DOI: 10.5061/dryad.rjdfn2z8c
title: Data from: A new Cenomanian acanthomorph fish from the El Chango quarry (Chiapas, South-Eastern Mexico) and its implications for the early diversification and evolutionary trends of acanthopterygians

description: A new Cenomanian spiny-rayed fish from El Chango quarry, Chiapas, South
 Eastern Mexico is described and included, together with Zoqueichthys
 carolinae and Pepemkay maya, in the most recent phylogenetic analysis of
 acanthomorph fishes encompassing both extant and extinct taxa. The
 topologies recovered from the parsimony phylogenetic analysis using both
 multistate, or composite, and contingent, or reductive, coding are
 compared against each other and with a Bayesian estimation. All the
 analyses corroborate the placement of Z. carolinae as a member of the
 division Lampripterygii, while both Choichix alvaradoi gen. et
 sp. nov. and P. maya are considered as incertae sedis members into the
 division Acanthopterygii. Although no apomorphic character states for C.
 alvaradoi were found, the unique combination of features supports the
 description of a new genus and species for the Upper Cretaceous of Mexico.
 The species herein described is the earliest diverging acanthopterygian
 lineage. The most outstanding character found is the absence of a true
 pelvic-fin spine that, together with its placement in the phylogenetic
 analysis, suggests the independent acquisition of the pelvic-fin spine in
 both paracanthopterygians and acanthopterygians from a segmented first
 soft ray. This extinct taxon represents, thus, an important piece to
 understand both the fish diversity through time and some steps in the
 early diversification of acanthopterygians.
description: 1. Description of methods
 used for collection/generation of data: The comparative anatomy study
 included data from acanthomorphs housed at the National Collection of
 Palaeontology of Mexico and the Palaeontological Museum Eliseo Palacios
 Aguilera. After
 the anatomical review, two phylogenetic analyses were performed. Both
 analyses are based on Davesne et al.´s (2016) matrix modified using the
 Mesquite software (Maddison & Maddison, 2018), to include the new
 fossil species, <em>Zoqueichthys carolinae</em> and
 <em>Pepemkay maya</em>, leaving a total of 29 terminals and an
 outgroup composed of Synodus Scopoli, 1777, Gymnoscopelus Günther, 1873,
 and †Ctenothrissa Woodward, 1899. The first analysis kept the composite
 (or multistate) coding of the original matrix. The second applied the
 reductive (or contingent) coding to reduce the use of multistate and
 polymorphic characters included in the original matrix, increasing the
 number of analysed features from the original 66 to 78
 characters. Parsimony and Bayesian methods
 were used to analyse both matrices. The parsimony analysis was performed
 in TNT (Goloboff et al. 2008), and the Bayesian inference was carried out
 in RevBayes (Höhna et al. 2016). For the parsimony analysis, a search with
 new technology using 10000 iterations of Ratchet with equal weights and
 100 replacements, was carried out over the most parsimonious trees (MPT)
 recovered in the first analysis. The group analysis support was estimated
 via bootstrap resampling, which implemented 1000 replications and was
 performed in TNT (Goloboff et al. 2008). For Bayesian inference, the
 simple MK model (Wright et al., 2019) was used with 15000 generations. The
 convergence of both analyses was evaluated with Tracer (Rambaut
 <i>et al</i>. 2018). 2. Methods for processing the
 data: Osteological description of the
 species studied; retrieved of the original matrix provided by Davesne et
 al. (2016); inclusion of the osteological of the species studied in the
 matrix; separation between both the composite and reductive dataset;
 running both the parsimony and Bayesian analysis; interpretation of the
 data; and mapping some specific character states. 3. Software-specific information
 needed to interpret the data: Mesquite: a modular system for
 evolutionary analysis. Version 3.51 Tree analysis using new
 technology (TNT) version 1.5 RevBayes: Bayesian phylogenetic
 inference using graphical models and an interactive model-specification
 language version 1.1 Tracer: a software package for
 visualising and analysing the MCMC trace files generated through Bayesian
 phylogenetic inference version 1.7.1
description: Both composite and reductive data matrix are separate; however,
 the exact steps used in the command lines were performed with the matrix
 containing all characters (i.e. Cantalice_2020_11_24.nex). Each character
 was properly activated or deactivated to perform both analyses.