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Thread: The mixed genetic origin of the first farmers of Europe

  1. #231
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    Quote Originally Posted by Riverman View Post
    Not intentional. Sorry.
    All good. No hard feelings.

    Quote Originally Posted by Riverman
    That's correct, but my hypothetical alternative to the conventional intepretation is that this bottleneck was caused by detrimental effects working on the population AFTER the ANA had split and back migrated. It doesn't really make a big difference whether they were actually sitting in North East Africa or the Near East, the point is they lived together with ancestral Eurasians almost directly up to the bottle neck event and separated in a relatively short time span before, either by staying behind, or moving back - or both in an originally fluent border situation.
    Can't say I necessarily disagree with this. It's a given that they were seemingly close relatives of the Proto-Eurasians and likely lived within close proximity of them whether somewhere in Africa or in the nearby Near East at some point and may have even have incurred some form of early admixture from them similar to what's in Mota. The point I was making was simply that people treating ANA like it's basically "Basal Eurasian" are misguided. What fundamentally makes most of the ancestry in Mota, Dinka, Mbutis and the like "SSA" also fits for it too and explains the clustering position of IBMs and the formal-stat models surrounding them. ANA so far seems a non-Eurasian (in the "genetic" sense) population and I can see you're not denying that so we have no real fundamental disagreement.

    Quote Originally Posted by Riverman View Post
    Absolutely, just read my comment above, which I wrote before yours. Also, the Eurasian bottleneck is not the same as moving out of Africa. It just means that there was a serious shrinking event - somewhere, caused by unknown factors. And I say its unlikely to have been the migratoin as such, but rather the deteriorating conditions.
    If you look at it like a tree with branches, its just that ANA is the latest branching event before the bottleneck and I suggest its POSSIBLE that this is because they migrated back, before the remaining Proto-Eurasians went through it. Just an alternative scenario, if you can tell me why its impossible, even though we seem to have evidence of human occupation much earlier, I'm listening.
    Peace.
    Once again, I'm not necessarily disagreeing with you on that at all. I'd have to do more reading on the archaeology and we'd need way more aDNA from North-Africa and West-Asia (like Arabia and the Levant) going way back to confirm or deny any of this. It sounds plausible enough to me and might even help explain Y-DNA E. Whether or not very early ANAs were strictly in North-Africa or had a spread in the nearby Near East is hardly worth arguing about when we're going back to time-frames that way back.

    Quote Originally Posted by Echo View Post
    For all I have seen people have just been calling it ANA.
    Your entire post is a weird strawman. I didn't at any point say I had a problem with calling it ANA. Why would I continue labelling it as such if I did? I was simply pointing out that it did not, as a component, partake in the Eurasian bottleneck just like most of the ancestry in Mota, Mbutis, Dinkas and so forth. It is not a Eurasian component, basically. Can you disprove this despite all the data pointing in that direction? Please do if you can. I'll be very interested. Now, whether you want to call that "SSA", "Non-Euraisan" or bamba-lamba-shamba-lamba is pure semantics. The point is that what fundamentally makes "SSA" components different from Eurasian ones was their not participating in the Eurasian bottleneck and ANA fits that mold. Simple as that. Honestly, even if I had the silly chauvinistic type tendencies you're implying... I'm both significantly Non-Eurasian ("SSA" or whatever) and Eurasian in ancestry. Why would it matter to me either way, my man?

    Quote Originally Posted by Echo View Post
    A notable problem of World Wide PCA Plot is that they are very sensible to drift.
    Yes, like the Eurasian bottleneck which is so imposing a genetic event that the plot refuses to notice the notable structure among African groups until you remove Eurasians:

     


    Introduce just one random Eurasian group and see what happens:

     


    There are clearly other drift events, seemingly among Eurasians, affecting the global plot but the basics are clear. Eurasian bottle neck groups to one side, groups who are mostly not descended from this bottleneck to another side and IBMs cluster right between in a manner that fits amazingly well with their proportions of ANA and Dzudzuana-like ancestry. Are you really not seeing this?

    Quote Originally Posted by Echo View Post
    This situation by itself doesn't make sense. We should see rather the opposite or a situation where Africans and Eurasians occupy an equal share of spaces relative to their respective genetic diversity.
    I've gotta ask. Do you believe ANA was a Eurasian bottleneck descended group? You think it belongs under "Main-Eurasian" in this qpGraph just like Basal-Eurasian? If so, can you please illustrate this? Please explain away the formal-stat based SSA-related affinities in IBMs and stuff like the earlier shared qpGraph. The Global PCA is just a side add-on for visual flare quite frankly and you haven't even managed to explain why it straight-forwardly depicts IBMs as a group nestled between Eurasian bottleneck descended groups and groups who didn't take a part in the bottleneck.
    Last edited by Awale; 11-30-2020 at 06:49 PM.

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    I don’t know why everyone is arguing, once the dna comes out, it will do the speaking. Right now all everyone is doing is throwing around their theories
    Last edited by maroco; 11-30-2020 at 06:56 PM.
    My results:
    Distance: 3.5693% / 0.03569309
    33.2 Early_European_Farmer
    24.8 Iberomaurusian
    17.6 Early_Levantine_Farmer
    11.0 Africa_Mesolithic
    6.8 Iran_Neolithic
    6.6 Steppe_Pastoralist

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    Quote Originally Posted by maroco View Post
    I don’t know why everyone is arguing, once the dna comes out it will do the speaking. Right now all everyone is doing is throwing around their theories
    This is a forum for discussion. What else would we do on here other than discuss and argue?

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  7. #234
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    Quote Originally Posted by Riverman View Post
    Not intentional. Sorry.

    Here is the bottom line:



    That's correct, but my hypothetical alternative to the conventional intepretation is that this bottleneck was caused by detrimental effects working on the population AFTER the ANA had split and back migrated. It doesn't really make a big difference whether they were actually sitting in North East Africa or the Near East, the point is they lived together with ancestral Eurasians almost directly up to the bottle neck event and separated in a relatively short time span before, either by staying behind, or moving back - or both in an originally fluent border situation.
    This is indeed not that new, there were various papers on the issue proposing that kind of back migration.



    And the reason might have been they were one population for a longer period of time or direct neighbours. How can anyone say with certainty whether ANA separated in a back migration or Proto-Eurasians moved out that late? I don't think they moved out that late, we now have more than enough evidence for AMH living outside of Africa longer before and I think the bottleneck event being simply best explained by deteriorating conditions affecting the central group of early Proto-Eurasians, living in Arabia probably.



    Absolutely, just read my comment above, which I wrote before yours. Also, the Eurasian bottleneck is not the same as moving out of Africa. It just means that there was a serious shrinking event - somewhere, caused by unknown factors. And I say its unlikely to have been the migratoin as such, but rather the deteriorating conditions.
    If you look at it like a tree with branches, its just that ANA is the latest branching event before the bottleneck and I suggest its POSSIBLE that this is because they migrated back, before the remaining Proto-Eurasians went through it. Just an alternative scenario, if you can tell me why its impossible, even though we seem to have evidence of human occupation much earlier, I'm listening.
    Peace.
    If you look at Lipson's trees the final version leaves ANA, Eurasian, the major part of Mota and East African ("Dinka") as a multifurcation because there is just too little structure to parse the phylogeny at this stage; different trees reach different conclusions in his supplements and there is no reason to associate ANA with Eurasian so closely. In general I would say the evidence is reasonably secure that there is some kind of "Neo-African" node that unites parts of West and East African ancestry (both "Dinka" and "Mota") and Eurasians and groups them apart from whatever more Basal elements they (and Mbuti, San etc.) have.

    Unless you're saying most of the ancestry of Africans outside HGs of the Central African forests and of Southernmost Africa ultimately derives from Arabia, I see no reason to associate this group of populations so closely to Eurasia, none at all. Why this need to associate the majority of African ancestry with Eurasians, when the evidence indicates multiregionalism in Africa (very deep divergences within Africa and the gradual emergence of behavioral modernity in NE, NW, S Africa near-simultaneously across the Middle Paleolithic)?
    Last edited by Ryukendo; 11-30-2020 at 07:28 PM.
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  9. #235
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    Quote Originally Posted by Awale View Post
    I didn't at any point say I had a problem with calling it ANA. Why would I continue labelling it as such if I did?]
    I didnt point out any particular individual. You said 'some people [...]', I also adressed 'some people [...]'. Basically we are just pointing out the general trends.

    I've gotta ask. Do you believe ANA was a Eurasian bottleneck descended group? You think it belongs under "Main-Eurasian" in this qpGraph just like Basal-Eurasian? If so, can you please illustrate this? Please explain away the formal-stat based SSA-related affinities in IBMs and stuff like the earlier shared qpGraph. The Global PCA is just a side add-on for visual flare quite frankly and you haven't even managed to explain why it straight-forwardly depicts IBMs as a group nestled between Eurasian bottleneck descended groups and groups who didn't take a part in the bottleneck.
    No, I'm going to because I don't take part in any of theory so.
    The Global PCA is just a side add-on for visual flare quite frankly and you haven't even managed to explain why it straight-forwardly depicts IBMs as a group nestled between Eurasian bottleneck descended groups and groups who didn't take a part in the bottleneck.
    I think it just makes sense since all African populations are nested in a chain of admixture events between divergent/deeper clades and neo-clades closer to Main Eurasians (without the necessary bottleneck/drift characterizing the lineage).

  10. #236
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    The Iberomaurusians are very interesting, their F4ratios pretty strongly indicate that they 55 Eurasian and 45 non-Eurasian but their Neanderthal admixture is much higher than you would expect from such a split.

    The bulk of their African ancestry is something that can't be distinguished easily from the main component in Shum_Laka, Dinka, and Mota. I can occasionally model them pretty well using Anatolia_Epipaleolithic + Dinka + some ENA population.


    Edit:

    I tried a broad modern right pop list including Dinka to model the Iberomaurusians as Shum_Laka + Anatolian and Dinka had massive Z-score of -9.7 which definitely indicates that there is some relationship there.
    Last edited by Mnemonics; 11-30-2020 at 09:43 PM. Reason: Additional info

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    Quote Originally Posted by Ryukendo View Post
    Unless you're saying most of the ancestry of Africans outside HGs of the Central African forests and of Southernmost Africa ultimately derives from Arabia, I see no reason to associate this group of populations so closely to Eurasia, none at all. Why this need to associate the majority of African ancestry with Eurasians, when the evidence indicates multiregionalism in Africa (very deep divergences within Africa and the gradual emergence of behavioral modernity in NE, NW, S Africa near-simultaneously across the Middle Paleolithic)?
    If I am not mistaken, this view comes from the structure of the yDNA and mtDNA trees. Sub-Saharan Africans share both yDNA and mtDNA with Eurasians, i.e. DE and L3'M'N. On one hand, with current ancient DNA, it is quite easy to argue that yDNA CF left Africa first and and DE stayed behind until Basal left Africa. However, with this in mind, mtDNA tree is asymmetric as there is only one exit out of Africa, i.e. M'N, but M'N' does not branch from L3'M'N to the exclusion of L3, because L3'M'N forms a single node. Therefore, both trees read together rather suggest that there was an early exit with CT and L3'M'N and an early back-migration of L3 and E.

    Owen mtDNA tree.GIF

    yfull y tree.GIF

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    Quote Originally Posted by Awale View Post
    .
    Taforalt in PCA doesn't act like a 45% african 55% eurasian population , they act like a 65% Eurasian just like they get in other admixture runs and calculators.

    In PCA they are more Eurasian shifted than Ethiopean Jews and Early Pastoral kenya who are about 55% Eurasian.

    Also Natufians don't act like a population with 13% african ancestry which is the ANA percentage in them according to the Dzudzuana paper , modern egyptians who show similar african percentage are more african shifted than natufians.



    So PCA is more aligning with there Admixture, or that ANA is not a simple african ancestry but an ancestry that does share some Eurasian tendencies maybe due to its phylogenetic position.
    I also want to mention that some recent papers didn't even take ANA into consideration and just continued treating Taforalt as 65% eurasian , 35% african.


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    Quote Originally Posted by Ramses View Post
    Taforalt in PCA doesn't act like a 45% african 55% eurasian population , they act like a 65% Eurasian just like they get in other admixture runs and calculators.

    In PCA they are more Eurasian shifted than Ethiopean Jews and Early Pastoral kenya who are about 55% Eurasian.
    Nope. I am using formal stats not stuff like G25 and ADMIXTURE which it supersedes and collate together both Eurasian and non-Eurasian ancestries in components like "Natufian". Formal-stats can suss out the more exact proportions of Eurasian Vs African ancestry like Mnemonics points out here:


    We've know this for years through studies as old as Pickrell et al. from 2013, Ramses but welcome to the party:

     


    Horners' "MENA" (like Natufian-like) scores are not equivalent to our actual base Eurasian ancestry. For example, like Mnemonics says, Somalis are about 44-45% MENA (what you display in your G25 based results) but the actual Eurasian ancestry is something like 38-40% and for Tigrinyas it is 50% which even weirdly aligns with our groups' mtDNA frequencies like I pointed out here. And in that respect they perfectly fit as a 55% Eurasian group by clustering just further of Tigrinyas.

    ...
    Last edited by Moderator; 11-30-2020 at 10:27 PM. Reason: Ad hominem

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    Quote Originally Posted by Awale View Post
    All good. No hard feelings.


    Yes, like the Eurasian bottleneck which is so imposing a genetic event that the plot refuses to notice the notable structure among African groups until you remove Eurasians:

     


    Introduce just one random Eurasian group and see what happens:

     


    There are clearly other drift events, seemingly among Eurasians, affecting the global plot but the basics are clear. Eurasian bottle neck groups to one side, groups who are mostly not descended from this bottleneck to another side and IBMs cluster right between in a manner that fits amazingly well with their proportions of ANA and Dzudzuana-like ancestry. Are you really not seeing this?
    I tell you why that kind of argument is problematic, its for two reasons:
    1. Its no real ANA and ANA is likely to have been quite diversified, which leads to the spread of "Neo-African" or "ANA-like" to the rest of Africa, but that much later. I saw various "ghost models" here and elsewhere, over the years. Some came close to the real thing, when it was retrieved, others were or are horribly wrong. Even by one look you see someone did a bad job. Now I'm not saying that for this ANA model, but I just want to caution against "taking it for the real thing", when it is not.

    2. If you put it on a PCA like that, people might say, "look, its closer to SSA", but there is a problem with that kind of interpretation. Because the closeness comes not just from ANA being close to modern SSA, but from the fact that modern SSA have ANA and ANA-like ancestry at a high proportion! So its close to arguing in favour of a closeness of let's say Egyptians and Yemenites to Ethio-Semites, which is real, only based on one aspect, but forgetting about the second: You get closer to another population on the PCA, if you share ancestry, regardless of the direction of the flow.
    So the real question is, where would Africans without that ANA-like/Neo-African ancestry be put on the PCA, and who would be closer then? I think we all know the answer, ANA would be closer to Eurasians. Even though modern SSA have a lot of ANA-like ancestry, they are still, just going by the model you used, which isn't the real thing, quite far apart.

    This means yes, ANA is not Eurasian proper, not Basal, not Main Eurasian, but its the closest neighbour by a margin from the African variation. And that's no coincidence.

    Quote Originally Posted by Ryukendo View Post
    If you look at Lipson's trees the final version leaves ANA, Eurasian, the major part of Mota and East African ("Dinka") as a multifurcation because there is just too little structure to parse the phylogeny at this stage; different trees reach different conclusions in his supplements and there is no reason to associate ANA with Eurasian so closely. In general I would say the evidence is reasonably secure that there is some kind of "Neo-African" node that unites parts of West and East African ancestry (both "Dinka" and "Mota") and Eurasians and groups them apart from whatever more Basal elements they (and Mbuti, San etc.) have.

    Unless you're saying most of the ancestry of Africans outside HGs of the Central African forests and of Southernmost Africa ultimately derives from Arabia, I see no reason to associate this group of populations so closely to Eurasia, none at all. Why this need to associate the majority of African ancestry with Eurasians, when the evidence indicates multiregionalism in Africa (very deep divergences within Africa and the gradual emergence of behavioral modernity in NE, NW, S Africa near-simultaneously across the Middle Paleolithic)?
    If there would have been this kind of deep multiregionalism, undistorted, they would be completely different people. The, like you said, Neo-African/ANA-like ancestry went over the continent in different waves and brought the populations closer together and closer to Eurasians, because this wave, its origin, was much closer Proto-Eurasians by default. So its important to change perspectives, exactly like I described for the PCA above. That ANA-like ancestry can be considered closer to SSA is because it constituted them, not because it was, originally, closer to Basal African H.s. That's a huge difference for the understanding. Because it implies that a related group to the Proto-Eurasians formed practically all of modern Africans, not "deep African ancestry" having flown into e.g. IBM.

    Once we get genomes of people before the "big back-migraton event" (Near East or North East Africa), the importance of the distinction will become apparent. Shum Laka was just some generations too late probably, Mota is probably the result of not just the first, but a second or third wave hitting East Africa. We're really dealing with more distant timings, because ANA-like ancestry is supposed to have spread minimum for 40.000 years in Africa when Mota was alive. That's obviously much too late for any kind of reference, especially since Eastern Africa was surely earlier hit by the expansion, than Western tropical Africa, the region where Shum Laka was found. So Mota is probably further away because it was an earlier branch of this Neo-Africans which moved down in the East and already mixed with locals as well.
    On the contrary, those found in the IBM were relatively "pure" and closer to the population's centre in North East Africa. With that perspective, all the events get turned around, if true. It makes clear what the centre vs. periphery dichotomy really was. Its absolutely ridiculous, like it was done with the South African finds, if some articles claimed that they found the cradle of humanity in South Africa and some authors even implied we all descend from a San-like people. First of all, the San are a modern H.s. group with its own evolutionary history and admixture events, they are no living fossil, secondly what is older about them, is because they came to be by an earlier branching event, in which they took more basal clades with them and preserved these in their fairly small and isolated population, until they made new contacts.

    The same will be seen with the non-Basal African ancestry in Mota: It was an earlier branching event creating it in comparison to the ANA-central groups in North Africa. The distance made them somewhat, not by a lot, more distant from Eurasians, together with the Basal admixture. The kind of arguments like this or that people descend from Mota, because they show similarities, is misleading, because it confuses source with target. The Mota HG were not source, but the target of gene flow. Like some hundreds of thousands of years earlier the ancestral San component was the target, not the source. Ultimately, the main source for most movements in recent Africa will be found to be either ANA-like (especially Niger-Kordofanian) or BEA-WEA (Afro-Asiatic). I think the connection is quite clear. And there were even earlier such expansions, among hunter gatherers, which being already lost under the newer layers and hard to recognise.
    If they can analyse older samples however, it will become evident.

    There can be no correct model or estimate without knowing the true baseline for a reference. And in the African context, we are very far from it. I mean in the African context we have something like Mota, which is for Europe like LBK. That's much too late.
    Last edited by Riverman; 11-30-2020 at 09:40 PM.

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