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The evolutionary and genetic origins of the specialized body plan of flatfish are largely unclear. We analyzed the genomes of 11 flatfish species representing 9 of the 14 Pleuronectiforme families and conclude that Pleuronectoidei and Psettodoidei do not form a monophyletic group, suggesting independent origins from different percoid ancestors. Genomic and transcriptomic data indicate that genes related to WNT and retinoic acid pathways, hampered musculature and reduced lipids might have functioned in the evolution of the specialized body plan of Pleuronectoidei. Evolution of Psettodoidei involved similar but not identical genes. Our work provides valuable resources and insights for understanding the genetic origins of the unusual body plan of flatfishes.

Background The monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related to other carangimorphs based on substantial sequencing efforts and diversely analytical methods. In this study, we examined why this particular result is often obtained. Results The mitogenomes of five flatfishes were determined. Select mitogenomes of representative carangimorph species were further employed for phylogenetic and molecular clock analyses. Our phylogenetic results do not fully support Psettodes as a sister group to pleuronectoids or other carangimorphs. And results also supported the evidence of long-branch attraction between Psettodes and the adjacent clades . Two chronograms, derived from Bayesian relaxed-clock methods, suggest that over a short period in the early Paleocene, a series of important evolutionary events occurred in carangimorphs. Conclusion Based on insights provided by the molecular clock, we propose the following evolutionary explanation for the difficulty in determining the phylogenetic position of Psettodes : The initial diversification of Psettodes was very close in time to the initial diversification of carangimorphs, and the primary diversification time of pleuronectoids, the other suborder of flatfishes, occurred later than that of some percomorph taxa. Additionally, the clade of Psettodes is long and naked branch, which supports the uncertainty of its phylogenetic placement. Finally, we confirmed the monophyly of flatfishes, which was accepted by most ichthyologists.

This paper reports the first complete sequence of the mitochondrial genome (mitogenome) of the yellow-striped flounder Pseudopleuronectes herzensteini (Pleuronectoidei: Pleuronectidae). Mitogenome evolution, and molecular phylogenetic reconstruction based on four to six techniques, including coalescent analysis, were performed for flatfish. The genome size of the specimen sampled was 16,845 bp, including 13 protein-coding genes, 22 tRNA genes, 12S, and 16S rRNA genes, and the control region, CR. The composition and arrangement of the genes are similar to those in other teleost fish, including the second mitogenome reported in this paper. The frequency of A, C, G, and T nucleotides in the P. herzensteini mitogenome is 27%, 29.2%, 17.6%, and 26.2%, respectively. The ratio of complementary nucleotides in the mitogenome of this and other species of the family was A+T:G+C (53.2: 46.8%) and do not deviate significantly from the expected equilibrium proportion. The submission to the global database (GenBank) of two new mitogenomes along with 106 analyzed GenBank sequences will contribute to phylogenetic studies of flounders at the family and suborder levels. Based on 26 and 108 nucleotide sequences of protein-coding genes (PCGs), we investigated the molecular phylogeny of flounders and performed analysis for two sets of sequences, including those of members of the family Pleuronectidae and the suborder Pleuronectoidei and estimated their importance in establishing the taxonomy at these two levels. Data obtained by up to six techniques of multigene phylogenetic reconstructions support monophyly within the family Pleuronectidae with high statistical confidence; however, conclusions regarding the phylogenetics at the suborder level require further investigation. Our results also revealed paraphyletic and weakly supported branches that are especially numerous at the suborder level; thus, there is a clear need for taxonomic revisions at the suborder, and possibly family levels. Genetic distance analysis reveals the suitability for DNA barcoding of species specimens at single genes as well as at whole mitogenome data.

Physiological and genetic responses of age 0+ Platichthys flesus were investigated in the eutrophicated and moderately contaminated Vilaine estuary, during a 6-month survey. The main objective of this study was to explore the biological responses of fishes during their juvenile period in an estuarine system in order to detect a possible selective pressure induced by the environmental stress. Our results showed a general convergence in physiological responses along the survey: an increase in genotoxicity was associated with an increase in mRNA expression of ATPase and betaine homocysteine methyltransferase. These results could suggest an increase of cellular damage, energetic request, and detoxification rate related to the growing exposure time to stress. Considering the aging of the cohort, the genetic characteristics of the Vilaine flounder cohort came closer to the one observed in a highly stressed system, the Seine estuary, suggesting a potential selective pressure mainly induced by the chemical stress.

The structure of the seismosensory system of Psettodes erumei was studied. General and specific features in comparison with the previously studied representatives of the suborder Pleuronectoidei were revealed. Similarity is manifested in the presence of four main head canals, coronal commissure, interrupted supratemporal commissure transformed into a supratemporal canal, and one trunk canal developed on both sides of the body. The seismosensory system of Psettodes erumei is characterized by several plesiomorphous characters: the presence of a sensory segment in lacrimale of the eyed side and supracleithrum, the absence of disruptions in all sensory canals, and a strong branching of cutaneous canaliculi. Specific features of P. erumei involve the presence of a large number of fontanels on angulo-articulare, connection on the eyed side of CIO sites in lacrimale and infraorbitale, and the underdevelopment of the bony vault of the sensory canal in praeoperculum.

Branching patterns of the trunk lateral line nerves were studied in 46 pleuronectiform species, representing nine families in two suborders. The dorsal fin longitudinal ramus (DFLR), derived from the main nerve (horizontal septum lateral line nerve), passed closely along the course of the middle trunk lateral line in all specimens examined, the dorsal longitudinal collector nerve (DLCN) partly coalescing with the DFLR along the arched part of the lateral line in Psettodes erumei (Psettodoidei), compared with the entire length of the latter in all other species (Pleuronectoidei). Citharidae, Paralichthyidae and Pleuronectidae were characterized by having a simple, elongated dorsal ramule; Bothidae was unique in having more than one dorsal ramule, forming a ladder-like network and peripherally giving off numerous minute branches; Poecilopsettidae and Samaridae possessed a few, short dorsal ramules; Soleidae and Cynoglossidae were characteristic in having a dendritic dorsal ramule. Secondary modifications of the course of the middle trunk lateral line were detected by nerve information, the arched part of the lateral line having been secondarily highly elevated in some genera of Pleuronectidae, but secondarily straightened in Samaridae.

Soleichthys maculosus, described from six specimens collected in shallow waters (37-63 m) off northern Australia, is readily distinguished from congeners by its unique ocular-side pigmentation featuring numerous, conspicuous white spots and blotches nearly as large as the eye diameter on a uniformly dark brown background without any crossbands, and in having two elongated, ocular-side pectoral-fin rays, with the second dorsalmost ray longer than the first, and without scales on the pectoral-fin rays. Soleichthys maculosus is most similar to S. siammakuti, a poorly-known species collected in the Gulf of Thailand, but differs from S. siammakuti in having the second dorsalmost ocular-side pectoral-fin ray longer than the first (vs. first ocular-side pectoral-fin ray longer in S. siammakuti), and in having different ocular-side pigmentation than that of S. siammakuti, which features yellow spots on dorsal and anal fins, two conspicuous white spots arranged in longitudinal series on the lateral line, and also a series of nine, light brown crossbands on a dark brown body.

Skull development after eye migration was studied in a bothid flounder Bothus myriaster (Bothidae). In the stage immediately following the migration, skull ossification was apparently weaker on the blind side than on the ocular side, such being related to the extensive dorsally directed shift of the blind side eye. The blind side frontal had two initial ossification sites;below (\"pseudomesial bar\" in Psettodes) and behind (\"frontal\" in bothids) the blind side eye. In bothids, the former was fused with the lateral ethmoid but autogenous to the latter during ontogeny. With increased eye size with growth, the otic region became progressively narrower. The late ossification of the region was considered to provide flexibility for cranial modifications owing to rapid eye enlargement.

A new bothid flounder, Engyprosopon marquisensis, is described from 11 specimens collected in deep waters (108-408m) off the Marquesas Islands (French Polynesia) during the French exploratory cruise MUSORSTOM 9 in 1997. Engyprosopon marquisensis is similar to E. bellonaensis from the Chesterfield Islands and Bellona Plateau in the Coral Sea and E. vanuatuensis from off Vanuatsu Island, but is easily distinguished from E. bellonaensis by the following combination of characters: narrow interorbital space in both sexes, small mouth, short caudal fin, large number of vertebrae, and fewer gill rakers. It differs from E. vanuatuensis by many scales in the lateral line, small eyes, short ocular-side upper jaw, and short blind-side lower jaw. Engyprosopon marquisensis is the deepest occurring (408m) species of the genus, and constitutes the second species of this genus with an eastern distribution.[PUBLICATION ABSTRACT]

A new bothid flounder, Engyprosopon vanuatuensis, is described on the basis of 15 specimens (9 males and 6 females, 41.1-55.8mm in standard length) collected from deep waters (163-165m) off Vanuatu Island in 1994 during the French exploratory cruise \"MUSORSTOM 8.\" The new species clearly differs from its congeners in having a short body, big eyes, large scales, and many gill rakers without serrations. Remarkable sexual dimorphism appears in interorbital width, anterior curve of head profile, rostral and orbital spines, length of ocular-side pectoral fin, small dots on eyes, and pigmentation of blind-side body.[PUBLICATION ABSTRACT]