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Thread: New DNA Papers

  1. #1801
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    A personal, reference quality, fully annotated genome from a Saudi individual
    Maxat Kulmanov, Rund Tawfiq, Hatoon Al Ali, Marwa Abdelhakim, Mohammed Alarawi, Hind Aldakhil, Dana Alhattab, Ebtehal Alsolme, Azza Althagafi, Angel Angelov, Salim Bougouffa, Patrick Driguez, Yang Liu, Changsook Park, Alexander Putra, Ana M Reyes-Ramos, Charlotte A E Hauser, Ming Sin Cheung, Malak S Abedalthagafi, Robert Hoehndorf
    doi: https://doi.org/10.1101/2022.11.05.515129
    This article is a preprint and has not been certified by peer review
    Abstract
    We have used multiple sequencing approaches to sequence the genome of a volunteer from Saudi Arabia. We use the resulting data to generate a de novo assembly of the genome, and use different computational approaches to refine the assembly. As a consequence, we provide a continguous assembly of the complete genome of an individual from Saudi Arabia for all chromosomes except chromosome Y, and label this assembly KSA001. We transferred genome annotations from reference genomes and predicted genome features using methods from Artificial Intelligence to fully annotate KSA001, and we make all primary sequencing data, the assembly, and the genome annotations freely available in public databases using the FAIR data principles.
    YFull: YF14620 (Dante Labs 2018)

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  3. #1802
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    Quote Originally Posted by pmokeefe View Post
    A personal, reference quality, fully annotated genome from a Saudi individual
    Maxat Kulmanov, Rund Tawfiq, Hatoon Al Ali, Marwa Abdelhakim, Mohammed Alarawi, Hind Aldakhil, Dana Alhattab, Ebtehal Alsolme, Azza Althagafi, Angel Angelov, Salim Bougouffa, Patrick Driguez, Yang Liu, Changsook Park, Alexander Putra, Ana M Reyes-Ramos, Charlotte A E Hauser, Ming Sin Cheung, Malak S Abedalthagafi, Robert Hoehndorf
    doi: https://doi.org/10.1101/2022.11.05.515129
    This article is a preprint and has not been certified by peer review
    Abstract
    We have used multiple sequencing approaches to sequence the genome of a volunteer from Saudi Arabia. We use the resulting data to generate a de novo assembly of the genome, and use different computational approaches to refine the assembly. As a consequence, we provide a continguous assembly of the complete genome of an individual from Saudi Arabia for all chromosomes except chromosome Y, and label this assembly KSA001. We transferred genome annotations from reference genomes and predicted genome features using methods from Artificial Intelligence to fully annotate KSA001, and we make all primary sequencing data, the assembly, and the genome annotations freely available in public databases using the FAIR data principles.
    This will be very interesting
    With high coverage Guanche sample 011
    SUCCESS p=.985
    55 Guanche.SG_11
    32 Canaanite_MLBA
    13 COG_MatangaiTuru_IA

    SUCCESS p=.978
    50 Guanche.SG_11
    40 BedouinB.DG
    11 COG_MatangaiTuru_IA

    G25 results

    Target: Me
    Distance: 1.4691% / 0.01469064 | R5P
    52.8 Berber_MAR_TIZ
    21.2 Yemenite_Mahra
    17.8 Greek_Cyclades_Amorgos
    5.4 Yoruba
    2.8 Bulala





    R11109 MALE 1 CE 1749.5 400 CE ARCHAEOLOGY Isola_Sacra Y-DNA: J-Y15222 mtDNA: X2m'n

  4. #1803
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    Haplogroups Reveal Ancient Lineages in the Modern-day Székely Population in Romania

    High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-day Székely Population in Romania
    Noémi Borbély, Orsolya Székely, Bea Szeifert, Dániel Gerber, István Máthé, Elek Benkő, Balázs Gusztáv Mende, Balazs Egyed, Horolma Pamjav, Anna Szécsényi-Nagy
    doi: https://doi.org/10.1101/2022.11.07.515481
    This article is a preprint and has not been certified by peer review

    Abstract
    Here we present 115 whole mitogenomes and 92 Y-chromosomal STR and SNP profiles from a Hungarian ethnic group, the Szekelys (in Romanian: Secuii, in German: Sekler) living in southeast Transylvania (Romania). The Szekelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Szekelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies, since complete mitochondrial DNA sequences and Y-chromosomal data containing 23 STRs have not been available from the region until now. We evaluated the results with population genetic and phylogenetic methods, in the context of the modern and ancient populations that are either geographically or historically related to the Szekelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighbouring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages and, in some cases, they could also be linked to ancient DNA data from Migration Period (5th-9th centuries AD) and Hungarian Conquest Period (10th century AD) populations.
    Last edited by pmokeefe; 11-09-2022 at 06:18 PM.
    YFull: YF14620 (Dante Labs 2018)

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  6. #1804
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    Quote Originally Posted by pmokeefe View Post
    High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-day Székely Population in Romania
    Noémi Borbély, Orsolya Székely, Bea Szeifert, Dániel Gerber, István Máthé, Elek Benkő, Balázs Gusztáv Mende, Balazs Egyed, Horolma Pamjav, Anna Szécsényi-Nagy
    doi: https://doi.org/10.1101/2022.11.07.515481
    This article is a preprint and has not been certified by peer review

    Abstract
    Here we present 115 whole mitogenomes and 92 Y-chromosomal STR and SNP profiles from a Hungarian ethnic group, the Szekelys (in Romanian: Secuii, in German: Sekler) living in southeast Transylvania (Romania). The Szekelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Szekelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies, since complete mitochondrial DNA sequences and Y-chromosomal data containing 23 STRs have not been available from the region until now. We evaluated the results with population genetic and phylogenetic methods, in the context of the modern and ancient populations that are either geographically or historically related to the Szekelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighbouring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages and, in some cases, they could also be linked to ancient DNA data from Migration Period (5th-9th centuries AD) and Hungarian Conquest Period (10th century AD) populations.
    The first link doesn't work, the DOI-link does.
    https://www.biorxiv.org/content/10.1...11.07.515481v1

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  8. #1805
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    Distribution of Y-chromosome haplogroups in Serbian population groups originating from historically and geographically significant distinct parts of the Balkan Peninsula

    Abstract
    Our study enrolled 1200 Serbian males originating from three geographical regions in the Balkan Peninsula inhabited by Serbs: present-day Serbia, regions of Old Herzegovina and Kosovo and Metohija. These samples were genotyped using the combination of 23 Y-chromosomal short tandem repeats (Y-STRs) loci and 17 Ychromosomal single nucleotide polymorphisms (Y-SNPs) loci for the haplotype and haplogroup analysis in order to characterize in detail Y chromosome flow in the recent history. Serbia’s borders have changed through history, forcing Serbs constantly to migrate to different regions of Balkan Peninsula. The most significant migration waves in the recent history towards present-day Serbia occurred from the regions of Old- Herzegovina and Kosovo and Metohija that lie in the south-west/south. High haplotype diversity and discrimination capacity were observed in all three datasets, with the highest number of unique haplotypes (381) and discrimination capacity (0.97) detected in the samples originating from the present-day Serbia. Haplogroup composition didn’t differ significantly among datasets, with three dominant haplogroups (I-M170, E-P170 and R-M198), and haplogroup I-M170 being the most frequent in all three datasets. Haplogroup E-P170 was the second most dominant in the dataset originating from geographical region of Kosovo and Metohija, whereas haplogroup R-M198 was the second most prevalent in the dataset from historical region of Old Herzegovina. Based on the phylogenetic three for haplogroup I constructed within this study, haplogroup I2a1-P37.2 was the most dominant within all three datasets, especially in the dataset from historical region of Old Herzegovina, where 182 out of 400 samples were derived for SNP P37.2. Genetic distances between three groups of samples, evaluated by the Fst and Rst statistical values, and further visualized through multidimensional scaling plot, showed great genetic similarity between datasets from Old Herzegovina and present-day Serbia. Genetic difference in the haplogroup distribution and frequency between datasets from historical region of Old Herzegovina and from geographical region of Kosovo and Metohija was confirmed with highest Fst and Rst vaules. In this study we have distinguished genetic structure, diversity and haplogroup frequencies within 1200 Serbian males from three datasets, relationships among them as well as with other Balkan and European populations, which is useful for studying recent demographic history.

    https://www.sciencedirect.com/scienc...72497322001089

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  10. #1806
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    Abstract
    The Hunyadi family is one of the most influential families in the history of Central Europe in the 14th–16th centuries. The family’s prestige was established by Johannes Hunyadi, a Turk-beater who rose to the position of governor of the Kingdom of Hungary. His second son, Matthias Hunyadi, became the elected ruler of the Kingdom of Hungary in 1458. The Hunyadi family had unknown origin. Moreover, Matthias failed to found a dynasty because of lacking a legitimate heir and his illegitimate son Johannes Corvinus was unable to obtain the crown. His grandson, Christophorus Corvinus, died in childhood, thus the direct male line of the family ended.
    In the framework of on interdisciplinary research, we have determined the whole genome sequences of Johannes Corvinus and Christophorus Corvinus by next-generation sequencing technology. Both of them carried the Y-chromosome haplogroup is E1b1b1a1b1a6a1c ∼, which is widespread in Eurasia. The father-son relationship was verified using the classical STR method and whole genome data. Christophorus Corvinus belongs to the rare, sporadically occurring T2c1+146 mitochondrial haplogroup, most frequent around the Mediterranean, while his father belongs to the T2b mitochondrial haplogroup, widespread in Eurasia, both are consistent with the known origin of the mothers. Archaeogenomic analysis indicated that the Corvinus had an ancient European genome composition.
    Based on the reported genetic data, it will be possible to identify all the other Hunyadi family member, whose only known grave site is known, but who are resting assorted with several other skeletons.



    https://www.cell.com/heliyon/fulltex...440(22)03019-5
    38.4 Mesolithic_North_Africa
    37.4 Anatolia_Barcin_Neolithic
    9.6 Levant_Natufian
    5.8 Caucasian_Neolithic
    4.6 Basal_Central/West_African
    2.2 West-Pontic_Steppe__Eneolithic_Sredny-Stog_Culture
    1.2 Wales_Meso
    0.4 CHN_Mid-Yellow-River_Mid-Neolithic_YangShao_Culture
    0.4 PER_LaGalgada_4100BP

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  12. #1807
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    A global analysis of matches and mismatches between human genetic and linguistic histories
    Chiara Barbieri , Damián E. Blasi, Epifanía Arango-Isaza, and Kentaro K. Shimizu
    PNAS - Vol. 119 | No. 47

    https://www.pnas.org/doi/10.1073/pnas.2122084119

    Significance
    There has been considerable debate about the extent to which our biological and linguistic histories match to each other, supported by examples of both matches and mismatches. We introduce a genomic database (GeLaTo, or Genes and Languages Together) to quantify matches and mismatches worldwide. While in most populations genetic and linguistic relations match, mismatches occur regularly as a result of language shift, and several language families follow diversification patterns different from that of the genomes. These findings reveal features of population contact in human history that were previously inaccessible to observation. Our database opens avenues for disentangling demographic and linguistic history and for comparing biological and linguistic modes of evolution.

    Abstract
    Human history is written in both our genes and our languages. The extent to which our biological and linguistic histories are congruent has been the subject of considerable debate, with clear examples of both matches and mismatches. To disentangle the patterns of demographic and cultural transmission, we need a global systematic assessment of matches and mismatches. Here, we assemble a genomic database (GeLaTo, or Genes and Languages Together) specifically curated to investigate genetic and linguistic diversity worldwide. We find that most populations in GeLaTo that speak languages of the same language family (i.e., that descend from the same ancestor language) are also genetically highly similar. However, we also identify nearly 20% mismatches in populations genetically close to linguistically unrelated groups. These mismatches, which occur within the time depth of known linguistic relatedness up to about 10,000 y, are scattered around the world, suggesting that they are a regular outcome in human history. Most mismatches result from populations shifting to the language of a neighboring population that is genetically different because of independent demographic histories. In line with the regularity of such shifts, we find that only half of the language families in GeLaTo are genetically more cohesive than expected under spatial autocorrelations. Moreover, the genetic and linguistic divergence times of population pairs match only rarely, with Indo-European standing out as the family with most matches in our sample. Together, our database and findings pave the way for systematically disentangling demographic and cultural history and for quantifying processes of shifts in language and social identities on a global scale.
    J1 FGC5987 to FGC6175 (188 new SNPs)
    MDKAs before Colonial Brazil
    Y-DNA - Milhazes, Barcelos, Minho, Portugal.
    mtDNA - Ilha Terceira, Azores, Portugal
    North_Swedish + PT + PT + PT @ 3.96 EUtest 4

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  14. #1808
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    Quote Originally Posted by RCO View Post
    A global analysis of matches and mismatches between human genetic and linguistic histories
    Chiara Barbieri , Damián E. Blasi, Epifanía Arango-Isaza, and Kentaro K. Shimizu
    PNAS - Vol. 119 | No. 47

    https://www.pnas.org/doi/10.1073/pnas.2122084119
    Very interesting to find out Hungarians represent the only example of linguistic enclave in this research, giving more food for thought for historians trying to come up with an explanation why did the language of some West Siberians become so widespread in Eastcentral Europe until modern times.

    "Hungarians are possibly one of the most studied cases of mismatch. They are genetically similar to their Indo-European speaking neighbors but maintain a separate linguistic identity as a member of the Uralic family. The Hungarian population preserved the language brought by the Magyars, who conquered the Carpathian Basin in the ninth century CE, while becoming genetically assimilated to their Indo-European–speaking neighbors through time. In our dataset, they are the only case of a linguistic enclave."
    Modern Ancestry
    1. East Alpine 52%
    2. Pannonian 25.2%
    3. Northeast German 15.8%
    4. Volga-Uralic (Bashkir) 7%
    Ancient Ancestry
    1. Yamnaya 47.2%
    2. Anatolia 39.0%
    3. WHG 11.6%
    4. Han 2.2%

  15. #1809
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    Delete

  16. #1810
    Population History and Genome Wide Association Studies of Birth Weight in a Native High Altitude Ladakhi Population

    Abstract
    Pathological low birth weight due to fetal growth restriction (FGR)is an important predictor of adverse obstetric and neonatal outcomes. It is more common amongst native lowlanders when gestating in the hypoxic environment of high altitude, whilst populations who have resided at high altitude for many generations are relatively protected. Genetic study of pregnant populations at high altitude permits exploration of the role of hypoxic in FGR pathogenesis, and perhaps of FGR pathogenesis more broadly.

    We studied the umbilical cord blood DNA of 316 neonates born to pregnant women managed at the Sonam Norboo Memorial Hospital, Ladakh (altitude 3540m) between February 2017-January 2019. Principal component, admixture and genome wide association studies (GWAS) were applied to dense single nucleotide polymorphism (SNP) genetic data, to explore ancestry and genetic predictors of low birth weight.

    Our findings support Tibetan ancestry in the Ladakhi population, with subsequent admixture with neighboring Indo-Aryan populations. Fetal growth protection was evident in Ladakhi neonates. Although no variants achieved genome wide significance, we observed nominal association of seven variants across genes (ZBTB38, ZFP36L2, HMGA2, CDKAL1, PLCG1) previously associated with birthweight.

    https://www.biorxiv.org/content/10.1....493635v1.full

    Ladakhi samples plot on a PCA between Tibetans and Indo-Aryans. I would guess that they plot between Balti and Tibetans on the G25 PCA.

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