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Thread: Root of Y-DNA phylogentic tree revised to 338,000 years (before Homo Sapiens)

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    3 out of 3 members found this post helpful.

    Arrow Root of Y-DNA phylogentic tree revised to 338,000 years (before Homo Sapiens)

    A very exciting new paper was released yesterday, confirming the announcement four months ago that the common ancestor to all human male lineages lived much longer ago than what believed so far.

    An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree (Mendez et al.)

    Abstract

    "We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins."


    The most amazing thing about this re-assessment is that the root of this new African branch (Y-haplogroup A00) is considerably older than the anatomically modern humans, known as Homo Sapiens. It is not until 200,000 years ago that hominids started exhibiting traits that could be characterised as anatomical modernity, while full behavioural modernity only developed from 50,000 years ago (in some parts of the world).

    This A00 lineage is at least 237,000 years old, but could be as old as 581,000 years old, based on the mutation rate used by the team of researchers. This bring us back to the Early to Middle Palaeolithic, a period where several (sub)species of hominids co-existed in Africa, Asia and Europe, including Homo erectus (1.8 million to 300,000 ybp), Homo rhodesiensis (300,000 to 125,000 ybp), Homo heidelbergensis (600,000 to 400,000 ybp), Denisovans (?), and of course Neanderthals (600,000 to 25,000 ybp).

    I have long supported the Multiregional origin of modern humans as opposed to the Recent African origin of modern humans taught in most schools. The discovery in 2010 that modern Eurasians did indeed have Neanderthal and Denisovan DNA was a first step in confirming the Multiregional origin theory. This paper adds another example of archaic admixture, from Central Africa this time. I believe that the reason why modern human racial groups display such phenotypical diversity is for the greatest part due to these archaic admixtures.

    I also believe that the definition of species, as applied to hominids, should be revised accordingly, since members are different species by definition cannot interbreed with one another. Therefore, all archaic humans should be considered as subspecies and not separate species.

    Genetic genealogy is a brand new science, which really took off in the last 5 to 10 years. It is likely that even older lineages will be found - if not in living people, at least in relatively recent ancient DNA from the last 10,000 years (like Ötzi).
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    I can see the wrong people misuse this information. It is basically saying that some ancient monkeys and sub-saharan africans are both y-dna group A.

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    WOW

    Good find Maciamo.

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    Wonder if they're going to announce Neanderthal and/Denisovan y-lines and mtd-DNA lines next... you know they have to be out there somewhere. I was of the same opinion Maciamo... the multi-regional makes too much sense to ignore. Although I will say in genetic terms we are still enormously still out of Africa within the last 120,000 years.

    **EDIT**
    Looks like my hybrid vigor theory with the Neanderthal/homo sapien mix gaining fifteen or so I.Q. points on BOTH parents is starting to hold some water. Standford, Harvard are you listening? Somebody needs to be writing my quotes down, I'm a genius.

    Or maybe just able to observe the obvious...

    BTW read the first part of my comment with the word "somewhere" in italics. Finding y-Neanderthal in modern man may not be as difficult as it would seem...
    Last edited by nordicfoyer; 02-03-13 at 02:45. Reason: honed dates

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    This is very interesting, I can imagine the excitement that will be going round some departments on reading this report. I admit to raising more than one surprised eyebrow myself when I read it and my own knowledge of genetics is rather small in comparison to some members on the board.

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    Quote Originally Posted by Maciamo View Post
    I have long supported the Multiregional origin of modern humans
    I'm glad our views get vindicated. There must be a thread or two where we argued our points before genetic evidence showed up.
    Be wary of people who tend to glorify the past, underestimate the present, and demonize the future.

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    Wow, very interesting findings, pushing back human history 100000 years isn't something you find out everyday. Its also very intriguing that this lineage was discovered in an African American male, as their predominant HG's are E1b1a and about 25% of African American Y-DNA is European in origin, so to find a relic lineage is extremely lucky.
    Also can anyone give me a few points on why a Multiregional model is more acceptable, RAO seems to compose 90 % of Human DNA, and the date of homo sapiens existence being pushed back dosent prove much of a variance in regions other than Africa. The oldest lineages outside of Africa are 60000 years old so where are the deep seeds that support the Multiregional hypothesis.

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    Quote Originally Posted by kamani View Post
    I can see the wrong people misuse this information. It is basically saying that some ancient monkeys and sub-saharan africans are both y-dna group A.
    You didn't understand anything.

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    Quote Originally Posted by Anthro-inclined View Post
    Also can anyone give me a few points on why a Multiregional model is more acceptable, RAO seems to compose 90 % of Human DNA, and the date of homo sapiens existence being pushed back dosent prove much of a variance in regions other than Africa.s.
    What's RAO ?

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    Quote Originally Posted by Maciamo View Post
    What's RAO ?
    Sorry, Recent African Origin

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    Quote Originally Posted by Maciamo View Post
    The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins."
    English is my first language and I don't understand what this means. Anyone care to translate? It sounds like they are making room for error-- either current or future. Here's some help from Merriam Webster:

    Stochastic
    1. (specifically) involving a random variable
    2. involving chance or probability

    from the Greek stochastikos-skillful in aiming

    Who wrote this-- someone in their legal department?

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    0 out of 3 members found this post helpful.
    Quote Originally Posted by Maciamo View Post
    You didn't understand anything.
    lol, maybe, but maybe I'm the only one who is calling it for what it is. Based on the article A predates humans (common human) by possibly 300.000 years, so A was originally partially monkey, so the bottom line: haplogroup A turned out to be monkey.

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by nordicfoyer View Post
    English is my first language and I don't understand what this means. Anyone care to translate?
    My best thought-by-thought translation:

    The A00 lineage was discovered in a commercial database testing black Americans, not black Africans. This demonstrates how the movement of people over time can cause individual samples to be geographically distant from the place of origin of their haplogroup. So, be careful when using the modern geographic location of outlier branches to try to determine where the haplogroup originated.
    Basically, it's saying that it was found in an American, not an African, so we can't say much about the geographic origin of the A00 haplogroup, nor would we be able to say much even if we found it in an African.

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    2 out of 2 members found this post helpful.
    Quote Originally Posted by kamani View Post
    lol, maybe, but maybe I'm the only one who is calling it for what it is. Based on the article A predates humans (common human) by possibly 300.000 years, so A was originally partially monkey, so the bottom line: haplogroup A turned out to be monkey.
    You're off by orders of magnitude. Apes diverged from monkeys ca. 30 million years ago. We even have Homo fossils dating to millions of years ago, so it wouldn't even be accurate to call it "ape" unless you're using the broad definition of the term "ape" which also includes Homo. Far from "calling it like it is," you're showing that you profoundly misunderstand this result.

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    Quote Originally Posted by sparkey View Post
    My best thought-by-thought translation:



    Basically, it's saying that it was found in an American, not an African, so we can't say much about the geographic origin of the A00 haplogroup, nor would we be able to say much even if we found it in an African.
    I agree Sparkey, that's what I concluded as well. The part I had difficulty understanding is what comes after that... specifically the before and after of "warrants caution during interpretation".

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    Quote Originally Posted by nordicfoyer View Post
    English is my first language and I don't understand what this means. Anyone care to translate? It sounds like they are making room for error-- either current or future. Here's some help from Merriam Webster:

    Stochastic
    1. (specifically) involving a random variable
    2. involving chance or probability

    from the Greek stochastikos-skillful in aiming

    Who wrote this-- someone in their legal department?
    noun stochos means target
    virb στοχευω means I am aiming, active voice
    noun στοχασμος means thoughts, calculations of probability, a sum of past and the possible results if a variation changed.
    virb στοχαζομαι means I am thinking, I am calculating, I find my mistakes, I make a sum of past, I am planning all possible future targets, passive voice,

    Stochastic Phenomena.
    the possible results of a procedure, that can not be described under a math law,
    mainly the unpredicted by maths result,
    the random effect size and possibility, that can cause results outside the calculated area

    example
    to predict weather many days ahead,
    or to create an earthquake in Pacific, after a jump of an elephant in Africa etc,

    generally
    to predict all possible results, according the 'if' input,
    so to 'aim' the target
    to predict or exclude possible results, of a random effect,
    When someone is showing/pointing the MOON
    many of us look the FINGER, the first time
    But some
    continue to see the finger AFTER second and third time,

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    Quote Originally Posted by sparkey View Post
    You're off by orders of magnitude. Apes diverged from monkeys ca. 30 million years ago. We even have Homo fossils dating to millions of years ago, so it wouldn't even be accurate to call it "ape" unless you're using the broad definition of the term "ape" which also includes Homo. Far from "calling it like it is," you're showing that you profoundly misunderstand this result.
    According to this the article timelines, we're tracing hg A to something that predates humans and neanderthals, and I'm going to leave it at that since is a controversial topic.

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    After hunting around, I've found some tidbits that might be of interest for this thread.

    The haplogroup study is currently behind a paywall, but should be available for public consumption soon. In the meantime, Dr. Thomas Krahn's (one of the key scientists on this project) presentation diagrams are able to be viewed. Dr. Krahn is employeed by FTDNA, and on the "about" section of FTDNA's website this is posted about the doctor: "He has discovered an uncountable number of new haplogroups".

    Also it seems like the STR's of this ancient line were studied independently of the SNP's by two seperate researchers/groups, and that each camps' findings eventually strengthened the others' claim. This should be more clear when the paper is out (Unfortunately for you all I'm incredibly cheap.)

    The "uncountable number" is what got my full attention here. If indeed there is an additional time frame extension/expansion of another y-DNA hg... what group would mostly likely be involved?

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    Quote Originally Posted by nordicfoyer View Post
    After hunting around, I've found some tidbits that might be of interest for this thread.

    The haplogroup study is currently behind a paywall, but should be available for public consumption soon. In the meantime, Dr. Thomas Krahn's (one of the key scientists on this project) presentation diagrams are able to be viewed. Dr. Krahn is employeed by FTDNA, and on the "about" section of FTDNA's website this is posted about the doctor: "He has discovered an uncountable number of new haplogroups".

    Also it seems like the STR's of this ancient line were studied independently of the SNP's by two seperate researchers/groups, and that each camps' findings eventually strengthened the others' claim. This should be more clear when the paper is out (Unfortunately for you all I'm incredibly cheap.)

    The "uncountable number" is what got my full attention here. If indeed there is an additional time frame extension/expansion of another y-DNA hg... what group would mostly likely be involved?
    I don't understand your question. The uncountable number of haplogroups discovered is over the past years working at FTDNA. This discovery of A00 is just an isolated case. The article won't mention other new discoveries.

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    Quote Originally Posted by Maciamo View Post
    I don't understand your question. The uncountable number of haplogroups discovered is over the past years working at FTDNA. This discovery of A00 is just an isolated case. The article won't mention other new discoveries.
    Agreed... this paper revolves around A00. I'm referring to future papers though. Well's original Out of Africa (during the last 120,000 years or so) hypothesis is slowing rupturing with Neanderthal mixing, Denisovan contributions, and now this A00 lineage. If a Neanderthal y-haplogroup (or maternal line) pops up... large segments of his theory will be null and void. Actually, a decent amount has already been proven inaccurate.

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    Quote Originally Posted by nordicfoyer View Post
    Agreed... this paper revolves around A00. I'm referring to future papers though. Well's original Out of Africa (during the last 120,000 years or so) hypothesis is slowing rupturing with Neanderthal mixing, Denisovan contributions, and now this A00 lineage. If a Neanderthal y-haplogroup (or maternal line) pops up... large segments of his theory will be null and void. Actually, a decent amount has already been proven inaccurate.
    Wells was not the first to propose the out of africa theory, in fact Charles Darwin first proposed an origin for humans in africa. Wells used genetics to back the theory, but the idea for an origin in africa is much older than Wells.
    Also, i dont think finding a Neanderthal or Denisovan Haplogroup will prove anything new, we already know that less than 4% of the non african human genome is of Neanderthal origin, and less than 6% of the melanesian and austrailian aborigine genome is Denisovan to. So i guess one could argue that a multiregional origin is partly valid, but most genetic evidence says that at least 90 percent of the human genetic compostion holds an origin in africa less than 70000 years ago.

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    I guess my sentence could be taken in such a way that implies Wells and Wells alone created this theory, that was not my intention.

    Wells did make his bread and butter trumpeting the Out of Africa theory, that we can be sure of...

    Neanderthal or Denisovan haplogroup would be a game changer in my book. Look at the online battles we have now between the alphabet soup of L,M,N,O,P... wait until one or two become a different "sub-species".

    Of course that's why I've been drawing attention to the numerous advancements of Neanderthal-- such as boat travel, fire starting 200,000 years before any homo sapien lines were capable, etc. Wells said "R1b were the first Europeans" one too many times for my taste.

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    Maybe I'm not figuring this right but it seems to me if they've found an early "A" - A00, that goes back so far before the species, then possibly all they have found it the paternal line in the precursor species (Homo heidelbergensis or some other 'step'). This then hardly speaks to multiregional origins, just as any minor included Neandertal or Denisovan DNA in the Homo sapiens genome only represents interactions between the species. I'm sure if we could determine human genomes over the last million years that we would find admixtures of Homo erectus in more recent species.

    As for the use of fire, it's no big deal when it was Homo erectus who first controlled it.

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    I'm surprised how many people use the words monkey or ape, talking about erectus, heiderbergensis or so, when its belongs to Homo genre. They were hominids.

    A fresh new. Hominid from Orce, Spain, dated in 1.400.000 years:

    http://www.iphes.cat/files/en_dent_humana_orce.pdf

    http://www.independent.co.uk/travel/...n-8518514.html

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    Quote Originally Posted by Lynn View Post
    Maybe I'm not figuring this right but it seems to me if they've found an early "A" - A00, that goes back so far before the species, then possibly all they have found it the paternal line in the precursor species (Homo heidelbergensis or some other 'step'). This then hardly speaks to multiregional origins, just as any minor included Neandertal or Denisovan DNA in the Homo sapiens genome only represents interactions between the species. I'm sure if we could determine human genomes over the last million years that we would find admixtures of Homo erectus in more recent species.





    As for the use of fire, it's no big deal when it was Homo erectus who first controlled it.
    I agree with your overall thinking actually. My point is that the RECENT Out of Africa theory--the one associated with Spencer Wells and his work The Journey of Man: A Genetic Odyssey back in 2002 -- would be shot full of holes if we find surviving Neanderthal and/or Denisovan haplogroups. It's already taken on a decent amount of water with Neanderthal/Denisovan admixtures and now this A00 haplogroup.

    And by pointing out Neanderthal's successes, I'm salting the fields for those in the future who might want to put him in the "dumb brute" class. If one of the haplogroups gets pushed back 600,000 years or so-- it will carry political overtones. To gloss over these potential implications ignores the last few thousand years worth of homosapien warfare.

    Or homo sapien's inhumanity to homo sapien... so to speak.

    **EDIT**
    When I used the term "recent" (capitalized above) I'm refering to ROA or Recent Out of Africa theory and not the "recentness" of Spencer Wells work in 2002. Sorry for the confusion if there was any.
    Last edited by nordicfoyer; 04-03-13 at 17:39.

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