Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau

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Abstract

Domestic yak, cattle, and their hybrids are fundamental to herder survival at high altitudes on the Tibetan Plateau. However, little is known about their history. Bos remains are uncommon in this region, and ancient domestic yak have not been securely identified. To identify Bos taxa and investigate their initial management, we conducted zooarchaeological analyses of 193 Bos specimens and sequenced five nuclear genomes from recently excavated assemblages at Bangga. Morphological data indicated that more cattle than yak were present. Ancient mitochondrial DNA and nuclear genome sequences identified taurine cattle and provided evidence for domestic yak and yak-cattle hybridization ~2500 years ago. Reliance on diverse Bos species and their hybrid has increased cattle adaptation and herder resilience to plateau conditions. Ancient cattle and yak at Bangga were closely related to contemporary livestock, indicating early herder legacies and the continuity of cattle and yak husbandry on the Tibetan Plateau.

Abstract

Early

management of domestic yak, taurine cattle and their hybrids on the high Tibetan Plateau dates to ~2500 years ago.

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The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker … (2009)

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk

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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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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.

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Author and article information

Contributors

Ningbo Chen:

ORCID: https://orcid.org/0000-0001-6624-5885

Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: Project administrationRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Zhengwei Zhang:

ORCID: https://orcid.org/0000-0002-8689-8776

Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Jiawen Hou:

ORCID: https://orcid.org/0009-0006-1980-0085

Role: Data curationRole: Formal analysisRole: InvestigationRole: SoftwareRole: ValidationRole: VisualizationRole: Writing - review & editing

Jialei Chen:

ORCID: https://orcid.org/0009-0009-7578-4958

Role: Data curationRole: Formal analysisRole: Validation

Xuan Gao: Role: Formal analysisRole: Investigation

Li Tang:

ORCID: https://orcid.org/0000-0002-1013-1499

Role: ResourcesRole: Writing - review & editing

Shargan Wangdue:

ORCID: https://orcid.org/0000-0002-4215-3959

Role: Investigation

Xiaoming Zhang:

ORCID: https://orcid.org/0000-0003-3139-2361

Role: ConceptualizationRole: InvestigationRole: Methodology

Mikkel-Holger S. Sinding:

ORCID: https://orcid.org/0000-0003-1371-219X

Role: Formal analysisRole: MethodologyRole: Writing - review & editing

Xuexue Liu:

ORCID: https://orcid.org/0000-0002-6871-2640

Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Jianlin Han:

ORCID: https://orcid.org/0000-0002-1527-3963

Role: Writing - review & editing

Hongliang Lü:

ORCID: https://orcid.org/0000-0003-3972-587X

Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Chuzhao Lei:

ORCID: https://orcid.org/0000-0002-7766-9728

Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Fiona Marshall:

ORCID: https://orcid.org/0009-0003-6719-9747

Role: ConceptualizationRole: MethodologyRole: Project administrationRole: SupervisionRole: ValidationRole: Writing - original draftRole: Writing - review & editing

Xinyi Liu:

ORCID: https://orcid.org/0000-0002-4767-4737

Journal

Journal ID (nlm-ta): Sci Adv

Journal ID (iso-abbrev): Sci Adv

Journal ID (publisher-id): sciadv

Journal ID (hwp): advances

Title: Science Advances

Publisher: American Association for the Advancement of Science

ISSN (Electronic): 2375-2548

Publication date Collection: 15 December 2023

Publication date (Electronic, pub): 13 December 2023

Volume: 9

Issue: 50

Electronic Location Identifier: eadi6857

Affiliations

[ ¹ ]Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China.

[ ² ]Center for Archaeological Science, Sichuan University, Chengdu 610065, P. R. China.

[ ³ ]Department of Archaeology, Max Planck Institute of Geoanthropology, Jena 07745, Germany.

[ ⁴ ]Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, Jena 07745, Germany.

[ ⁵ ]Institute for Conservation and Research of Cultural Relics of Tibet Autonomous Region, Lhasa 850000, China.

[ ⁶ ]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming 650201, P. R. China.

[ ⁷ ]Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen DK-1350, Denmark.

[ ⁸ ]National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China.

[ ⁹ ]Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse 31000, France.

[ ¹⁰ ]Yazhouwan National Laboratory, Sanya 572024, P. R. China.

[ ¹¹ ]CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China.

[ ¹² ]Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA.

Author notes

[* ]Corresponding author. Email: luhl@ 123456scu.edu.cn (H.L.); leichuzhao1118@ 123456nwafu.edu.cn (C.L.); fmarshal@ 123456wustl.edu (F.M.); liuxinyi@ 123456wustl.edu (X.L.)

[†]

These authors contributed equally to this work.

Author information

Ningbo Chen https://orcid.org/0000-0001-6624-5885

Zhengwei Zhang https://orcid.org/0000-0002-8689-8776

Jiawen Hou https://orcid.org/0009-0006-1980-0085

Jialei Chen https://orcid.org/0009-0009-7578-4958

Li Tang https://orcid.org/0000-0002-1013-1499

Shargan Wangdue https://orcid.org/0000-0002-4215-3959

Xiaoming Zhang https://orcid.org/0000-0003-3139-2361

Mikkel-Holger S. Sinding https://orcid.org/0000-0003-1371-219X

Xuexue Liu https://orcid.org/0000-0002-6871-2640

Jianlin Han https://orcid.org/0000-0002-1527-3963

Hongliang Lü https://orcid.org/0000-0003-3972-587X

Chuzhao Lei https://orcid.org/0000-0002-7766-9728

Fiona Marshall https://orcid.org/0009-0003-6719-9747

Xinyi Liu https://orcid.org/0000-0002-4767-4737

Article

Publisher ID: adi6857

DOI: 10.1126/sciadv.adi6857

PMC ID: 10848728

PubMed ID: 38091398

SO-VID: 71fcba51-a2f5-49f3-8509-7675cfee9f94

Copyright © Copyright © 2023 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

History

Date received : 16 May 2023

Date accepted : 07 November 2023

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;

Award ID: 32372854

Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;

Award ID: 32102523

Funded by: FundRef http://dx.doi.org/10.13039/501100002808, Carlsbergfondet;

Award ID: CF20-0355

Funded by: National key R&D program of China;

Award ID: 2021YFC1523600

Funded by: National Key Basic Research Programs of China;

Award ID: SQ2021YFF1000041

Funded by: FundRef http://dx.doi.org/10.13039/501100002858, China Postdoctoral Science Foundation;

Award ID: 2021T140564

Funded by: FundRef http://dx.doi.org/10.13039/501100002858, China Postdoctoral Science Foundation;

Award ID: 2020M683587

Funded by: Natural Science Basic Research Program of Shaanxi;

Award ID: 2021JQ-137

Funded by: The Chinese Government’s contribution to the CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources in Beijing;

Award ID: 2023-YWF-ZX-02

Funded by: FundRef http://dx.doi.org/10.13039/501100005236, Chinese Universities Scientific Fund;

Award ID: 2452021153

Funded by: The earmarked fund;

Award ID: CARS-37

Funded by: National Science Foundation of USA;

Award ID: 2017247

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Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau

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Most cited references 88

The Sequence Alignment/Map format and SAMtools

Fast and accurate short read alignment with Burrows–Wheeler transform

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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