Descent, marriage, and residence practices of a 3,800-year-old pastoral community in Central Eurasia

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Significance

To date, knowledge about the biological side of familial organization in prehistoric societies has been limited. In particular, little is known about the structure of Bronze Age society in Eurasia at the village or household levels. Here, the skeletal community of a burial mound in the Southern Urals was studied using integrative methods from the fields of archaeology, anthropology, and palaeogenomics. It is suggested that the descent system of the 3,800-y-old livestock herders at Nepluyevsky was patrilineal and primarily determined by consanguinity between brothers. Monogamy was the marriage norm, and postmarital residence was patrilocal, with female membership being transferred to the husband’s group.

Abstract

Our understanding of prehistoric societal organization at the family level is still limited. Here, we generated genome data from 32 individuals from an approximately 3,800-y-old burial mound attributed to the Bronze Age Srubnaya-Alakul cultural tradition at the site of Nepluyevsky, located in the Southern Ural region of Central Eurasia. We found that life expectancy was generally very low, with adult males living on average 8 y longer than females. A total of 35 first-degree, 40 second-degree, and 48 third-degree biological relationships connected 23 of the studied individuals, allowing us to propose a family tree spanning three generations with six brothers at its center. The oldest of these brothers had eight children with two women and the most children overall, whereas the other relationships were monogamous. Notably, related female children above the age of five were completely absent from the site, and adult females were more genetically diverse than males. These results suggest that biological relationships between male siblings played a structural role in society and that descent group membership was based on patrilineality. Women originated from a larger mating network and moved to join the men, with whom they were buried. Finally, the oldest brother likely held a higher social position, which was expressed in terms of fertility.

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Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2009)

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk

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The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Aaron McKenna, Matthew Hanna, Eric R. Banks … (2010)

Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS--the 1000 Genome pilot alone includes nearly five terabases--make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.

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Author and article information

Contributors

Jens Blöcher:

ORCID: https://orcid.org/0000-0003-0398-1994

Joachim Burger

Journal

Journal ID (nlm-ta): Proc Natl Acad Sci U S A

Journal ID (iso-abbrev): Proc Natl Acad Sci U S A

Journal ID (publisher-id): PNAS

Title: Proceedings of the National Academy of Sciences of the United States of America

Publisher: National Academy of Sciences

ISSN (Print): 0027-8424

ISSN (Electronic): 1091-6490

Publication date (Electronic, pub): 21 August 2023

Publication date (Print, pub): 5 September 2023

Publication date PMC-release: 21 February 2024

Volume: 120

Issue: 36

Electronic Location Identifier: e2303574120

Affiliations

[1] ^aInstitute of Organismic and Molecular Evolution, Palaeogenetics Group , Johannes Gutenberg University, Mainz 55128, Germany

[2] ^bCentre for Palaeogenetics , Stockholm 10691, Sweden

[3] ^cDepartment of Bioinformatics and Genetics, Swedish Museum of Natural History , Stockholm 10405, Sweden

[4] ^dDepartment of Zoology, Stockholm University , Stockholm 10691, Sweden

[5] ^eInstitute of Archaeological Sciences, Johann Wolfgang Goethe University , Frankfurt am Main D-60629, Germany

[6] ^fResearch Institute and Museum of Anthropology, Lomonosov Moscow State University , Moscow 125009, Russia

[7] ^gDepartment of Biology, University of Padova , Padova 35131, Italy

[8] ^hDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology , Leipzig 04103, Germany

[9] ⁱLaboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace , Komotini 69100, Greece

[10] ^jInstitute of History and Archaeology, Ural Branch of the Russian Academy of Science , Ekaterinburg 620108, Russia

Author notes

¹To whom correspondence may be addressed. Email: jbloech@ 123456uni-mainz.de or jburger@ 123456uni-mainz.de .

Edited by Eske Willerslev, University of Cambridge, Cambridge, United Kingdom; received March 3, 2023; accepted July 17, 2023 by Editorial Board Member Richard G. Klein