Computational protocol: Redescription and Phylogenetic Placement of †Hemicalypterus weiri Schaeffer, 1967 (Actinopterygii, Neopterygii) from the Triassic Chinle Formation, Southwestern United States: New Insights into Morphology, Ecological Niche, and Phylogeny

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Protocol publication

[…] To ascertain the phylogenetic relationships of †Hemicalypterus weiri to other neopterygian fishes, both parsimony and maximum likelihood cladistic analyses were performed based on a morphological character matrix of 100 characters and 54 taxa. The morphological data matrix was assembled using Mesquite Version 3.04 build 725 []. The data matrix is built upon [], which used many of the characters from López-Arbarello [] for ginglymodian fishes. Two other studies [, ] have also used either the whole matrix or a subsample of the matrix from [] for their respective analyses of holostean fishes. Two additional characters (the presence of a suprapreopercular bone, and the number of infraorbitals anterior to the orbit, characters 96 and 97 in this matrix, respectively) from [] were added to the matrix because of their use in further delineating ginglymodian relationships. Three characters include an additional character state for each, as first proposed in []: character 1 includes a state 4—dorsal fin originates posterior to pelvic fins and extends opposite to anal fin; character 22 includes a character state 3—length of postparietals (parietals of traditional terminology) more than half of the parietal (frontal of traditional terminology); character 23 includes a character state 2—parietals (frontals) only slightly longer than their maximum width.Two synapomorphic characters for †Dapediidae from [, ] were newly included in this study: character 94—body deeply fusiform to nearly circular (absent 0, present 1); character 95—hem-like dorsal and anal fins (absent 0, present 1).To further elucidate a relationship to teleostean fishes, three additional teleostean synapomorphic characters were added to this matrix based on []: character 98—tube-like, canal-bearing, anterior arm of the antorbital (absent 0, present 1); character 99—two vertebral centra fused into occipital condyle in adults (absent 0, present 1); character 100—hypural articulating with a few caudal rays (absent 0 present 1).The following characters are newly added to this study: character 91—morphology of the premaxillary teeth (unicuspid 0, bicuspid/bifid 1, multicuspid 2); character 92—ventral ridge scales (absent 0, present 1); character 93—thickness of scales posteriad (no reduction in thickness 0, reduced in thickness or lost 1).One character from [] was modified to include an additional state for this study. Character 83, the morphology of the dorsal ridge scales, includes a newly defined character state 3 for scales that are toothed or spinose, meaning the present of multiple spines per dorsal ridge scale.Coding for †Callipurbeckia minor was changed for character 29 from [] and []: the circumorbital ring closes in ontogeny in C. minor (López-Arbarello personal communication); this character coding has been changed from 0 to 1 in this study. Coding of †Siemensichthys from [] was changed for two characters based on []: character 7 is changed from? to 0; character 10 is changed from? to 1.Additional holostean taxa listed below are added to the data matrix based upon examination of specimens and interpretation of previous studies; each of these taxa have been chosen because previous hypotheses have purported a potential affinity to †Hemicalypterus. As †Hemicalypterus has been hypothesized to be related to semionotids within Holostei, five additional holostean fishes were included to further resolve the relationships of holostean fishes: the ionoscopid fish †Archaeosemionotus connectens; ginglymodian fishes †Lepidotes elvensis, †Camerichthys lunae, and †Kyphosichthys grandei; and the archaeomaenid fish †Aetheolepis mirabilis. Scores for †Archaeosemionotus connectens are based on []; scores for †Lepidotes elvensis are based on []; scores for †Camerichthys are based on []; scores for †Kyphosichthys are based on []; scores for †Aetheolepis mirabilis are based on [] and examination of photographs of specimens.Other studies as outlined above have hypothesized a close relationship between †Hemicalypterus and dapediid fishes, and so several taxa are included in the analysis that are putative members of †Dapediidae (†Dapediiformes): †Sargodon tomicus, †Dapedium caelatum, †Dapedium stollorum, †Dapedium punctatum, †Dapedium pholidotum, †Dandya ovalis, †Paradapedium egertoni, †Tetragonolepis oldhami, †Tetragonolepis semicincta, and †Heterostrophus phillipsi. Character scores of each taxon for the morphological data matrix are based on the following: scores for †Tetragonolepis semicincta are based on [] and personal examination of specimens; scores for †Tetragonolepis oldhami and †Paradapedium egertoni are based on []; scores for †Sargodon tomicus and †Dandya ovalis are based on []; scores for †Dapedium stollorum and †Dapedium punctatum are based on [, , , ] and personal examination of specimens; scores for †Dapedium pholidotum are based on [] and personal examination of specimens; scores for †Heterostrophus phillipsi are based on [, ] and examination of high-resolution photographs of the type material, freely provided by the JISC GB3D Type Fossils Online Project (found at http://www.3d-fossils.ac.uk).Please see the Electronic Supplemental Information documents for the complete list and description of phylogenetic characters and specimen materials examined () and morphological data matrix (). [...] A parsimony-based analysis was performed using PAUP* Version 4.0a147 for Macintosh []. Characters were unordered and given equal weight. Multistate characters were treated as polymorphisms. The starting tree in the heuristic search was obtained via stepwise addition, and branch-swapping was done with tree-bisection-reconnection (TBR). Branches were collapsed if maximum branch length was zero. Symmetric resampling bootstraps [] were performed with 100 replicates. The subholostean †Perleidus was designated as the outgroup taxon in the analyses.A maximum likelihood analysis was conducted using the software Garli Version 2.01 [] using a single partition with the Lewis MK model modified for only variable characters (MKv) as recommended for morphological data []. Characters were unordered, and polymorphisms were treated as missing data. Five separate likelihood analyses were conducted, with the tree having the best likelihood score presented here in order to evaluate evolutionary relationships. A nonparametric bootstrap analysis [] was performed on the dataset with 100 random pseudoreplicates. As in the parsimony analysis, †Perleidus was rooted as the outgroup. […]

Pipeline specifications

Software tools Mesquite, PAUP*, GARLI
Application Phylogenetics
Organisms Danio rerio