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Thread: Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria[

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    Quote Originally Posted by Chad Rohlfsen View Post
    This is an interesting turnout. The apparent North African in Kostenki and BK-1653 look legit. I put in those edges because the f2 between ShumLaka and them was near 2 and the worst two left.

    Attachment 44465Attachment 44466Attachment 44467
    ShumLaka is showing no internal drift though, that indicates something isn't right.
    Have you tried adding an East-Asian population like Jomon/Boisman/DevilsGate? I'm stuck in the roadblock of trying to figure out why they are so close to Goyet.
    Last edited by Kale; 04-29-2021 at 12:14 AM.
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    Quote Originally Posted by Kale View Post
    ShumLaka is showing no internal drift though, that indicates something isn't right.
    Have you tried adding an East-Asian population like Jomon/Boisman/DevilsGate? I'm stuck in the roadblock of trying to figure out why they are so close to Goyet.
    Shared Bacho Kiro-related ancestry? Or perhaps another ancient Central Asian population (most likely IUP-related)?

    In some models there is a slight admix edge of Goyet in Tianyuan but it's often the other way around too (Tianyuan->Goyet)

    For me these are the most probable scenarios along with Goyet-> ANE -> Boisman or something like that.
    Last edited by Max_H; 04-30-2021 at 10:32 AM.

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    Everything I've tried so far results in a super-bottlenecked lineage though (at least as severe as the OOA bottleneck or sometimes 3-4x more severe). Maybe that did happen, but it's just not very appealing, large drift branches usually indicate something is wrong and it's just fudging for damage control.
    Goyet > ANE > Boisman doesn't work, Boisman/Jomon are closer to Goyet than ANE.
    Goyet > Boisman or Boisman > Goyet both work, but with heavy bottlenecks.

    To repost a graph from earlier, this is the most satisfying solution I've come across so far, the bottleneck is 35 or 52 versus 33 for OOA.
    I also like it because rather than Tianyuan and Goyet being a small amount of some hugely bottlenecked IUP branch, Tianyuan is 100% IUP and Goyet 52% of a modestly drifted BachoKiro (-excess Neanderthal)
     

    digraph G {
    size = "7.5,10";
    Root -> South_Africa_2000BPSG [ label = "14" ];
    Root -> X [ label = "14" ];
    X -> AEA [ label = "16" ];
    AEA -> MotaSG [ label = "140" ];
    AEA -> OOA [ label = "33" ];
    OOA -> OOA1 [ label = "2" ];
    OOA -> ZlatyKunSG [ label = "143" ];
    OOA1 -> pUST [ label = "2" ];
    pUST -> pUST1 [ label = "35" ];
    pUST1 -> pUST2 [ label = "17" ];
    pUST -> Ust_IshimDG [ label = "3" ];
    OOA1 -> IUP [ label = "5" ];
    IUP -> BK1 [ label = "6" ];
    BK2 -> BachoKiro_IUP [ label = "62" ];
    pGOY -> pGOY2 [ label = "0" ];
    pGOY2 -> GoyetQ116_1 [ label = "130" ];
    BKG2 -> BachoKiro_Gravettian [ label = "137" ];
    IUP -> E1 [ label = "6" ];
    E1 -> E2 [ label = "1" ];
    E2 -> Tianyuan [ label = "130" ];
    E2 -> E3 [ label = "7" ];
    PKB -> PrimorskyKrai_Boisman_MN [ label = "25" ];
    W1 -> W2 [ label = "2" ];
    W2 -> W3 [ label = "5" ];
    W3 -> Kostenki14 [ label = "131" ];
    pSUN -> SunghirSG [ label = "11" ];
    pANE -> ANE [ label = "3" ];
    ANE -> MA1SG [ label = "139" ];
    ANE -> Yana_UPSG [ label = "10" ];
    pONG -> OngeDG [ label = "33" ];
    BK1 -> BK2 [ style=dotted, label = "96%" ];
    pUST2 -> pGOY [ style=dotted, label = "48%" ];
    pGOY2 -> BKG1 [ style=dotted, label = "74%" ];
    BKG1 -> BKG2 [ style=dotted, label = "97%" ];
    E3 -> PKB [ style=dotted, label = "92%" ];
    pUST2 -> W1 [ style=dotted, label = "40%" ];
    W3 -> pSUN [ style=dotted, label = "98%" ];
    W2 -> pANE [ style=dotted, label = "75%" ];
    E3 -> pONG [ style=dotted, label = "40%" ];
    X -> BK2 [ style=dotted, label = "4%" ];
    BK1 -> pGOY [ style=dotted, label = "52%" ];
    W3 -> BKG1 [ style=dotted, label = "26%" ];
    X -> BKG2 [ style=dotted, label = "3%" ];
    pUST1 -> PKB [ style=dotted, label = "8%" ];
    OOA1 -> W1 [ style=dotted, label = "60%" ];
    X -> pSUN [ style=dotted, label = "2%" ];
    E1 -> pANE [ style=dotted, label = "25%" ];
    pUST -> pONG [ style=dotted, label = "60%" ];
    }
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    Quote Originally Posted by Kale View Post
    Everything I've tried so far results in a super-bottlenecked lineage though (at least as severe as the OOA bottleneck or sometimes 3-4x more severe). Maybe that did happen, but it's just not very appealing, large drift branches usually indicate something is wrong and it's just fudging for damage control.
    Goyet > ANE > Boisman doesn't work, Boisman/Jomon are closer to Goyet than ANE.
    Goyet > Boisman or Boisman > Goyet both work, but with heavy bottlenecks.

    To repost a graph from earlier, this is the most satisfying solution I've come across so far, the bottleneck is 35 or 52 versus 33 for OOA.
    I also like it because rather than Tianyuan and Goyet being a small amount of some hugely bottlenecked IUP branch, Tianyuan is 100% IUP and Goyet 52% of a modestly drifted BachoKiro (-excess Neanderthal)
     

    digraph G {
    size = "7.5,10";
    Root -> South_Africa_2000BPSG [ label = "14" ];
    Root -> X [ label = "14" ];
    X -> AEA [ label = "16" ];
    AEA -> MotaSG [ label = "140" ];
    AEA -> OOA [ label = "33" ];
    OOA -> OOA1 [ label = "2" ];
    OOA -> ZlatyKunSG [ label = "143" ];
    OOA1 -> pUST [ label = "2" ];
    pUST -> pUST1 [ label = "35" ];
    pUST1 -> pUST2 [ label = "17" ];
    pUST -> Ust_IshimDG [ label = "3" ];
    OOA1 -> IUP [ label = "5" ];
    IUP -> BK1 [ label = "6" ];
    BK2 -> BachoKiro_IUP [ label = "62" ];
    pGOY -> pGOY2 [ label = "0" ];
    pGOY2 -> GoyetQ116_1 [ label = "130" ];
    BKG2 -> BachoKiro_Gravettian [ label = "137" ];
    IUP -> E1 [ label = "6" ];
    E1 -> E2 [ label = "1" ];
    E2 -> Tianyuan [ label = "130" ];
    E2 -> E3 [ label = "7" ];
    PKB -> PrimorskyKrai_Boisman_MN [ label = "25" ];
    W1 -> W2 [ label = "2" ];
    W2 -> W3 [ label = "5" ];
    W3 -> Kostenki14 [ label = "131" ];
    pSUN -> SunghirSG [ label = "11" ];
    pANE -> ANE [ label = "3" ];
    ANE -> MA1SG [ label = "139" ];
    ANE -> Yana_UPSG [ label = "10" ];
    pONG -> OngeDG [ label = "33" ];
    BK1 -> BK2 [ style=dotted, label = "96%" ];
    pUST2 -> pGOY [ style=dotted, label = "48%" ];
    pGOY2 -> BKG1 [ style=dotted, label = "74%" ];
    BKG1 -> BKG2 [ style=dotted, label = "97%" ];
    E3 -> PKB [ style=dotted, label = "92%" ];
    pUST2 -> W1 [ style=dotted, label = "40%" ];
    W3 -> pSUN [ style=dotted, label = "98%" ];
    W2 -> pANE [ style=dotted, label = "75%" ];
    E3 -> pONG [ style=dotted, label = "40%" ];
    X -> BK2 [ style=dotted, label = "4%" ];
    BK1 -> pGOY [ style=dotted, label = "52%" ];
    W3 -> BKG1 [ style=dotted, label = "26%" ];
    X -> BKG2 [ style=dotted, label = "3%" ];
    pUST1 -> PKB [ style=dotted, label = "8%" ];
    OOA1 -> W1 [ style=dotted, label = "60%" ];
    X -> pSUN [ style=dotted, label = "2%" ];
    E1 -> pANE [ style=dotted, label = "25%" ];
    pUST -> pONG [ style=dotted, label = "60%" ];
    }
    As always very interesting to see your qpGraphs. This one is particular seems to a large extent to agree with the literature published on these samples, even down to the 25% Tianyuan (in this case IUP) affinity in ANE. However if it's not too much trouble could you include Loschbour (since it had an ENA signal, I suspect Goyet or ANE-related) in your graph? I've seen qpGraphs which show Loschbour contribute to East Asians instead, so it would be interesting to see how that relationship came about.

    Lastly, just for reference, would you have any D stats handy showing Boisman closer to Goyet than ANE?

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    Quote Originally Posted by Kale View Post
    Basal Eurasian is an outdated concept Ust_Ishim was instrumental in defining that concept, and then we found Ust_Ishim's brother Oase in Europe, and now I'm sure these BachoKiro folks will join that club.
    I think calling it the y-hg IJ branch would be more accurate at this point.
    "Basal Eurasian" was never a qualified term, anyhow - but a cruch made to fill a gap.

    The truth of the matter - afaik - is that there's been a pretty advanced "flint-culture" throughout Western Eurasia since EUP. There's still no reason to assume, presume or believe that the population registered within the sub-arctic periods of EUP and MUP were of 'different kinds' - as in different 'species'. The most marked difference known was between two various sub-species, one being 'proto-Cro-magnons', the other 'Neanders'. Apparently they mixed, thus producing one basis for "modern man". Apparently they both mixed with other 'kinds' - aka sub-species - of humans, such as the Denisovans - producing another basis for 'modern men'.

    During the last last 120 millennia of the Paleolithic the climate started fluctuating more radically - showing amplitudes of both cold and hot not seen before - in the 15 million year long climate-curves of the MIS-scale. The period in question is called the Weichsel stadial and signify the period when the global ice-cap filling the Arctic cricle - paralell to the Antarctic ice - started to break up and melt away, producing climatical variations not seen in the antarctic waters or the tropical habitats of the equatorial zone.

    To survive the climatical fluctiations of the northern hemisphere a pretty advanced set of skills and knowledge were needed - as in botany, zoology, pyrotech and mineralogy, to develop the technology neccesary to maintain a decent, productive and reproductive life - throughout the sub-arctic and temperate parts of western Eurasia, where the major hubs of paleolithic populations existed, producing sculls, bones and techno-complexes that o-b-v-i-o-u--l-y share all of the most important characteristics. Like soild houses with effective heating, where TOOLS of flint, pots of brimstone and clothes from fuhrs, skins, hemp and flax could be produced - during all seasons and weathers...

    The EXTREME cold-periods registered across the northern hemisphere during the Late Weichsel is unique to the climatical history of the planet. The effect is well known - as the LGM and the Younger Dryas severey decimated ALL biotopes above the 40th parallell, eradicating all larger mammals to extinction level and - as the ragnarök of the Younger Dryas dropped the median temperature with 10-15 degrees (Celsius) - 2 out of 3 mamalian species known from Paleolithic Europe simply ceased to exist. Thus the Cave-bears (U. spelaeus) of LUP Bulgaria disappearede by the LGM while the last ones known camped in Bisacany until the extreme cold-dip of the YD.

    From the hand few individuals of peoples and other large mammals - surviving these extremes in climatical refugias from where the continent was RE-populated - we got a compltely new shuffle of the Eurasian genomes within all larger species today thriving in the temperate and sub-arctic climates, north of the Meds, the Arabian Sea and the Indian Ocean. Thus we have several sets of "Founding Fathers" to identify - as the various, patrilinear cultures were able to establish permanent cultures - able to reproduce, multiply and grow s-t-e-a-d-i-l-y and balanced - from the royal pioneers of The First Families into the Extended Families that brought the first cultures into high-cultures able to build Higher Civilizations and thus become specific "aetnicities" (genus), whose social stability and cultural evolution was founded on a histoical identity - as A (kind of) people, born as branches, twigs and limbs of the same "stem", aka the same (ancestral) y-dna. The term "family-three" do have a historical background. In fact there would be no 'civilizations' to study without the family-threes of y-dna ABCDF as well as the post-glacial lines of GHIJK-T. Who all came out of the very same ice-time.

    That may imply that all paleolithic y-dna from Western Eurasia was eradicated - and the present lines a result of a VERY limited circle of y-dna F, each producing the post-glaial and PRESENT variants of GHIJK-T. Without a thorough understanding of the SEVERE bottle-necks of LGM/YD - and the conseuent founder-effects (blaiming macro-dad F) - there will be no logic found able to explain the PRESENT genomes of Eurasia. However shrude, sharp and ingenious your logo-pops may be, they can't meet reality without the help of historical knowledge as well as self-critical thinking and SOUND, rather than politcally correct common sense.



    Quote Originally Posted by Kale View Post
    What was the extent of area effected by the Campanian Eruption by the way?
    https://www.researchgate.net/figure/...fig5_293756222

    Quote Originally Posted by K33 View Post
    You think Oase was just Ust Ishim-like with excess Neanderthal ancestry?

    BTW I have grown interested in phylogenies doing away w/Basal Eurasian primarily after the Buran Kaya sample was found to basically be a regular Gravettian. I had thought he would have more affinity w/WHG. And if WHG wasn't hiding out in Paleolithic SE Europe I have trouble understanding where else they came from.
    If not in the pretty dry and (very) cold climate of (LUP) oriental Europe, their chances to survive and thrive was substatially better in the more humid, milder and greater biodiversity of occidental Europe.


    John Hawks question from 2001 is still not answered properly - but, thanks to guys like you, we're closing in... ;-)
    https://johnhawks.net/weblog/reviews...ic_europe.html
    Last edited by Boreas; 05-05-2021 at 02:44 PM.

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    Upper Palaeolithic layers and Campanian Ignimbrite/Y-5 tephra in Toplitsa cave, Northern Bulgaria


    Toplitsa cave, located in the Eastern Balkans (Northern Bulgaria), was excavated in 2011 with the main goal of investigating deposits encompassing the transition from the Middle to Upper Palaeolithic. (...)

    We present a preliminary assessment of the stratigraphy and report on the identification of large amounts of glass shards belonging to the CI eruption (ca. 39,000 years old (ka BP)) in TP II Layers 2 and 3, below which there is a well preserved hearth. This fire-pit carved in Layer 5 (TP II) and underlying the Y-5 tephra is the most significant find. Two Ursus spelaeus teeth from the underlying Layer 5 have been radiocarbon dated to 49,770–45,750 calibrated years before present (cal BP; 95.4% probability) and to 48,210–45,050 cal BP (95.4% probability). The lithics found in Layer 5 are technologically consistent with the Initial Upper Palaeolithic (IUP) or possibly with other transitional Middle to Upper Palaeolithic assemblages.

    Layer 5 from TP II in Toplitsa overlaps chronologically with other regional records. These include the final Middle Palaeolithic with leaf points from Musselievo (estimated to ca. 50–45 ka cal BP), the transitional Middle to Upper Palaeolithic assemblage from Temnata Cave Layer VI (trench II, which is covered by CI tephra and has been dated to older than 39 ka BP), the earliest laminar Upper Palaeolithic (i.e. IUP) from Temnata Cave Layer 4 (trench I, dating from 47.6 to 40.5 ka cal BP), the IUP from Bacho Kiro Cave Layers J and I (dating to 46.0–43.3 ka cal BP) and Kozarnika cave Layer 6/7 (dated to ca. 49.1–44.0 ka cal BP).
    https://www.sciencedirect.com/scienc...52409X21001243

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    Quote Originally Posted by Max_H View Post
    As always very interesting to see your qpGraphs. This one is particular seems to a large extent to agree with the literature published on these samples, even down to the 25% Tianyuan (in this case IUP) affinity in ANE. However if it's not too much trouble could you include Loschbour (since it had an ENA signal, I suspect Goyet or ANE-related) in your graph? I've seen qpGraphs which show Loschbour contribute to East Asians instead, so it would be interesting to see how that relationship came about.

    Lastly, just for reference, would you have any D stats handy showing Boisman closer to Goyet than ANE?
    outgroup pop1 pop2 pop3 d-value std.err. z-score
    South_Africa_2000BP.SG Onge.DG Yana_UP.SG GoyetQ116_1 -0.00185 0.000588 -3.15
    South_Africa_2000BP.SG Tianyuan Yana_UP.SG GoyetQ116_1 -0.00129 0.0007 -1.84
    South_Africa_2000BP.SG Japan_Jomon Yana_UP.SG GoyetQ116_1 0.00171 0.000635 2.7
    South_Africa_2000BP.SG PrimorskyKrai_Boisman_MN Yana_UP.SG GoyetQ116_1 0.00154 0.000543 2.84
    South_Africa_2000BP.SG Mongolia_N_East Yana_UP.SG GoyetQ116_1 0.00373 0.000575 6.48

    Mbuti.DG Onge.DG Yana_UP.SG GoyetQ116_1 -0.00123 0.000561 -2.19
    Mbuti.DG Tianyuan Yana_UP.SG GoyetQ116_1 -0.000665 0.000673 -0.988
    Mbuti.DG Japan_Jomon Yana_UP.SG GoyetQ116_1 0.00233 0.000599 3.9
    Mbuti.DG PrimorskyKrai_Boisman_MN Yana_UP.SG GoyetQ116_1 0.00216 0.000514 4.21
    Mbuti.DG Mongolia_N_East Yana_UP.SG GoyetQ116_1 0.00435 0.000555 7.84

    Chimp.REF Onge.DG Yana_UP.SG GoyetQ116_1 -0.0012 0.000652 -1.83
    Chimp.REF Tianyuan Yana_UP.SG GoyetQ116_1 -0.00063 0.000754 -0.836
    Chimp.REF Japan_Jomon Yana_UP.SG GoyetQ116_1 0.00237 0.000697 3.4
    Chimp.REF PrimorskyKrai_Boisman_MN Yana_UP.SG GoyetQ116_1 0.0022 0.000611 3.6
    Chimp.REF Mongolia_N_East Yana_UP.SG GoyetQ116_1 0.00439 0.000646 6.79

    Mongolia_N_East are the most severe offender I've found yet, that level of affinity is crazy, these don't even reach significance.
    South_Africa_2000BP.SG GoyetQ116_1 Yana_UP.SG Mongolia_N_East = z -1.88
    Mbuti.DG GoyetQ116_1 Yana_UP.SG Mongolia_N_East = z -1.57

    I need to run these stats on my admixtools1 machine, something seems off here.

    EDIT:
    Yeah ok with admixtools1...
    South_Africa_2000BP.SG Onge.DG Yana_UP.SG GoyetQ116_1 = z -2.1
    South_Africa_2000BP.SG Tianyuan Yana_UP.SG GoyetQ116_1 = z -1.0
    South_Africa_2000BP.SG Japan_Jomon Yana_UP.SG GoyetQ116_1 = z -1.1
    South_Africa_2000BP.SG PrimorskyKrai_Boisman_MN Yana_UP.SG GoyetQ116_1 = z -2.4
    South_Africa_2000BP.SG Mongolia_N_East Yana_UP.SG GoyetQ116_1 = z -2.0

    That makes more sense. I've narrowed down the problem to the function f2_from_precomp.

    Here's a d-stat using 'The prefix of genotype files' for data.
    South_Africa_2000BP.SG GoyetQ116_1 Tianyuan Mongolia_N_East -9.48e-4 6.40e-4 -1.48 0.139 660799
    And using 'A directory which contains pre-computed f2-statistics'
    South_Africa_2000BP.SG GoyetQ116_1 Tianyuan Mongolia_N_East -0.00131 0.000627 -2.10 0.0359

    Basically the same. Also matches results I've gotten using admixtools1 in Linux.

    But using 'f2_from_precomp'
    South_Africa_2000BP.SG GoyetQ116_1 Tianyuan Mongolia_N_East 0.00428 0.000666 6.43 1.28e-10
    Woa what happened here?

    Can anyone else replicate this?
    Last edited by Kale; 05-05-2021 at 08:16 AM.
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    deleted
    Last edited by mauors; 05-05-2021 at 03:35 PM.

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    I did the following test: first I extract precomputed f2 stats for the 4 populations using
    Code:
    extract_f2("../data/v44.3_1240K_public", "../data/admixtools_f2s/test", pops=c("South_Africa_2000BP.SG", "Mongolia_East_N", "Russia_Yana_UP.SG", "Belgium_UP_GoyetQ116_1_published_all", "China_Tianyuan"), maxmem=2000)
    Then I compute the Dstat in the following way
    From genotype:
    Code:
    qpdstat("../data/v44.3_1240K_public", "South_Africa_2000BP.SG", "Belgium_UP_GoyetQ116_1_published_all", "China_Tianyuan", "Mongolia_East_N")
    South_Africa_2000BP.SG Belgium_UP_GoyetQ116_1_published_all China_Tianyuan Mongolia_East_N -0.000695958469743563 0.000721000029152948 -0.965268296259565 0.334410446981141 422439
    From f2 prefix:
    Code:
    qpdstat("../data/admixtools_f2s/test", "South_Africa_2000BP.SG", "Belgium_UP_GoyetQ116_1_published_all", "China_Tianyuan", "Mongolia_East_N")
    South_Africa_2000BP.SG Belgium_UP_GoyetQ116_1_published_all China_Tianyuan Mongolia_East_N -0.000697150324074302 0.000728270311373421 -0.957268631148193 0.338431684094258
    From precomputed:
    Code:
    f2s <- f2_from_precomp("../data/admixtools_f2s/test")
    qpdstat(f2s, "South_Africa_2000BP.SG", "Belgium_UP_GoyetQ116_1_published_all", "China_Tianyuan", "Mongolia_East_N")
    South_Africa_2000BP.SG Belgium_UP_GoyetQ116_1_published_all China_Tianyuan Mongolia_East_N -0.0010869765810988 0.0011223392842114 -0.968491967081547 0.332798728899118
    So it's about the same, ~ -0.96. Could it be the version of the program?

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    Hmmm, try setting maxmiss to 1 or 0.5 in extract_f2, that's what's setting it off for me. Maxmiss unspecified like you ran I get sane results.
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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