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Thread: Genetic Genealogy & Ancient DNA in the News (DISCUSSION ONLY)

  1. #3261
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    How about that bizarro Romania_EBA sample from the ossicles paper? F3 outgroup nmonte...

    First half kind of what you'd expect...

    Steppe: 31.65%
    "Afanasievo_Mongolia_I6221" 20.65
    "Ukraine_Dereivka_CA" 10.9
    "Afanasievo_EloBashi" 0.05
    "Afanasievo_KarasukIII" 0.05

    Euro-Farmer: 15.50%
    "Hungary_LCA_Baden" 12.55
    "Ukraine_Ilatka_GAC" 1.05
    "Bulgaria_Varna_CA" 0.95
    "Hungary_CA" 0.8
    "Hungary_MN" 0.1
    "Czech_MN_Baalberge" 0.05

    Then the other half...
    "Kazakhstan_Kumsay_EBA" 42.4
    "Tajikistan_Sarazm_CA" 9.55

    Noise...
    "Cameroon_ShumLaka_900BP" 0.8
    "Cameroon_ShumLaka_3100BP.SG" 0.05
    "Mota.SG" 0.05

    Columns:,Anatolia_Barcin_N,Levant_N,Iran_GanjDareh _N,CHG.SG,Taforalt,Vanuatu_ancient,Taiwan_Hanben_I A,PrimorskyKrai_Boisman_MN,Peru_Laramate_900BP,Kar elia_HG,IronGates_Meso1,Yamnaya_Samara,Ust_Ishim.D G
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    Not DNA, so I am posting it here:

    https://www.nature.com/articles/s41586-020-2153-8

    Article Published: 01 April 2020

    The dental proteome of Homo antecessor


    Frido Welker, Jazmín Ramos-Madrigal, Petra Gutenbrunner, Meaghan Mackie, Shivani Tiwary, Rosa Rakownikow Jersie-Christensen, Cristina Chiva, Marc R. Dickinson, Martin Kuhlwilm, Marc de Manuel, Pere Gelabert, María Martinón-Torres, Ann Margvelashvili, Juan Luis Arsuaga, Eudald Carbonell, Tomas Marques-Bonet, Kirsty Penkman, Eduard Sabidó, Jürgen Cox, Jesper V. Olsen, David Lordkipanidze, Fernando Racimo, Carles Lalueza-Fox, José María Bermúdez de Castro, Eske Willerslev & Enrico Cappellini

    Nature (2020)
    Abstract

    The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1,2,3,4,5. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge6,7,8. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)9,10 and Homo erectus from Dmanisi (Georgia)1, two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor—that is, similar to that of modern humans—may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.

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    Quote Originally Posted by rozenfeld View Post
    Not DNA, so I am posting it here:

    https://www.nature.com/articles/s41586-020-2153-8

    Article Published: 01 April 2020

    The dental proteome of Homo antecessor


    Frido Welker, Jazmín Ramos-Madrigal, Petra Gutenbrunner, Meaghan Mackie, Shivani Tiwary, Rosa Rakownikow Jersie-Christensen, Cristina Chiva, Marc R. Dickinson, Martin Kuhlwilm, Marc de Manuel, Pere Gelabert, María Martinón-Torres, Ann Margvelashvili, Juan Luis Arsuaga, Eudald Carbonell, Tomas Marques-Bonet, Kirsty Penkman, Eduard Sabidó, Jürgen Cox, Jesper V. Olsen, David Lordkipanidze, Fernando Racimo, Carles Lalueza-Fox, José María Bermúdez de Castro, Eske Willerslev & Enrico Cappellini

    Nature (2020)
    Abstract

    The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1,2,3,4,5. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge6,7,8. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)9,10 and Homo erectus from Dmanisi (Georgia)1, two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor—that is, similar to that of modern humans—may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.
    This is very interesting! It indicates that hominids colonized Eurasia several times in the last 2 million years.

    After reading the abstract and having access to supplementary materials, it's not yet clear to me what is the relationship between H. antecessor and H. erectus: is the former directly descended from the latter? Do they represent two independent migrations? In this case, is H. antecessor closer to Neanderthals/Denisovans/modern humans than H. erectus?

    What are the implications of these findings? Is it possible that the ancestors of Neanderthals/Denisovans/modern humans lived in Asia rather than in Africa? Of course we'd need aDNA from archaic African hominids to clarify this...

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  7. #3264
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    Cherifi & Amrani (preprint), "Evaluation of DNA conservation in Nile-Saharan environment, Missiminia, in Nubia: Tracking maternal lineage of 'X-Group'"


    Just an old-school HVS-1 mtDNA pilot study, but hopefully a sign of better things to come. Samples collected by archaeologists in the 1970s from a necropolis near Abri, in the Nile valley of northern Sudan. They successfully typed 11 samples (of 15 attempted): 8 from the X-Group period (~AD 350-500), 2 from the earlier Meroitic period, and 1 from the following Christian period. The results were: the two Meroitic both listed as H2 (but really that just means matching the reference sequence in HVS-1); the X-Group L1b, L2, L3b, L3e, N*, T1a, and 2 cases of X; and the Christian sample W1. I wouldn't count on HVS-1 assignments being reliable at all, though. The L1b and T1a look okay at least.

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  9. #3265
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    https://www.genetics.org/content/ear...ics.120.303167
    A locus-specific analysis of one such shared deletion suggests the existence of a direct introgression event from the Altai Neanderthal lineage into the ancestors of extant East Asian populations.
    I wonder if this implies a Northern route to East Asia for the ancestors of modern East-Asians? Too bad they didn't test say Papuans or Australians for this as well.
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  11. #3266
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    Quote Originally Posted by Milkyway View Post
    Modern alleles in archaic human Y chromosomes support origin of modern human paternal lineages in Asia rather than Africa

    Hongyao Chen, Shi Huang

    Recent studies have shown that hybridization between modern and archaic humans was commonplace in the history of our species. After admixture, some individuals with admixed autosomes carried the modern Homo Sapiens uniparental DNAs, while the rest carried the archaic versions. Coevolution of admixed autosomes and uniparental DNAs is expected to cause some of the sites in modern uniparental DNAs to revert back to archaic alleles, while the opposite process would occur (from archaic to modern) in some of the sites in archaic uniparental DNAs. This type of coevolution is one of the elements that differentiate the two different models of the Y phylogenetic tree of modern humans, rooting it either in Africa or East Asia. The expected reversion to archaic alleles is assumed to occur and is easily traceable in the Asia model, but is absent in the Africa model due to its infinite site assumption, which also precludes the independent or convergent mutation to modern alleles in archaic uniparental DNAs since mutations are assumed to occur randomly across a neutral genome, and convergent evolution is assumed not to occur. Here, we examined newly published high coverage Y chromosome sequencing data of two Denisovan and two Neanderthal samples to determine whether they carry modern-Homo Sapiens alleles in sites where they are not supposed to according to the Africa model. The results showed that a significant fraction of the sites that, according to the Asia model, should differentiate the original modern Y from the original archaic Y carried modern alleles in the archaic Y samples here. Some of these modern alleles were shared among all archaic humans while others could differentiate Denisovans from Neanderthals. The observation is best accounted for by coevolution of archaic Y and admixed modern autosomes, and hence supports the Asia model, since it takes such coevolution into account.
    "The rooting of mtDNA tree in Asia independently confirms an earlier paper
    (Johnson et al., 1983), and has been verified by ancient findings regarding mitochondrial DNA that shows
    the earlier appearance of haplogroup R compared to N, which challenges rooting the human mtDNA tree
    in Africa"

    True but once we have genomes from the 55kybp time-frame that should change, those would likely be N. Plus Oase1 is not much younger that Ust Ishim.

    "As modern humans migrated to new places and admixed with local archaic humans, coevolution alongside admixed
    autosomes may have caused certain sites in modern uniparental DNAs to mutate back to archaic alleles,
    or certain sites in archaic uniparental DNAs to mutate into modern alleles
    "

    Looks implausible.

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    On Eurogenesblog Arza provided links for samples' data from the Swiss plateau regarding the transition from Late Neolithic to Bronze Age. Probably, someone can squeeze something from those files.

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    Quote Originally Posted by Hodo Scariti View Post
    On Eurogenesblog Arza provided links for samples' data from the Swiss plateau regarding the transition from Late Neolithic to Bronze Age. Probably, someone can squeeze something from those files.

    The paper said this :


    Genetic transition in the Swiss Late Neolithic and Early Bronze Age

    Furtwaengler et al.

    Recent studies have shown that the beginning of the Neolithic period as well as final stages of the Neolithic were marked by major genetic turnovers in European populations.The transition from hunter-gatherers to agriculturalists and farmers/farming in the 6 th millennium BP coincided with a human migration from the Near East. In the 3 rd millennium BP a second migration into Central Europe occurred originating from the Pontic steppe linked to the spread of the Corded Ware Complex ranging as far southwest as modern day Switzerland. These genetic processes are well studied for example for the Middle-Elbe-Saale region in Eastern Germany, however, little is known from the regions that connect Central and Southern Europe. Here, we investigate genomic data from 69 individuals from the Swiss Plateau and Southern Germany that span the transition of the Neolithic to the Bronze Age (5500 to 4000 BP). Our results show a similar genetic process as reported for the Middle-Elbe-Saale region suggesting that the migration from the Pontic steppe reached all the way into the Swiss plateau. The high quality of the ancient genomic data also allowed an analysis of core families within multiple burials, the determination and qualification of different ancestry components and the determination of the migration route taken by the ancestors of the Late Neolithic populations in this region. This study presents the first comprehensive genome wide dataset from Holocene individuals from the Swiss plateau and provides the first glimpse into the genetic history of this genetically and linguistically diverse region.











    Arza provided other informations about Swiss plateau findings.

    MX211 G2a2a1a2a1 G-S11565/etc*(xL166,PF3143^)

    MX275_rmdup R1b1a1b1a1a2 R-P312*(xS450,DF17,M167,L165,L617,L881,A431,S359,S45 3,L356,BY247,Z2248,Y18211)

    MX257_rmdup R1b1a1b1a1a R-PF6543/etc*(xFGC14885,A1243,L729.2,S265,S24013,JFS0001,L4 8,S500,FGC427,S12025,A2148,S26140,L326,A8045)

    Aesch21_rmdup G2a G-CTS6753/etc*(xFGC666,Z6278,Z3238)

    MX258_rmdup R1b1a1b1a1a2 R-P312*(xS450,DF17,Z205,L165,L881,DF81,Z29990,S7402, Z37,FGC5513,A93,BY2589,DF99)

    SNPRA58 G2a2a1a2a G-PF3238*(xZ6215^,PF3242^,BY21539,Y140842,FGC2310)

    MX283_rmdup R1b1a1b1a1a2 R-P312*(xS450,DF17,Z262,L165,L617,L881,A431,S359,CTS 6519.1,L409,CTS7958,Z143,L100,PF6584,F1493.2,L1358 ,BY247,L238,DF99,Y18210)

    SX29_rmdup I2a1a2~ I-Z2575*(xAMM068,A812,Y13569,S20061)

    SX11_rmdup G2a2 G-CTS4367*(xPF3184,Z3238)

    MX191 I2a1a2~ I-AM01260/etc*(xAMM058,S12452)

    Aesch14_rmdup G2a2a1a2a1 G-Z6130^*(xFGC5672^,PF3143^)

    MX279_rmdup R1b1a1b1a1a2 R-P312*(xS450,M167,L165,A431,F1343,S453,L408,CTS1595 ,S259,L1358,L21,L238)

    SNPRA64 R1b1a1b1a1a2 R-P312*(xS227,L881,A431,F1343,S453,L356,FGC5512,BY25 88,Z2248,DF19)

    MX254_2_rmdup R1b1a1b1a1a2 R-P312*(xZ272,M167,L165,L617,L881,A431,F1343,DF81,L3 56,L192.1,Z2245,DF99,Y18211)

    SNPRA61 G2a2a1a2a1 G-Z6130^/etc*(xZ6134^,Y18934^,Z6241)

    MX288_rmdup R1b1a1b1a1a2 R-P312*(xS227,L617,L881,A431,S359,CTS11567,L356,Z260 ,Z2245,L1199,DF99,Y18210)

    Aesch23_rmdup G2a2a1a2a1 G-FGC2271/etc*(xFGC5696^,PF3242^)

    SNPRA63 R1b1a1b1a1a2 R-P312*(xZ212,S457,L165,L617,L881,S359,CTS11567,L739 ,L196,FGC12403,L552,FGC22513,Z37,PF6578,F1493.2,L1 358,S245,DF99)

    Aesch25_rmdup R1b1a1b1a1a R-L151*(xM405,P312,FGC37115)

    MX188 I2a1a2~ I-AM01271/etc*(xAMM078,F3145)

    MX182 G2a2a1a2a1 G-Z6130^*(xZ6215^,Y18934^)

    MX192 I2a1a2~ I-AM01260/etc*(xAMM053,S13737)

    MX212 G2a2a1a2a1 G-FGC2271/etc*(xZ6287,Z6226^)

    MX210 G2a2a1a2a1 G-PF3240/etc*(xL167,PF3143^)

    SX20_rmdup R1b1a1b1a1a2 R-P312*(xS1217,M167,L165,L617,L881,A431,F1343,CTS115 67,S255,L196,S1468,S7402,FGC22963,FGC31485,FGC2251 3,CTS4333,Z143,L4,PF6578,F1493.2,L21,Y18213)

    Aesch19_rmdup G2a2a1a2a1 G-Z6130^/etc*(xL166,PF3143^)

    MX150 G2a2a1a2 G-L91*(xZ6207,PF3143^,Z6772,FGC2376,ZS3311.2)

    Aesch1_rmdup G2a2a1a2a1 G-PF3239/etc*(xL166,PF3143^)

    MX219 G2a2a G-PF3181*(xBY47532,Z31437,Z34559)

    MX209 G2a2a1a2a1 G-Z6130^*(xZ6206^,BY180368^,Z6243)

    MX252_rmdup R1b1a1b1a1a2 R-P312*(xDF27,L408,CTS188,Z37,PF6584,S259,F1493.2,L1 358,S461,DF99)

    Aesch22_rmdup G2a2a1a2a1 G-S11565*(xL167,PF3242^)
    Last edited by etrusco; 04-09-2020 at 08:17 AM.

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    Quote Originally Posted by Milkyway View Post
    Modern alleles in archaic human Y chromosomes support origin of modern human paternal lineages in Asia rather than Africa

    Hongyao Chen, Shi Huang

    Recent studies have shown that hybridization between modern and archaic humans was commonplace in the history of our species. After admixture, some individuals with admixed autosomes carried the modern Homo Sapiens uniparental DNAs, while the rest carried the archaic versions. Coevolution of admixed autosomes and uniparental DNAs is expected to cause some of the sites in modern uniparental DNAs to revert back to archaic alleles, while the opposite process would occur (from archaic to modern) in some of the sites in archaic uniparental DNAs. This type of coevolution is one of the elements that differentiate the two different models of the Y phylogenetic tree of modern humans, rooting it either in Africa or East Asia. The expected reversion to archaic alleles is assumed to occur and is easily traceable in the Asia model, but is absent in the Africa model due to its infinite site assumption, which also precludes the independent or convergent mutation to modern alleles in archaic uniparental DNAs since mutations are assumed to occur randomly across a neutral genome, and convergent evolution is assumed not to occur. Here, we examined newly published high coverage Y chromosome sequencing data of two Denisovan and two Neanderthal samples to determine whether they carry modern-Homo Sapiens alleles in sites where they are not supposed to according to the Africa model. The results showed that a significant fraction of the sites that, according to the Asia model, should differentiate the original modern Y from the original archaic Y carried modern alleles in the archaic Y samples here. Some of these modern alleles were shared among all archaic humans while others could differentiate Denisovans from Neanderthals. The observation is best accounted for by coevolution of archaic Y and admixed modern autosomes, and hence supports the Asia model, since it takes such coevolution into account.
    Sigh A bit late April Fools' Day...

    China's output in many fields is already first-grade, at par with Europe and the US or better, but for that to extend to human evolution, they need to empower more people like Qiaomei Fu and fewer nationalistic troll-researchers like these two jokers here.

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