taxonID	type	description	language	source
03DCAA7BFFF1FFD9E35A6818FE4AF62A.taxon	discussion	The monophyly of Citharoidea (Citharidae) receives low support in (BS % = 56) in the concatenated ML analysis. Sampling of this family in previous multilocus studies, for example (Betancur‐R., Broughton, et al., 2013; Betancur‐R., Li, et al., 2013; Campbell et al., 2013; Harrington et al., 2016) have found high support for monophyly of Citharidae. Low support for the monophyly of this family in molecular phylogenetic study was previously shown in mitogenomic phylogenies (Campbell, López, et al., 2014), sampling to date, however, has not included more than three genera of this lineage. This study includes Brachypleura, representing four of the five genera in the family, only leaving Paracitharus unsampled. The earliest‐branching lineage of the family based on these four genera and the molecular data presented here is Brachypleura. Consequently, the low support for monophyly of this family here may be a result of the short internodes in the tree in this region. Numerous studies have doubted the monophyly of Citharidae, for example (Chapleau, 1993; Cooper & Chapleau, 1998 b; Hensley, 1997; Hensley & Ahlstrom, 1984); however, Hoshino (2001) established synapomorphies for Citharidae and indicated them to be monophyletic.	en	Campbell, Matthew A., Chen, Wei-Jen, Chanet, Bruno, Chen, Jhen-Nien, Lee, Mao-Ying (2019): Origins and relationships of the Pleuronectoidei: Molecular and morphological analysis of living and fossil taxa. Zoologica Scripta 48 (5): 640-656, DOI: 10.1111/zsc.12372, URL: https://doi.org/10.1111/zsc.12372
03DCAA7BFFF1FFD8E35A6E12FBC4F3FF.taxon	discussion	Flatfish taxonomy has long overlooked the family‐level diversity present in Pleuronectoidei. The earliest flatfish classification simply placed all fifteen known species into a single genus, Pleuronectes, within the order Thoracici without any family divisions present (Linnaeus, 1758). Later, Pleuronectidae of Cuvier contained five subfamilies, the Cynoglossinae, Hippoglossinae, Platessinae, Pleuronectinae and Soleinae (Cuvier, 1817). Additional complexity with flatfish taxonomy was advanced with the concept of flatfishes as a suborder, the Heterosamata, and two families — the Pleuronectidae and Soleidae (Jordan & Evermann, 1896). Subsequently, Regan (1910) proposed two suborders of the Psettodoidea with the single family of Psettodidae and the Pleuronectoidea with two divisions (Pleuronectiformes and Soleiformes). The Pleuronectiformes of Regan (1910) had two families, the Bothidae and Pleuronectidae, and a Soleiformes with two families, the Soleidae and Cynoglossidae. Since then, the largest divisions within the suborder Pleuronectoidei have followed a division between pleuronectids and their relatives (superfamily Pleuronectoidea; Nelson (2006 )) and soleids and their relatives (superfamily Soleoidea; Nelson (2006 )) such as Norman (1934) proposing three families for the flatfish lineage, Psettodidae, Bothidae and Pleuronectidae. From the two divisions with Pleuronectoidei, the distinction of Citharidae became evident in further investigations. Hubbs (1945) defined a Citharidae (Citharinae + Brachypleurinae) closely related to Scophthalmidae, and these being most closely related to all other Pleuronectoidea indicating another major division within the flatfish lineage and a concept that has been reflected in subsequent classifications (Chapleau, 1993; Hensley & Ahlstrom, 1984). The citharids composed of the genera Brachypleura, Citharoides, Citharus, Lepidoblepharon, and Paracitharus were demonstrated by Hoshino (2001) to be monophyletic — contradicting Chapleau (1993) who indicated they were paraphyletic — and the earliest‐branching lineage of Pleuronectoidei. The current taxonomy of the Pleuronectoidei may be characterized by three superfamilies: Citharoidea, Pleuronectoidea and Soleoidea (Chanet et al., 2004; Hoshino, 2001; Nelson, 2006). In this study, we find support for these three superfamilies.	en	Campbell, Matthew A., Chen, Wei-Jen, Chanet, Bruno, Chen, Jhen-Nien, Lee, Mao-Ying (2019): Origins and relationships of the Pleuronectoidei: Molecular and morphological analysis of living and fossil taxa. Zoologica Scripta 48 (5): 640-656, DOI: 10.1111/zsc.12372, URL: https://doi.org/10.1111/zsc.12372
03DCAA7BFFF0FFDAE0196C47FDB4F4F2.taxon	discussion	Pleuronectoidea is identified to contain the families Scophthalmidae, Pleuronectidae, Paralichthyidae and Bothidae. Scophthalmidae is the earliest‐branching lineage of the Pleuronectoidea and sister to the remainder of this clade with high support (Figures 1 and 2). This placement receives support from several studies (Betancur‐R., Li, et al., 2013; Campbell et al., 2013; Harrington et al., 2016; Near et al., 2012), but is not widely supported across multilocus and mitochondrial DNA‐based studies. Alternative placements of Scophthalmidae closely related to Rhombosoleidae and Achiropsettidae are found in other data sets, not exclusively those based on mitochondrial genomes (Betancur‐R., Broughton, et al., 2013; Campbell, Chen, et al., 2014; Shi et al., 2018). Some morphological classifications have indicated that Scophthalmidae is closely related to Citharidae, for example (Chapleau, 1993; Hubbs, 1945); however, the most recent studies provide additional evidence that Scophthalmidae is a lineage within Pleuronectoidea (Chanet et al., 2004; Hoshino, 2001). Early flatfish classification schemes placed all species in Pleuronectidae and it continued to contain many fishes of uncertain affinity. More recent efforts have advanced the understanding of composition and inter‐relationships within this family (Cooper & Chapleau, 1998 a; Vinnikov, Thomson, & Munroe, 2018). The placement of Pleuronectidae as the sister lineage to one lineage of the polyphyletic Paralichthyidae (Paralichthyidae I) and Bothidae to another (Paralichthyidae II) in this study was demonstrated in early molecular phylogenetic studies and has continued to be apparent with larger samplings of lineages and characters, for example (Berendzen & Dimmick, 2002; Campbell, López, et al., 2014; Harrington et al., 2016). Non‐monophyly of paralichthyids is well known from both anatomical and molecular studies (Azevedo, Oliveira, Pardo, Martínez, & Foresti, 2008; Berendzen & Dimmick, 2002; Chanet et al., 2004; Chapleau, 1993; Khidir, Chapleau, & Renaud, 2005; Pardo et al., 2005). The affinities of some paralichthyids with pleuronectids and some with bothids have long been indicated by classifications, with all or some of these fishes being considered most closely related to one or both of these other families, for example (Hensley, Amaoka, Hensley, Moser, & Sumida, 1984; Hubbs, 1945; Norman, 1934). We identify a clade including Paralichthys and relatives (Paralichthys, Pseudorhombus, Xystreurys) — Paralichthyidae I in this study — as sister to the Pleuronectidae. Paralichthyidae II is composed of Cyclopsetta, Etropus and Citharichthys in this study and is sister to the Bothidae (Figures 1 and 2). A polyphyletic Paralichthyidae may be resolved through the creation of two families, Paralichthyidae and Cyclopsettidae. Previously, Hensley and Ahlstrom (1984) indicated a Cyclopsetta group and a Pseudorhombus group. Based on our analyses and others, Paralichthyidae presumably contains 10 genera including the Pseudorhombus group: Ancylopsetta, Cephalopsetta, Gastropsetta, Hippoglossina, Lioglossina, Paralichthys, Pseudorhombus, Tarphops, Verecundum and Xystreurys (Chapleau, 1993). Cyclopsettidae contains at least four genera, Cyclopsetta, Etropus and Citharichthys, which were examined in this study, and Syacium. Syacium, while not examined here, based on previous anatomical and molecular work should be considered a member of Cyclopsettidae (Chapleau, 1993; Hensley & Ahlstrom, 1984; Pardo et al., 2005). Within the Cyclopsettidae, the monophyly of genera requires further evaluation, for example (Azevedo et al., 2008; Betancur‐R., Broughton, et al., 2013; Betancur‐R., Li, et al., 2013). Morphological support for a sister relationship between Cyclopsettidae and Bothidae, as shown in this study, is present as both clades have vertebral apophyses and lack a first neural spine (Hensley & Ahlstrom, 1984). We included two fossils in our total evidence analysis that belong in the Pleuronectoidea (Figure 2). The relationships of Eobothus mimimus † have long been uncertain, and the mostresolved placement of Eobothus mimimus † to date has been as a member of the Pleuronectoidea. Eobothus minimus † had previously been indicated to be a bothid species (Berg, 1940, 1941; Blot, 1980; Norman, 1934; Patterson, 1993 b), a scophthalmid species (Chabanaud, 1936, 1940, 1949) and later a crown pleuronectoid (Chanet, 1997). Eobothus minimus † may not be considered a member of an extant family, as it shares derived characteristics with Bothidae, Pleuronectidae, Paralichthyidae (I & II), Scophthalmidae and Brachypleura (Chanet, 1999). Chanet (1999) considered Eobothus minimus † to be incertae sedis within a “ bothoid ” lineage of Brachypleura, Scophthalmidae, Paralichthyidae (I & II), Bothidae and Pleuronectidae. Here, we refine the placement so that Eobothus mimimus † forms part of a three‐branch polytomy (Eobothus mimimus †, (Pleuronectidae, Paralichthyidae I), (Bothidae, Paralichthyidae II )). Eobothus mimimus † is more closely related to Bothidae, Paralichthyidae (I & II) and Pleuronectidae than Scophthalmidae or Brachypleura. The results of our total evidence analysis indicate that E. minimus † is most likely a member of an extinct family‐level lineage within Pleuronectoidea. Oligobothus pristinus † has previously been clearly placed in the Bothidae and we recover that relationship (Baciu & Chanet, 2002).	en	Campbell, Matthew A., Chen, Wei-Jen, Chanet, Bruno, Chen, Jhen-Nien, Lee, Mao-Ying (2019): Origins and relationships of the Pleuronectoidei: Molecular and morphological analysis of living and fossil taxa. Zoologica Scripta 48 (5): 640-656, DOI: 10.1111/zsc.12372, URL: https://doi.org/10.1111/zsc.12372
03DCAA7BFFF3FFDBE0126D1FFD6DF495.taxon	discussion	The third superfamily in Pleuronectoidei is composed of eight families in this study and its monophyly is well supported (Figure 1, BS = 82 %, Figure 2, PP = 0.97). There is weak support in the ML analysis (Figure 1, BS = 35 %) and moderate support in the Bayesian combined approach (Figure 2, PP = 0.63) for a monophyletic group of Achiridae, Paralichthodidae, Rhombosoleidae and Achiropsettidae and Numidiopleura enigmatica †. This study includes representation of Achiridae, Paralichthodidae, the two divergent lineages of Rhombosoleidae, and Achiropsettidae for the first time to our knowledge in a phylogenetic study and indicates these families in total may form a monophyletic assemblage and Rhombosoleidae is paraphyletic. Support for arrangements among the families Achiridae, Paralichthodidae, Rhombosoleidae and Achiropsettidae is low, indicated by support values in the ML analysis and a polytomy in the Bayesian combined analysis. The placement of Achiridae as most closely related to Soleidae + Cynoglossidae is well supported from a morphological perspective (Chanet et al., 2004; Chapleau, 1993; Hoshino, 2001). Nonetheless, here and other studies Achiridae is shown to be closely related to Paralichthodidae, Rhombosoleidae and Achiropsettidae (Betancur‐R., Li, et al., 2013; Harrington et al., 2016), though see Shi et al. (2018) for another placement. Chapleau and Keast (1988) indicate a relationship of (Samaridae (Achiridae (Soleidae + Cynoglossidae ))). It may be possible that this disagreement between placements of Achiridae may result from the particular species examined in anatomical works. Paralichthodidae has held different placements in alternative classification schemes, with integration into Chapleau (1993) ’ s data set placing it as a family and earliest‐branching member of Soleoidea (Cooper & Chapleau, 1998 b). Our analysis refines placement of the lineage to indicate near relatives of Achiridae, Rhombosoleidae and Achiropsettidae. Rhombosoleidae is demonstrated to be paraphyletic, with Rhombosolea most closely related to Mancopsetta with maximal support values in the ML analysis (BS = 100 %) and moderate support in the Bayesian combined analysis (PP = 0.60). Sampling in mitogenomic studies have not included Oncopterus, but show very high support for a sister relationship between Rhombosoleidae and Achiropsettidae (Campbell, López, et al., 2014; Shi et al., 2018). Oncopterus darwinii is unlike other rhombosoleids as it is found in the Southwest Atlantic and all other rhombosoleids are distributed mainly around Australia and New Zealand (Nelson, 2006). In our time‐calibrated tree, this monotypic genus is indicated to diverge as an independent lineage 36.51 mya as well. As a resolution for the paraphyly of Rhombosoleidae, we suggest that the monotypic family Oncopteridae be created containing the single species Oncopterus darwinii. Rhombosoleidae then includes nine genera and 18 species: Ammotretis, Azygopus, Colistium, Pelotretis, Peltorhamphus, Psammodiscus, Rhombosolea and Taratretis (Nelson, 2006). Our findings support a sister relationship between Rhombosoleidae as defined above and Achiropsettidae. One of the fossils in our analysis, Numidiopleura enigmatica †, is placed with Achiridae, Paralichthodidae and (Oncopteridae, (Rhombosoleidae + Achiropsettidae). When Numidiopleura enigmatica † was first described, it was thought to be a missing link between Psettodes and Pleuronectoidei (Gaudant & Gaudant, 1969). However, cladistic analysis of this fossil by Chanet (1997) resolved it as Pleuronectoidei incertae sedis. Here, we find that N. enigmatica † represents extinct family diversity within the Soleoidea, with close affinities to Rhombosoleidae and Achiropsettidae. Numidiopleura enigmatica † is the oldest representative of this putative clade. Reconciling the position of N. enigmatica † from a biogeographic standpoint is problematic as the fossil is from the Mediterranean and the distribution of inferred relatives is in the Southern Hemisphere. A cautious interpretation is necessary as the fossil of N. enigmatica † is lost and of uncertain age. Within Soleoidea, four other families form a monophyletic assemblage — Samaridae, Poecilopsettidae, Soleidae and Cynoglossidae — with well‐supported monophyly (BS = 86 %, PP = 0.82, Figures 1 and 2). The monophyly and same branching arrangements of these four families have been documented in three previous studies utilizing independent data sets (Campbell et al., 2013; Campbell, López, et al., 2014; Harrington et al., 2016). Note that in Figure 2 of Harrington et al. (2016), Aseraggodes xenicus is incorrectly labelled as a cynoglossid, although it is a soleid. Alternative branching arrangements of Samaridae, Poecilopsettidae, Soleidae and Cynoglossidae are presented in a recent mitogenomic study, but the families are monophyletic (Shi et al., 2018). The fossil Eobuglossus eocenicus † while recently not considered a soleid by (Near et al., 2012) is demonstrated to be a soleid, in line with previous hypotheses (Chanet, 1994; Chapleau & Keast, 1988). Research in flatfish alpha taxonomy is active and room for continued development of the beta taxonomy of the Pleuronectoidei is present. Two notable genera were not examined in this study, Tephrinectes and Thysanopsetta, suggested by Hensley and Ahlstrom (1984) to be removed from Paralichthyidae. Detailed anatomical investigation of Tephrinectes indicates it is a distinct lineage from Paralichthyidae (Hoshino, 2001; Hoshino & Amaoka, 1998). Further investigations may reveal more family‐level diversity within Pleuronectoidei either through the identification of new distinct lineages or refinement of known genera.	en	Campbell, Matthew A., Chen, Wei-Jen, Chanet, Bruno, Chen, Jhen-Nien, Lee, Mao-Ying (2019): Origins and relationships of the Pleuronectoidei: Molecular and morphological analysis of living and fossil taxa. Zoologica Scripta 48 (5): 640-656, DOI: 10.1111/zsc.12372, URL: https://doi.org/10.1111/zsc.12372
03DCAA7BFFF5FFDCE0126987FC3CF6D8.taxon	description	5.1.1 | Diagnosis Diagnostic characters are compiled following the information from Hensley and Ahlstrom (1984) and Chapleau (1993). Cyclopsettidae is recognized from other families by this combination of features: Eyes on the left side; the urinary papilla relatively close the blind side; ocular‐side pelvic fin located at the mid‐ventral line of the body; blind‐side pelvic fin base is more anterior than that of the ocular side; 17 caudal‐fin rays, and all fin rays are supported by hypurals, not located on preural, neural nor haemal spines; five hypurals and hypural 5 fused with the epural; first neural spine absent; and vertebral apophyses present. 5.1.2 | Composition This family includes four genera, Citharichthys, Cyclopsetta (type genus), Etropus and Syacium evidenced from anatomical and molecular data sources and currently 45 recognized species (Chapleau, 1993; Fricke, Eschmeyer, & Fong, 2018; Hensley & Ahlstrom, 1984; Pardo et al., 2005). The monophyly of all genera in this family has not been shown in molecular studies (Azevedo et al., 2008; Betancur‐R., Broughton, et al., 2013; Betancur‐R., Li, et al., 2013). 5.1.3 | Distribution Eastern (Senegal to Angola) and western (U. S. A to Brazil) Atlantic, Eastern Pacific (Baja California to Peru), distributed in brackish waters and marine coastal waters into the deep sea (2000 m).	en	Campbell, Matthew A., Chen, Wei-Jen, Chanet, Bruno, Chen, Jhen-Nien, Lee, Mao-Ying (2019): Origins and relationships of the Pleuronectoidei: Molecular and morphological analysis of living and fossil taxa. Zoologica Scripta 48 (5): 640-656, DOI: 10.1111/zsc.12372, URL: https://doi.org/10.1111/zsc.12372
03DCAA7BFFF5FFDCE35A6B3AFB61F2A2.taxon	description	5.2.1 | Diagnosis The diagnostic characters follow the information from Norman (1934) and Chapleau (1993). Oncopteridae is recognized by this combination of features: Eyes on the right side; large foramen on branchial septum between lower pharyngeals and urohyal; origin of dorsal fin anterior of eyes above blind‐side nostrils; first dorsal‐fin ray specialized, enlarged, hard, curved, and movable, and connects with first strongly developed basal bone of the fin, contained in a deep groove on blind‐side head; pelvic fins asymmetric and separated by anal fin, ocular‐side pelvic fin located much more anterior than that of the blind side; six pelvic‐fin rays; lateral line with distinctive semi‐circular curve above the pectoral fin and several transverse supratemporal accessory branches from main lateral line to dorsal edge of body. 5.2.2 | Composition This family includes a single genus, Oncopterus, with a single species Oncopterus darwinii Steindachner, 1874. 5.2.3 | Distribution Southwestern Atlantic (Brazil to Argentina), distributed in shallow coastal waters (20 – 80 m).	en	Campbell, Matthew A., Chen, Wei-Jen, Chanet, Bruno, Chen, Jhen-Nien, Lee, Mao-Ying (2019): Origins and relationships of the Pleuronectoidei: Molecular and morphological analysis of living and fossil taxa. Zoologica Scripta 48 (5): 640-656, DOI: 10.1111/zsc.12372, URL: https://doi.org/10.1111/zsc.12372
