Thomas A. Munroe

Addressing Gene Tree Discordance and Non-Stationarity to Resolve a Multi-Locus Phylogeny of the Flatfishes (Teleostei: Pleuronectiformes)

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).

Systematics, distribution and ecology of commercially important paralichthyid flounders occurring in Argentinean-Uruguayan waters (Paralichthys, Paralichthyidae): an overview

Abstract Species of Paralichthys Girard are the most important flatfishes to commercial fisheries in nearshore waters of Argentina and Uruguay. Recent commercial catches increased from 3000 tonnes (t) in 1984 to 11000 t in 1995, representing more than

Taxonomic status of three nominal species of Indo-Pacific symphurine tonguefishes (Symphurus: Cynoglossidae: Pleuronectiformes)

65 million in export income for 1995. Although their commercial importance has long been recognized, paralichthyid flounders in this region are not well studied, either from a systematic or an ecological viewpoint. Six nominal species have been reported from Argentinean and Uruguayan waters: Paralichthys bicyclophorus, P. brasiliensis, P. isosceles, P. orbignyanus, P. patagonicus and P. simulans. However, species descriptions are often vague and incomplete, and reported distributions are dubious. Variations in scale morphology, meristic and morphometric characters were used to differentiate among the Paralichthys species co-occurring in this area. Of six species previously reported from this region, only three, P. isosceles, P. orbignyanus and P. patagonicus, are valid. P. bicyclophorus is regarded as a junior synonym of P. patagonicus; P. simulans is a junior synonym of P. orbignyanus; while P. brasiliensis, although reported from coastal waters of Argentina and Uruguay for many years, does not occur there. Paralichthys spp. were collected on the continental shelf and in estuaries in the south Atlantic between 34–55°S. P. orbignyanus and P. patagonicus inhabit marine and estuarine locations and extend as far south as 43°S. The former is a shallow-water, euryhaline species occurring to about 20 m. In contrast, P. patagonicus has higher densities between 36–40°S at 70–100 m depth. P. isosceles occurs mainly on the inner continental shelf between 43–45°S at 70–100 m depth, and reaches its southern limit at about 47°S.

Concerted Evolution of Duplicate Control Regions in the Mitochondria of Species of the Flatfish Family Bothidae (Teleostei: Pleuronectiformes).

The taxonomic status of three rarely captured, nominal species of Indo-Pacific symphurine tonguefishes,Symphurus trifasciatus (Alcock, 1894),S. microrhynchus (Weber, 1913), andS. holothuriae Chabanaud, 1948, is resolved.Symphurus microrhynchus, previously known only from three specimens, is redescribed based on 12 specimens.Symphurus holothuriae, previously reported only from the holotype, is a junior subjective synonym ofS. microrhynchus. Symphurus trifasciatus is redescribed based on six specimens, including the lectotype designated in this study.Symphurus microrhynchus is distinguished from congeners by a combination of meristic features, head and opercle shape, dorsalfin position, and features of its pigmentation. The species occurs in relatively shallow tropical waters from Zanzibar through French Polynesia (the only reported occurrence of a shallow-waterSymphurus from a locality on the Pacific Plate), including Indonesia, Papua New Guinea, Vietnam, and northwestern Australia.Symphurus trifasciatus, known from deep waters along both coasts of the Indian subcontinent and adjacent waters, has an overall similarity in body shape and meristic features reminiscent of those inS. microrhynchus, but differs notably in having a longer and wider head, a distinctive opercle shape, number of scale rows on the head, and pigmentation pattern.

New Western Indian Ocean Tonguefish (Pleuronectiformes: Cynoglossidae, Symphurus)

Mitogenomes of flatfishes (Pleuronectiformes) exhibit the greatest diversity of gene rear-rangements in teleostean fishes. Duplicate control regions (CRs) have been found in the mito-genomes of two flatfishes, Samariscus latus (Samaridae) and Laeops lanceolata (Bothidae), which is rare in teleosts. It has been reported that duplicate CRs have evolved in a concerted fashion in fishes and other animals, however, whether concerted evo-lution exists in flatfishes remains unknown. In this study, based on five newly sequenced and six previously reported mitogenomes of lefteye flounders in the Bothidae, we explored whether duplicate CRs and concerted evolution exist in these species. Results based on the present study and previous reports show that four out of eleven bothid species examined have duplicate CRs of their mitogenomes. The core regions of the duplicate CRs of mitogenomes in the same species have identical, or nearly identical, sequences when compared to each other. This pattern fits the typical characteristics of concerted evolution. Additionally, phylogenetic and ancestral state reconstruction analysis also provided evidence to support the hypothesis that duplicate CRs evolved concertedly. The core region of concerted evolution is situated at the conserved domains of the CR of the mitogenome from the termination associated sequences (TASs) to the conserved sequence blocks (CSBs). Commonly, this region is con-sidered to regulate mitochondrial replication and transcription. Thus, we hypothesize that the cause of concerted evolution of the duplicate CRs in the mtDNAs of these four bothids may be related to some function of the conserved sequences of the CRs during mitochondrial rep-lication and transcription. We hope our results will provide fresh insight into the molecular mechanisms related to replication and evolution of mitogenomes.

Symphurus hondoensis Hubbs, 1915, a valid species of western Pacific tonguefish (Pleuronectiformes: Cynoglossidae)

Abstract Symphurus monostigmus, described on the basis of two males (48.8 and 54.6 mm SL) collected on the inner continental shelf at 65–110 m off the coast of KwaZulu-Natal, South Africa, is distinguished from congeners by the following combination of characters: an irregular, conspicuous dark spot overlying the anteroventral ocular-side body cavity; a 1-2-2-2-2 pattern of interdigitation of dorsal-fin pterygiophores and neural spines; 14 caudal-fin rays; 86 dorsal-fin rays; 73–74 anal-fin rays; 48 total vertebrae; five hypurals; black peritoneum (posterior region only); ocular side uniformly yellowish-white with numerous, darker reddish-brown freckles especially noticeable along dorsal and ventral contours of body (freckles coalesced into several darker blotches on dorsal and ventral margins on posterior half of body), blind side uniformly yellowish-white, and dorsal and anal fins without conspicuous spots or ocelli. Symphurus monostigmus is most similar to S. macrophthalmus, but differs from that species in ID pattern (1-2-2-1-2 in S. macrophthalmus) and its smaller eye (100–138 vs. 211 in thousandths of HL) with much smaller pupil (pupil diameter/eye diameter 28–32% vs. ca. 54% in S. macrophthalmus).

A New Species of Trinectes (Pleuronectiformes: Achiridae) from the Upper Río San Juan and Río Condoto, Colombia

Symphurus hondoensis Hubbs, 1915, originally described only from the holotype taken in 390–542 m in Suruga Bay Japan, has long been considered a junior synonym ofS. strictus Gilbert, 1905, known from waters off Hawaii, Japan, the Philippine Islands, and South Africa. Based on new information from the holotype and a specimen recently captured from deep waters (789–815 m) off Amami-Oshima Island, southern Japan,S. hondoensis is now established as a valid species.Symphurus hondoensis is unique among congeners in having the combination of a 1–2–3 pattern of interdigitation of proximal dorsal pterygiophores and neural spines, 10 abdominal vertebrae, 14 caudalfin rays, 111–113 dorsal-fin rays, 95 anal-fin rays, 59 total vertebrae, 105–106 scales in longitudinal series, blind side nearly as darkly pigmented as the ocular surface, and a black peritoneum. Recognition ofS. hondoensis increases the number of described species ofSymphurus in waters off Japan to three (S. orientalis Bleeker,S. strictus, andS. hondoensis), with at least one more underscribed species occurring in deepwater hydrothermal vent areas off southern Japan.

Symphurus ocellaris, a new shallow-water symphurine tonguefish collected off Pacific Panama (Pleuronectiformes: Cynoglossidae)

A new species of American sole, captured in freshwater tributaries of the Río San Juan and Río Condoto, near Andagoya, Colombia, is described from four specimens collected by H. G. F. Spurrell around 1913. These fish were deposited in the fish collection of the British Museum (Natural History) and originally identified as Solea panamensis Steindachner, 1876. In the 1960s, Carl L. Hubbs and John A. Bollinger re-examined the specimens and determined that they represented an undescribed species, as indicated by labels placed in jars containing these specimens and through correspondence with staff at the British Museum. However, no formal description of this nominal species was published and its taxonomic status remained unclear. Our re-examination of these specimens and comparisons with all other described species of Trinectes support the conclusions of Hubbs and Bollinger that they are not Solea panamensis, now considered a junior subjective synonym of Trinectes fonsecensis (Günther, 1862), and that they represent an undescribed species. Formal description of the new species, Trinectes hubbsbollinger, named in recognition of the initial discoverers, is provided herein. Trinectes hubbsbollinger is distinguished from its congeners by the combination of 7–8 lightly pigmented, transverse chromatophore lines on the ocular side of the body, ocular-side lower lip with short fimbriae with few branches, few or no cirri on the scaleless area surrounding the ocular-side anterior naris, and absence of pectoral-fin rays.

Description of a new cryptic, shallow-water tonguefish (Pleuronectiformes: Cynoglossidae: Symphurus) from the western North Pacific Ocean

ABSTRACT Symphurus ocellaris is described on the basis of a holotype (73.2 mm SL) and paratype (42.3 mm SL) collected in the environs of Coiba Island, Gulf of Chiriqui, Pacific Panama, at 24 m and 7.4 m, respectively. This species is distinguished from congeners by the combination of: a 1–3–4 pattern of interdigitation of dorsal-fin pterygiophores and neural spines (ID pattern), 12 caudal-fin rays, presence of an ocellated spot on the caudal fin in both sexes, 51 total vertebrae, 96–97 dorsal-fin rays, 80–81 anal-fin rays, 85–86 longitudinal scale rows, a pupillary operculum, unpigmented peritoneum, uniformly pigmented blind side, and ocular-side background coloration lacking prominent dark spots or conspicuous crossbands. Symphurus ocellaris is only the second known species in the genus characterized by a 1–3–4 ID pattern. Among eastern Pacific Symphurus, S. callopterus also has a 1–3–4 ID pattern and 12 caudal-fin rays, but lacks the ocellated caudal spot, has a different ocular-side pigmentation, and has higher, non-overlapping meristic features. The only other eastern Pacific tonguefish with an ocellated caudal-fin spot, S. fasciolaris, differs in having 10 caudal-fin rays, a 1–4–3 ID pattern, and ocular-side pigmentation featuring prominent spots and crossbands.

A new species of Soleichthys (Soleidae: Pleuronectiformes) from tropical seas off northern Australia

Combined results based on morphological characters and analyses of partial sequences of the 16s rRNA and coI genes confirm the validity of a new, cryptic, symphurine tonguefish from the western North Pacific Ocean. Symphurus leucochilus n. sp., a diminutive species reaching sizes to c. 67 mm standard length, is described from nine specimens that were collected from fish-landing ports and from trawls made at c. 150 m off Taiwan and Japan. Symphurus leucochilus shares many similar features with those of Symphurus microrhynchus and that of several undescribed species that are morphologically similar to S. microrhynchus. Symphurus leucochilus has also been misidentified as Symphurus orientalis in fish collections because of shared similarities in some aspects of their morphology. The new species differs from all congeners by the following combination of meristic, morphological and pigmentation features: a predominant 1-2-2-2-2 pattern of interdigitation of proximal dorsal-fin pterygiophores and neural spines; 12 caudal-fin rays; 89-92 dorsal-fin rays; 76-80 anal-fin rays; 49-51 total vertebrae; four hypurals; 75-83 longitudinal scale rows; 32-35 transverse scales; 15-17 scale rows on the head posterior to the lower orbit; absence of a fleshy ridge on the ocular-side lower jaw and a membranous connection between the anterior nostril and lower part of the eye; a narrow interorbital space and dorsal-fin origin anterior to the vertical through the anterior margin of the upper eye; absence of both dermal spots at bases of anterior dorsal-fin rays and melanophores on the isthmus; uniformly yellow to light-brown ocular-side colouration without bands; dorsal and anal fins with alternating series of dark rectangular blotches and unpigmented areas; a uniform white blind side and a bluish-black peritoneum. Despite overall similarities in morphology between S. leucochilus and S. orientalis, as well as between two of the nominal species morphologically similar to S. microrhynchus, analyses of partial 16s rRNA and coI gene sequences show that S. leucochilus, S. orientalis and the two other nominal species represent three distinct lineages within the genus Symphurus.