Non-homogeneous processes and, in particular, base compositional non-stationarity have long been recognized as a critical source of systematic error. But only a small fraction of current molecular systematic studies methodically examine and effectively account for the potentially confounding effect of non-stationarity. The problem is especially overlooked in multi-locus or phylogenomic scale analyses, in part because no efficient tools exist to accommodate base composition heterogeneity in large data sets. We present a detailed analysis of a data set with 20 genes and 214 taxa to study the phylogeny of flatfishes (Pleuronectiformes) and their position among percomorphs. Most genes vary significantly in base composition among taxa and fail to resolve flatfish monophyly and other emblematic groups, suggesting that non-stationarity may be causing systematic error. We show a strong association between base compositional bias and topological discordance among individual gene partitions and their inferred trees. Phylogenetic methods applying non-homogeneous models to accommodate non-stationarity have relatively minor effect to reduce gene tree discordance, suggesting that available computer programs applying these methods do not scale up efficiently to the data set of modest size analysed in this study. By comparing phylogenetic trees obtained with species tree (STAR) and concatenation approaches, we show that gene tree discordance in our data set is most likely due to base compositional biases than to incomplete lineage sorting. Multi-locus analyses suggest that the combined phylogenetic signal from all loci in a concatenated data set overcomes systematic biases induced by non-stationarity at each partition. Finally, relationships among flatfishes and their relatives are discussed in the light of these results. We find support for the monophyly of flatfishes and confirm findings from previous molecular phylogenetic studies suggesting their close affinity with several carangimorph groups (i.e., jack and allies, barracuda, archerfish, billfish and swordfish, threadfin, moonfish, beach salmon, and snook and barramundi).

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Symphurus thermophilus n. sp., described from 16 specimens collected by submersibles, ROV, epibenthic sled and dredge, occurs on a variety of substrata at several active hydrothermal sites located at 239–733 m between 21°N and 35°S in the western Pacific Ocean. Symphurus thermophilus, the only pleuronectiform fish known to inhabit hydrothermal vent areas, is characterized by the combination of a 1–2–2–2–2 pattern of interdigitation of dorsal proximal pterygiophores and neural spines, 14 caudal-fin rays, 5 hypurals, 9 abdominal vertebrae, 47–51 total vertebrae, 88–94 dorsal-fin rays, 74–80 anal-fin rays, 100–112 scales in longitudinal series, ocular-side pigmentation pattern featuring 5–8, black, mostly incomplete crossbands, uniformly white blind side, and black peritoneum. Of specimens examined, seven including the holotype, were collected on Kaikata Seamount off southern Japan; one specimen was collected at the Kasuga-2 hydrothermal vent, Marianas Islands; and six were collected at sites on the Kermadec Ridge. In addition to specimens captured, many other S. thermophilus were observed from submersibles and ROVs at hydrothermal sites in the western Pacific including those in the Marianas Islands, at Nikko Seamount near Minami-Iohjima Island, and at Minami-Ensei Knoll, Mid-Okinawa Trough. Many of the specimens examined have skeletal anomalies including fused bones in the caudal skeleton, and missing or partially developed and/or misshapen fin rays.

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International audience* The status of marine biodiversity in the Eastern Central Atlantic (ECA), especially of coastal and pelagic fishes, is of concern owing to a number of threats including overharvesting, habitat loss, pollution, and climate change combined with inadequate policy responses, legislation, and enforcement.ăă* This study provides the first comprehensive documentation of the presence, status, and level of extinction risk, based on IUCN Red List assessment methodology, for more than 1800 marine species, including all taxonomically described marine vertebrates (marine mammals, sea turtles, seabirds, fishes); complete clades of selected marine invertebrates (sea cucumbers, cone snails, cephalopods, lobsters, reef-building corals); and marine plants (mangroves, seagrasses).ăă* Approximately 8% of all marine species assessed in the ECA are in threatened categories, while 4% are listed as Near Threatened, 73% are Least Concern, and 15% are Data Deficient. Fisheries and overharvesting are the biggest threats to living marine resources in the ECA, with 87% of threatened species across all taxonomic groups affected by both large- and small-scale targeted fisheries, excessive capture as by-catch, or unsustainable harvest.ăă* The results of this study will transform the current state of knowledge and increase capacity for regional stakeholders to identify and enact marine conservation and research priorities, as a number of species are identified as having high conservation and/or research priorities in the region.ăă* Through the process of marine species data collection and risk assessments conducted over the past 5 years, several key conservation actions and research needs are identified to enable more effective conservation of marine biodiversity in the ECA, including increased governance, multilateral collaboration, taxonomic training, and improved reporting of fisheries catch and effort

Aphoristia (= Symphurus) orientalis Bleeker 1879, collected from an unspecified depth and location in Japanese waters, is the first described species of symphurine tonguefish from Indo-Pacific waters. The original description with accompanying illustration is based on the unique holotype specimen and provides limited diagnostic characters for this taxon. Subsequent to its description, the holotype of A. orientalis has been lost. Limited diagnostic information and loss of the holotype have caused considerable confusion to subsequent systematic studies regarding the identity of this and similar tonguefish species occurring in the Indo-West Pacific region. Several, often-cited, taxonomic accounts purportedly redescribing S. orientalis are erroneous because they include more than one species in these redescriptions. These erroneous redescriptions not only confused the species concept of S. orientalis (Bleeker), but also confounded the systematics of similar Indo-West Pacific tonguefishes. Symphurus novemfasciatus Shen and Lin, described on two specimens collected in southern Taiwan, shares many morphological and pigmentation features similar to those of S. orientalis. Morphological data from a large series of tonguefishes collected in Taiwanese and Japanese waters, as well as molecular data from a smaller number of specimens from these locations, including the type locality of S. novemfasciatus, confirm the presence of only one species, S. orientalis (Bleeker), among these specimens. Symphurus novemfasciatus Shen and Lin is therefore regarded as a junior subjective synonym of S. orientalis. Symphurus orientalis is redefined based on a large series of specimens identified by a consistent set of morphological criteria, and a neotype is designated to stabilize nomenclature and systematics of this species. Symphurus orientalis differs from congeners by its combination of: a predominant 1–2–2–2–2 pattern of interdigitation of proximal dorsal-fin pterygiophores and neural spines, 12 caudal-fin rays, 9 abdominal and 52–55 total vertebrae, four hypurals, 96–101 dorsal-fin rays, 82–89 anal-fin rays, 87–99 longitudinal scale rows, 37–42 transverse scales, 5–11 (usually) distinct, complete or incomplete, blackish-brown crossbands on the ocular side, uniformly white blind side, and conspicuous bluish-black peritoneum. Documenting morphological variation for S. orientalis represents the most important step towards clarification of the identity of this and other symphurine tonguefish species from this region. Reliable identification of specimens of S. orientalis also provides the foundation for evaluating the status of several other, poorly-known, nominal species of Indo-West Pacific tonguefishes that have features similar to those of S. orientalis. Improved identifications will lead to better knowledge on the geographic distribution of S. orientalis and these other species, as well as to improve estimates of biodiversity and the biogeography of Indo-West Pacific symphurine tonguefishes.