"What if you're wrong" – haplogroup J

By Razib Khan | June 28, 2011 2:52 pm

Back when this sort of thing was cutting edge mtDNA haplogroup J was a pretty big deal. This was the haplogroup often associated with the demic diffusion of Middle Eastern farmers into Europe. This was the “Jasmine” clade in Seven Daughters of Eve. A new paper in PLoS ONE makes an audacious claim: that J is not a lineage which underwent recent demographic expansion, but rather one which has been subject to a specific set of evolutionary dynamics which have skewed the interpretations due to a false “molecular clock” assumption. By this assumption, I mean that mtDNA, which is passed down in an unbroken chain from mother to daughter, is by and large neutral to forces like natural selection and subject to a constant mutational rate which can serve as a calibration clock to the last common ancestor between two different lineages. Additionally, mtDNA has a high mutational rate, so it accumulates lots of variation to sample, and, it is copious, so easy to extract. What’s not to like?

First, the paper, Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe:

R-lineage mitochondrial DNA represents over 90% of the European population and is significantly present all around the planet (North Africa, Asia, Oceania, and America). This lineage played a major role in migration “out of Africa” and colonization in Europe. In order to determine an accurate dating of the R lineage and its sublineages, we analyzed 1173 individuals and complete mtDNA sequences from Mitomap. This analysis revealed a new coalescence age for R at 54.500 years, as well as several limitations of standard dating methods, likely to lead to false interpretations. These findings highlight the association of a striking under-accumulation of synonymous mutations, an over-accumulation of non-synonymous mutations, and the phenotypic effect on haplogroup J. Consequently, haplogroup J is apparently not a Neolithic group but an older haplogroup (Paleolithic) that was subjected to an underestimated selective force. These findings also indicated an under-accumulation of synonymous and non-synonymous mutations localized on coding and non-coding (HVS1) sequences for haplogroup R0, which contains the major haplogroups H and V. These new dates are likely to impact the present colonization model for Europe and confirm the late glacial resettlement scenario.

John Hawks has written at length of the possible distortions that selection might produce in our understanding of the history of mtDNA lineages, and therefore our understanding of the history of the population groups which these genealogies are used as proxies for. So I won’t review that much. I find the dynamics that they’re detecting possible, even plausible. But I don’t see why the authors having introduced skepticism start to conjure up positive visions of what is the true nature of the demographics which underpin these mtDNA phylogenies, now that they’ve “corrected” for variation in the power of the molecular clock to let use look through the glass clearly.

Readers with more fluency in the mtDNA literature can probably pick it apart. At the end of the day I’m always wondering what do the subfossils tell us? In other words, ancient DNA. Inferences from contemporary populations have been a total hash at a finer grain than that of continents, so you probably shouldn’t rest on that leg alone.

Finally, I thought this paper was of interest because it’s an inversion of R1b1b2. That’s a Y chromosomal haplogroup which was once presumed to be Paleolithic but now seems likely to be Neolithic. These authors are claiming that a mtDNA haplogroup which was once presumed to be Neolithic is actually Paleolithic. All this I think indicates that we should be modulating outward our error bars whenever we make assertions based on uniparental data with any time depth and below a very coarse level of spatial granularity.

  • http://washparkprophet.blogspot.com ohwilleke

    mtDNA hg R had to be at least 45,000 years old because it has descedants in the aboriginal Australians and in Papua New Guinea. An estimate of 54,500 years isn’t far off from reasonable calibrations based on that point.

    The notion that “[t]his lineage played a major role in migration “out of Africa””, however, doesn’t pass the smell test. Essentially everyone of ancesteral Eurasian descent alive today are matriline descendants of someone who had mtDNA L3, and there are a lot of mutations from that point to the most basal of the mtDNA haplogroups in R. You need to go from L3 to N to R to descendant mtDNA hgs at a time when the population level production of new mutations would have been limited by a much smaller effective population than the one seen post-Neolithic.

    Also, the TMCA date for mtDNA hg J is very likely not the date when it arrives in Europe in any meaningful frequency. Paleolithic European hunter-gatherer mtDNA from ancient is predominantly U4 and U5, and I can’t recall any instance of Paleolithic European hunter-gatherers having with mtDNA hg J of any kind. We can infer from its presence in the Americas, the mtDNA hg X must have been present in Siberian Paleolithic hunter-gatherers, probably (unlike other mtDNA hgs in the Americas) by a “Northern route.” We can pin some mtDNA M hgs to the Paleolithic by their island isolations (Andamanese; Japanese). But, there are really very few mtDNA hgs that we can definitively calibrate as Paleolithic in anything approximating their modern geographic distribution.

    Moreover, we also have pretty convincing evidence from a growing number of separate lines of evidence that there was immense population genetic upheaval in Europe with limited continuity from era to era first between the pre-LGM and post-LGM when Europe was repopulated from Southern refugia (and possibly new influxes of people from outside Europe), then in the Neolithic, and to a lesser degree later.

    J may have “brewed” and diversified in the Near East for tens of thousands of years, but there is very little evidence to suggest that it is a Paleolithic arrival in Europe. If anything, this study tells us most importantly that mtDNA mutation rate clocks aren’t reliable. We can rely on the phylogeny, but other means of calibrating dates are almost always going to be more trustworthy.

    Even if it is an ancient hg, the distribution and other evidence point to a fairly recent (i.e. predominantly Neolithic) arrival in Europe.

  • http://washparkprophet.blogspot.com ohwilleke

    Footnote: Ancient DNA data here. mtDNA J first appears in Neolithic Germany ca. 5400 BCE. Not one of the 50 paleolithic mtDNA samples (even those from societies that made the Paleolithic-Neolithic transition very late) that could be types were J. Nor were any of the 22 early Neolithic mtDNA samples from Syria, Turkey, Italy, or Portugal. The only cases of J prior to 3300 BCE are in the LBK where it is a minor component of a hetrogeneous mix, with a wider range and more prominent inclusion in the mix thereafter. Thus, not only is it not found in pre-Neolithic samples, the ancient DNA suggests that hg J was not part of the Cardial Pottery Neolithic and instead came in a later wave to that part of Europe.

    The timing and distribution is suggestive of the idea that J may not only have spread into Europe with farmers, but that it may have spread specifically with dairy farmers.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    thanks. assumed you’d have something to say about this :-) this was one of my major issues too: “Also, the TMCA date for mtDNA hg J is very likely not the date when it arrives in Europe in any meaningful frequency.” also, it doesn’t look like they cited the aDNA papers.

  • Eurologist

    I wonder, if you look at a good number of lineages but with relatively few mutations, to what extent different ratios of synonymous versus non-synonymous will just naturally occur by chance, without invoking selection processes.

    I find the use of “different mutation rates” confusing in the paper when the authors really mean bottlenecks and expansion and different population sizes.

    As to R1b1b2 being neolithic, that is far from being settled.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    As to R1b1b2 being neolithic, that is far from being settled.</i

    you read the posts on this weblog, wouldn’t you get that i would agree with that assessment?

  • Andrew Lancaster

    “R1b1b2. That’s a Y chromosomal haplogroup which was once presumed to be Paleolithic but now seems likely to be Neolithic.”

    I’d say every few months the peer reviewed literature gets closer to saying it is post-Neolithic, or at least not in the first one or two waves of the Neo-lithic. Amongst some of us in the genetics genealogy crowd, it has for some time been considered likely to be Bronze Age, and associated with Indo European. (This hypothesis was not even one of the 3 tested in the most recent article you have very recently covered. But it seems consistent with the findings.)

    Of course this is a clade that hobbyists have a lot of resources for, because most have European ancestry, and this was acknowledged in one recent paper. The data sets are bigger than any normal academic study, made up of volunteers, and commercial testing looking for new clade defining SNPs is now becoming standard.

    Best Regards
    Andrew

  • pconroy

    #6 – yes, in the genetic genealogy community, some branches of R1b1b2, especially R-L21 – which is dominant in Ireland and Britain may only be 5,500 years old and R-L21 M222+ (Ui Neill) may be 2,500 yo.

    Incidentally a new SNP DF23 has just been found, which lies between R-L21 and M222 downstream. So this is good news for people like me, as it should finally bring us nearer to determining the source population of M222. The betting is almost equally Ireland and Scotland, but some like the R-L21 list owner think England. I think it’s going to be among the Belgae in the Low Countries…

  • Andrew Lancaster

    pcconroy

    I reckon we are still pretty far from being able to for example name an exact Celtic nation as the vector which spread a particular R1b clade. I know people want it to happen. It would be fascinating!

    But it is hard for me to imagine what kind of data could actually lead to a strong conclusion about such things, unless it be from ancient DNA?

    On the other hand it is dangerous to predict that science will not work out a way! :)

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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