DOI: 10.5061/dryad.f4qrfj708
title: Data from: Median-Joining Networks and Bayesian phylogenies often do not tell the same story

description: 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 (AU) test to compare 85 cases of branching patterns
 of cycle-free MJNs and Bayesian Inference (BI) phylogenies using datasets
 from 55 empirical studies. By rooting the MJN analyses to provide
 directionality, we report substantial disagreement between computed MJNs
 and posterior distributions on BI phylogenies. The branching patterns in
 MJNs and BI phylogenies show significantly different relationships in
 37.6% of cases. Among the relationships that do not significantly differ,
 96.2% show alternative sets of relationships. Our results indicate that
 the two methods provide different measures of relatedness in a
 phylogenetic sense. Finally, our analyses also support previous
 observations of the statistical hypothesis testing by reconfirming the
 over-conservativeness of the Shimodaira-Hasegawa test versus the AU test.
description: # 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 stores sequence alignment, 50% majority rule consensus phylogeny constructed from MRBAYES version 3.2.2, transformed MJN topology using the root identified from the BI topology, for the 85 cases evaluated. Note the topologies are missing in cases 28,33,34,70 and sequence alignment is missing in cases 22,25 due to the corruption in the original files.