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Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation

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RT @Grimmiges: This week on #GWoN an example (#plant, #oak) for why it's always a good idea to have other do, what you can do by heart: htt…
Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation https://t.co/6CsmbAqjs1
This week on #GWoN an example (#plant, #oak) for why it's always a good idea to have other do, what you can do by heart: https://t.co/UyZ7fdGE2x PS Don't miss the pre-print/data @PeerJPreprints: https://t.co/JopOgDixMe https://t.co/SINTe0D4MO
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Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation https://t.co/crF7ZssIiQ
PeerJ: Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation https://t.co/QdvhKg0eEn
Our preprint on Cerris #oaks is now online @PeerJPreprints https://t.co/3J6Ipr7CRc #OpenData Naturally with more networks than trees. #Biodiversity #Biogeography #EvolutionaryStudies #Taxonomy https://t.co/b6tMs4V9Fj
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Supplemental Information

Investigated specimens and related information

We also report the accession numbers of the sequences retrieved from GenBank and used to complement the investigated dataset.

DOI: 10.7287/peerj.preprints.26995v1/supp-1

TrnH-psbA Haplotype list

incuding results of the BLAST identity matches on GenBank

DOI: 10.7287/peerj.preprints.26995v1/supp-2

List of the identical 5S-IGS clones sequences

This list reports all the identical 5S-IGS cloned sequences in the investigated dataset. Colors according to species list.

DOI: 10.7287/peerj.preprints.26995v1/supp-3

Online Supplementary Archive

This Online Supporting Archive includes data and analysis files of Simeone et al. "Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation" in several subfolders

DOI: 10.7287/peerj.preprints.26995v1/supp-4

5S-IGS Clone-based RaxML tree

The tree was rooted on Q. baloot and Q. floribunda. Taxa colors as in Fig. 1, 2a and File S1. Branch bootstrap support (1-100) is reported

DOI: 10.7287/peerj.preprints.26995v1/supp-5

Networks based on transformed 5S-IGS data showing inter-individual average (AVG) clonal distance relationship

individuals represented by more than 2, 3 and 5 clones are included ( cut-offs specimens are indicated)

DOI: 10.7287/peerj.preprints.26995v1/supp-6

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Marco Cosimo Simeone conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Simone Cardoni performed the experiments, prepared figures and/or tables, approved the final draft.

Roberta Piredda analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Francesca Imperatori performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

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

Guido W Grimm conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

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

DNA Deposition

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

All sequence data generated as part of this study are available on GenBank (http://www.ncbi.nlm.nih.gov/genbank/) under accession numbers LT963519-LT963530 and LT971421-LT972071.

Data Deposition

The following information was supplied regarding data availability:

Primary data and analyses are provided for download in the Online Supplementary Archive (OSA) at the journal's homepage (mirrored at www.palaeogrimm.org/data).

Funding

This project was funded by a Swedish Research Council (VR) grant to TD. Sequencing was made possible using funds from a VR ‘ForsAss’ grant (no. 2008–3726) to GWG. GWG has been funded by the Austrian Science Fund FWF ‘Lise-Meitner mobility’ grant (project no. M1751-B16). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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