Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

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Abstract

Early natural historians—Comte de Buffon, von Humboldt, and De Candolle—established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.

Abstract

Water availability dictates patterns of global phylogenetic beta diversity in tropical plants.

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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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Basic local alignment search tool.

Stephen F Altschul, Warren Gish, Webb Miller … (1990)

A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.

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Author and article information

Contributors

Jens J. Ringelberg:

ORCID: https://orcid.org/0000-0003-0567-5210

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

Erik J. M. Koenen:

ORCID: https://orcid.org/0000-0002-4825-4339

Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Benjamin Sauter: Role: Investigation

Anahita Aebli:

ORCID: https://orcid.org/0000-0002-5736-2219

Role: Investigation

Juliana G. Rando:

ORCID: https://orcid.org/0000-0002-3714-8231

Role: Data curationRole: Investigation

João R. Iganci:

ORCID: https://orcid.org/0000-0002-5740-3666

Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: InvestigationRole: ResourcesRole: Writing - review & editing

Luciano P. de Queiroz:

ORCID: https://orcid.org/0000-0001-7436-0939

Role: ResourcesRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Daniel J. Murphy:

ORCID: https://orcid.org/0000-0002-8358-363X

Role: Data curationRole: ResourcesRole: Writing - review & editing

Myriam Gaudeul: Role: ResourcesRole: Writing - review & editing

Anne Bruneau:

ORCID: https://orcid.org/0000-0001-5547-0796

Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: ResourcesRole: ValidationRole: Writing - review & editing

Melissa Luckow: Role: InvestigationRole: Writing - review & editing

Gwilym P. Lewis:

ORCID: https://orcid.org/0000-0003-2599-4577

Role: Resources

Joseph T. Miller:

ORCID: https://orcid.org/0000-0002-5788-9010

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

Marcelo F. Simon:

ORCID: https://orcid.org/0000-0002-5732-1716

Role: Funding acquisitionRole: InvestigationRole: ResourcesRole: Writing - review & editing

Lucas S. B. Jordão:

ORCID: https://orcid.org/0000-0002-9501-0548

Role: Resources

Matías Morales:

ORCID: https://orcid.org/0000-0001-5540-9725

Role: Data curationRole: Funding acquisitionRole: InvestigationRole: ResourcesRole: ValidationRole: Writing - review & editing

C. Donovan Bailey:

ORCID: https://orcid.org/0000-0002-3123-4083

Role: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: SupervisionRole: Validation

Madhugiri Nageswara-Rao: Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - review & editing

James A. Nicholls:

ORCID: https://orcid.org/0000-0002-9325-563X

Role: Data curationRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: Writing - original draft

Oriane Loiseau:

ORCID: https://orcid.org/0000-0002-9852-857X

Role: Formal analysis

R. Toby Pennington:

ORCID: https://orcid.org/0000-0002-8196-288X

Role: ConceptualizationRole: Data curationRole: MethodologyRole: ResourcesRole: ValidationRole: Writing - review & editing

Kyle G. Dexter:

ORCID: https://orcid.org/0000-0001-9232-5221

Role: ConceptualizationRole: MethodologyRole: Writing - review & editing

Niklaus E. Zimmermann:

ORCID: https://orcid.org/0000-0003-3099-9604

Role: ConceptualizationRole: Data curationRole: MethodologyRole: SupervisionRole: Writing - review & editing

Colin E. Hughes:

ORCID: https://orcid.org/0000-0002-9701-0699

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

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: February 2023

Publication date (Electronic, pub): 17 February 2023

Volume: 9

Issue: 7

Electronic Location Identifier: eade4954

Affiliations

[ ¹ ]Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland.

[ ² ]Programa de Pós Graduação em Ciências Ambientais, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Rua Prof. José Seabra de Lemos, 316, Bairro Recanto dos Pássaros, 47808-021 Barreiras-BA, Brazil.

[ ³ ]Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus s/n, 96010-900 Capão do Leão-RS, Brazil.

[ ⁴ ]Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, 91501-970 Porto Alegre-RS, Brazil.

[ ⁵ ]Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n, Novo Horizonte, 44036-900 Feira de Santana-BA, Brazil.

[ ⁶ ]Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia.

[ ⁷ ]School of Biological, Earth and Environmental Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia.

[ ⁸ ]School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia.

[ ⁹ ]Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France.

[ ¹⁰ ]Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, Canada.

[ ¹¹ ]School of Integrative Plant Science, Plant Biology Section, Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USA.

[ ¹² ]Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK.

[ ¹³ ]Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.

[ ¹⁴ ]Embrapa Recursos Genéticos e Biotecnologia, 70770-901 Brasília-DF, Brazil.

[ ¹⁵ ]Programa de Pós-Graduação em Botânica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, 22460-030 Rua Pacheco Leão-RJ, Brazil.

[ ¹⁶ ]Instituto de Recursos Biológicos, CIRN-CNIA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Buenos Aires, Argentina.

[ ¹⁷ ]Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQB Ciudad Autónoma de Buenos Aires, Argentina.

[ ¹⁸ ]Facultad de Agronomía y Ciencias Agroalimentarias, Universidad de Morón, B1708JPD Morón, Buenos Aires, Argentina.

[ ¹⁹ ]Department of Biology, New Mexico State University, Las Cruces, NM 88001, USA.

[ ²⁰ ]United States Department of Agriculture - Agricultural Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL 33158, USA.

[ ²¹ ]Australian National Insect Collection, CSIRO, Clunies Ross Street, Acton, ACT 2601, Australia.

[ ²² ]School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK.

[ ²³ ]Department of Geography, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK.

[ ²⁴ ]Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK.

[ ²⁵ ]Department of Environmental System Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland.

[ ²⁶ ]Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland.

Author notes

[* ]Corresponding author. Email: jens.ringelberg@ 123456gmail.com

[†]

Present address: Department of Evolutionary Biology and Ecology, Université Libre de Bruxelles, Faculté des Sciences, Campus du Solbosch - CP 160/12, Avenue F.D. Roosevelt 50, 1050 Bruxelles, Belgium.

[‡]

Present address: Departement Bau und Umwelt, Abteilung Umweltschutz und Energie, Kirchstrasse 2, 8750 Glarus, Switzerland.

Author information

Jens J. Ringelberg https://orcid.org/0000-0003-0567-5210

Erik J. M. Koenen https://orcid.org/0000-0002-4825-4339

Anahita Aebli https://orcid.org/0000-0002-5736-2219

Juliana G. Rando https://orcid.org/0000-0002-3714-8231

João R. Iganci https://orcid.org/0000-0002-5740-3666

Luciano P. de Queiroz https://orcid.org/0000-0001-7436-0939

Daniel J. Murphy https://orcid.org/0000-0002-8358-363X

Anne Bruneau https://orcid.org/0000-0001-5547-0796

Gwilym P. Lewis https://orcid.org/0000-0003-2599-4577

Joseph T. Miller https://orcid.org/0000-0002-5788-9010

Marcelo F. Simon https://orcid.org/0000-0002-5732-1716

Lucas S. B. Jordão https://orcid.org/0000-0002-9501-0548

Matías Morales https://orcid.org/0000-0001-5540-9725

C. Donovan Bailey https://orcid.org/0000-0002-3123-4083

James A. Nicholls https://orcid.org/0000-0002-9325-563X

Oriane Loiseau https://orcid.org/0000-0002-9852-857X

R. Toby Pennington https://orcid.org/0000-0002-8196-288X

Kyle G. Dexter https://orcid.org/0000-0001-9232-5221

Niklaus E. Zimmermann https://orcid.org/0000-0003-3099-9604

Colin E. Hughes https://orcid.org/0000-0002-9701-0699

Article

Publisher ID: ade4954

DOI: 10.1126/sciadv.ade4954

PMC ID: 10957106

PubMed ID: 36800419

SO-VID: acc32d35-ba27-4934-a9ef-c6a92c7b61f6

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 License 4.0 (CC BY).

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date received : 19 August 2022

Date accepted : 17 January 2023

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;

Award ID: DEB-1135733

Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;

Award ID: 1238731

Funded by: FundRef http://dx.doi.org/10.13039/501100000038, Natural Sciences and Engineering Research Council of Canada;

Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;

Funded by: FundRef http://dx.doi.org/10.13039/501100001711, Swiss National Science Foundation;

Award ID: 310003A_156140

Funded by: FundRef http://dx.doi.org/10.13039/501100001711, Swiss National Science Foundation;

Award ID: 31003A_182453/1

Funded by: FundRef http://dx.doi.org/10.13039/501100001711, Swiss National Science Foundation;

Award ID: P2ZHP3_199693

Funded by: FundRef http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;

Award ID: 480530/2012-2

Funded by: FundRef http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;

Award ID: PROTEX 440487

Funded by: FundRef http://dx.doi.org/10.13039/501100006181, Fundação de Amparo à Pesquisa do Estado da Bahia;

Award ID: JCB0030/2016

Funded by: FundRef http://dx.doi.org/10.13039/501100003074, Agencia Nacional de Promoción Científica y Tecnológica;

Award ID: PICT 2016-0021

Funded by: FundRef http://dx.doi.org/10.13039/501100002923, Consejo Nacional de Investigaciones Científicas y Técnicas;

Award ID: PIP 11220110100250B

Funded by: FundRef http://dx.doi.org/10.13039/501100006181, Fundação de Amparo à Pesquisa do Estado da Bahia;

Award ID: PTX0004

Funded by: FundRef http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;

Award ID: 305570/2021-8

Funded by: FundRef http://dx.doi.org/10.13039/501100002322, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior;

Award ID: Finance Code 001

Funded by: FundRef http://dx.doi.org/10.13039/501100010677, Instituto Nacional de Tecnología Agropecuaria;

Award ID: 2019-PD-E2-I038-002

Funded by: FundRef http://dx.doi.org/10.13039/501100010677, Instituto Nacional de Tecnología Agropecuaria;

Award ID: 2019-PE-E6-I114-001

Funded by: FundRef http://dx.doi.org/10.13039/501100006181, Fundação de Amparo à Pesquisa do Estado da Bahia;

Award ID: APP0096

Funded by: FundRef http://dx.doi.org/10.13039/501100020014, Embrapa Recursos Genéticos e Biotecnologia;

Funded by: FundRef http://dx.doi.org/10.13039/501100020423, Georges and Antoine Claraz Foundation;

Funded by: National Environment Research Council (NERC);

Funded by: Universidad de Morón;

Award ID: PID UM 06-002-16

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Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

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China Tropical Medicine

Most cited references 194

Trimmomatic: a flexible trimmer for Illumina sequence data

Fast and accurate short read alignment with Burrows–Wheeler transform

Basic local alignment search tool.

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