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The use of next generation sequencing to solve phylogenetic incongruences in Orchidaceae Juss

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RT @antonelli_lab: Our preprint has been published today in @PeerJPreprints https://t.co/FBlRd2cNIV #Biodiversity #EvolutionaryStudies #Gen…
RT @antonelli_lab: Our preprint has been published today in @PeerJPreprints https://t.co/FBlRd2cNIV #Biodiversity #EvolutionaryStudies #Gen…
RT @rnomics: The use of next generation sequencing to solve phylogenetic incongruences in Orchidaceae Juss https://t.co/DuZKaqncAI…
The use of next generation sequencing to solve phylogenetic incongruences in Orchidaceae Juss https://t.co/DuZKaqncAI Background. Current evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However…
Our preprint has been published today in @PeerJPreprints https://t.co/FBlRd2cNIV #Biodiversity #EvolutionaryStudies #Genomics #PlantScience @GGBC_GU
220 days ago
PJpreprint: The use of next generation sequencing to solve phylogenetic incongruences in Orchidaceae Juss https://t.co/fVPTxyJxKT
220 days ago
The use of next generation sequencing to solve phylogenetic incongruences in Orchidaceae Juss https://t.co/96OdDIMhIt
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Supplemental Information

DNA sequence alignment with loops

The file contains the chloroplast sequence alignment and a Mr Bayes analysis block that excludes poorly aligned sites, but includes the entire inverted loop regions.

DOI: 10.7287/peerj.preprints.26530v1/supp-1

DNA sequence alignment with loops down-weighted

The file contains the chloroplast sequence alignment and a Mr Bayes analysis block that excludes poorly aligned sites, as well as down-weighting the inverted loop regions by excluding all but one character in each inverted loop.

DOI: 10.7287/peerj.preprints.26530v1/supp-2

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Narjara Lopes de Abreu conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Ruy José Válka Alves conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Sérgio Ricardo Sodré Cardoso conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Yann JK Bertrand analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Filipe Sousa performed the experiments, analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Climbiê Ferreira Hall analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Bernard E Pfeil analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Alexandre Antonelli conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

Field collection permission was granted by the following government agencies:

1. Ministério do Meio Ambiente - MMA

2. Instituto Chico Mendes de Conservação da Biodiversidade - ICMBio

3. Sistema de Autorização e Informação em Biodiversidade - SISBIO

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

DNA Sequences have been deposited at EMBL/ENA under accession numbers ERS2203551-ERS2203590.

Funding

A.A. is supported by grants from the Swedish Research Council (B0569601), the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013, ERC Grant Agreement n. 331024), the Swedish Foundation for Strategic Research, the Knut and Alice Wallenberg Foundation, the Biodiversity and Ecosystems in a Changing Climate programme, and the Faculty of Science at the University of Gothenburg. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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