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Thread: SNP naming and phylogenetics - equivalents, synonyms and whatever

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    Lightbulb SNP naming and phylogenetics - equivalents, synonyms and whatever

    Quote Originally Posted by George Chandler View Post
    I'm not trying to divert the thread as I understand it relates to the Hinxton remains. If you think of the same phylogenetic SNP line as a building with each new level being an SNP they don't occupy the same level unless they are a different name for the same SNP. They don't occupy the same level on the tree just because nothing diverts from that SNP node as of yet. Looking at L459 everyone who has tested the main subgroups under DF13 has tested positive for L459 (unless something recent has changed that). How can you say that L459 and DF13 are on the same level? It's a direct line with one being above and one being positioned below.
    You are still very confused about phylogenetic equivalent SNPs and you should start a new thread about it can that go on for as many pages as you like until you understand what they are. No one ever said that L459 and DF13 are on the same level and if you want to discuss that please do it in a new thread.
    Last edited by ArmandoR1b; 10-21-2014 at 03:23 PM.

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    Quote Originally Posted by ArmandoR1b View Post
    You are still very confused about phylogenetic equivalent SNPs and you should start a new thread about it can that go on for as many pages as you like until you understand what they are. No one ever said that L459 and DF13 are on the same level and if you want to discuss that please do it in a new thread.
    No I don't have any interest in starting a new thread because I do understand. The statement was made that Z245 and L21 are on the same level. This is not true and if it were that would mean that DF13 and L459 were on the same level as well (which they aren't). One is above and one is below in the Phylogenetic line in the same way one is above and one is below in the same phylogenetic line when comparing Z245 and L21. There are branches coming off the L21 node and there are no branches coming off the Z245 node which I'm aware of. Believe whatever you want to believe but you're wrong.

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    Quote Originally Posted by George Chandler View Post
    I'm not trying to divert the thread as I understand it relates to the Hinxton remains. If you think of the same phylogenetic SNP line as a building with each new level being an SNP they don't occupy the same level unless they are a different name for the same SNP. They don't occupy the same level on the tree just because nothing diverts from that SNP node as of yet. Looking at L459 everyone who has tested the main subgroups under DF13 has tested positive for L459 (unless something recent has changed that). How can you say that L459 and DF13 are on the same level? It's a direct line with one being above and one being positioned below.
    I'm going to try to explain this quickly, if no one minds.

    When we say that Z245 and L21 are "on the same level", we don't really mean that literally; we mean we do not know at present which one came first. Let's pretend for a minute Z245 came first. Imagine a man who has two sons. One of them is Z245+ and L21- (ancestral for L21) like his dad. The other son is not only Z245+ but has a brand spanking new SNP: L21.

    The Z245+ L21- son dies without leaving any male descendants behind to carry on a Z245+ L21- y-dna line. The other son, however, the Z245+ L21+ guy, has several sons who are also Z245+ L21+, and they likewise have male descendants who survive to carry on that y-dna line.

    So there you have it: all the L21+ guys are also Z245+, but we do not know how it happened because the Z245+ L21- line is dead and long gone. Perhaps it happened the way I imagined above, or perhaps it happened the other way around: that is, L21 came first and Z245 after.

    If we knew, we could place those SNPs in the proper phylogenetic order; but we don't know, so we have to place them on the same phylogenetic level. See?

    If we could just find someone who is Z245+ and L21-, or L21+ and Z245-, we would have the answer, but we don't have the answer because thus far we have not found such a person.

    Maybe Hinxton 1 will provide the answer if there is a clear L21- result from him?

    Hope that cleared things up.
    Last edited by rms2; 10-21-2014 at 03:46 PM.

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    Quote Originally Posted by George Chandler View Post
    No I don't have any interest in starting a new thread because I do understand. The statement was made that Z245 and L21 are on the same level. This is not true and if it were that would mean that DF13 and L459 were on the same level as well (which they aren't). One is above and one is below in the Phylogenetic line in the same way one is above and one is below in the same phylogenetic line when comparing Z245 and L21. There are branches coming off the L21 node and there are no branches coming off the Z245 node which I'm aware of. Believe whatever you want to believe but you're wrong.
    Wow, I can't believe you have such a deep misunderstanding of phylogenetic equivalent SNPs.

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    Quote Originally Posted by rms2 View Post
    I'm going to try to explain this quickly, if no one minds.

    When we say that Z245 and L21 are "on the same level", we don't really mean that literally; we mean we do not know at present which one came first. Let's pretend for a minute Z245 came first. Imagine a man who has two sons. One of them is Z245+ and L21- (ancestral for L21) like his dad. The other son is not only Z245+ but has a brand spanking new SNP: L21.

    The Z245+ L21- son dies without leaving any male descendants behind to carry on a Z245+ L21- y-dna line. The other son, however, the Z245+ L21+ guy, has several sons who are also Z245+ L21+, and they likewise have male descendants who survive to carry on that y-dna line.

    So there you have it: all the L21+ guys are also Z245+, but we do not know how it happened because the Z245+ L21- line is dead and long gone. Perhaps it happened the way I imagined above, or perhaps it happened the other way around: that is, L21 came first and Z245 after.

    If we knew, we could place those SNPs in the proper phylogenetic order; but we don't know, so we have to place them on the same phylogenetic level. See?

    If we could just find someone who is Z245+ and L21-, or L21+ and Z245-, we would have the answer, but we don't have the answer because thus far we have not found such a person.

    Maybe Hinxton 1 will provide the answer if there is a clear L21- result from him?

    Hope that cleared things up.
    I understand exactly what you've written and it means "uncertain phylogenetic placement under P312", or like the SNP list shows "under investigation". I can see that someone has looked at the ISOGG tree and they don't know where to place the SNP so they stick next to the closest one. You get a list of SNP who's phylogenetic placement is unknown. When you have newer people learning about SNP's and people are saying it's on the same level it's confusing. I'm not sure who decided to start using that terminology but seriously?

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    Quote Originally Posted by George Chandler View Post
    I understand exactly what you've written and it means "uncertain phylogenetic placement under P312", or like the SNP list shows "under investigation". I can see that someone has looked at the ISOGG tree and they don't know where to place the SNP so they stick next to the closest one. You get a list of SNP who's phylogenetic placement is unknown. When you have newer people learning about SNP's and people are saying it's on the same level it's confusing. I'm not sure who decided to start using that terminology but seriously?
    Quote Originally Posted by George Chandler View Post
    Maybe people who try to make themselves appear smarter than they are by creating and using big words in a manner which is incorrect and then spamming them to others should..such as yourself for example. Take your own advice.
    You are still extremely confused about the meaning of phylogenetically equivalent. It isn't our fault that you can't understand it's meaning. It doesn't matter that you don't agree with it. It's term has been in use for a long time and it is used by professionals. You need to accept that it's meaning is here to stay and you won't be able to change it. People will continue to use the term whether you like it or not.

    The term exists in the ISOGG Glossary -
    http://www.isogg.org/tree/ISOGG_Glossary.html

    It is also used the following published studies -

    http://www.plosone.org/article/info%...l.pone.0041634

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113241/

    http://www.plosone.org/article/info:...l.pone.0005792

    http://www.plosone.org/article/info%...l.pone.0049170

    If you disagree so much with the term you should write to ISOGG and the authors of all of those published studies.

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    Quote Originally Posted by ArmandoR1b View Post
    You are still extremely confused about the meaning of phylogenetically equivalent. It isn't our fault that you can't understand it's meaning. It doesn't matter that you don't agree with it. It's term has been in use for a long time and it is used by professionals. You need to accept that it's meaning is here to stay and you won't be able to change it. People will continue to use the term whether you like it or not.

    The term exists in the ISOGG Glossary -
    http://www.isogg.org/tree/ISOGG_Glossary.html

    is also used the following published studies -

    http://www.plosone.org/article/info%...l.pone.0041634

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113241/

    http://www.plosone.org/article/info:...l.pone.0005792

    http://www.plosone.org/article/info%...l.pone.0049170

    If you disagree so much with the term you should write to ISOGG and the authors of all of those published studies.
    Look at what I said previously..stating that yes I agree with when you say L21 is phylogenetically equivalent to Z245 "under P312. You keep bouncing from the term "on the same level" and "phylogenetically equivalent". The quote you used in the isogg definitions I agree with and how it's used being that it shows a relationship between 2 SNP's of the same line of what ever the SNP is.

    I quote "for example, Y-DNA haplogroup M is defined by the following SNPs: M4, M5, M106, M186, M189, P35, which are said to be phylogenetically equivalent"

    The conversation then goes to the term that Rich mentioned which is that "on the same level" he is using which defines a known SNP position with the close proximity SNP who's position is unknown and they are positioned on the same level of the isogg tree.

    You can't just say SNP 1 and SNP 2 are phylogenetically equivalent without defining the haplogroup or upper SNP along with the SNP's you are saying are phylogenetically equivalent.

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    George -

    I thought I explained it very carefully. When we do not know which of two or several or many SNPs occurred first - and probably never will know - they must be placed on the same level, but it is not difficult to understand what that means. When you have several different SNPs on the same phylogenetic level, that means a bottleneck occurred in which only one y-dna line survived: the one positive for the whole damned array of them.

    That's the way it is.

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    Quote Originally Posted by George Chandler View Post
    Look if you, isogg and the rest of the world want to confuse new people who are trying to learn by incorrectly saying the are on the same level while not stating that the SNP placement is unknown go ahead. It's bad terminology and is difficult to understand for new people just starting out and trying to learn. If you want to incorrectly state that that they are phylogenetically equivalent while giving no explanation to the haplogroup or SNP you're talking about that's your choice as I didn't expect you to say anything else but "that's the way it is".
    But it's not incorrect, George. That is the terminology. You are right that it must be explained from time to time, but it's no mistake. They are different SNPs on the same phylogenetic level, and thus phylogenetically equivalent, because they cannot be ordered any other way, and we don't want to leave any of them out.

    Okay, that's all I have to say on the subject.

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    Lightbulb SNP naming and phylogenetics - equivalents, synonyms and whatever

    Quote Originally Posted by George Chandler View Post
    Look at what I said previously..stating that yes I agree with when you say L21 is phylogenetically equivalent to Z245 "under P312. You keep bouncing from the term "on the same level" and "phylogenetically equivalent". The quote you used in the isogg definitions I agree with and how it's used being that it shows a relationship between 2 SNP's of the same line of what ever the SNP is.
    You had stated "I can see that someone has looked at the ISOGG tree and they don't know where to place the SNP so they stick next to the closest one. You get a list of SNP who's phylogenetic placement is unknown." which means you are confused as at to why Z245 was placed as a phylogenetically equivalent to L21. It means that they know that every time someone is tested for both L21 and Z245 they are always positive for both. I have stated that before. It also means that everyone that descends from L21 and Z245 tests positive for both. Therefore they phylogenetically equivalent until someone comes around that is either L21+ Z245- or L21- and Z245+. That is how they choose where to place the more newly discovered SNP. It isn't because "they don't know where to place the SNP" It is quite the opposite. They know exactly where to place the SNP until test results from someone prove otherwise. There is absolutely no way to know which is ancestral to which until either L21+ Z245- or L21- and Z245+ is found.

    I figured stating that it is "on the same level" would be easier for people to understand and you state above it is now your main point of contention then you go on to tell rms2 that "Look if you, isogg and the rest of the world want to confuse new people who are trying to learn by incorrectly saying the are on the same level while not stating that the SNP placement is unknown go ahead. It's bad terminology and is difficult to understand for new people just starting out and trying to learn. If you want to incorrectly state that that they are phylogenetically equivalent while giving no explanation to the haplogroup or SNP you're talking about that's your choice as I didn't expect you to say anything else but "that's the way it is". " which shows that the bouncing of terms is not your main point of contention. It shows that you are still confused.

    Being on the same level is the same as phylogenetically equivalent because of the example I pointed out in the first paragraph. Z245 is not phylogenetically equivalent to U152, a "brother" of L21, and therefore it is not on the same level as U152. Z245 is phylogenetically equivalent to L21 and therefore it is on the same level. L21 and U152 are on different levels in the phylogenetic tree. I think your confusion here is from looking at diagram such as https://dl.dropboxusercontent.com/u/...dency_Tree.jpg and thinking that L21, U152, DF27. DF19, DF99. and L238 are on the same level which is not how the term is used.

    Quote Originally Posted by George Chandler View Post
    I quote "for example, Y-DNA haplogroup M is defined by the following SNPs: M4, M5, M106, M186, M189, P35, which are said to be phylogenetically equivalent"
    There is absolutely no difference between that example and S145/M529/L21 * L459 * S245/Z245 * Z260 * S461/Z290 as found at http://www.yfull.com/tree/R1b1a2a1a2c/ other than the asterisks at YFull and commas at ISOGG.

    YFull has a more up to date tree. ISOGG takes longer to update the tree. I start with ISOGG then I go to YFull to find changes or additions. YFull shows Z245 and L21 to be phylogenetically equivalent.

    Quote Originally Posted by George Chandler View Post
    The conversation then goes to the term that Rich mentioned which is that "on the same level" he is using which defines a known SNP position with the close proximity SNP who's position is unknown and they are positioned on the same level of the isogg tree.

    You can't just say SNP 1 and SNP 2 are phylogenetically equivalent without defining the haplogroup or upper SNP along with the SNP's you are saying are phylogenetically equivalent.
    The position of L21 and Z245 are known in relation to each other and other SNPs. We have absolutely no proof which is ancestral to which in regards to L21 and Z245 but we know that they are below P312 and above DF63 and Z2542/CTS8221. Therefore the haplogroup or upper SNP has been defined. Therefore, they get placed as being phylogenetically equivalent until L21+ Z245- or L21- and Z245+ is found.

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