Data supporting phylogenetic reconstructions of the Neotropical clade Gymnotiformes

Data is presented in support of model-based total evidence (MBTE) phylogenetic reconstructions of the Neotropical clade of Gymnotiformes “Model-based total evidence phylogeny of Neotropical electric knifefishes (Teleostei, Gymnotiformes)” (Tagliacollo et al., 2016) [1]). The MBTE phylogenies were inferred using a comprehensive dataset comprised of six genes (5277 bp) and 223 morphological characters for an ingroup taxon sample of 120 of 218 valid species and 33 of the 34 extant genera. The data in this article include primer sequences for gene amplification and sequencing, voucher information and GenBank accession numbers, descriptions of morphological characters, morphological synapomorphies for the recognized clades of Gymnotiformes, a supermatrix comprised of concatenated molecular and morphological data, and computer scripts to replicate MBTE inferences. We also included here Maximum-likelihood and Bayesian topologies, which support two main gymnotiform clades: Gymnotidae and Sternopygoidei, the latter comprised of Rhamphichthyoidea (Rhamphichthyidae+Hypopomidae) and Sinusoidea (Sternopygidae+Apteronotidae).


Specifications
Data is with this article and in the GenBank public repository at GenBank: 26616344 Value of the data Data summary for the most comprehensive phylogenetic study of Gymnotiformes to date, including an ingroup taxon sampling of 33 (94%) recognized genera and 120 (57%) of all valid species.
New molecular sequences for 149 specimens and descriptions of morphological characters for 166 specimens.
Supermatrix comprised of six genes (5277 bp) and 223 morphological characters used to reappraise relationships of Gymnotiformes

Data
The data provided below include supporting information to replicate phylogenetic analyses of Tagliacollo et al. [1]. The information is comprised of: (1) taxon sampling used in the phylogenetic analyses, (2) molecular and morphological datasets including GenBank accession numbers, description of morphological characters, and synapomorphies used to diagnose clades, and 3) detailed description of methodological procedures and parameters used in Tagliacollo et al. [1] to estimate phylogenetic relationships of the Neotropical clade Gymnotiformes. Furthermore, supplementary materials include the following: (1) computer scripts used in Tagliacollo et al. [1] to run MBTE analyses, (2) a matrix of morphological characters, (3) a supermatrix of combined molecular and morphological, (4) a list of analyzed material (specimens and lots), and (5) maximum-likelihood and bayesian phylogenetic trees.
Experimental design, materials and methods

Sequence alignments
Forward and reverse sequences were assembled in Geneious 5.5.6. The IUPAC ambiguity code of nucleotides was applied in cases where nucleotide identity was dubious. We combined newly generated data with available sequences from previous studies [2][3][4][5][6][7]. Each gene was independently aligned using MAFFT 5.3 [8] under default parameters. To detect potential errors such as amplification of pseudogenes, paralogous copies or potential laboratory cross-contamination, each gene alignment was analyzed in PhyML 3.0 [9]. Sequences suspiciously misplaced in the resulting gene trees were then re-amplified.

Morphological dataset
3.1. Description of characters used in the morphological dataset 1. Body shape 1.0: body laterally compressed, body width at pectoral fin base less than 70% its depth. 1: Body cylindrical or subcylindrical, roughly circular in cross section, body depth at pectoral girdle approximately equal to its width. 2. Body shape 2.0: body laterally compressed. 1: Body dorsoventrally flattened. Newly coded herein. 3. Body shape profile. "Body Depth," character 2 in Albert, 2001. 0: Body relatively deep in profile, depth at pectoral girdle more than 11% total length. 1: Body elongate, slender, depth less than 11% total length. 4. Snout length short. 0: preorbital length about one-third total head length in mature specimens. 1: Snout short, preorbital length less than one-third total head length ([10]- Fig. 13). 5. Snout long. 0: Length of the snout (preorbital length) about one-third total head length in mature specimens. 1: Snout elongate, frontal, vomer and anterior portion of parasphenoid elongate; preorbital length longer than one-third total head length or greater in mature specimens ([10]-Figs. 11-17). 6. Gape large. 0: Rictus of mouth extends ventral to nasal capsule, gape forming less than one-third total head length. 1: Rictus extends posterior to a vertical through eye, gape forming more than one-third total head length. 7. Gape short. 0: Rictus extends ventral to nasal capsule, gape more than three times eye diameter, oriented parallel with long axis of head. 1: Rictus extends to a vertical with mental symphysis, gape very small, less than twice diameter of eye, oriented oblique to long axis of head.
8. Oral opening in adults. 0: Upper and lower jaws of equal length, oral aperture terminal. 1: Lower jaw extends anterior to upper, oral aperture superior. 2: Upper jaw extends anterior to lower, oral aperture inferior. 9. Position of nasal capsule. 0: Nasal capsule, including olfactory epithelium and olfactory sensory neurons, positioned relatively posteriorly on snout; located closer to eye than to anterior tip of snout; posterior nares closer to anterior margin of eye than to anterior nares. 1: Anterior position of nasal capsule; located closer to tip of snout than to eye; posterior nares closer to anterior nares than to anterior margin of eye ([10]- Fig. 19 Fig. 1). 80. Sphenoid region. 0: Sphenoid region of neurocranium less than one-third total head length in mature specimens, combined axial length of orbitosphenoid and pterosphenoid about equal to length of preorbital region. 1: Sphenoid region of neurocranium more than one-third total head length, combined axial length of the orbitosphenoid and pterosphenoid bones greater than preorbital region. 2: Sphenoid region of neurocranium more than one-third total head length, combined axial length of the orbitosphenoid and pterosphenoid bones greater than preorbital region, orbit positioned at anterior third of head. 81. Orbitosphenoid shape. 0: Orbitosphenoid well ossified in median nasal septum, orbitosphenoid broad, its ventral margin longer than its dorsal margin. 1: Anterior margin of orbitosphenoid not ossified, orbitosphenoid narrow, its ventral margin about as long or shorter than its dorsal margin. 82. Orbitosphenoid margin. "Sphenoid fenestra" (Character 74) in [10]. olfactory tract shorter length of olfactory lobe. 1: Olfactory bulb remote from rest of forebrain; olfactory tract longer than length of olfactory lobe ([13]-character 123). 105. Eyeball extrinsic muscles. 0: Extrinsic eyeball muscles and fibers of nervous innervation robust, their diameters greater than that of in situ collagen fibers. 1: Extrinsic eyeball muscles and innervating nerves small or absent, their diameters about the same as collagen fibers ( [17]). 106. Accessory optic system. 0: Accessory optic tract large, easily visible in histological sections; neurons of tract organized into a distinct tegmental cell cluster (i.e., accessory optic nucleus). 1: Accessory optic tract reduced or absent; discrete accessory optic nucleus not visible in sections ( [32,33]). 107. Integumental taste buds. 0: Taste buds present on head in characiforms, and over entire integumental surface in siluriforms; diameters of nerves V and VII equal to or larger than that of other cranial nerves in isthmal region; primary facial and vagal sensory nuclei larger than medial octaval nucleus. 1: Taste buds entirely absent from extra-oral integument; nerves V and VII smaller than other cranial nerves of isthmal region; primary facial and vagal sensory nuclei smaller than medial octaval nucleus. 108. Schreckstoff/club cells. 0: Schreckstoff (alarm substance), club cells, and fright response present in Ostariophysi. 1: Schreckstoff, club cells, and fright response absent ([13]-character 117). 109. Passive electroreception. 0: No ability to detect weak ambient electric fields. 1: Structures and behavioral capacity to detect weak low frequency ambient electric fields, used in predation; associated neural structures in peripheral (e.g., ampullary electroreceptor organs) and central (e.g., electrosensory lateral line lobe, nucleus electrosensorius) nervous systems [34,35]. 110. Ampullary organ rosettes. 0: Ampullary organs distributed individually in integument. 1: Ampullary organs clustered in rosettes [36]. 111. Active electroreception. 0: Passive, low frequency electroreception, used in predation; neural apparatus for detecting low frequency electric currents. 1: Electrogeneration and high frequency electroreception, used in communication and navigation (in addition to predation); neural apparatus for producing and detecting high frequency electric currents [37,38]. 112. Tuberous electroreceptors. 0: One class of tuberous electroreceptor organs. 1: Two classes of morphologically distinct tuberous electroreceptor organs [39]. 113. Preotic lateralis ganglia. 0: All preotic lateral line nerve ganglia form from separate placodes, their axonal bundles entering brain separately. 1: Anterodorsal, anteroventral, and preopercularmandibular lateral line nerve ganglia fused during ontogeny, their axons entering brain in a single bundle [17].   [24]. 220. Humeral accessory EO. 0: No humeral electric organ. 1: Humeral electric organ extending dorsally from pectoral fin base, and then posteriorly along horizontal myoseptum a distance less than length of pectoral fin [51]. 221. Neural EO. 0: Main electric organ of mature specimens ontogenetically derived from hypaxial musculature. 1: Main electric organ of mature specimens derived from electromotor neurons which innervate larval hypaxial organ [50,52]. 222. EOD form. 0: EOD of mature specimens produced as discrete non-overlapping pulses with alternating periods of current flow and no current flow; capacity for EOD frequency modulations present; cells of pacemaker nucleus organized into two separate clusters. 1: EOD produced as a continual series of discharges to form a quasi-sinusoidal pattern of current emission; no capacity for EOD frequency modulations; relay and pacemaker cells mingled in a single medullary nucleus [53]. 223. EOD monophasic in adults. 0: EOD of mature specimens with two (sometimes three or four) phases; EOD characterized by both head-positive and head-negative depolarizations. 1: Monophasic EOD of juveniles retained into maturity; EOD characterized exclusively by head-positive depolarizations. 2: Monophasic hyperpolarization from negative baseline [49,54].

Maximum-likelihood (ML)
MBTE-ML analyses datasets were conducted in [62] using a supermatrix of concatenated molecular and morphological data. Models of nucleotide evolution were estimated in PartitionFinder v.1.1.1 [63]. Mkv model [64] was used for the morphological dataset. MBTE-ML analyses consisted of two independent runs, each one starting from a BioNJ starting tree and using the Subtree Pruning and Regrafting (SPR) algorithm to search for tree improvement in terms of likelihood scores. All other parameters were set as default. To assess node support, 100 non-parametric bootstrap replications were performed for each independent tree search resulting in a total of 200 pseudo-replicates. A consensus tree with bootstraps was computed using the function SumTrees from DendroPy 3.7.0 [65]. Computer scripts to replicate analyses are shown in Supplementary 1.

Bayesian inference (BI)
MBTE-BI analyses were conducted in MrBayes 3.2 [66] using a supermatrix of concatenated molecular and morphological data. Models of nucleotide evolution were estimated in PartitionFinder v.1.1.1 [63]. Mkv model [64] was used for the morphological dataset. MBTE-BI analysis consisted of two runs (four chains each) of the Metropolis-Coupled Markov Chain Monte Carlo (MC 3 ). Each run was comprised of 5.0 Â 10 7 generations with model parameter values and a single tree sampled every 5 Â 10 3 generation. All other parameters were set as default. To ensure adequate mixing of the MCMC, effective sample size values (ESS 4200) were inspected for parameter estimates in Tracer 1.5. The two independent runs were summarized with "sump" and "sumt" commands in MrBayes 3.2 [66]. The initial 25% of sampled topologies were discarded as burn-in procedure. The remaining topologies were used to construct a 50% majority-rule consensus tree. Posterior probabilities were visualized in FigTree 1.4.0. Computer scripts to replicate analyses are shown in Supplementary 1.

List of synapomorphies used to diagnose clades
Node 175: GYMNOTIFORMES ch. 3-Body shape profile. "Body Depth," character 2 in Albert, 2001. / 1: Body elongate, slender, depth less than 11% total length. ch. 7-Gape short. / 1: Rictus extends to a vertical with mental symphysis, gape very small, less than twice diameter of eye, oriented oblique to long axis of head.
ch. 14-Position of eye. / 1: Eye completely covered by epidermis in adults; orbital margin not free. ch. 72-Lateral ethmoid size. / 1: Lateral ethmoid reduced in size; four peripheral margins not contacting other bony surfaces.
ch. 106-Accessory optic system. / 1: Accessory optic tract reduced or absent; discrete accessory optic nucleus not visible in sections.
ch. 107-Integumental taste buds. / 1: Taste buds entirely absent from extra-oral integument; nerves V and VII smaller than other cranial nerves of isthmal region; primary facial and vagal sensory nuclei smaller than medial octaval nucleus.
ch. 166-Anterior coracoid process. / 1: Anterior coracoid process not extending to a vertical with contact of dorsomedial limb of coracoid with cleithrum.
ch. 220-Humeral accessory EO. / 1: Humeral electric organ extending dorsally from pectoral fin base, and then posteriorly along horizontal myoseptum a distance less than length of pectoral fin.
ch. 166-Anterior coracoid process. / 1: Anterior coracoid process not extending to a vertical with contact of dorsomedial limb of coracoid with cleithrum.
ch. 9-Position of nasal capsule. / 1: Anterior position of nasal capsule; located closer to tip of snout than to eye; posterior nares closer to anterior nares than to anterior margin of eye.
ch. 30-Scales on middorsum. / 1: Scales absent from head, anterior portion of dorsal midline, and area dorsal to pectoral fins. ch. 33-Lateral line pores. / 1: Posterior lateral line pores tubular; tube length more than three times pore diameter.
ch. 124-Endopterygoid anterior process. / 1: Entire extent of ligament ossified, forming a bony strut anterior to orbit; process equally as wide along most of its length. ch. 205-Gas bladder. / 1: Anterior chamber of gas bladder encapsulated in a thick, opaque layer of tissue.
ch Node 265: Eigenmanninae clade ch. 4-Snout length short. / 1: Snout short, preorbital length less than one-third total head length. ch. 26-Body translucence. / 1: Body translucent in living specimens, yellow or pink hue in living specimens, yellow or hyaline in formalin-fixed specimens, melanophores sparse or absent on lateral body surface.
ch. 83-Sphenotic process. / 1: Dorsolateral margin of sphenotic bearing a transversely oriented crest or process exposed on dorsolateral edge, anterior margin not underlying frontal.
ch. 9-Position of nasal capsule. / 1: Anterior position of nasal capsule; located closer to tip of snout than to eye; posterior nares closer to anterior nares than to anterior margin of eye.
ch. 30-Scales on middorsum. / 1: Scales absent from head, anterior portion of dorsal midline, and area dorsal to pectoral fins.
ch. 45-Anterior maxillary shelf. / 1: Anterior process of maxilla large and broad, extending more than one half the length of the descending blade in mature specimens.
ch. 63-Mesethmoid, tip shape. / 0: Portion of mesethmoid anterior to ventral ethmoid horizontal; its dorsal surface anterior and posterior to ventral ethmoid approximately parallel; its ventral surface parallel with dorsal surface.
ch. 68-Median septum of ventral ethmoid. / 1: Ossified median septum of ventral ethmoid elongate in mature specimens, longer than deep, extending posterior to posterior margin of lateral process.
ch. 74-Base lateral ethmoid. / 1: Lateral ethmoid narrow or tubular; length of its base less than one-third length of its anterior margin.
ch. 78-Dorsal margin of frontals. / 1: Portion of frontal anterior to orbit concave in lateral profile ch. 105-Eyeball extrinsic muscles. / 1: Extrinsic eyeball muscles and innervating nerves small or absent, their diameters about the same as collagen fibers.
ch. 123-Endopterygoid ascending process. / 1: Small ascending process of endopterygoid in juveniles obliterated by growth along dorsal margin of bone; no endopterygoid process in adults.
ch. 46-Maxilla descending blade. / 1: Descending blade of maxilla broad, connective tissue membrane along its anteroventral margin ossified to form a thin shelf; anterior portion of maxilla rhomboid in lateral view.
Node 289: MegadontognathusþApteronotus clade ch. 21-Pigment contrast. / 1: High contrast dark brown or black and white pigments on body surface.
ch. 123-Endopterygoid ascending process. / 1: Small ascending process of endopterygoid in juveniles obliterated by growth along dorsal margin of bone; no endopterygoid process in adults.
ch. 202-Posterior parapophyses. / 0: Parapophyses of posterior precaudal vertebra small, their ventral margins oblique to long axis of body, not contacting one another along midline.
Node 300: Platyurosternarchus clade ch. 6-Gape large. / 1: Rictus extends posterior to a vertical through eye, gape forming more than one-third total head length. ch. 7-Gape short. / 0: Rictus extends ventral to nasal capsule, gape more than three times eye diameter, oriented parallel with long axis of head.
ch. 125-Mesopterygoid dentition. / 0: Numerous small teeth distributed in an irregular field on anterior portion of ventral surface of endopterygoid.
ch. 182-Number posterior DHS. / 0: Two or three DHSs posterior to large anterior spine. ch. 188-Number anal-fin rays. / 3: 200-299 rays. Taxa coded by modal number of anal-fin rays. Node 301: Sternarchorhynchus clade ch. 8-Oral opening in adults. / 0: Upper and lower jaws of equal length, oral aperture terminal. ch. 9-Position of nasal capsule. / 1: Anterior position of nasal capsule; located closer to tip of snout than to eye; posterior nares closer to anterior nares than to anterior margin of eye.
ch. 45-Anterior maxillary shelf. / 0: Anterior process of maxilla extending as a shelf of bone less than one-third the length of the descending blade.
ch. 81-Orbitosphenoid shape. / 1: Anterior margin of orbitosphenoid not ossified, orbitosphenoid narrow, its ventral margin about as long or shorter than its dorsal margin.
ch. 30-Scales on middorsum. / 2: Scales absent along entire middorsum. ch. 31-Scale shape. / 1: Scales dorsal to lateral line rhomboid, their long axis oriented oblique to long axis of body, their dorsoventral axes longer than their longitudinal axes.
ch. 81-Orbitosphenoid shape. / 1: Anterior margin of orbitosphenoid not ossified, orbitosphenoid narrow, its ventral margin about as long or shorter than its dorsal margin.
ch. 85-Parasphenoid ventral margin. / 1: Ventral margin of parasphenoid flexed sharply on either side of the basicranial region; ventral margin of sphenoid region oblique relative to long axis of neurocranium.
ch. 9-Position of nasal capsule. / 1: Anterior position of nasal capsule; located closer to tip of snout than to eye; posterior nares closer to anterior nares than to anterior margin of eye.
ch. 154-Hypobranchial 2. / 1: Anterior tip of second hypobranchial with a large medially oriented process, contacting contralateral third hypobranchial across midline by means of a cartilaginous bridge.
ch. 47-Maxilla descending blade. / 1: Ventral margin of descending blade with a sharp angle about two-thirds distance to its tip; ventral margin posterior to this angle relatively straight.
ch. 84-Parasphenoid lateral process. / 0: Lateral margins of parasphenoid extending as broad dorsolateral processes anterior to prootic, extending to a horizontal with trigeminal foramen.