Thomas, Many thanks for this. I guess the "inconsistent" calls could be parallel mutations in different lines.... We are presumably dealing with very long time frames, so parallel mutation might be expected. As limited as this data is, and perhaps being very ancient DNA, prone to contamination and error, can any rough inferences be seen as to the time of branching from the line to humans? Clearly from your information it seems before A00. John. Sent from my iPad > On 25/11/2015, at 8:53 pm, Thomas Krahn via <genealogy-dna@rootsweb.com> wrote: > > Dear Ian, > > Thanks very much for your updates and analysis. > > I have made something similar with the Y chromosome side for Denisova8. > This is of course way more speculative since the few reads most of the > time only have a 1x coverage and the most part consists of huge gaps. > Anyways, since there are no Neanderthal Y sequences, we're grasping for > straws. Finally some really ancient Y-DNA. > > https://drive.google.com/file/d/0B2lGDNiBM85QUllVS1g3eFVSdHc/view > > I was actually surprised that in context with gorilla, chimp and A00 > sequences, some of the base changes made sense. We can see multiple A0-T > markers that we previously discovered from A00 samples confirmed. At > least 20 mutations match up with chimp and gorilla and can therefore be > attributed to the novel branch A00-T with significant confidence. > Note that this number of 20 ancestral Denisova8 alleles is significantly > higher than the 8 phylogenetic inconsistent mutations that I've found. > > I have also registered 130 mutations that could potentially be derived > in Denisova, however they are purely speculative. > I have not filtered them for quality or for stable regions. Only > consider them with a grain of salt. They are not worth a publication, > but when more ancient Y-DNA sequences become available they may be used > for comparison. > > Thomas > > >> On 11/24/2015 11:39 AM, Ian Logan via wrote: >> List >> >> Readers might be interested to see the mitochondrial details >> and abstract that accompany this paper: >> >> "Nuclear and mitochondrial DNA sequences from two Denisovan individuals" >> Sawyer,S., Renaud,G., Viola,B., Prufer,K., Kelso,J. and Paabo,S. >> >> A free download on: >> http://www.pnas.org/content/early/2015/11/11/1519905112.full.pdf >> >> The date of divergence of the Denisovan line from the modern human line >> would appear to be around 900-1,000 kya. >> >> > > > ------------------------------- > To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Dear John, I've changed the topic so that we don't hijack Ian's thread. https://drive.google.com/file/d/0B2lGDNiBM85QUllVS1g3eFVSdHc/view I should have mentioned that there is another tab (Sheet 2) in the file that shows the phylogeny roughly as I see it. Considering 20 mutations consistent with the hypothesis that a A00-T branch exists, versus only 8 mutations that speak for any alternative constellation (e.g. Denisova-A0-T with A00 on a different branch or Denisova as a branch of Chimp etc.), I'm very confident that the given phylogeny is the correct one. If those were random mutations, we'd expect about 3/4 of them to not match the A00-T hypothesis and only 1/4 to match it. Yes, you are right that the "inconsistent" calls could be back- or parallel mutations. But there is also a significant margin of technical error. At a layer of 1x there are simply a lot of bogus base calls with NGS sequencing. I'm already very pleased that there is at least some weak evidence that confirms the phylogeny we've found from our A00 samples. The whole field of non-contemporary human Y chromosome research is in very early stages. The biggest problem is the lack of male DNA samples. All Neanderthal samples are females, as well as the gorilla sequence at UCSC. I had to make my own hg19 mapping for the gorilla Tzambo from the Great Ape Genome Project. http://biologiaevolutiva.org/greatape/ http://www.ncbi.nlm.nih.gov/sra/SRX243503[accn] That's why I think it's important to support Bonnie Schrack's A00 Cameroon Project: https://experiment.com/projects/go-west-young-man-in-search-of-the-a00-haplogroup-among-peoples-of-western-cameroon We have now several hundred samples and almost 40 of them are in A00. It is now important to pick selected samples for NGS sequencing and someone needs to pay for that. I have always helped Bonnie with free extra SNP tests, but NGS testing also exceeds my personal budget. So please consider donating a little to this project. How about taking a coupon code for your own Big Y and pledging the difference to the Cameroon A00 project :) Thanks, Thomas On 11/25/2015 09:39 AM, AJ Marsh wrote: > Thomas, > > Many thanks for this. > > I guess the "inconsistent" calls could be parallel mutations in different lines.... We are presumably dealing with very long time frames, so parallel mutation might be expected. > > As limited as this data is, and perhaps being very ancient DNA, prone to contamination and error, can any rough inferences be seen as to the time of branching from the line to humans? Clearly from your information it seems before A00. > > John. > > Sent from my iPad > >> On 25/11/2015, at 8:53 pm, Thomas Krahn via <genealogy-dna@rootsweb.com> wrote: >> >> Dear Ian, >> >> Thanks very much for your updates and analysis. >> >> I have made something similar with the Y chromosome side for Denisova8. >> This is of course way more speculative since the few reads most of the >> time only have a 1x coverage and the most part consists of huge gaps. >> Anyways, since there are no Neanderthal Y sequences, we're grasping for >> straws. Finally some really ancient Y-DNA. >> >> https://drive.google.com/file/d/0B2lGDNiBM85QUllVS1g3eFVSdHc/view >> >> I was actually surprised that in context with gorilla, chimp and A00 >> sequences, some of the base changes made sense. We can see multiple A0-T >> markers that we previously discovered from A00 samples confirmed. At >> least 20 mutations match up with chimp and gorilla and can therefore be >> attributed to the novel branch A00-T with significant confidence. >> Note that this number of 20 ancestral Denisova8 alleles is significantly >> higher than the 8 phylogenetic inconsistent mutations that I've found. >> >> I have also registered 130 mutations that could potentially be derived >> in Denisova, however they are purely speculative. >> I have not filtered them for quality or for stable regions. Only >> consider them with a grain of salt. They are not worth a publication, >> but when more ancient Y-DNA sequences become available they may be used >> for comparison. >> >> Thomas >> >> >>> On 11/24/2015 11:39 AM, Ian Logan via wrote: >>> List >>> >>> Readers might be interested to see the mitochondrial details >>> and abstract that accompany this paper: >>> >>> "Nuclear and mitochondrial DNA sequences from two Denisovan individuals" >>> Sawyer,S., Renaud,G., Viola,B., Prufer,K., Kelso,J. and Paabo,S. >>> >>> A free download on: >>> http://www.pnas.org/content/early/2015/11/11/1519905112.full.pdf >>> >>> The date of divergence of the Denisovan line from the modern human line >>> would appear to be around 900-1,000 kya. >>> >>> >> >> ------------------------------- >> To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message