15 files

Collection of morphological matrices (some including extinct taxa) and related phylogenetic inferences

Version 4 2020-09-14, 13:20
Version 3 2019-02-25, 13:05
Version 2 2018-09-10, 09:09
Version 1 2018-09-10, 08:43
posted on 2020-09-14, 13:20 authored by Guido GrimmGuido Grimm
This file set contains (version 3) information, and analysis files, related to morphological data matrices collected from literature (including some we published) to sum up some principal features of these matrices, mainly how tree(un)like they are.

Version 3 includes
XLXS-File OverviewTables summarising general signal information (behaviour under parsimony and NJ tree-building in relation to matrix and individual Delta Values, a measure for treelikeness.

Content of 7z-Archives

Cycadales.7z includes the matrices of Stevenson (Mem. NY Bot. Garden, 57: 8–55, 1990) and my extension of it (Grimm GW. 1999. Diploma thesis. Eberhard Karls Universität) including extinct (potential) cycads as well as some inference based on them.

HuffonMcMahon.7z includes the matrix and analysis files used for the graphics labelled HM04* and shown in the related post on Genealogical World of Phylogenetic Networks (GWoN): The curious case(s) of tree-like matrices with no synapomorphies.

SookiasTestData.7z includes the Crocodilian morpho-matrix included in the SI of the Sookias (PaleorXiv, 2019) and analysis files used for the graphics shown in the related GWoN post: Has homoiology been neglected in phylogenetics? includes NEXUS-reformatted dinosaur matrices provided as supplement to
Hartman et al., PeerJ, 2018: birds and related Theropoda with 505 taxa and 700 characters
Yang et al., PeerJ, 2020: Ornithischia 62 (one duplicate) taxa, 263 characters.

Important note: When using the NEXUS-formatted matrix files cite the original literature. Cite this collection, if you want to refer to results/inferences done by me (links below) or included here.

Matrices are provided in NEXUS format (*.nex), trees in NEWICK (*.tre – single tree; *.tree[s] – tree collections) and networks in Splits-NEXUS format (*.nxs; *.dist; use SplitsTree to open and view files): MPT = most-parsimonious tree samples, BioNJ = neighbour-joining tree fulfilling the least-squares optimality criterion, MD = neighbour-net splits graphs using simple (Hamming) mean morphological pairwise distances, NJBS and PBS = NJ and parsimony bootstrap pseudoreplicates.