Y-DNA ages

The concept "molecular clock" has been and is still for me almost equal to pseudo-science: many people talk of it as if it'd be proof of something when it has zero weight as evidence and almost all estimates are necessarily wrong (often by a lot).

While the concept may be acceptable for speculative purposes, the resulting statistics have no more value than your favorite holy book for the key purpose of explaining reality.

In the case of Y-DNA "molecular clock" age estimates are always based on a handful of STR markers, which do not seem but a pointer and not the real stuff. The real stuff is in the SNPs instead but the problem is that, right now, we know only a few of the many that must be lurking in the actual Y chromosomes that all men carry in their cells. As the exact amount of SNPs in any given lineage is unknown, there is no way of counting them and, that way, establishing the relative chronology of the Y-DNA phylogeny.

However this will change soon if is not already doing so, because full chromosome sequencing is every day cheaper and that is what has allowed, for example the 1000 Genomes Project. A few weeks ago, an open access paper by A. Van Geylesteen et al., emphasized this immediate future in which our knowledge of the Y-DNA tree will almost literally explode. 

But the fact is that there is at least one person who has been already working in the open with that perspective in mind. Terry D. Robb, at his site mostly dedicated to haplogroup I1, published some months ago a (partial) Y-DNA tree of Humankind (update 10 or this PDF) that calculates haplogroup relative ages based on nucleotide differences between the Y-chromosome sequences of the 1000 Genomes Project. 

It is still not rocket science but it is getting quite close. A problem may be that some haplogroups are too thinly represented (actually only R1b, O3 and E1b have large enough samples to be fairly safe about them internally) but while this may be a problem for coalescence ages (because maybe key sublineages are not represented), it should not be at all for divergence ones, i.e. the node where they separate from their closest relatives. So we cannot be certain that the apparent coalescent relative age of, for example, haplogroup D (n=17) is correct but we can be quite certain that the relative age of its divergence from its "brother" E at the DE node is good. 

The other and main problem is calibration. And this is the only (albeit important) aspect where I disagree with Robb's method. He insists on scholastically using academic references from only the population genetics literature (which systematically produces too recent "ages") and ignores archaeological references altogether. Therefore I have taken his graph and modified that part as follows:

click to expand
As you can see, I calibrated by equating age(CF) = 80,000 years ago. This is based on Petraglia 2007 and other materials that establish that there was modern human presence in South Asia since c. 80,000 BP, before and after the Toba ash layer (74 Ka BP). A minor doubt would be if that date would better correspond with Y-DNA F (which in my calibration above shows up right after the Toba event) but that would have made all ages even older (not really a problem for me but I feel alright with this calibration).

The result is somewhat shocking because it pushes the age of A0 to c. 265,000 years ago, making it effectively pre-Sapiens by all the archaeological record (earliest remains at Omo 2 are c. 190,000 years old).  Relatedly, it would push the age of A00 (assuming everything else in the Méndez paper is correct) to c. 450,000 years ago. But after the initial surprise... why not? After all most of us have Neanderthal admixture and they must have diverged a million year ago or earlier. And some peoples even have minor Homo erectus admixture most likely, diverging some 1.8 Ma years ago probably. 

Whatever the case, this graph above, with my much necessary recalibration, is the most reasonable "molecular clock" you can get nowadays for the human patrilineal phylogeny. All the STR sorcery is just that: pseudo-science.

Update (July-13-2013): must be 25% older in fact

Since new evidence piles up in favor of a 100,000 BP arrival to South and SE Asia by H. sapiens, all the dates suggested above should be re-calibrated by adding 25%.

I hope to rewrite this page soon with the new probable chronology.  But let's advance that this new calibration produces the following approximate ages for the best sampled haplogroups:
  • CF'DE:
    • CF: ~100 Ka (calibration point)
      • F: ~92 Ka
        • MNOPS: ~76 Ka
          • NO: ~60 Ka
              • O: ~ 52 Ka
          • P: ~68 Ka
            • R1 ("R" in the graph): ~ 48 Ka (Aurignacian)
              • R1b: ~34 Ka (Gravettian)
        • IJ: ~69 Ka
          • I ~48 Ka (Aurignacian)
    • DE: ~115 Ka
      • E: ~99 Ka
        • E1b: ~78 Ka
It's quite curious how now everything seems to fit incredibly well. The scientific method does pays off after all the grudges. 

Update (Jan-9-2014): Dienekes has collected some of the most recent scholarly age chronological estimates of Y-DNA. The estimates seem to be getting significantly more informative and, of course, older. However the DE/CF split c. 80 Ka BP is still a bit too recent to be realistic according to what archaeology tells us about the migration out of Africa, which is an impossible to ignore calibration point.

The DE/CF split should be roughly coincident with the preliminary migrations to Arabia c. 125 Ka ago, while the C/F split and the F node itself should be of roughly c. 100 Ka ago.

In any case, you can find those graphs in: link 1, link 2. Maybe in some years scholarly genetic research on this matter will finally achieve a half-decent match with archaeologically based likelihood. But not quite yet.



    Fuerteventura and Lanzarote shelter many rock simple Iberian scripts that we identified in 2000 [http://www.visionlibros.com/detalles.asp?id_Productos=10978 ]
    This is concordant with the fact that some ancient Canarian mummies share genetic traits with Europeans.
    Were Iberian scripts made by Iberian fishers who were after tuna-fish?This may be likely [http://basques-iberians.blogspot.com.es/2013/11/las-escrituras-ibero-guanches-de.html ].Or scripts may have been done by some Iberian population established in Canary Islands.Otherwise,Canary Islanders could have born Iberian script to Iberian Peninsula; this last hypothesis seems unlikely.This type of script has not been found in Africa elsewhere.
    [http://commons.wikimedia.org/wiki/File:Iberian-Guanche_inscriptions.pdf?uselang=es ]

    1. It's interesting what you mention but, please, stay on topic.

      Maybe make a search for "Iberian script", "Canarian" or "Guanche" in the navigation bar above. Thanks. There are some entries on those matters and then, of course, I'm open to well written interesting guest articles. If so, try emailing me (email at my profile, remove the "DELETETHIS" anti-spam inset).

  2. Out of interest, is A00 at the root of the Y-DNA tree purely because of calculations based on internal variations within the Y-DNA, or is it based on external factors like archeological evidence?

    My thinking is that if it is based purely on Y-DNA variances there could be other potential roots such as F? Or am I missing something?

    1. You're missing the outgroup, usually the chimpanzee, one of our closest relatives and a well researched one. The root is unmistakable because at some remote point, maybe 10-13 million years ago, we also share a male ancestor with our ape cousins. So the point where the tree converges with the extremely long branch that goes to chimpanzees: that node is the root.

      We could use Neanderthals too but I don't know if we have a sufficient quality such genome. The Denisova genome is very good quality but both are female. Chimps work fine anyhow.

    2. But indeed there was a time when such thing was not clear. If you follow the history of mtDNA research (older than Y-DNA one, as it's easier to extract and analyze the data), they first just named haplogroups quite randomly. They began with Native Americans and they got A, B, C and D, then came East Asians and got E, F and G (in addition to the previous), then European lineages were named (H, I, J, and K initially), then they found an African lineage and called it L and and Indian one that was called M. Then someone realized that most of the previous haplogroups could be grouped either under M or in a new category called N. It took some more time for researchers to realize that macro-haplogroups M and N were part of L. It's a curious alphabetic story. Unlike with Y-DNA (which was more confusing, as different authors used different names until 2001), mtDNA retained the historical nomenclature. But for more than a decade it has been very clear where the root is, in both the mtDNA and the Y-DNA sides. I don't recall the precise studies which first established this but I bet they are well known by experts (more experts than myself) and studied in the faculties.

    3. Thanks for your reply. So for the A00 to be at the root, Y-DNA must be available from chimpanzees and it has to be closer to A00 than the other haplogroups?

      I'm no expert and have only done a basic Google search, but it appears that the chimpanzee Y-DNA hasn't been fully sequenced and for the parts that have they vary widely from humans. Would the variation be too wide to determine, for example, that A00 is closer than F?


    4. "So for the A00 to be at the root, Y-DNA must be available from chimpanzees and it has to be closer to A00 than the other haplogroups?"

      That's a misunderstanding: all branches are (aprox.) equally long from the root node, what is closer to the chimpanzee is the root node, from which A00 and the rest (A0-T is called semi-officially by ISOGG) hang in exactly equal footing.

      ·→ Chimp root
      ·→ Human root

      And from the Human root:

      ·→ A00
      ·→ A0-T

      Naturally the branches are not to any sort of scale, just indicative.

      "... it appears that the chimpanzee Y-DNA hasn't been fully sequenced and for the parts that have they vary widely from humans".

      You can still track the phylogenetic relation: you don't need the full sequence for it. Human haplogroups haven't been determined by analyzing the full sequence of each sample (not at all) but by gradually finding new markers (SNPs = single nucleotide polymorphisms) that are stable enough that don't change in the whole human evolution or even much larger periods, so either you have it and belong to the haplogroup defined by it or not (and must test for other SNPs for upstream or parallel branches), for full security is better to have more than just one SNP tested, I guess but usually one is enough (unstable SNPs, which are rare, are removed from the table as soon as they are determined as such). Sequencing the whole Y chromosome is not worth the effort: even if nowadays is much much much cheaper than it used to be, the problem lays in processing all the other information, on which little is known most often (one thing is to have the full texts and another thing knowing what they mean, as they are not written in plain English). Even when SNPs are not available (what may happen at phylogenetic levels not yet properly researched) geneticists use the so-called microsatellites or STR (short tandem repeats) as method to estimate the approximate phylogeny: it's less reliable but better than nothing - and it'd be reliable for such extremely long branches as the ones joining humans and chimps to our common male ancestor, as there's no room for noise but it's rather a featureless very long line. I presume that the root was first calculated that way.

      "Would the variation be too wide to determine, for example, that A00 is closer than F?"

      Both are similarly close, what is (slightly) closer to the chimpanzee Y-chromosome is the common root from which both branches (and all the others) ultimately hang, the so called "Y chromosome Adam" (which was probably not a H. sapiens but maybe something like H. rhodesiensis, as A00 and maybe even A0 stems are too old for the known paleoanthropology of our species or phenotype).

      Have you per chance been listening to German Dziebel? I haven't discussed these issues since, many years ago, we both agreed grudgingly to stop bothering each other. His ideas are utter nonsense based only on his personal interpretation of cultural anthropology (kinship systems). He somehow believes that a "soft science" like that one can topple a "hard" one like genetics and biology. He's very wrong (but stubborn, extremely stubborn).

  3. Thanks for explaining that. I misunderstood how the tree was formed, essentially thinking that the haplogroups in the tree are static and, for example, A00 hadn't changed since the branch (which demonstrates my lack of knowledge in the area!).

    Nonetheless, I still think the tree can be rotated and the branches remain valid? So for example in the diagram on this page, the tree could be rotated so that F is where Y is?

    My background is computer science and I'm wondering whether the method to produce the tree relies solely on the Y-DNA of the leaves or whether it requires further external information like an older ancestor or some other heuristic to arrive at the commonly presented structure?

    I haven't heard of German Dziebel.

    1. A00 hasn't changed much except for the fact that more and more known SNPs have been added to the list. But it is a recent (2013) and also very exceptional finding, so I don't think it'll be moving around much.

      In the A00 discovery entry you have a very clear tree, incl. the outgroup "chimp". In the A0 discovery entry, from 2011, yo have instead the tree rooted as in the one in this entry with the chimp outgroup just implicit (one with a chimp outgroup is surely available in the original paper but won't check right now).

      "Nonetheless, I still think the tree can be rotated and the branches remain valid? So for example in the diagram on this page, the tree could be rotated so that F is where Y is?"

      No, you can't. Unless you'd be willing to accept that chimpanzees, gorillas, orangutans and surely a host of other mammal species are patrilineal descendants from that "first F" carrier. That they are, for simplicity and focus, not included in the tree does not mean that they are not included in an implicit way. Your proposal means that, at least patrilineally, all other apes, monkeys, etc. descend from humans. I don't think you will be able or willing to assume the implications of such abhorrent claim but, even if you were, it would not stand scientific scrutiny anyhow and nobody else would accept it.

      "the method to produce the tree relies solely on the Y-DNA of the leaves or whether it requires further external information like an older ancestor or some other heuristic to arrive at the commonly presented structure?"

      Requires an outgroup (chimp), I told you already. But once established, this one is not anymore strictly necessary because we know already which is the "Adam" sequence and can proceed out of it. Of course when we get new upstream haplogroups like A0 and A00, what doesn't happen every day, the chimp sequence comes handy again.

      "I haven't heard of German Dziebel".

      Never mind then. Just that he also wanted to upset the phylogeny for his own reasons and place the origin of Humankind in America (against all the available data, not just genetic but also archaeological and paleoanthropological).

  4. Thanks for the heads up, Hiromi. I'm just not paying any attention to anthro-news as of late, so I missed that:

    → http://www.nature.com/nature/journal/vaop/ncurrent/full/nature17993.html

    That's gonna shut up more than one mouth for good, hopefully. Glad to feel vindicated once again, really. :)

    "... is all this dna stuff legit or pseudo-science when it comes to actual phylogeny of Y-DNA and mt".

    To put it simple: phylogeny is legit and it works very well. What is not that legit is age estimation, which is riddled with a lot of vices and biases: particularly scholastic inertia and academic arrogance, often bordering pseudoscience as result. In the above (dated) page I tried to put forward an alternative and maybe more rigorous age estimation, always with due caution.

    Facts are facts in the end and I'm very glad that we finally have not just a pre-Indoeuropean R1b guy in West Europe but also a pre-Neolithic one.

    Ironically, there is at least one person who is going to be even happier: Prof. Caramelli, who along with some other die-hards like Oppenheimer, has been arguing for a much greater component of Paleolithic Continuity based on R1b. Recently I was the one to defend a large fraction of Neolithic replacement vs his "mostly continuity" argument in a soon-to-be published book about Basque and Sardinian origins.

    A lot remains to be understood anyhow and I still say: "sample Atlantic Europe, please", there is where the real clues should be, at least re. modern European R1b.

  5. @Maju, you seem to know way too much about yDNA J1, can I please have your say on my J1 ZS3684 subclade? https://www.yfull.com/tree/J-ZS3684/

    1. No, sorry. What I know is the generic leftover of reading and debating about almost two decades of research on these matters, so for example I know that J1 in the Nile is very diverse, close to West Asian diversity, suggesting that it is very old there, while in NW Africa it is instead much less diverse, what tells us it is much more recent there than farther East.

      What can I know of a "new subclade" that is presented to me without its upstream phylogeny? Well, what says there: one from "Nor" (Norway?) and the other from "Ind" (India?), although I always ignore age estimate claims, because I'm persuaded they are wrong and way too recent in all cases.

      I'd suggest you do that: lose focus on your particular lineage, research all J1 with patience, making maps and trees (by hand even) and you'll learn something too.

  6. So you suggest that J1 is an African lineage?
    --IJ split into I and J and I is basically found in Europe only, is not it more likely that that happened more likely in Europe for both of them, and again J split into J1 and J2 somewhere around Black Sea shore?
    --Is the diversity of J1 found around Nile is greater than the one found around Caucasus?
    --Indian ZS3684 has Khabra as their surname, no associated with any religion is known but it does sound close to Heber, Hebrew, Khabur River, Kaboura(Kabul) Khybar Pass and Khabarda(kabardin).

    On YFullTree https://www.yfull.com/tree/J1/, one just have to see which are the SNPS that are in direct line from J1 to Zs3684, that is my direct paternal line, other offshoots are great..... granduncles only, so it matters not where they are or were found in the past.

    1. "So you suggest that J1 is an African lineage?"

      Not at all. It is an Asian lineage: ultimately as every lineage derived from F or CF and specifically because it is apparent that the origin of the lineage is in West Asia (Kurdistan or Palestine areas probably). What I say is that it is old enough in NE Africa (from Egypt to the Horn) to be considered quasi-native of that region and not a marker of any recent expansion from West Asia. IMO it may have been there since approx. the LSA (African equivalent of the Upper Paleolithic and almost certainly the same phenomenon at the root), much as T in East Africa or mtDNA X1 or M1 in those same regions.

      So, yeah, IJ surely split into I (to Europe) and J (in West Asia) c. 50 Ka ago but, soon after, J split into J1 and J2 and J1 began pouring into NE Africa. This is because J1 is almost as diverse in NE Africa as it is in West Asia: there's no obvious founder effect at all, it has been there since soon after J1 coalesced.

      In Ethiopia we see that there are no differences between Semites and other populations re. this marker, so it is clearly not a Semitic marker (J2 is instead).

      Instead in NW Africa it is surely a Capsian or early Afroasiatic marker from c. 10 Ka ago, as at least E1b-M78 is as well. These populations originated in Nubia as far as we can tell but the overall Afroasiatic origin is maybe further south, towards the Ethiopia-South Sudan border.

      "Is the diversity of J1 found around Nile is greater than the one found around Caucasus?"

      I don't know of any recent comprehensive study of J1 across all its relevant geography but old studies show extremely similar diversity levels in West Asia and NW Africa. A recent study, if my memory is correct, limited to West Asia, suggested the origin could be in the Kurdistan area, like J2. I still think that the very diverse Palestinians are being neglected in this research and that it is possible that J1 arose in the Levant instead.

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  8. Is there any other information I should provide you with to have a better idea, like CSV file from YFull? I am Kit # 285562 at FTDNA. Thanks.

    1. I'm not into personal genetics. I try to help people who make questions about their lineages but it's not my main interest at all. I'm interested in population genetics as something collective, as something that help us to unravel prehistory. I don't know which my haplogroups are: I don't care, they are irrelevant; I know who my grandparents were and each of their known genealogies up to a point, why would I need to know more: each generational step into the past my own genetic self is more and more fragmented, below 5% looks very much pointless, isn't it? (A great-great-grandparent would be ~6% and well into the 19th century). You can go further and further but less than 1% your specific DNA is like no relation at all, right? Genealogy is a bit fraudulent, not just genetic genealogy - at least that's my opinion.

  9. Thank you very much for your time and effort. Autosomal Soup is like the fallen autumn leaves that no one can tell which tree they come from, changeable drastically just in one generation, thus of the least importance to me. My Y lineage which can be traced back to antiquity is most important to me and then the mtDNA which happen to be H14a.

    Obviously I was mistaken about your interests and expertise so have given you all this trouble for nothing, I apologize for that. Thanks again.

    1. The sum of your Y-DNA and mtDNA in your genetic makeup is pretty much negligible, even more so if you'd be a woman, because then we'd only count the mtDNA, which is really tiny. No, that's not what people is made of, and never mind that more than 99% of your genetics is shared with every single other human on Earth. You are not your DNA only or even mainly and we are not our ancestors in any case but ourselves, our selves in which DNA plays a role setting up the basis but which are plastic selves that we can and we do alter in the course of our lives.

      It's like having a huge library, which is pretty much the same for us all. But we do decide which books we do prefer and how to apply the knowledge in them to reality. Biological determinism is all kinds of wrong.

    2. I don't think that we know yet the full importance of the yDNA and mtDNA but one thing is for sure that one without a yDNA will end up with an extra hole instead, and the importance of mtDNA furnace at least need no explanation either, I think.

      Humans also have 98.8% dna similarity to the Chimpanzees, so it actually are these small differences that seem to make the big differences.

      A man is stuck with his yDNA and so is also the story of females when it comes to the mtDNA, while in the case of aDNA Soup one have the power to change the mix for one's next generation. What changes the least is the most important, while what is changeable the most is akin to illusion. I thanks you again for sharing your thoughts in this matter.

    3. For me Y-DNA and mtDNA lineages are just neutral markers, sure they do have effects but (if we ignore the deletereous mutations that will unavoidably go extinct soon, as they did in the past again and again) there is no demonstrated relationship between these lineages and any sort of extra efficiency, there's no apparent positive selection affecting these lineages, hence neutral, evolutionarily pointless, all the same more or less (all Y-DNA will make you male, all mtDNA will do cellular breathing all the same).

      "Humans also have 98.8% dna similarity to the Chimpanzees"...

      Sure thing but the genetic distance to other humans is much much smaller, if we split from chimpanzees some 8-17 million years ago, we only split from other major human groups (aka "races") some 200-50 thousand years. So there's no possible comparison because the scale is 100 times smaller, our fellow humans are about 100 times closer than chimpanzees only in divergence time.

      Also chimpanzees have a very curious evolutionary history: they have evolved more than us (relative to gorilla and orangutan) and also they must have admixed with proto-gorillas soon after their split with our branch, because they carry a gorilla derived chromosome.

      See: http://forwhattheywereweare.blogspot.com/2013/01/chromosome-scale-evolution-among.html

      So maybe rather than us being highly evolved proto-chimpanzees, at least in many aspects, it is chimpanzees which are highly evolved proto-humans and with a gorilla touch that we lack. In any case we're talking of 100 times greater difference than with other Homo sapiens.

      "What changes the least is the most important"...

      Prove me its significance in the phenotype. I'm very sure that most of your traits or mine are totally unrelated to the Y-DNA. My paternal grandfather was blond with blue eyes and bald, I sport very resistant black curly hair and brown eyes, almost certainly all traits inherited from my grandmothers.

      But guess it's a matter of faith, so believe whatever you want.

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  11. Sir; If you will, please provide the archeological linkages at least some to your y-dna split timelines. If for no other purpose to help educate myself and other less educated peoples on these subjects.

    1. Be more specific in your request, please. The entry is full of links and those links have invariably other links in them, some of them probably also relevant, so there's a lot to read only from that. And your request is so vague and generic that I'm tempted to redirect you to Google, Wikipedia and your local library. ;)

      So what exactly are you wondering about?

  12. Hi Maju, how art thou?

    I've been getting more into Y-DNA as of late, I think after recently learning about A-M13's game of hopscotch (EEFs-Sardinia-Ireland) it must have rekindled a deeper interest on my paternal-line. I was at first averse to your staunch stance against the "molecular clock" age estimation of Y-DNA, in large part because I just paid for a second BigY test and would hate to think it's a complete waste of money.

    On reading over your critique a second time, I started seeing a few key points more clearly. I think the keyword "speculative" in your second opening paragraph (top of the page) is what I missed earlier. Also, after reviewing several samples from NGS provider Yfull's Ytree, it's clear their subclade TMRCA estimates are limited to the available samples of a given subclade. The samples within a given subclade can have a stark variance in coverage and detected SNPs:

    R-Y16143: http://imgur.com/yVi8NMe
    Source: https://www.yfull.com/tree/R-Y16143/

    My opinion could be biased here but I think as long as NGS interpretation providers like Yfull openly show their formula and don't try to sell false ideas of exactitude, there shouldn't be any quarrels -- some academics might think differently but *I'd like to think most customers in the commercial DNA testing industry understand speculation and confidence intervals.

    Now, I know you've clearly stated you're disinterest for considering age estimations and private genealogies but I hope you'll make an exception here since this is rather ancient and dealing with a broader scope of populations:

    I'd like your opinion on a Sicilian A-M13 (37 STR) which happens to be my closest match; this factors genetic distance and steps compared to over 53 A-M13s in 20 countries. It's rather surprising since several other African A-M13s have higher genetic distances (Sudan, Chad, Ethiopia, Algeria, Egypt). What's most intriguing, our speculative TMRCA (~1947ybp) happens to roughly overlap Rome's first penetration into Upper-Nubia (22 BC).

    Evidently, there appears to be a historical event for a small Nubian population (1,000 persons) entering Sicily in 22 BC. If interested, I've summarized the findings here: http://www.anthrogenica.com/showthread.php?11679-A-M13-in-a-Sicilian-man

    The Sicilian's BigY results should be in within the next few weeks. Even after thoroughly reading this thread and understanding the limited speculative nature of these estimates, I'm still, perhaps foolishly, eager to see the results ;)

  13. There are some serious issues in the usual approach to "molecular-clock-o-logy" in the academy:

    1. They tend to scholastically repeat old references, in turn referred to even older references, rather than "risking" using innovative approaches or referring to the few studies that dare to point to older reference frames based on more up-to-date data. In the end this results in persistent calibration errors such as considering the out-of-Africa migration to be a mere 60-70 Ka old, when it's certailnly 125-100 Ka old based on updated archaeology, or considering the Homo-Pan split to be a mere 5-6 Ma old, when it's surely older than 7 Ma (Sahelanthropus is unmistakably in our hominid line) and probably some 8-13 Ma old. So my rule of thumb when faced with such methods is to add 50-100% time to all nodes, and this usually seems to work quite well.

    2. Another school, Y-DNA only, uses "pedigree" methods based on observed father-son mutation rates BUT dangerously ignoring that novel mutations are evolutionarily untested and very often will fail (sterility or other problems hindering quality reproduction), hence the effective mutation rate must be significantly slower, how much? Can't tell but there used to be a current which promoted an "evolutionary rate" (corrected after observed rates) that somehow has fallen into oblivion without never being properly challenged scientifically.

    3. In mtDNA it has been observed that effective mutation rates vary a lot from branch to branch, incidentally the most basally diverse the branch (notably M and H, which are huge star-like structures) the less it seems to accumulate mutations. On the opposite side those lines like U which branch almost systematically in pairs (sign of slow but successive expansions with a small population size) have much more rapid effective mutation rates. To me this strongly suggests that in larger populations new lineages have strong difficulties in becoming consolidated (in mtDNA even fastest mutation rates are very very slow, of the order of millennia, so mother lineages survive along daughter ones and in much larger numbers unless the pop. size is very small) and my few attempts to use the proper maths here seem to support this notion (simulations above certain Ne threshold, maybe Ne=>10, will tend to eliminate novel or mutant lineages, resulting in a very conservative pool of lines). So basically it'll be only at the margins, where pops. are very small, where mutation rates will be accelerated.

    4. Commercial DNA testing tends to favor the shortest possible rates. Why? Because it's much easier to sell to their customers a Viking era ancestry than a Magdalenian era one, for example. As it is becoming a big business, this commercial interest tends to infect even the academy.

    So big issues here, really.

  14. "I'd like to think most customers in the commercial DNA testing industry understand speculation and confidence intervals."

    Just search for "DNA test" at YouTube: at least initially most don't understand shit! Everything is oh-so-shocking!, even the <1% Jewish affinity segment and stuff like that. Maybe they learn with time but initially they are all the time quite naive.

    "I'd like your opinion on a Sicilian A-M13 (37 STR) which happens to be my closest match; this factors genetic distance and steps compared to over 53 A-M13s in 20 countries."

    I don't have the materials to know, sorry. Also I don't know enough: Wikipedia says it is only a very distant relative to the Khoisan A sublineages and that it seems centered in Sudan (the presence of A in the Sudanese corridor was indeed known since long ago, so I guess it's all this sublineage). Therefore I'd imagine that it spread northwards with other comparable Sudan-centered lineages like E1b-M78, which is clearly associated in Europe to Neolithic, in Palestine to Natufian Epipaleolithic and in general can be a marker of Afroasiatic (but maybe also East Sudanic, which could well be a relative of Basque language, at least in part) ethno-linguistic expansion northwards (to North Africa and the Levant primarily, later to Europe via the Neolithic). That's my best guess and therefore I'd think it may have spread since c. 12.000 years ago.

    Anyway, my rule of thumb for standard age estimates: add 50-100% to them and see if that fits well with something archaeologically or historically meaningful. Not knowing which is the standard age estimate for A-M13, I can't apply the "method" directly but maybe you can.

    Notice anyhow that Sicilians are quite anomalously ultra-levantine for Europe. IMO this probably (? - just a "good theory" I have) indicates that the Shekelesh (surely Semitic mercenaries in the Sea Peoples narrations) are the later Sicel/Siculi, which probably went westward in alliance with the Shardana (Sardinians) and Teresh (Tyrsenians or Etruscans, probably of Trojan affinity, cf. Tauresi, Lemnian language) to fight against Italic (Indoeuropean penetration in Italy). The Etruscans managed to consolidate their niche but the Sicels were expelled from Central Italy and established themselves in (East) Sicily and Calabria.

    I mention this because surely, therefore, their A-M13 notable frequencies may well be rooted in Bronze Age Levant, or maybe in Egypt itself. Unlike other "Sea Peoples" who seem correlated to some specific geography, the Shekelesh are only described by their name, which seems to derive from "shekel" (a very old Levantine type of money or weight) and the fact that they were circumcised (not European, Anatolian nor Berber therefore: surely Semitic) that's why I think they could well be a loose group of Semitic mercenaries.

    My brief inroads into Sicilian genetics do not suggest that Roman slavery left any significant genetic signature nor that the brief Muslim conquest had significant impact. However it is very clear that Siciians and Maltese have very unusual West Asian (Levant-type) admixture for Europeans and, barring a very odd founder effect in the Neolithic, it's reasonable to think it has to do with the migrations of the Bronze Age collapse period, a very turbulent one, a true "end of times" in all the Mediterranean region and part of the rest.

    My two cents.

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  16. Hello,
    I tested my haplogroups recently. I live in France with 46 % french-german yDNA, 25 % diverse NW Europe, 16 % spanish-portuguese, 13 % british, 0,6 % Italian... Therefore, my mitDNA is haplogroup T. My mom sometimes said she had Spanish origins. Is it surprising to get a T haplogroup with almost 0% Italian origin while spanish is so high in your opinion ? THanks. Great job, your website is very instructive.

    1. MtDNA T is common across Europe and has in principle Neolithic origins (i.e. it arrived from West Asia some 9-7000 years ago, along with J, N1, N2 and X, and unlike most H and U). I'm surprised you say it's rare in Italy, so I'll check that claim. Hold on.

    2. See this: http://forwhattheywereweare.blogspot.com/2014/02/italian-haploid-genetics-second-round.html

      T is common in Italy (12%). Your claim is wrong.

  17. Hey Maju I'm Zachary. I've been studying Dna and haplogroups for 3 yrs now. It all started when I did a cheap Y Chromosome test and got L-M22. Yr later I did FTDNA Big Y 700 and my Haplogroup (L2) is L-FT13849. Its under L-SK1414. I've studied all European and middle eastern haplogroup and L is a mystery. My father's lineage is from Gottshee Austria 1330-1941. Prior to Gottshee Austria my father's lineage is from South Tyrol. We love the mountains like u Basques. I have a distant match in Sicily, and a exact match in Cyprus. Another match in Kuwait but that individual did a basic test not the big Y. My Mtdna is H1ao1. Cheers 🍻 pal

    1. Y-DNA L is quite clearly from South Asia (roughly Pakistan as center) and from memory has also some presence in West Asia. It does look a bit odd in Austria indeed but, on the good side, it gives you a unique family history and not just being another amorphous one from the crowd, and a family mystery to investigate or at least speculate about. There are probably many ways in which this lineage may have arrived to Europe: my first guess would be that relatively modern and maybe associated to Ottoman expansion in the Balcans, but I and others have been wrong before when following this kind of more obvious apparent explanations.

      The Sicily and Cyprus matches may suggest some other origin instead, maybe in the Sea Peoples' later derivation to Italy, which produced the Etruscans (probably the Teresh > Tyrsenoi from somewhere near Troy) and the Sicels/Siculi (Shekelesh, maybe some sort of proto-Phoenicians, Syrian-related genetically in any case, Semitic by name and tradition of circumcision).

      There's one ancient population precisely in and around Tyrol, the Rhaetians, who seem to be Etruscan-related somehow: https://en.wikipedia.org/wiki/Rhaetian_language

      ... hence my second thought would be to consider them as source of your peculiar lineage.

      See also: https://en.wikipedia.org/wiki/Rhaetian_people

      If Etruscan related I can't but consider that Rhaeti and Rasna (Rassena, Rasnal), the Etruscan endonym, which produces Tyrsenos by addition of "ty-" (surely "tu", probably the Etruscan article "the", as "ta" means "this"), are qute similar (if we allow for evolution and Roman typical confusion when observing other peoples).

      In any case I'd say those Rhaeti and in general the Earliest Iron Age flows from the East Mediterranean to Italy (and by extension Tyrol) are a good lead.

      Alternatively it could be something Jewish or Romani (Gypsy) or your random Indian coming with Marco Polo (or whichever other less famous oriental trader, or even the holding of Cyprus by Crusaders and Venice) but I kind of like the Rhaetian lead better. The main Y-DNA marker of such "Pelasgo-Tyrsenian" (and to lesser extent Semitic) flows is J2, which was also re-expanded by Rome (what makes it a bit confusing in this case). I wonder how much J2 is there in Tyrol, if more common than elsewhere in the area (barring Italy), then it may be a signature of Tyrsenian settlement.


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