>the very huge list of firmly confirmed phyloequivalent snps to M253 and P40 (I1 snps)When we talk about SNPs being phyloequivalent, does that only mean that they are phyloequivalent for modern I1? For example, if all modern I1s are M253+ P40+ and both SNPs can define haplogroup I1, are we likely to find some remains eventually that are perhaps P40+ but M253- and represent some intermediate stage? Matthew Simonds > From: [email protected] > To: [email protected] > Date: Wed, 8 Jan 2014 14:12:40 -0700 > Subject: [yDNAhgI] Update on Ancient I in Europe > > Here’s an update on what has recently been learned about haplogroup I ydna in ancient Europe. Bones of several males from 8000 b.p. were examined for their dna: Loschbour was from a Luxuemberg site, four male dna Motala 2,3,9,12 > were from a Swedish site. Another male from Swedish site, Motala6, seems not to be confirmed haplogroup I, but his true haplogroup is still unidentified though thought Q for awhile. Their ydna analysis of these ancient males is discussed in depth in the paper “Ancient human genomes suggest three ancestral populations for presentday Europeans”. > > As of a month ago, the hobby community had collected a number of phyloequivalent ysnps to M423, mainly from Geno2: the full list is M423, L178, L1224, CTS8486, CTS8239, CTS7218, CTS5985, CTS5375, CTS1802, CTS176, CTS1293, CTS11030. > Multiple customers of Geno2 chip or WTY and from the L161 “Isles” clades or from the L621 “Dinaric” clade were found derived for ALL of these 12 ysnps. Everyone else in haplogroup I was found ancestral for All of them. > > In the cited paper, however, only L178 and M423 were tested on these ancient dna samples. They took their snps to test from ISOGG list, and as we know that list always lags present knowledge because of the procedure of inclusion into their list. The ancient dna samples are not necessarily readable on any given snp site, so it is important to have that ancient dna tested on alternative sites of equivalence if unreadable on any particular site. So I sent the 10 snp sites listed above for which they did not test to authors of the cited paper. They very kindly looked up the allele values for the additional snps which could be read. > > Loschbour was readable for all 12 snps with results: derived for CTS8239, CTS7218, CTS5985, CTS176, CTS1293, L178, M423, but ancestral for the other five snps including L1224. > > Motala12 was readable for 9 of the 12 snps with results which exactly matched Loschbour. Unreadable snps were CTS8239, L1224, M423. > > Motala3 was readable for only 3 of the 12 snps with results matching Loschbour: CTS7218+, CTS176+, CTS1293+ > > Motala2 was readable for only 1 of the 12 snps and disagreed with first three dna samples, being CTS1293- > > Motala9 was not readable for any of the 12 snps. > > Loschbour and Motala12 (and probably Motala3) establish a new branch line of the I Tree which is today probably extinct or severely tiny in present population. It splits the 12 snps into ancestrals and deriveds. See “Tree and Map for haplogroup I” for position of this new branch of the tree. > > So we concentrate on what we might further learn about Motala2 and Motala9 samples using the rich catalog of well placed ysnps that has resulted from Geno2 and other products done by hobbyists. > > All we know about Motala9 is that he is P38+ but P40-. All we know about Motala2 is that he is P38+ M253+ Z79- L703- L37- L621-. So both are haplogroup I, but that’s about all we know. > Motala9 could be most anything within haplogroup I except a modern I1. He could be anything in I2...... and could be a new ancient branch on the ancestral I1 line which branched off prior to P40. That’s a time range of 22,000 years b.p. up to about 4500 years b.p. Similarly Motala2 could have branched off of the ancestral I1 line anytime before M253, and Motala still has much of I2...... for his location. > > So there is much work that authors of this paper can do using our Geno2 generated rich lists of phylogenetically equivalent snps for many of the key branch segments of the I tree. Motala2 and Motala9 could conceivably be placed fairly well in the haplogroup I tree, giving us much better incite into presence of our haplogroup in northern Europe 8000 years ago. I have sent several sets of the confirmed phylogenetically equivalent snp lists to them and hopefully they will see if they are readable for Motala2 and Motala9. > > What I have not put together yet, waiting to see if they will use it or that Motala2 and Motala9 are not confirmed to be part of I2....., is the very huge list of firmly confirmed phyloequivalent snps to M253 and P40 (I1 snps). Since that branch line segment is so long, 22000 years ago up to 4500 years ago, the list of well confirmed equivalent snps is probably presently approaching 100 in number. If Motala2 or Motala9 are confirmed I2..... then no sense checking them on all those I1 snps. > > So there could be much more of value to be extracted from these ancient dna samples from a complete use of their full genome measurements plus the hobby community’s most up to date list of well confirmed and well placed ysnps. > I hope they will continue to work with us as they did on the initial set of ysnps equivalent to M423 and L178 which produced such informative results. > > Footnote: If Motala6 is indeed not confirmed haplogroup Q as the cited paper concluded, then a complete list of phylogenetically equivalent snps to P38 should probably be tested to see if he is haplogroup I or not? > > > > > > > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > ------------------------------- > 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

Probably the most common usage of "phyloequivalent" would have to mean that for all TESTED modern samples, a set of snps showed derived and ancestral states in unison. We don't know what the entire population turn out to be unless we measured it. So some ancient dna samples might split a phyloequivalence seen in all present day tests, and that is indeed what we saw in the M423 L178 plus 10 more snps case I described. As far as P40 and M253 are concerned, they are on a branch line about 17,500 years long and have dozens and dozens of KNOWN phyloequivalent snps. So P40 and M253 define just two points within that 17500 years branch segment. There could be bones with dna from between those points, prior to both those points, or after both of those points. And concerning those two points, we have not the foggiest idea whether P40 is earlier than M253, or vice versa. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Matthew Simonds Sent: Wednesday, January 08, 2014 3:12 PM To: [email protected] Subject: Re: [yDNAhgI] phyloequivalent ysnps‏ >the very huge list of firmly confirmed phyloequivalent snps to M253 and P40 >(I1 snps)When we talk about SNPs being phyloequivalent, does that only mean >that they are phyloequivalent for modern I1? For example, if all modern I1s >are M253+ P40+ and both SNPs can define haplogroup I1, are we likely to >find some remains eventually that are perhaps P40+ but M253- and represent >some intermediate stage? Matthew Simonds > From: [email protected] > To: [email protected] > Date: Wed, 8 Jan 2014 14:12:40 -0700 > Subject: [yDNAhgI] Update on Ancient I in Europe > > Here’s an update on what has recently been learned about haplogroup I ydna > in ancient Europe. Bones of several males from 8000 b.p. were examined > for their dna: Loschbour was from a Luxuemberg site, four male dna Motala > 2,3,9,12 > were from a Swedish site. Another male from Swedish site, Motala6, seems > not to be confirmed haplogroup I, but his true haplogroup is still > unidentified though thought Q for awhile. Their ydna analysis of these > ancient males is discussed in depth in the paper “Ancient human genomes > suggest three ancestral populations for presentday Europeans”. > > As of a month ago, the hobby community had collected a number of > phyloequivalent ysnps to M423, mainly from Geno2: the full list is M423, > L178, L1224, CTS8486, CTS8239, CTS7218, CTS5985, CTS5375, CTS1802, CTS176, > CTS1293, CTS11030. > Multiple customers of Geno2 chip or WTY and from the L161 “Isles” clades > or from the L621 “Dinaric” clade were found derived for ALL of these 12 > ysnps. Everyone else in haplogroup I was found ancestral for All of them. > > In the cited paper, however, only L178 and M423 were tested on these > ancient dna samples. They took their snps to test from ISOGG list, and as > we know that list always lags present knowledge because of the procedure > of inclusion into their list. The ancient dna samples are not necessarily > readable on any given snp site, so it is important to have that ancient > dna tested on alternative sites of equivalence if unreadable on any > particular site. So I sent the 10 snp sites listed above for which they > did not test to authors of the cited paper. They very kindly looked up > the allele values for the additional snps which could be read. > > Loschbour was readable for all 12 snps with results: derived for CTS8239, > CTS7218, CTS5985, CTS176, CTS1293, L178, M423, but ancestral for the other > five snps including L1224. > > Motala12 was readable for 9 of the 12 snps with results which exactly > matched Loschbour. Unreadable snps were CTS8239, L1224, M423. > > Motala3 was readable for only 3 of the 12 snps with results matching > Loschbour: CTS7218+, CTS176+, CTS1293+ > > Motala2 was readable for only 1 of the 12 snps and disagreed with first > three dna samples, being CTS1293- > > Motala9 was not readable for any of the 12 snps. > > Loschbour and Motala12 (and probably Motala3) establish a new branch line > of the I Tree which is today probably extinct or severely tiny in present > population. It splits the 12 snps into ancestrals and deriveds. See > “Tree and Map for haplogroup I” for position of this new branch of the > tree. > > So we concentrate on what we might further learn about Motala2 and Motala9 > samples using the rich catalog of well placed ysnps that has resulted from > Geno2 and other products done by hobbyists. > > All we know about Motala9 is that he is P38+ but P40-. All we know about > Motala2 is that he is P38+ M253+ Z79- L703- L37- L621-. So both are > haplogroup I, but that’s about all we know. > Motala9 could be most anything within haplogroup I except a modern I1. He > could be anything in I2...... and could be a new ancient branch on the > ancestral I1 line which branched off prior to P40. That’s a time range of > 22,000 years b.p. up to about 4500 years b.p. Similarly Motala2 could > have branched off of the ancestral I1 line anytime before M253, and Motala > still has much of I2...... for his location. > > So there is much work that authors of this paper can do using our Geno2 > generated rich lists of phylogenetically equivalent snps for many of the > key branch segments of the I tree. Motala2 and Motala9 could conceivably > be placed fairly well in the haplogroup I tree, giving us much better > incite into presence of our haplogroup in northern Europe 8000 years ago. > I have sent several sets of the confirmed phylogenetically equivalent snp > lists to them and hopefully they will see if they are readable for Motala2 > and Motala9. > > What I have not put together yet, waiting to see if they will use it or > that Motala2 and Motala9 are not confirmed to be part of I2....., is the > very huge list of firmly confirmed phyloequivalent snps to M253 and P40 > (I1 snps). Since that branch line segment is so long, 22000 years ago up > to 4500 years ago, the list of well confirmed equivalent snps is probably > presently approaching 100 in number. If Motala2 or Motala9 are confirmed > I2..... then no sense checking them on all those I1 snps. > > So there could be much more of value to be extracted from these ancient > dna samples from a complete use of their full genome measurements plus the > hobby community’s most up to date list of well confirmed and well placed > ysnps. > I hope they will continue to work with us as they did on the initial set > of ysnps equivalent to M423 and L178 which produced such informative > results. > > Footnote: If Motala6 is indeed not confirmed haplogroup Q as the cited > paper concluded, then a complete list of phylogenetically equivalent snps > to P38 should probably be tested to see if he is haplogroup I or not? > > > > > > > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > ------------------------------- > 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