A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

The New World Vulture [ Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [ Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution.

Abstract

14,000 year old DNA reveals the evolutionary dynamics and adaptations of South American vultures.

Related collections

Most cited references 73

Record: found
Abstract: found
Article: found

Is Open Access

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.

0 comments Cited 15544 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

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

0 comments Cited 13663 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

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

0 comments Cited 10189 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Per G. P. Ericson:

ORCID: http://orcid.org/0000-0002-4143-9998

per.ericson@nrm.se

Yanhua Qu:

ORCID: http://orcid.org/0000-0002-4590-7787

quyh@ioz.ac.cn

Journal

Journal ID (nlm-ta): Commun Biol

Journal ID (iso-abbrev): Commun Biol

Title: Communications Biology

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2399-3642

Publication date (Electronic): 23 August 2022

Publication date PMC-release: 23 August 2022

Publication date Collection: 2022

Volume: 5

Electronic Location Identifier: 857

Affiliations

[1 ]GRID grid.425591.e, ISNI 0000 0004 0605 2864, Department of Bioinformatics and Genetics, , Swedish Museum of Natural History, ; P.O. Box 50007, SE-10405 Stockholm, Sweden

[2 ]GRID grid.410350.3, ISNI 0000 0001 2174 9334, Institut de Systématique, Evolution, Biodiversité (ISYEB), , UMR7205 CNRS MNHN UPMC EPHE Sorbonne Université, Muséum National d’Histoire Naturelle, ; 75005 Paris, France

[3 ]GRID grid.510921.e, Centre for Palaeogenetics, ; Stockholm, Sweden

[4 ]GRID grid.412367.5, ISNI 0000 0001 0123 6208, Department of Laboratory Medicine, , Örebro University Hospital; Södra Grev Rosengatan, ; SE-70185 Örebro, Sweden

[5 ]GRID grid.217197.b, ISNI 0000 0000 9813 0452, Department of Biology and Marine Biology, , University of North Carolina; Wilmington, ; 601S. College Road, Wilmington, NC 28403 USA

[6 ]GRID grid.10548.38, ISNI 0000 0004 1936 9377, Department of Archaeology and Classical Studies, , Stockholm University, ; SE-10691 Stockholm, Sweden

[7 ]GRID grid.35937.3b, ISNI 0000 0001 2270 9879, Bird Group, Department of Life Sciences, , Natural History Museum, ; Akeman St, Tring, Herts UK

[8 ]GRID grid.425591.e, ISNI 0000 0004 0605 2864, Department of Palaeobiology, , Swedish Museum of Natural History, ; P.O. Box 50007, SE-10405 Stockholm, Sweden

[9 ]GRID grid.9227.e, ISNI 0000000119573309, Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, , Chinese Academy of Sciences, ; Beijing, 100101 China

Author information

Per G. P. Ericson http://orcid.org/0000-0002-4143-9998

Yanhua Qu http://orcid.org/0000-0002-4590-7787

Article

Publisher ID: 3811

DOI: 10.1038/s42003-022-03811-0

PMC ID: 9399080

PubMed ID: 35999361

SO-VID: c2b333af-6ac2-4f96-b5a0-5c381e52287f

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 20 May 2022

Date accepted : 5 August 2022

Funding

Funded by: FundRef https://doi.org/10.13039/501100004359, Vetenskapsrådet (Swedish Research Council);

Award ID: 621-2017-3693

Award Recipient : Per G. P. Ericson

Custom metadata

Keywords: palaeontology,population genetics

Data availability:

Keywords: palaeontology, population genetics

Comments

Comment on this article

scite_

Most referenced authors 1,779

See all reference authors

A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture

Read this article at

Abstract

Abstract

Related collections

Glossa: a journal of general linguistics

Most cited references 73

Trimmomatic: a flexible trimmer for Illumina sequence data

The Sequence Alignment/Map format and SAMtools

Fast and accurate short read alignment with Burrows–Wheeler transform

Author and article information

Contributors

Journal

Affiliations

Author information

Article

History

Funding

Categories

Custom metadata

Comments

Comment on this article

Similar content 164

Most referenced authors 1,779