Median-Joining Networks and Bayesian phylogenies often do not tell the same story

Inferring phylogenies among intraspecific individuals often yields unresolved relationships (i.e., polytomies). Consequently, methods that compute distance-based abstract networks, like Median-Joining Networks (MJNs), are thought to be more appropriate tools for reconstructing such relationships than traditional trees. Median-Joining Networks visualize all routes of relationships in the form of cycles, if needed, when traditional approaches cannot resolve them. However, the MJN method is a distance-based phenetic approach that does not involve character transformations and makes no reference to ancestor-descendant relationships. Although philosophical and theoretical arguments challenging the implication that MJNs reflect phylogenetic signal in the traditional sense have been presented elsewhere, an empirical comparison with a character-based approach is needed given the increasing popularity of MJN analysis in evolutionary biology. Here, we use the conservative Approximately Unbiased (..., , , # Data from: Median-Joining Networks and Bayesian phylogenies often do not tell the same story

[https://doi.org/10.5061/dryad.f4qrfj708](https://doi.org/10.5061/dryad.f4qrfj708)

The following three files are Supplementary Materials for: Kong, Sánchez-Pacheco, and Murphy (2023) Median-Joining Networks and Bayesian phylogenies often do not tell the same story. Bulletin of the Society of Systematic Biologists.

## Description of the data and file structure

**1\. Supp1\-Kong\-et\-al\-BSSB\-2023\-data\.csv**
A `.csv` file that contains information on the sequence length, nucleotide model selected, *p*-values from the AU and SH tests, and the source where the sequences were extracted from for the 85 cases evaluated is summarized.

**2\. Supp2\-Kong\-et\-al\-BSSB\-2023\-MJNs\.zip**
Computed MJN using NETWORK version 4.6.1.2 for cases 1 to 85 in `pdf` format.

**3\. Supp3\-Kong\-et\-al\-BSSB\-2023\-Nexus\.zip**
Each `Mesquite` executable (partially executable by `PAUP*`) Nexus (`.nex`) file ...