1)In my Wiliam_Daugherty FTDNA FF Project, in addition to autosomal data, I have been comparing yDNA information. Based on yDNA tests of five descendants of three of William's sons, and pending autosomal DNA confirmation, I think that I have a good idea at the 60 marker level what William Daugherty's yDNA was. When all test results become available over the next couple of months I expect that we will be out to 67 markers. We have a very solid paper trail as well. The derivation process involves a 2 out of three or better yDNA marker match to be accepted as the Patriarch's derived yDNA. I think that this derived information can be broadly useful and would like to find some way of adding these sort of results to the FTDNA database. Perhaps a moderate fee to FTDNA for evaluation of our research would be appropriate as well as appropriate disclaimers on the derived yDNA result. 2)Over the next several months to a year, I may have constructed as many as three separate "pseudo-autosomal DNA test results" for three different people. I am interested in refining these "pseudo results against" real results in various databases with out skewing real database results. I would like to see some way of doing this at FTDNA, GEDmatch and perhaps as Ancestry.com as well. Please let me know your thoughts Sam Eaton

This is a question I recently posed at 23andMe, but perhaps someone here can answer it as well.  In messing with my raw data file (a text file of the 500K tested SNPs under the 23andMe V2 chip), something caught my eye.  Specifically, the number of CC pairs was almost identical to the number of GG pairs (i.e., within 0.5% of each other, with both at roughly 100K), the number of AA pairs was almost identical to the number of TT pairs (roughly 88K), the number of AG pairs was almost identical to the number of CT pairs (roughly 72K), and the number of AC pairs was almost identical to the number of GT pairs (roughly 16K). AT and CG pairs hardly appeared at all, but the counts for both were broadly similar, well under 1000 in each case.  Can someone explain the mechanism that makes these counts themselves occur in pairs?  No doubt it's something basic, but the answer is not immediately obvious to me. Thanks. Ruy Cardoso

A bit of a disappointing sale at 23andMe today. Details on my blog: http://www.yourgeneticgenealogist.com/2011/11/23andme-cyber-monday-discount-today.html CeCe   www.yourgeneticgenealogist.com www.studiointv.com

I was more thinking about second opinions about the methods used. I can so far not say anything than that the mutations the software identify is truly there by visual inspection. Some mutations is only seen in a individual in one extremee, and on the other extreme there are some haplotypes that is completly pan-european. Anders ________________________________ Fra: tewilder <[email protected]> Til: [email protected] Sendt: Fredag, 25. november 2011 0.12 Emne: Re: [AUTOSOMAL-DNA] Fennoscandian BGA: Mutation Shared Matrix There are those of us who are interested, buy who because of mixed ancestry can't be subjects in your research.

In the lack of any interest I should add that mutations in haplotypes exclusive to Fennoscandia appears to cluster to ethnicities. Mutations seen in Norwegians appears mostly in other Norwegians especially the most common shared only between two persons, the same for Swedes, Finns and the Saami. However there appears to be sharing between regions for the most shared mutations. There also appears to be regional clustering in the north of Fennoscandia across borders. I have visually controlled many haplotypes found lately and they appears consistent with the occurance of mutations in haplotypes giving  unique haplotypes not seen outside Fennoscandia. This means that autosomal haplogroups are definable and detectable. Anders ________________________________ Fra: Anders Pålsen <[email protected]> Til: [email protected] Sendt: Tirsdag, 22. november 2011 14.29 Emne: [AUTOSOMAL-DNA] Fennoscandian BGA: Mutation Shared Matrix Mutation Sharing Matrix consist currently known unique haplotype mutations map for Fennoscandia shared with two or more individuals on chromosome 1.  These mutations is currently only known in Fennoscandia. Anders http://fennoscandia.blogspot.com/2011/11/fennoscandian-mutation-sharing-matrix.html

There are those of us who are interested, buy who because of mixed ancestry can't be subjects in your research. There are DNA segments in my family that are most typical of Norwegians but show up where ever there was substantial Viking settlement. On the other hand, my mtDNA shows the north of Fennoscandia across borders matching that you mention. It seems to me that there is some DNA that has a coastal Norwegian and Viking dispersion, and other old inland cross border types. But these are early days yet, and there is nothing people outside the research group can do yet except wait for more discoveries and a practical method to apply them. On 11/24/2011 1:42 PM, Anders Pålsen wrote: > In the lack of any interest I should add that mutations in haplotypes exclusive to Fennoscandia appears to cluster to ethnicities. Mutations seen in Norwegians appears mostly in other Norwegians especially the most common shared only between two persons, the same for Swedes, Finns and the Saami. However there appears to be sharing between regions for the most shared mutations. There also appears to be regional clustering in the north of Fennoscandia across borders. I have visually controlled many haplotypes found lately and they appears consistent with the occurance of mutations in haplotypes giving unique haplotypes not seen outside Fennoscandia. This means that autosomal haplogroups are definable and detectable. > > > Anders > > > > ________________________________ > Fra: Anders Pålsen<[email protected]> > Til: [email protected] > Sendt: Tirsdag, 22. november 2011 14.29 > Emne: [AUTOSOMAL-DNA] Fennoscandian BGA: Mutation Shared Matrix > > Mutation Sharing Matrix consist currently known unique haplotype mutations map for Fennoscandia shared with two or more individuals on chromosome 1. > > These mutations is currently only known in Fennoscandia. > > > Anders > > http://fennoscandia.blogspot.com/2011/11/fennoscandian-mutation-sharing-matrix.html > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message >

I hear that there may be a 23andMe sale on Monday. CeCe www.yourgeneticgenealogist.com www.studiointv.com

Mutation Sharing Matrix consist currently known unique haplotype mutations map for Fennoscandia shared with two or more individuals on chromosome 1.  These mutations is currently only known in Fennoscandia. Anders http://fennoscandia.blogspot.com/2011/11/fennoscandian-mutation-sharing-matrix.html

List, As seen from this posting trying to reconstruct a autosomal haplotype could be complex but can give informative history. The core haplotype appears to be simple and effective in proving Fennoscandinavian ancestry despite its tiny size, while the extended haplotype can provide clues to its age and history. However most Fennoscandians do not have these specific mutations so not having these do not disprove Fennoscandian ancestry. . This method using core haplotypes with limited distributed mutations appears to be very accurate in pinpointing ancestry Read more and illustrations at the Fennoscandia BGA blogg: http://fennoscandia.blogspot.com/2011/11/fennoscandian-autosomal-haplotype-and.html Anders

Hi Fran A sister gets an X form each of her parents. A brother would only get an X only from his Mum. The X a brother would inherit from his Mother initially has come form her parents [so half the material of the mothers x has come from the maternal grandfather and half from maternal grandmother] While the sister's X [X from her father has come from her paternal grandmother and from her mother's x has come from both her maternal grandfather and from her maternal grandmother ] Essentially as you go back the parts of the X are being mixed up with mixes of DNA coming down the female side. A son passes his X once to his son but that son pass on his mothers x A daughter passes her X to both sons and daughters. The son passes it once but only to his son. The daughters continue to pass the Mother's x down the generations [becoming less with each generation] until it disappears having been replaced by more recent generations X material. Karen Karen On Fri, Nov 18, 2011 at 2:18 AM, Frances Meng <[email protected]> wrote: > Dear Tim, > > To hopefully clarify my question, I meant from my paternal grandmother's X which to me meant my father's family. Could you please explain your answer? Do you mean my brother is only receiving his X from our mother and nothing from our father's mother? My brother and I only share 1/2 base pair on our X. > > My paternal uncle and I share several long blocks on our X,some are 1/2 and others have green stripes [full]. Is this just coming from my paternal grandmother and not my paternal grandfather's mother? > > Which grandmothers contribute to our combined ch. X? From your answer I'm assuming that my brother can only receive his from our mother because he is XY but I can receive it from both of my grandmothers since I'm XX. > > Could you please explain to me how this works? We were tested by Family Tree dna and our ch.X results were not given to us. > > Thanks. > Fran > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message >

Thanks for your reply Tim. I have to make a correction about #1. Its not 500kb but maximum 500 consecutive SNP. I also tried some more parameters after this posting at #1. I reduced it first to maximum 100 SNP but it only reduced to 1324 unique haplotype clusters from the initial 1344. Reducing it further to max 10 SNP only reduced to 1189 unique haplotype clusters. Reducing it even more to 5 SNP reduced only to 962 unique haplotype clusters. First if reducing it to 2 SNP it dropped much down getting only 277 unique haplotype clusters remained. Using maximum 1 SNP crashed the software. It make sense that allowing for larger haplotypes generate more unique haplotypes than allowing only for smaller haplotypes. So what I infer from this is that these unique haplotype clusters is rather small and not very large. These numbers have been generated from software made for finding genetic diseases from haplotypes where you mark individuals with certain traits cases and check them vs the controls. If there is any haplotype strongly associated with a trait the associated haplotype is found. These haplotypes are usually not very large. Just check the SNP used by 23andme health section.. So is also the cases with these haplotypes. The software do for many haplotypes infer parent-child relationships between them indicating that haplotype mutations are in the picture at least when I check at the individual level. Anders ________________________________ Fra: Tim Janzen <[email protected]> Dear Anders,     Thanks for doing this analysis.  Can you tell us what your definition of a haplotype was in this situation?  Was it a specific number of matching consecutive SNPs?  My personal opinion is that reason #1 is the primary reason why relatively few autosomal haplotypes were seen in your analysis. ... Tim Janzen

A male passes only Y's to his sons. Males pass their X only to their daughters. > -----Original Message----- > From: [email protected] [mailto:autosomal-dna- > [email protected]] On Behalf Of Karen Hodges > Sent: Friday, November 18, 2011 10:55 PM > To: [email protected] > Subject: Re: [AUTOSOMAL-DNA] Base Pair With Full Match > <snip> > > A son passes his X once to his son but that son pass on his mothers > x > <snip>

Dear Anders, Thanks for doing this analysis. Can you tell us what your definition of a haplotype was in this situation? Was it a specific number of matching consecutive SNPs? My personal opinion is that reason #1 is the primary reason why relatively few autosomal haplotypes were seen in your analysis. I think that this situation again brings up a topic that we discussed on the ISOGG list in February: DNA recombination hotspots. Slide 29 in the presentation at www.stats.ox.ac.uk/~mcvean/DTC/BIOINF/Lectures/Recombination.ppt indicates that there are about 33,000 recombination hotspots found in the Phase II HapMap project. Slide 31 explains that the hotspot motif CCTCCCTNNCCAC accounts for 40% of all human hotspots. There is also a good review article on this topic in Nature Reviews Genetics, March 2010, p. 221-233. It would be helpful to have a complete list of these blocks and their associated boundaries. Eventually it makes sense for us to start looking at phased haplotypes for each block that is bounded by a hotspot and then try to associate each haplotype with a specific ancestor or series of ancestors. Some of these haplotype blocks have ancient origins going back to Neanderthal or Denisovan ancestors. Such blocks would contain about 30 SNPs on average using 23andMe version 3 data. Sincerely, Tim Janzen -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Anders Pålsen Sent: Friday, November 18, 2011 2:39 AM To: [email protected] Subject: [AUTOSOMAL-DNA] Autosomal Haplotype Clustering Patterns - Actual or Error? List, I have found this pattern of haplotype clustering within individuals from Norway, Sweden and Finland on Chr 1 using 38.5k SNP: This raises the questions why its like this. I suspect its the following reasons: 1. The effect of recombination splitting or killing haplotypes. However the maximum haplotype size in clusters is 500kb questions recombination as the effect. 2. The effect of limited population data. Its possible more individuals and populations would reduce the number of unique haplotype clusters. 3. The effect of undetected errors in the genotypes. However no correlation between high unique haplotypes found in individuals and high detected genotype error rate for these. 4. The effect of incorrect phasing as the result of errors in genotype or/and ordinary phasing error as result of the model used. 5. The effect of haplotype or mutation extinction. Recent individual haplotypes or mutations have limited spread generally, while older haplotype clusters or mutations have larger geographic spread. Do anyone else have more suggestions to explain this? Anders

Aaah...that's the tricky bit. On 18 November 2011 20:23, Ann Turner <[email protected]> wrote: > Thanks for the offer. I would need raw data for the matching party as well, > preferably someone has also tested a father and mother. > > Ann > > On Thu, Nov 17, 2011 at 9:20 PM, Samantha John <[email protected] > >wrote: > > > Ann, > > > > I could send you my son and both his parents, or me and both mine, all > done > > at 23andMe if you wish? In both cases, especially my son's, there are > > matches with him that can't be pinned down to either parent. > > > > Regards > > Sam > > > > On 18 November 2011 06:19, CeCe Moore <[email protected]> wrote: > > > > > > > > Ann, > > > > > > I think I have a set that I can send you. I could also send you mine > and > > > my parents, but my dad is at FTDNA and my mom is at 23andMe, so I don't > > > know if that would work. > > > > > > CeCe > > > > > > > > > www.yourgeneticgenealogist.com > > > www.studiointv.com > > > > > > > > > ---------------------------------------- > > > > From: [email protected] > > > > Date: Thu, 17 Nov 2011 08:19:52 -0800 > > > > To: [email protected] > > > > Subject: Re: [AUTOSOMAL-DNA] Fundamental autosomal DNA question > > > > > > > > No, unfortunately. I need raw data with father/mother/child trios on > > both > > > > sides of the match so I can use phased data. That's not easy to come > > by. > > > > > > > > Ann > > > > > > > > On Thu, Nov 17, 2011 at 7:41 AM, CeCe Moore <[email protected]> > > > wrote: > > > > > > > > > Ann, > > > > > Thanks for sharing your experience. > > > > > Have you looked at the raw data on those long segments (over 10 cM) > > to > > > > > determine if they really are IBS? I find those lengths very > > surprising. > > > > > With your data, you noted that about 95 percent of the time what I > > said > > > > > earlier will hold true, but that other 5 percent is troubling. I > > > certainly > > > > > would like us all to be able to be confident of the validity of the > > 10 > > > cM > > > > > blocks and above, if not the 7 cM and above. > > > > > CeCe > > > > > Sent via BlackBerry by AT&T > > > > > > > > > > -----Original Message----- > > > > > From: Ann Turner <[email protected]> > > > > > Date: Thu, 17 Nov 2011 12:19:52 > > > > > To: <[email protected]> > > > > > Subject: Re: [AUTOSOMAL-DNA] Fundamental autosomal DNA question > > > > > > > > > > One way to study the problem is with father/mother/child trio data. > > If > > > the > > > > > child has a match not found in either parent, it is possible > (indeed > > > I'd > > > > > say likely) that the segment is Identical by State, not Identical > by > > > > > Descent. > > > > > > > > > > Ancestry Finder at 23andMe lets you look at segments down to 5 cM / > > 700 > > > > > SNPs. For actual numbers in one case, my son has a total of 231 > > > segments > > > > > listed with names attached. 67 of those are found only in the child > > > (29%). > > > > > The breakdown by segment size is > > > > > > > > > > 4/76 > 7 cM, longest 11.1 cM (5%) [This seems consistent with a 95% > > > > > confidence interval] > > > > > 7/37 6-7 cM (19%) > > > > > 56/119 < 6 cM (47%) > > > > > > > > > > FTDNA seems to have a cutoff of 7.7 cM / 500 SNPs (that's by > > empirical > > > > > observation -- has anyone found a shorter longest segment?). I have > > > data > > > > > for one father/mother/child trio that seems particularly dicey, > with > > > 22/100 > > > > > matches in the child not found in either parent. The segment sizes > > > ranged > > > > > from 7.7 to 12.90, with a median of 8. Other trios I've looked at > > seem > > > to > > > > > run about 15%. > > > > > > > > > > Ann Turner > > > > > > > > > > On Wed, Nov 16, 2011 at 1:02 PM, CeCe Moore <[email protected] > > > > > wrote: > > > > > > > > > > > > > > > > > When I say "legitimately" match, I mean an IBD segment that would > > > meet > > > > > the > > > > > > company's matching threshold, not a segment made up of stretches > of > > > IBD > > > > > and > > > > > > IBS pieced together. > > > > > > > > > > > > I'm not saying that it is impossible for a match over ~7 cMs to > be > > > IBS, > > > > > > but very unlikely. (I was going to write ~10 cMs in my response, > > but > > > > > > thought that might be a bit conservative.) I know that it is > > > > > theoretically > > > > > > possible, but in my thousands of hours of atDNA research, I have > > yet > > > to > > > > > see > > > > > > proof of one. Can you please show me an example of an IBS match > > over > > > 7 > > > > > cMs? > > > > > > (I know that Ann Turner has seen lots of them between 5cMs-7cMs. > > > We'll > > > > > see > > > > > > if she responds with a larger one.) > > > > > > > > > > > > If enough of a portion of the segment is IBS that it doesn't show > > up > > > in > > > > > > your parent (i.e.- make the company's threshold), then it will > > > obviously > > > > > > reduce the authentic match to a point that is not worth > pursuing. I > > > have > > > > > > chased far too many matches under 7 cMs to recommend doing the > > same. > > > > > > > > > > > > > > > > ------------------------------- > > > > > To unsubscribe from the list, please send an email to > > > > > [email protected] with the word 'unsubscribe' > > without > > > > > the quotes in the subject and the body of the message > > > > > > > > > > > > > > > ------------------------------- > > > > > To unsubscribe from the list, please send an email to > > > > > [email protected] with the word 'unsubscribe' > > without > > > > > the quotes in the subject and the body of the message > > > > > > > > > > > > > ------------------------------- > > > > To unsubscribe from the list, please send an email to > > > [email protected] with the word 'unsubscribe' without > > > the quotes in the subject and the body of the message > > > > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > > [email protected] with the word 'unsubscribe' without > > > the quotes in the subject and the body of the message > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' without > > the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

Ann, I could send you my son and both his parents, or me and both mine, all done at 23andMe if you wish? In both cases, especially my son's, there are matches with him that can't be pinned down to either parent. Regards Sam On 18 November 2011 06:19, CeCe Moore <[email protected]> wrote: > > Ann, > > I think I have a set that I can send you. I could also send you mine and > my parents, but my dad is at FTDNA and my mom is at 23andMe, so I don't > know if that would work. > > CeCe > > > www.yourgeneticgenealogist.com > www.studiointv.com > > > ---------------------------------------- > > From: [email protected] > > Date: Thu, 17 Nov 2011 08:19:52 -0800 > > To: [email protected] > > Subject: Re: [AUTOSOMAL-DNA] Fundamental autosomal DNA question > > > > No, unfortunately. I need raw data with father/mother/child trios on both > > sides of the match so I can use phased data. That's not easy to come by. > > > > Ann > > > > On Thu, Nov 17, 2011 at 7:41 AM, CeCe Moore <[email protected]> > wrote: > > > > > Ann, > > > Thanks for sharing your experience. > > > Have you looked at the raw data on those long segments (over 10 cM) to > > > determine if they really are IBS? I find those lengths very surprising. > > > With your data, you noted that about 95 percent of the time what I said > > > earlier will hold true, but that other 5 percent is troubling. I > certainly > > > would like us all to be able to be confident of the validity of the 10 > cM > > > blocks and above, if not the 7 cM and above. > > > CeCe > > > Sent via BlackBerry by AT&T > > > > > > -----Original Message----- > > > From: Ann Turner <[email protected]> > > > Date: Thu, 17 Nov 2011 12:19:52 > > > To: <[email protected]> > > > Subject: Re: [AUTOSOMAL-DNA] Fundamental autosomal DNA question > > > > > > One way to study the problem is with father/mother/child trio data. If > the > > > child has a match not found in either parent, it is possible (indeed > I'd > > > say likely) that the segment is Identical by State, not Identical by > > > Descent. > > > > > > Ancestry Finder at 23andMe lets you look at segments down to 5 cM / 700 > > > SNPs. For actual numbers in one case, my son has a total of 231 > segments > > > listed with names attached. 67 of those are found only in the child > (29%). > > > The breakdown by segment size is > > > > > > 4/76 > 7 cM, longest 11.1 cM (5%) [This seems consistent with a 95% > > > confidence interval] > > > 7/37 6-7 cM (19%) > > > 56/119 < 6 cM (47%) > > > > > > FTDNA seems to have a cutoff of 7.7 cM / 500 SNPs (that's by empirical > > > observation -- has anyone found a shorter longest segment?). I have > data > > > for one father/mother/child trio that seems particularly dicey, with > 22/100 > > > matches in the child not found in either parent. The segment sizes > ranged > > > from 7.7 to 12.90, with a median of 8. Other trios I've looked at seem > to > > > run about 15%. > > > > > > Ann Turner > > > > > > On Wed, Nov 16, 2011 at 1:02 PM, CeCe Moore <[email protected]> > wrote: > > > > > > > > > > > When I say "legitimately" match, I mean an IBD segment that would > meet > > > the > > > > company's matching threshold, not a segment made up of stretches of > IBD > > > and > > > > IBS pieced together. > > > > > > > > I'm not saying that it is impossible for a match over ~7 cMs to be > IBS, > > > > but very unlikely. (I was going to write ~10 cMs in my response, but > > > > thought that might be a bit conservative.) I know that it is > > > theoretically > > > > possible, but in my thousands of hours of atDNA research, I have yet > to > > > see > > > > proof of one. Can you please show me an example of an IBS match over > 7 > > > cMs? > > > > (I know that Ann Turner has seen lots of them between 5cMs-7cMs. > We'll > > > see > > > > if she responds with a larger one.) > > > > > > > > If enough of a portion of the segment is IBS that it doesn't show up > in > > > > your parent (i.e.- make the company's threshold), then it will > obviously > > > > reduce the authentic match to a point that is not worth pursuing. I > have > > > > chased far too many matches under 7 cMs to recommend doing the same. > > > > > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > > [email protected] with the word 'unsubscribe' without > > > the quotes in the subject and the body of the message > > > > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > > [email protected] with the word 'unsubscribe' without > > > the quotes in the subject and the body of the message > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

List, I have for a longer time wondered how to be able to find autosomal mutations or autosomal haplotypes in easier ways than reading manually trough and tenthousand or more haplotypes to each other. I recently found out (or it seems) how to find your own unique haplotype or mutations/recent mutations with limited geographic or individual spread in the genome using software and methodogy originally made for finding genetic diseases. In this software scientists typically define a trait or the occurance of a disease in cases and compare these to the controls. If there is a very strong correlation between the diseases and the cases but not the controls you have detected a genetic disease. However nobody says you cant change "disease" with something else you want to investigate, so what happend if you define a individual as a "disease"? I phased a panel of 138 individuals with 41k SNP's in chromosome 1 resulting in 277 haplotypes where 1 individual was defined as having a disease trait for both haplotypes. The software quickly indicated trough haplotype clustering that 2 SNP allele was absolutely unique for this individual (or at least in this panel). Further 3 SNP was found to be found in in the "disease" individual and some others in various degree. The first SNP had very limited distribution within Scandinavia only found in 3 individuals where 2 haplotypes was found in the "disease" individual. The second SNP was found more widespread with 4 individuals found in both Europe and Scandinavia, also here matching with 2 haplotypes from the "disease" individual. The third SNP was found in 3 individuals found in Scandinavia and in Europe also here including 2 haplotypes from the "disease" individual. Then after having identified candidate SNP its time to reconstruct the actual haplotype and its ability to differentiate. Its cool to find unique SNP or unique haplotypes however they are very private or worthless in geneology if they dont show up in someone else. Lets therefor look at the first SNP that was also found among others than the "disease" individal, also here the software do the job:. SNP as 1 locus or haplotype scaled up from single locus to unique haplotype: C-> 120 of 277 haplotypes for 4 ind. CTC -> 58 of 277 haplotypes for 4 ind. TCCTC -> 3 of 277 haplotypes for 3 ind CCCTC -> 55 of 277 haplotypes for 1 ind. ATTCCTC -> 2 of 277 haplotypes for 2 ind. CTTCCTC -> 1 of 277 haplotypes for 1 ind. ACCCCTC ->55 of 277 haplotypes for 1 ind. GATTCCTC ->2 of 277 haplotypes for 2 ind. ACTTCCTC ->1 of 277 haplotypes for 1 ind. AACCCCTC ->1 of 277 haplotypes for 1 ind. And finally all haplotypes fully differensiated: GGCCAGATTCCTC -> 1 of 277 haplotypes for 1 ind. AGCCAGATTCCTC-> 1 of 277 haplotypes for 1 ind. AGCCAACTTCCTC -> 1 of 277 haplotypes for 1 ind. GGCTAAACCCCTC-> 1 of 277 haplotypes for 1 ind. The haplotype at its largest is only 74k or 0.074 Mb making these likely very stable haplotypes unlikely to recombine. So then only imagination and the genetic correlation with these sets of imigations sets the limit from here, a natural forward step would be as these kind of haplotypes are very stable to make autosomal haplotype trees to attempt tracing human migrations similar to Y-SNP and mitokondria SNP. Anders

List, I have found this pattern of haplotype clustering within individuals from Norway, Sweden and Finland on Chr 1 using 38.5k SNP: Unique haplotypes not shared with others - 1 344 (typical between 15 to 50 per individual) Haplotypes shared between 2 ind - 157 Haplotypes shared between 3 ind - 30 Haplotypes shared between 4 ind - 3 Haplotypes shared between 5 ind - 2 Haplotypes shared between 6 ind - 2 As this shows widespread haplotype clusters are much rarer than those shared with only two individuals, but the "unique" haplotype clusters appears to be absolutely highest at the individual level. This raises the questions why its like this. I suspect its the following reasons: 1. The effect of recombination splitting or killing haplotypes. However the maximum haplotype size in clusters is 500kb questions recombination as the effect. 2. The effect of limited population data. Its possible more individuals and populations would reduce the number of unique haplotype clusters. 3. The effect of undetected errors in the genotypes. However no correlation between high unique haplotypes found in individuals and high detected genotype error rate for these. 4. The effect of incorrect phasing as the result of errors in genotype or/and ordinary phasing error as result of the model used. 5. The effect of haplotype or mutation extinction. Recent individual haplotypes or mutations have limited spread generally, while older haplotype clusters or mutations have larger geographic spread. Do anyone else have more suggestions to explain this? Anders

Thanks for the offer. I would need raw data for the matching party as well, preferably someone has also tested a father and mother. Ann On Thu, Nov 17, 2011 at 9:20 PM, Samantha John <[email protected]>wrote: > Ann, > > I could send you my son and both his parents, or me and both mine, all done > at 23andMe if you wish? In both cases, especially my son's, there are > matches with him that can't be pinned down to either parent. > > Regards > Sam > > On 18 November 2011 06:19, CeCe Moore <[email protected]> wrote: > > > > > Ann, > > > > I think I have a set that I can send you. I could also send you mine and > > my parents, but my dad is at FTDNA and my mom is at 23andMe, so I don't > > know if that would work. > > > > CeCe > > > > > > www.yourgeneticgenealogist.com > > www.studiointv.com > > > > > > ---------------------------------------- > > > From: [email protected] > > > Date: Thu, 17 Nov 2011 08:19:52 -0800 > > > To: [email protected] > > > Subject: Re: [AUTOSOMAL-DNA] Fundamental autosomal DNA question > > > > > > No, unfortunately. I need raw data with father/mother/child trios on > both > > > sides of the match so I can use phased data. That's not easy to come > by. > > > > > > Ann > > > > > > On Thu, Nov 17, 2011 at 7:41 AM, CeCe Moore <[email protected]> > > wrote: > > > > > > > Ann, > > > > Thanks for sharing your experience. > > > > Have you looked at the raw data on those long segments (over 10 cM) > to > > > > determine if they really are IBS? I find those lengths very > surprising. > > > > With your data, you noted that about 95 percent of the time what I > said > > > > earlier will hold true, but that other 5 percent is troubling. I > > certainly > > > > would like us all to be able to be confident of the validity of the > 10 > > cM > > > > blocks and above, if not the 7 cM and above. > > > > CeCe > > > > Sent via BlackBerry by AT&T > > > > > > > > -----Original Message----- > > > > From: Ann Turner <[email protected]> > > > > Date: Thu, 17 Nov 2011 12:19:52 > > > > To: <[email protected]> > > > > Subject: Re: [AUTOSOMAL-DNA] Fundamental autosomal DNA question > > > > > > > > One way to study the problem is with father/mother/child trio data. > If > > the > > > > child has a match not found in either parent, it is possible (indeed > > I'd > > > > say likely) that the segment is Identical by State, not Identical by > > > > Descent. > > > > > > > > Ancestry Finder at 23andMe lets you look at segments down to 5 cM / > 700 > > > > SNPs. For actual numbers in one case, my son has a total of 231 > > segments > > > > listed with names attached. 67 of those are found only in the child > > (29%). > > > > The breakdown by segment size is > > > > > > > > 4/76 > 7 cM, longest 11.1 cM (5%) [This seems consistent with a 95% > > > > confidence interval] > > > > 7/37 6-7 cM (19%) > > > > 56/119 < 6 cM (47%) > > > > > > > > FTDNA seems to have a cutoff of 7.7 cM / 500 SNPs (that's by > empirical > > > > observation -- has anyone found a shorter longest segment?). I have > > data > > > > for one father/mother/child trio that seems particularly dicey, with > > 22/100 > > > > matches in the child not found in either parent. The segment sizes > > ranged > > > > from 7.7 to 12.90, with a median of 8. Other trios I've looked at > seem > > to > > > > run about 15%. > > > > > > > > Ann Turner > > > > > > > > On Wed, Nov 16, 2011 at 1:02 PM, CeCe Moore <[email protected]> > > wrote: > > > > > > > > > > > > > > When I say "legitimately" match, I mean an IBD segment that would > > meet > > > > the > > > > > company's matching threshold, not a segment made up of stretches of > > IBD > > > > and > > > > > IBS pieced together. > > > > > > > > > > I'm not saying that it is impossible for a match over ~7 cMs to be > > IBS, > > > > > but very unlikely. (I was going to write ~10 cMs in my response, > but > > > > > thought that might be a bit conservative.) I know that it is > > > > theoretically > > > > > possible, but in my thousands of hours of atDNA research, I have > yet > > to > > > > see > > > > > proof of one. Can you please show me an example of an IBS match > over > > 7 > > > > cMs? > > > > > (I know that Ann Turner has seen lots of them between 5cMs-7cMs. > > We'll > > > > see > > > > > if she responds with a larger one.) > > > > > > > > > > If enough of a portion of the segment is IBS that it doesn't show > up > > in > > > > > your parent (i.e.- make the company's threshold), then it will > > obviously > > > > > reduce the authentic match to a point that is not worth pursuing. I > > have > > > > > chased far too many matches under 7 cMs to recommend doing the > same. > > > > > > > > > > > > > ------------------------------- > > > > To unsubscribe from the list, please send an email to > > > > [email protected] with the word 'unsubscribe' > without > > > > the quotes in the subject and the body of the message > > > > > > > > > > > > ------------------------------- > > > > To unsubscribe from the list, please send an email to > > > > [email protected] with the word 'unsubscribe' > without > > > > the quotes in the subject and the body of the message > > > > > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' without > > the quotes in the subject and the body of the message > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' without > > the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

CeCe - our Maker gave humans the ability to choose our reaction to what happens - given this ability, I choose to enjoy. Thanks for the feedback - it makes my (long) day.... Jim Bartlett On 11/17/11, CeCe Moore<[email protected]> wrote: I love your attitude Jim! CeCe [1]www.yourgeneticgenealogist.com [2]www.studiointv.com ---------------------------------------- > Date: Thu, 17 Nov 2011 15:31:20 -0600 > From: [3][email protected] > To: [4][email protected]; [5][email protected] > Subject: [AUTOSOMAL-DNA] Finding Real Ancestors [was Numbers differences between FTDNA and 23 & me] > > > Mary Alice, > > I agree with you! > > I can assure you that the Common Ancestors (husband/wife) that each of my > atDNA matches and I agree upon, are not just surname matches, they are real > people with birth, marriage, and death dates and places and, in all cases, > at least two children: one child is my ancestor and the other child is the > ancestor of my match. They are the same family for both of us in the same > place and time. Each and every person in each of our direct lineages is a > real person (incidently with a unique ahnentafel number). Almost all of > these lines can also be found in trees at GEDmatch.com; FamilySearch.org; > and usually other on-line sites as well as genealogy libraries. > > Are these 100 percent guaranteed, bet-the-farm certainties? Who can say that > about any genealogy. And besides that, there could easily be an NPE in one > or both of our lineages. If so - then clearly the atDNA segment we share > could not have come through this line. There is always that possibility. > These situations can only be uncovered by detailed Y-DNA and mtDNA testing > to veryfy each and every paper link. > > There is also the possibliity that our shared atDNA segment came from a > different Common Ancestor. In fact several of my atDNA matches and I have > more that one set of known Common Ancestors - so a DNA segment could come > from either one of the lines (but not both). I have now documented at least > 7 sets of cousins (from first to 8th) among my ancestors. So a match with > one of them in the path to theCommon Ancestor provides two possible paths > for the DNA segment to come down to me. > > The difficulty in finding a Common Ancestor is mostly due, IMO, to not > knowing all of our ancestors! At the 4th cousin level, I don't know 12.5 > percent of my ancestors; at the 5th cousin level 25 percent; 6th cousin > level 43 percent; 7th cousin level 58 percent, 8th cousin level 69 percent, > etc. That represents a LOT of places a Common Ancestor could be hiding - > maybe just beyond a brick wall, maybe well beyond that. It's no wonder we > don't match many of our atDNA matches. But that won't stop me from trying > ... References 1. http://www.yourgeneticgenealogist.com/ 2. http://www.studiointv.com/ 3. mailto:[email protected] 4. mailto:[email protected] 5. mailto:[email protected]

Ann, Thanks for sharing your experience. Have you looked at the raw data on those long segments (over 10 cM) to determine if they really are IBS? I find those lengths very surprising. With your data, you noted that about 95 percent of the time what I said earlier will hold true, but that other 5 percent is troubling. I certainly would like us all to be able to be confident of the validity of the 10 cM blocks and above, if not the 7 cM and above. CeCe Sent via BlackBerry by AT&T -----Original Message----- From: Ann Turner <[email protected]> Date: Thu, 17 Nov 2011 12:19:52 To: <[email protected]> Subject: Re: [AUTOSOMAL-DNA] Fundamental autosomal DNA question One way to study the problem is with father/mother/child trio data. If the child has a match not found in either parent, it is possible (indeed I'd say likely) that the segment is Identical by State, not Identical by Descent. Ancestry Finder at 23andMe lets you look at segments down to 5 cM / 700 SNPs. For actual numbers in one case, my son has a total of 231 segments listed with names attached. 67 of those are found only in the child (29%). The breakdown by segment size is 4/76 > 7 cM, longest 11.1 cM (5%) [This seems consistent with a 95% confidence interval] 7/37 6-7 cM (19%) 56/119 < 6 cM (47%) FTDNA seems to have a cutoff of 7.7 cM / 500 SNPs (that's by empirical observation -- has anyone found a shorter longest segment?). I have data for one father/mother/child trio that seems particularly dicey, with 22/100 matches in the child not found in either parent. The segment sizes ranged from 7.7 to 12.90, with a median of 8. Other trios I've looked at seem to run about 15%. Ann Turner On Wed, Nov 16, 2011 at 1:02 PM, CeCe Moore <[email protected]> wrote: > > When I say "legitimately" match, I mean an IBD segment that would meet the > company's matching threshold, not a segment made up of stretches of IBD and > IBS pieced together. > > I'm not saying that it is impossible for a match over ~7 cMs to be IBS, > but very unlikely. (I was going to write ~10 cMs in my response, but > thought that might be a bit conservative.) I know that it is theoretically > possible, but in my thousands of hours of atDNA research, I have yet to see > proof of one. Can you please show me an example of an IBS match over 7 cMs? > (I know that Ann Turner has seen lots of them between 5cMs-7cMs. We'll see > if she responds with a larger one.) > > If enough of a portion of the segment is IBS that it doesn't show up in > your parent (i.e.- make the company's threshold), then it will obviously > reduce the authentic match to a point that is not worth pursuing. I have > chased far too many matches under 7 cMs to recommend doing the same. > ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message