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Thread: New paper on mtDna in Iberia

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    New paper on mtDna in Iberia

    Ruth Barral-Arca et al

    See:

    http://journals.plos.org/plosone/art...l.pone.0159735

    "The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA) variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested) is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM), prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype frequencies."

    To my knowledge haplogroup U is not nested in HVO, so this statement doesn't inspire confidence.

    Also, since these aren't complete genome sequences, I don't think conclusions about then they arrived are totally reliable.


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    Well, I was hoping this study could settle once and for all the doubt about the origins of haplogroup u6, if the maximum place of variation was very near the straight of gibraltar than, it would have probably come from noth africa but that maximum is present in huelva which is about 150 km away from gibraltar. Also if haplogroup L came "only" with slave-trade it woulb be expected that it's maximum varitation should be in lisbon but it is far way in the algarve region, that to my knowledge (correct me if I am wrong) wasn't a slave trading place, actually lisbon was the only place I know in Portugal.

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    As far as mtDna U6 is concerned, I don't know how anyone could do a better job for it using modern dna than Bernard Secher et al: https://bmcevolbiol.biomedcentral.co...71-2148-14-109

    It's dense, and you can't reduce the findings to a single soundbite, but that's a mark of how good it is, in my opinion. It's pretty clear, for example, which subclades of it came from North Africa and when.

    When I saw the title of this paper I thought perhaps they'd done the same for some of the other mtDna lineages in Spain, particularly for the "L" lineages, but that's not the case.

    I think they limited themselves themselves to filling in some of the blanks by sampling in areas not sampled before, and then looking at the sum total of all the mtDna data compiled for Iberia so far, which is great, since that hadn't been done before. This is everything that has ever been done, so the general parameters are correct. The problem is that if you are interested in population genetics, you're interested when and with whom these lineages entered an area, and for that you need whole genome sequences of modern samples and ancient dna as well.

    This is the general picture:
    mtDna Iberian peninsula.jpg

    If this link doesn't work, please let me know. It's acting up.

    As far as the "L" being on a south/north cline, rather than centered around Lisbon, for example, I think that you can get founder effects in small towns and rural areas that you might not get in a capital city with its constant influx of new people. MtDna, like yDna, is very subject to drift.

    The settlement of SSA people in southern Portugal, in particular, as well as in Lisbon, was well known, I thought. I definitely remember reading about it. A quick search led me to this:

    https://www.academia.edu/7345366/Por...ole_Portuguese

    Go to S2.1. It explains how under population in the rural south led to the settlement of Sub-Saharan workers there, enough so that they constituted 10% or more of the workforce at one point. Given the difference between SSA mtDna versus yDna, I think there was probably less resistance to admixture with the women than the men.

    The Ramos Timhorao who is referenced as the source for those facts in the article has written an entire book on the subject, unfortunately not translated from the Portuguese, which is called "Blacks in Portugal". It's a google book, as well as being available for purchase. You might find that helpful.
    https://books.google.com/books/about...d=_nmkAAAACAAJ
    Last edited by Angela; 20-08-16 at 21:31.

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    It occurred to me to check the eupedia map on mtDna "L". Maciamo has the swathe of "L" going across the southern areas of Iberia into Spain at higher levels than shown in this paper. Perhaps he can take a look. Perhaps they actually didn't include all the studies, or perhaps their methodology was different. The distribution within southern Portugal is also a bit different.


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    The problem with the L lineages is that they are most probably in iberia since along time ago, i suspect they came with whoever brought e-m81. The problem would be to distinguish those lineages which i believe are the majority from the lineages that came with the slave trade, that coulb have been done if they tested for deep clades but probably it wasn't the objective of the study afterall. About the methodology giving less L lineages than previous studies, maybe the previous studies just got "lucky" with the area tested, still the averages for western iberia in the study are quite different from maciamo's averages.
    Only one question out of curiosity, have U6 or L lineages beeen found in ancient dna studies in iberia? thank you

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    Not to my knowledge, Sue Biking.

    This is the paper on the ancient U6 found in Romania. I don't think we'd be far off if we concluded that most of the U6 went east to west across North Africa and then into Iberia, but Secher does a great job of tracking it subclade by subclade.
    http://www.nature.com/articles/srep25501

    There's some correlation with E-M81, but it's by no means perfect. One thing that could have been done, in addition to getting way down into the subclades, is to see if the largest number of the yDna SSA lineages, even if there aren't very many of them, track with the numbers for "L" particularly in the southwest.

    I don't think they're at all implying that all the "L" came with SSA y lineages or predominantly SSA people autosomally. It seemed to me they're saying that it's an overlay.


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    Quote Originally Posted by Angela View Post
    Not to my knowledge, Sue Biking.

    This is the paper on the ancient U6 found in Romania. I don't think we'd be far off if we concluded that most of the U6 went east to west across North Africa and then into Iberia, but Secher does a great job of tracking it subclade by subclade.
    http://www.nature.com/articles/srep25501

    There's some correlation with E-M81, but it's by no means perfect. One thing that could have been done, in addition to getting way down into the subclades, is to see if the largest number of the yDna SSA lineages, even if there aren't very many of them, track with the numbers for "L" particularly in the southwest.

    I don't think they're at all implying that all the "L" came with SSA y lineages or predominantly SSA people autosomally. It seemed to me they're saying that it's an overlay.

    I forgot to add this link to the Candela Hernandez et al paper on mtDna "L" .

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624789/

    These authors did it the way it should be done, in my opinion, with whole genome sequences. Unfortunately, they only did it for western and eastern Andalucia.

    "Regarding lineage L, the sub-haplogroups L1 (L1b), L2 (L2a, L2b) and L3 (L3d, L3f, L3h, L3x) again distinguish western (3.92%) from eastern (1.28%) Andalusians. In the analyzed Berber samples, the L1b registered an average of 7% (~6–8%). In Figuig Berbers, L3e appears conspicuously represented (21.3%), which is a finding that is not shared by the other two Moroccan Berber populations (3–8%). The evolutionary origins of the L0, L1, L2 and L3 lineages are located in sub-Saharan Africa [41]. The neat markers of mtDNA L lineages among North Africans again support the view that the Sahara desert has not been an insurmountable barrier to the populations that border it ([15,38,42], among others)."

    "The analysis performed by [26] on the phylogeography of L sequences observed in Iberia and remaining Europe pointed to 65% of its introduction in recent times (Romanization period, Islamic expansion and Atlantic slave trade), and 35% at older times, as earlier as 11ky. The complete sequence based FA for U6 agrees more with these results, attributing a half-half proportion of sequences in both periods, showing the higher resolution of complete mitogenomes. The historical-based expectation of a higher proportion of newly introduced U6 lineages in Andalusia was confirmed: 70% against 30% in the earlier migration."

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    Well I personally did not know about that study which is quite interesting. About the topic study, at least we have more samples to work with. Hopefully Maciamo will use these samples to update the mt-dna data about the iberian peninsula though it seems to me it will only alter the averages of lineages that have a small presence in iberia like x,w,i,l etc.

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    I just took now into account, where is haplogroup K in the percentages, is it under U has K itself derived from u8 or is it in the other categorie, categorie which is almost non existent in portugal but very high in the iberian plateau.
    PS: don´t mind the 21% other in center portugal since looking at the images I do not see the part of the circle with its color.

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    Y-DNA haplogroup
    proly R1B

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    The paper seems very interesting but I just read it fast now.
    What it seems weird are the large variations of H maternal line in different areas of Spain.

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    Quote Originally Posted by suebiking View Post
    I just took now into account, where is haplogroup K in the percentages, is it under U has K itself derived from u8 or is it in the other categorie, categorie which is almost non existent in portugal but very high in the iberian plateau.
    PS: don´t mind the 21% other in center portugal since looking at the images I do not see the part of the circle with its color.
    Suebiking,

    Go to the Supplementary Info section to which I link below, and click on Tables S1 and S2. Once there, if you scroll all the way to the right, you'll see the designations for both the new samples they collected and the ones they used that were previously published. You'll find "K" in there.

    http://journals.plos.org/plosone/art...0159735#sec013

    @mihaitzatelo,

    Yes, I noticed that too.

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    Thanks, I missed it.

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