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Thread: Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes

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    Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes

    Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes
    Reyhan Yaka, et al.
    Highlights
    •Genetic kinship estimated from co-buried individuals’ genomes in Neolithic Anatolia
    •Close relatives are common among co-burials in Aşıklı and Boncuklu
    •Many unrelated infants found buried in the same building in Çatalhöyük and Barcın
    •Neolithic societies in Southwest Asia may have held diverse concepts of kinship

    Summary
    The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,1 mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,2 household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük, and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.
    YFull: YF14620 (Dante Labs 2018)

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    Link to table with newly sequenced haplogroups.
    Five Y Haplogroups:
    G2a2b, G2a2a1, H3a1, C1a2(X2)

    Table Z2 (mentioned below), is a spreadsheet file which can be downloaded here.

    Mitochondrial DNA and Y chromosome analyses
    Mitochondrial DNA
    We obtained mitochondrial genomes with mean coverages between 0.4- and 258-fold per individual (Table Z1). In order to assess the mitochondrial haplogroups, we called consensus mitochondrial sequences of each individual using samtools (version 1.9) mpileup and variant caller tools143 with parameters set for aDNA; namely, filtering for sites that have a minimum depth of 3 and a base and mapping quality score of at least 30.147 We assigned mtDNA haplogroups of each individual based on SNPs at informative nucleotide positions of the mitochondrial genome using HaploGrep2v2.1.1 (https://haplogrep.i-med.ac.at/).148
    The results are presented in Table Z2 and Figure S1E. We observed haplogroup K1a4, one of the common haplogroups in Neolithic farmer populations,149 in three individuals from Aşıklı (128, 129, 133). Two Aşıklı individuals (131, 136) belonged to T2c1a and the remaining three individuals from Aşıklı (2, 33, 40) belonged to haplogroups H2a2a, U3a and N1a1a1, respectively. We also found haplogroup K1a4 in one Çatalhöyük individual (30006) and a subtype of haplogroup K1 (K1a) in three individuals (2728, 2842, 1885). Three Çatalhöyük individuals (21981, 11739, 20217) belonged to three subtypes of K1 (K1a17, K1b1, K1a4b), respectively. Three individuals from Çatalhöyük (8587, 2017, 5747) belonged to subtypes of T2 (T2e, T2, T2c1) and one (5357) belonged to N1a1a1, one of the most abundant haplogroup in Near Eastern and European farmer populations.149,150 The remaining Çatalhöyük individuals (2033, 2779, 21855) belonged to subtypes of H2a2a (H2a2a1d, H2a2a, H2a2a1), respectively.
    Y chromosome
    We used the yHaplo program (version 1.0.19)151 to assign Y chromosome haplogroups of one Aşıklı and four Çatalhöyük male individuals. We genotyped each male individual based on 13,508 ISOGG (International Society of Genetic Genealogy, http://isogg.org, version 11.04) consortium SNPs, excluding strand-ambiguous SNPs (C/G and A/T) and by randomly choosing one allele for each of 13,508 ISOGG SNPs. We called all single base substitutions using BAM files mapped to hs37d5 and samtools mpileup (version 1.9)143 (filtering the sites with a mapping quality and a base quality of lower than 30. We also excluded insertions/deletions and sites that displayed multiple alleles.
    We observed haplogroup G2a2b in Aşıklı33 male individual. Two individuals from Çatalhöyük (5357 and 2779) were assigned to haplogroup C1a2 and the remaining two Çatalhöyük individuals (1885 and 2033) belonged to haplogroups, G2a2a1 and H3a1, respectively (Table Z2).
    Last edited by pmokeefe; 04-14-2021 at 06:55 PM.
    YFull: YF14620 (Dante Labs 2018)

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    "Ancient genome data produced for this study is deposited at the European Nucleotide Archive (ENA) under the accession number PRJEB39316 as BAM files." --- from the paper

    Project: PRJEB39316
    We present genetic kinship networks of individuals co-buried within domestic structures in Neolithic Anatolia, produced using ancient genomes. In the 9th and early 8th millennia BCE, in phases of Aşıklı and Boncuklu Höyük characterised by small curvilinear buildings, siblings and parent-offspring predominate co-burials, evidencing a nuclear family element in kin relationships. In Çatalhöyük and Barcın of the 7th millennium BCE, characterised by larger rectangular buildings, we find a lower frequency of genetic kin among co-burials, suggesting that the buildings were used by non-genetic kin groups. Furthermore, the frequent co-burials of first-degree related females in Neolithic Anatolia appear distinct from patriarchal burial patterns described for post-7th millennium BCE Europe, highlighting the shifting nature of kinship through the Neolithic.
    Secondary Study Accession:ERP122819
    Study Title:Variable Kinship Patterns in Neolithic Anatolia Revealed by Ancient Genomes
    Center Name:Middle East Technical University
    Study Name:Kinship in Neolithic Anatolia
    YFull: YF14620 (Dante Labs 2018)

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    Fastqs and BAMs are already available at ENA ftp. Links can be found using NCBI.

    https://www.ncbi.nlm.nih.gov/sra/?term=PRJEB39316
    Last edited by teepean47; 04-14-2021 at 05:55 PM.

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    No surprise there, to say the least:

    Aceramic Neolithic-period populations had lower within-group genetic diversity (measured using the f3-statistic) than did Ceramic Neolithic groups (Figures 1D and S2C, and Tables Z8 and Z9) and carried a higher fraction of short runs of homozygosity (ROH) than most Ceramic Neolithic genomes (Figure S3G). This temporal increase in diversity, also noted in earlier studies,20 could be explained by two non-exclusive scenarios, namely population growth and genetic admixture. By testing D(Outgroup, X; Aceramic Anatolian, Ceramic Anatolian), where X represents an early Holocene Zagros or Levantine population, we found results compatible with southern and eastern gene flow into Central and West Anatolia between roughly 7,500 and 6,500 cal BCE (Figure 1E and Table Z4) as previously suggested.21,26 Using qpAdm, we could also model Ceramic Neolithic Anatolian populations as mixtures of c.90% Aceramic Neolithic Anatolian ancestry (estimate ± 1 standard error: 89%–92% ± 2%–4%) and c.10% Levantine ancestry (8%–11% ± 2%–4%) (models that included Zagros or Caucasus populations were not supported) (Table Z10). Notably, the timing of increased population mobility is contemporaneous with a stronger reliance on agriculture and animal husbandry as food sources, a shift to larger buildings, likely population growth, and possible shifts in patterns of social organization, as we describe below.
    Last edited by Lupriac; 04-14-2021 at 06:14 PM.

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    Quote Originally Posted by pmokeefe View Post
    Link to table with newly sequenced haplogroups.
    Five Y Haplogroups:
    G2a2b, G2a2a1, H3a1, C1a2(X2)

    Table Z2 (mentioned below, is a spreadsheet file which can be downloaded here.

    Mitochondrial DNA and Y chromosome analyses
    Mitochondrial DNA
    We obtained mitochondrial genomes with mean coverages between 0.4- and 258-fold per individual (Table Z1). In order to assess the mitochondrial haplogroups, we called consensus mitochondrial sequences of each individual using samtools (version 1.9) mpileup and variant caller tools143 with parameters set for aDNA; namely, filtering for sites that have a minimum depth of 3 and a base and mapping quality score of at least 30.147 We assigned mtDNA haplogroups of each individual based on SNPs at informative nucleotide positions of the mitochondrial genome using HaploGrep2v2.1.1 (https://haplogrep.i-med.ac.at/).148
    The results are presented in Table Z2 and Figure S1E. We observed haplogroup K1a4, one of the common haplogroups in Neolithic farmer populations,149 in three individuals from Aşıklı (128, 129, 133). Two Aşıklı individuals (131, 136) belonged to T2c1a and the remaining three individuals from Aşıklı (2, 33, 40) belonged to haplogroups H2a2a, U3a and N1a1a1, respectively. We also found haplogroup K1a4 in one Çatalhöyük individual (30006) and a subtype of haplogroup K1 (K1a) in three individuals (2728, 2842, 1885). Three Çatalhöyük individuals (21981, 11739, 20217) belonged to three subtypes of K1 (K1a17, K1b1, K1a4b), respectively. Three individuals from Çatalhöyük (8587, 2017, 5747) belonged to subtypes of T2 (T2e, T2, T2c1) and one (5357) belonged to N1a1a1, one of the most abundant haplogroup in Near Eastern and European farmer populations.149,150 The remaining Çatalhöyük individuals (2033, 2779, 21855) belonged to subtypes of H2a2a (H2a2a1d, H2a2a, H2a2a1), respectively.
    Y chromosome
    We used the yHaplo program (version 1.0.19)151 to assign Y chromosome haplogroups of one Aşıklı and four Çatalhöyük male individuals. We genotyped each male individual based on 13,508 ISOGG (International Society of Genetic Genealogy, http://isogg.org, version 11.04) consortium SNPs, excluding strand-ambiguous SNPs (C/G and A/T) and by randomly choosing one allele for each of 13,508 ISOGG SNPs. We called all single base substitutions using BAM files mapped to hs37d5 and samtools mpileup (version 1.9)143 (filtering the sites with a mapping quality and a base quality of lower than 30. We also excluded insertions/deletions and sites that displayed multiple alleles.
    We observed haplogroup G2a2b in Aşıklı33 male individual. Two individuals from Çatalhöyük (5357 and 2779) were assigned to haplogroup C1a2 and the remaining two Çatalhöyük individuals (1885 and 2033) belonged to haplogroups, G2a2a1 and H3a1, respectively (Table Z2).
    Interesting!
    https://www.yfull.com/tree/H-Z5864/

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    Quote Originally Posted by parasar View Post
    I think it's a H2 wrongly assigned H3a1.

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    Quote Originally Posted by thejkhan View Post
    I think it's a H2 wrongly assigned H3a1.
    Perhaps someone can check the BAM ERS4811100 https://www.ncbi.nlm.nih.gov/sra/ERX4279393[accn]
    "We used the yHaplo program (version 1.0.19)151 to assign Y chromosome haplogroups of one Aşıklı and four Çatalhöyük male individuals. We genotyped each male individual based on 13,508 ISOGG (International Society of Genetic Genealogy, http://isogg.org, version 11.04) consortium SNPs, excluding strand-ambiguous SNPs (C/G and A/T) and by randomly choosing one allele for each of 13,508 ISOGG SNPs. We called all single base substitutions using BAM files mapped to hs37d5 and samtools mpileup (version 1.9)143 (filtering the sites with a mapping quality and a base quality of lower than 30. We also excluded insertions/deletions and sites that displayed multiple alleles."

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