Project 2435: Juan Marcos Mirande. 2017. Combined phylogeny of ray-finned fishes (Actinopterygii) and the use of morphological characters in large-scale analyses. Cladistics. 33 (4):333-350.
This project has 24 documents.

Please find here additional documents associated with this project. Occasionally MorphoBank receives matrices that are not formatted to parse to the database, these can also be found here, along with others and are presented 'as is' from the scientist.

24 Documents

1 (Downloaded 4 times )
Fig. 1. General topology of the consensus of most parsimonious trees obtained from: (a) combined dataset weighting each character separately (SEP); (b) grouping contiguous characters to weight them collectively (GR3, GR9, G27, GEN, MOL); (c) combined dataset grouping by positions (MOL); (d) combined dataset with equal weights (EQW). The final hypothesis herein proposed is shaded. The number of analysed species for each category is shown in parentheses.
2 (Downloaded 2 times )
Fig. 2. General topology of the final hypothesis (GR3) showing relationships between orders (Fit = 4619.23957; Length = 2,634,502 steps). Subtrees of the Ovalentaria and Carangiaria are shown separately. The subtree of the Eupercaria is shown in Fig. 3. More details are provided in Table 3 and in the Supplementary Online Material.
3 (Downloaded 4 times )
Fig. 3. General topology of the final hypothesis (GR3) showing relationships within the Eupercaria (Fit = 4619.23957; Length = 2,634,502 steps). The subtree of the Perciformes is shown separately. More details are provided in the Table 3 and in the Supplementary Online Material.
Appendix S01 (Downloaded 5 times )
Dataset, including the 14,141 species having at least one sequence and the Accession numbers. The first block correspond to morphological data. When open with TNT, only the 8104 species herein analyzed remains active (S1_dataset.tnt; execute with TNT).
Appendix S02
List of sequences removed from the final dataset for possible contamination or identification problems (S2_removed.txt).
Appendix S03 (Downloaded 1 time )
List of the number of sequences analyzed by each species (S3_in.txt)
Appendix S04 (Downloaded 7 times )
List of morphological characters. References correspond to papers in which the definition and coding of characters are based. ** EDIT FOR MORPHOBANK REPOSITORY: In the morphological dataset, characters start from 0. Therefore, character numbers in this list are the number in the dataset plus 1 **
Appendix S05 (Downloaded 2 times )
TNT script used to assign states from literature to morphological characters. (S5_morphology.tnt).
Appendix S06 (Downloaded 4 times )
Dataset of 8104 species restricted to first block of data, including taxonomy of species. (S6_names.tnt; execute with TNT).
Appendix S07 (Downloaded 7 times )
Consensus trees for analyses under different parameters in TNT format. Trees, from 0 to 7, correspond to SEP, GR3, GR9, G27, GEN, POS, EQW, and MOL (S7_constrees.tre; open with TNT after loading dataset.tnt file).
Appendix S08 (Downloaded 29 times )
General topology of the final hypothesis (consensus of GR3) showing relationships between families (Fit= 4620.20103; Length= 2,639,520 steps). Black dots on branches show nodes supported by all the performed analyses (S8_families.svg; open with a web browser).
Appendix S09 (Downloaded 4 times )
Agreement subtree (2500 spp) showing only the relationships shared by most parsimonious trees obtained in all the analyses, prunning taxa or clades floating with different parameters of search (S9_agreement.zip; open with a web browser).
Appendix S10 (Downloaded 2 times )
Agreement subtree (3710 spp) showing only the relationships shared by most parsimonious trees obtained in the analyses of the combined dataset without grouping or grouping contiguous columns to collectively weight them against their average homoplasy (SEP, GR3, GR9, G27, and GEN) (S10_agreementIW.svg; open with a web browser).
Appendix S11 (Downloaded 37 times )
General topology of the final hypothesis (consensus of GR3) (Fit= 4620.20103; Length= 2,639,520 steps). First number on branches represent the number of the node and the second one is the Bremer support. Nodes with a question mark after the second node are monophyletic in all the trees used to calculate supports and, therefore, are considered as highly supported (S11_GR3bremer.svg; open with a web browser).
Appendix S12 (Downloaded 2 times )
General topology of the final hypothesis (consensus of GR3) (Fit= 4620.20103; Length= 2,639,520 steps) showing morphological synapomorphies. Numbers between bars are the morphological characters supporting those clades. After the last bar, node numbers are shown, corresponding to those of Appendices S11, S20, and S21 (S12_morphosynap.svg; open with a web browser).
Appendix S13 (Downloaded 2 times )
General topology of the consensus of most parsimonious trees under SEP (Fit= 3157.58185; Length= 2,647,426 steps) (S13_SEP.svg; open with a web browser).
Appendix S14 (Downloaded 1 time )
General topology of the consensus of most parsimonious trees under GR9 (Fit= 4758.99827; Length= 2,639,476 steps) (S14_GR9.svg; open with a web browser)..
Appendix S15 (Downloaded 2 times )
General topology of the consensus of most parsimonious trees under G27 (Fit= 4827.49437; Length= 2,639,826 steps) (S15_G27.svg; open with a web browser).
Appendix S16 (Downloaded 2 times )
General topology of the consensus of most parsimonious trees under GEN (Fit= 4902.70047; Length= 2,639,497 steps) (S16_GEN.svg; open with a web browser).
Appendix S17 (Downloaded 1 time )
General topology of the consensus of most parsimonious trees under POS (Fit= 4044.83082; Length= 2,642,422 steps) (S17_POS.svg; open with a web browser).
Appendix S18 (Downloaded 1 time )
General topology of the consensus of most parsimonious trees under equal weights (EQW) (Length= 2,629,862 steps) (S18_EQW.svg; open with a web browser).
Appendix S19 (Downloaded 3 times )
General topology of the consensus of most parsimonious trees in the molecule-only analysis (MOL) (Fit= 4616.26673; Length= 2,639,474 steps) (S19_MOL.svg; open with a web browser).
Appendix S20 (Downloaded 2 times )
Expanded results and discussions relative to those of the manuscript. All discussed clades are illustrated in Figs. 1–3 of the manuscript, and online Appendices S8, S11, and S12.
Appendix S21 (Downloaded 3 times )
List of autapomorphies and synapomorphies obtained under GR3. Node numbers correspond to those of the Appendix S11 (apom.txt).