Post by Ish Gebor on Feb 4, 2020 13:53:32 GMT -5
Neanderthals
A000T A8835
A000 A10805
A000a A21565
A000b A10801
A000b1 A10765
A00-T PR2921www.marres.education/haplogroups.htm
Recent data on Y chromosomes by Mendez et al 43 found evidence to support a model that placed the Neanderthal lineage as an outgroup to the modern human Y chromosomes, including A00,...
Out of Africa a Southern route to Arabia (Pg. 117)
Ancestral DNA, Human Origins, and Migrations
We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup.
We called bases for both the Neandertal and A00 sequences by using SAMtools
To reduce the potential impact of postmortem DNA damage, we restricted this analysis to coordinates covered by at least three sequencing reads. We further restricted to the subset of Poznik et al.19 regions in which the human reference sequence is based on bacterial artificial chromosome clones derived from the RP-11 individual, 20 a known carrier of haplogroup R1b. This left ∼7.83 Mb of sequence within which to assign variants to the appropriate branches (Figure S2, Appendix A). Using the known age of the Ust’-Ishim individual and the constrained optimization procedure described in Rasmussen et al., 21 we obtained parametric bootstrap estimates for TAR as well as for the mutation rate and the TMRCA of haplogroup K-M526 (Appendix A). Briefly, we sampled from the process that generated the observed tree (Figure S2) by simulating the number of single nucleotide variants (SNVs) on each branch as a Poisson draw with mean equal to the observed number of mutations. To obtain bootstrap samples of the three parameters, we maximized their joint likelihood for each tree replicate.
The 17 sites that are incompatible with the tree are principally due to recurrent and back mutations. Because the reference has accumulated more mutations than Ust’-Ishim since their common ancestor, it is expected that more incompatible sites unite A00 and Ust’-Ishim than unite the reference and A00. Indeed, 10 of the 13 mutations map to branches ancestral to the reference sequence (but not Ust’-Ishim) in the 1000 Genomes Project (see Web Resources). Likewise, one of the other four mutations could have recurred in the reference and A00. Our approach cannot detect mutations that occurred on both the lineage leading to A00 and on the lineage leading to K-M526; however, the expected number of such mutations is quite small.
Recurrent Mutations
Four mutations were inconsistent with tree ii in Figure 1A. Non-A0 lineages in the 1000 Genomes panel34 share the reference allele at coordinate 2,710,154, and individuals in haplogroups B through T share the reference allele at 23,558,260. The two others were at coordinates 9,386,241 and 15,024,530.
Four mutations were inconsistent with tree ii in Figure 1A. Non-A0 lineages in the 1000 Genomes panel34 share the reference allele at coordinate 2,710,154, and individuals in haplogroups B through T share the reference allele at 23,558,260. The two others were at coordinates 9,386,241 and 15,024,530.
The Divergence of Neandertal and Modern Human Y Chromosomes
doi.org/10.1016/j.ajhg.2016.02.023
The father of all men is 340,000 years old
Albert Perry carried a secret in his DNA: a Y chromosome so distinctive that it reveals new information about the origin of our species. It shows that the last common male ancestor down the paternal line of our species is over twice as old as we thought.
One possible explanation is that hundreds of thousands of years ago, modern and archaic humans in central Africa interbred, adding to known examples of interbreeding – with Neanderthals in the Middle East, and with the enigmatic Denisovans somewhere in southeast Asia.
Albert Perry carried a secret in his DNA: a Y chromosome so distinctive that it reveals new information about the origin of our species. It shows that the last common male ancestor down the paternal line of our species is over twice as old as we thought.
One possible explanation is that hundreds of thousands of years ago, modern and archaic humans in central Africa interbred, adding to known examples of interbreeding – with Neanderthals in the Middle East, and with the enigmatic Denisovans somewhere in southeast Asia.
