Visitors   Views   Downloads
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

Supplemental Information

Bacterial gene trees and supertrees in Newick format.

DOI: 10.7287/peerj.preprints.18v1/supp-1

Eukaryotic supertree files in Newick format

DOI: 10.7287/peerj.preprints.18v1/supp-2

Sample EvolSimulator configuration file

DOI: 10.7287/peerj.preprints.18v1/supp-3

Inferred LGT events between 13 bacterial classes.

Inferred LGT events between 13 bacterial classes. (a) LGT heatmap. The colour side bars indicate class. The row and column order is the same. The number of transfers is shown in a white-yellow-red colour scale with darker colours indicating a higher proportion of transfer events. Colour intensity is relative to the largest number of transfers in a row. Relationships with fewer than 5% of the maximum transfer events for a row or only a single transfer event were filtered out. (b) LGT affinity graph of the bacterial classes. Each node of the graph represents a bacterial class scaled relative to the number of represented taxa (2-75). Two genera are connected by an edge if the number of inferred LGT events between them exceeds 5% of their shared genes. The shade of an edge is proportional to this ratio of LGT events to shared genes; black edges indicate relationships with at least as many LGT events as shared genes. The thickness of an edge scales relative to the actual number of inferred transfers (30-1414) with thicker edges indicating more transfers.

DOI: 10.7287/peerj.preprints.18v1/supp-4

The LGT affinity neighbourhood of genus Clostridium.

The LGT affinity neighbourhood of genus Clostridium. Each node of the graph represents a bacterial genus coloured by class and scaled relative to the number of represented taxa (1-13). Two genera are connected by an edge if the number of inferred LGT events between them exceeds 5% of their shared genes. The shade of an edge is proportional to this ratio of LGT events to shared genes; black edges indicate relationships with at least as many LGT events as shared genes. The thickness of an edge scales relative to the actual number of inferred transfers (2-125) with thicker edges indicating more transfers.

DOI: 10.7287/peerj.preprints.18v1/supp-5

Accuracy of SPR, RF and MRP supertrees

A comparison of the accuracy of SPR, RF and MRP supertrees as measured by the minimal SPR distance between simulated species histories and any rooting of the supertree under varying rates of random or divergence-biased simulated LGT events.

DOI: 10.7287/peerj.preprints.18v1/supp-6

Additional Information

Competing Interests

The authors have no competing interests.

Author Contributions

Chris Whidden conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper.

Norbert Zeh conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper.

Robert G Beiko conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper.

Data Deposition

The following information was supplied regarding the deposition of related data:

Dryad.org [accession in progress]

Funding

This work was funded by the Natural Sciences and Engineering Research Council of Canada via grants to N.Z. and R.G.B., and a graduate fellowship to C.W. C.W. was also supported by the Killam Trusts. N.Z. and R.G.B. acknowledge the support of the Canada Foundation for Innovation and the Canada Research Chairs Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies