses mutation rates recently estimated by Kong et al.,14 who performed high-coverage whole genome sequencing on 78 human pedigrees.
the estimated TMRCA for the tree incorporating A00 as the basal lineage would be 209 kya, which is only slightly older than current estimates of the TMRCA of mtDNA and the age of the oldest AMH fossil remains. We note, however, that the higher mutation rate produces an estimate for the common ancestor of all non-African Y chromosome haplogroups (C through T) of ~39 kya6 (i.e., versus ~63 kya for the mutation rate used here). It is difficult to reconcile the younger estimate with the timing of the out-of-Africa dispersal on the basis of the analyses of autosomal DNA21 and the fossil record outside of Africa.22–25 Regardless of which mutation rate is applied, the analysis of relative ages of nodes26 shows that the TMRCA of the A00-rooted tree is 67% older (95% CI ¼ 35%–126%) than that of the A0-rooted tree.
Upon searching a large pan-African database consisting of 5,648 samples from ten countries (Cameroon, Nigeria, Ghana, Senegal, Uganda, Tanzania, Malawi, Zimbabwe, Mozambique, and South Sudan), we identified 11 Y chromosomes that were invariant and identical to the A00 chromosome at five of the six Y-STRs (2 of the 11 chromosomes carried DYS19-16, whereas the others carried DYS19-15). These 11 chromosomes were all found in a sample of 174 (~6.3%) Mbo individuals from western Cameroon (Figure 2).
38 which show that the earliest divergence events involved the ancestors of extant traditional hunter-gatherers. 39–41 Given what we know about the coalescent process, the lack of dense sampling in sub-Saharan Africa (especially compared with Europe) has most likely contributed to the failure to identify more cases of incongruence between genealogical and population divergence. The large sample size of African Americans was critical for the discovery of the A00 lineage given its very low frequency estimate in sub-Saharan Africa
AMHs.46 Interestingly, the Mbo live less than 800 km away from a Nigerian site known as Iwo Eleru, where human skeletal remains with both archaic and modern features were found and dated to ~13 kya.47 Further
ty. Finally, the discovery of the A00 lineage demonstrates the power of public participation in the scientific process—a venture