The complete mitochondrial genome of Acanthogobius lactipes and its phylogenetic analysis.

Acanthogobius lactipes is a demersal, euryhaline fish belonging to the suborder Gobiodei. This study sequenced and described the complete mitochondrial genome of A. lactipes for the first time. The circular genome of A. lactipes is 16,592 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. The overall A, C, G, and T contents were 27.78, 27.31, 17.52, and 27.39%, respectively. Based on the 13 protein-coding genes, the phylogenetic tree showed that A. lactipes formed a well-supported cluster with the genus Acanthogobius and rooted with other family Oxudercidae species.

Schindleria parva, a new species of Schindler's fish (Teleostei: Schindleriidae: Schindleria) from Jeddah, Saudi Arabia, Red Sea.

Schindleria parva, a new species of the family Schindleriidae, is described from two specimens collected from the central Red Sea of Saudi Arabia. The new species is characterized by lack of pigmentation on the body, possession of an inconspicuous gas bladder and the presence of small teeth on the premaxillae. The holotype is a female of 11 mm standard length (SL) (11.9 mm total length) and the paratype is a male of 9 mm SL. Dorsal fin rays 10 (9) anal fin rays 9 (7). The body depth at pectoral-fin origin 5% (4%) of SL, depth at anal-fin origin 8% (7%) SL, predorsal length 63% (65%) SL, preanal length 72% (72%) SL, the first anal-fin ray situated below the fourth dorsal-fin ray), a total of 23 + 16 myomeres. The female contained a series of 30 rectangular eggs in a single row, whereas the male is characterized by a short rod-like urogenital papilla. Species of the genus Schindleria are likely the smallest marine vertebrates on the planet and S. parva is likely the smallest Schindleria species in the Red Sea. The global diversity of Schindleria is likely underestimated due to the paedomorphic features of this genus. Its fast generation times make it a species-rich genus of high turnover rates, thus potentially highly important for the trophic food webs of coral reefs. Thus, this finding advances knowledge on the biodiversity of the Red Sea, highlights its conservation significance, and contributes towards the understanding of the complexity of the coral-reef fish community.

Diversification and colonization processes in Gobioidei predicted based on mitochondrial 12S rRNA with focusing on Oxudercidae.

Gobioidei is one of the largest vertebrate taxa with over 2000 species observed around the globe. The largest group in Gobioidei is gobies that had been classified as one family, Gobiidae, based on morphological features. Molecular phylogenetic studies revealed that gobies consisted of two monophyletic families, Gobiidae and Oxudercidae, in which 19 lineages have been proposed, despite some claims arisen about the relationship among these lineages or species. We analyzed 58 Gobioidei species, including 45 East Asian oxudercids, based on 12S rRNA sequences to reconstruct the spatiotemporal diversification history of gobies. Our analysis yielded the results compatible with the previous reports in a large framework. The common ancestor of Gobiidae and Oxudercidae were estimated to appear at 38.66 Mya. Genus-level splits occurred in Gobiidae and Oxudercidae predominantly at Miocene and late Miocene to early Pleistocene, respectively. Gobies have likely originated in many parts of the northern and western Pacific Ocean, of which a large proportion of Oxudercidae have adapted to various environments in the North Pacific.

A new species of Corcyrogobius (Teleostei: Gobiidae) from Île de Ngor, Senegal.

Corcyrogobius pulcher sp. nov. is described from off Île de Ngor, Dakar, Senegal. Corcyrogobius pulcher is distinguished from its two congeners by having the rear edge of the jaws ending posteriorly below mideye, second dorsal fin I/9, pectoral fin rays 17, pelvic fins oval or truncated posteriorly, scales in lateral series 26-27, anterior oculoscapular head canal with pore ß, suborbital row b of sensory papillae anteriorly beginning below vertical of posterior edge of eye, dark vertical caudal bar, branchiostegal membrane without intense dark spot, cheek with two oblique whitish stripes, the first going from the eye downwards and forward to the posterior jaws, the second on the preopercular, alternating with brown oblique stripe going from behind the eye downwards and forward across the cheek. Furthermore, mitochondrial COI-barcoding data unambiguously support the species-level distinctiveness of the three Corcyrogobius species. A key to the species of Corcyrogobius is provided.

New species of Silhouettea (Teleostei: Gobiidae) from Qeshm Island, Iran and the DNA barcoding of the Persian Gulf and Oman Sea gobies.

Silhouettea ghazalae sp. nov. is described from Qeshm Island, Persian Gulf. Silhouettea ghazalae sp. nov. is distinguished from congeners by having: small mental fold present on chin, head length 31.4-32.4% of standard length, head width 24.5% of standard length, second dorsal fin I/11, anal fin I/13, breast with large cycloid scales, predorsal area naked, suborbital row b anteriorly beginning below anterior edge of pupil, posteriorly ending below pore ß, suborbital row c anteriorly extending more than row b and posteriorly extending less than row b, suborbital row cp oblique with four papillae, body with four ill-defined midlateral blotches and the fifth a triangular mark on the caudal fin base, no clearly defined pale saddles on back, and the first dorsal fin pigmented with dots and with dark blotch present anteriorly. A key to Silhouettea species is provided. A dataset including novel and publicly available mtDNA COI sequences of 12 species from the Persian Gulf and Oman Sea gobies belonging to eight genera have been assembled in order to provide a reference dataset for DNA barcoding studies. The new species is further characterised by a minimum K2P distance of 21% to its closest relatives in our dataset, Cabillus tongarevae in the mtDNA COI barcode region.

Two new species of Hetereleotris (Perciformes: Gobiidae) from the Red Sea.

Two new species of the gobiid genus Hetereleotris, H. aurantiaca sp. nov. and H. semisquamata sp. nov., are described from the Red Sea, the former from Saudi Arabia at Jeddah from the cave at depth of 14-16 m, and the latter from the southern Egypt from reef flat. Hetereleotris aurantiaca sp. nov. is distinguished from its congeners by having dorsal-fin rays VI + I,10; anal-fin rays I,9; pectoral-fin rays 14, all rays branched; pelvic-fin rays I,5, the fin separated and without frenum, 5th ray unbranched; anterior nostril with a long tube without process from the rim, posterior nostril a pore with erected rim; no tentacle above eye; posterior angle of jaws extending posteriorly to below posterior edge of pupil; no opercular spine; no mental frenum; pelvic fins longer than pectoral fins; squamation reduced to a few scales on caudal peduncle at caudal-fin base; no head canals; by presence, size and pattern of suborbital rows of sensory papillae; and orange head and yellowish orange body with five faint brown bars. Hetereleotris semisquamata sp. nov. is distinctive among its congeners by unique scale pattern (scales cycloid, the squamation reduced, tapering from caudal-fin base along lateral midline towards pectoral fin where nearly reaching its base) and by coloration (head and body whitish, with brown line from eye to end of upper lip, dark brown band across interorbital area and continuing obliquely from eye to corner of opercle, broad dark brown band below first dorsal fin continuing into fin, and moderately broad dark brown bar on caudal-fin base). Furthermore, it is characterized in having dorsal-fin rays VI + I,11, anal-fin rays I,10, pectoral-fin rays 16, and absence of head canals. In addition to descriptions of two species, a key to all species of Hetereleotris is provided. Hetereleotris psammophila is reported outside the Gulf of Aqaba for the first time.

Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness.

The use of genome-scale data to infer phylogenetic relationships has gained in popularity in recent years due to the progress made in target-gene capture and sequencing techniques. Data filtering, the approach of excluding data inconsistent with the model from analyses, presumably could alleviate problems caused by systematic errors in phylogenetic inference. Different data filtering criteria, such as those based on evolutionary rate and molecular clocklikeness as well as others have been proposed for selecting useful phylogenetic markers, yet few studies have tested these criteria using phylogenomic data. We developed a novel set of single-copy nuclear coding markers to capture thousands of target genes in gobioid fishes, a species-rich lineages of vertebrates, and tested the effects of data-filtering methods based on substitution rate and molecular clocklikeness while attempting to control for the compounding effects of missing data and variation in locus length. We found that molecular clocklikeness was a better predictor than overall substitution rate for phylogenetic usefulness of molecular markers in our study. In addition, when the 100 best ranked loci for our predictors were concatenated and analyzed using maximum likelihood, or combined in a coalescent-based species-tree analysis, the resulting trees showed a well-resolved topology of Gobioidei that mostly agrees with previous studies. However, trees generated from the 100 least clocklike frequently recovered conflicting, and in some cases clearly erroneous topologies with strong support, thus indicating strong systematic biases in those datasets. Collectively these results suggest that data filtering has the potential improve the performance of phylogenetic inference when using both a concatenation approach as well as methods that rely on input from individual gene trees (i.e. coalescent species-tree approaches), which may be preferred in scenarios where incomplete lineage sorting is likely to be an issue.

Revising the distribution of a threatened goby, Apocryptodon punctatus (Perciformes, Oxudercidae), in Japan with the discovery of an isolated population.

Five specimens of a threatened goby, Apocryptodon punctatus (21.2-40.1 mm in standard length), were collected at a mudflat site of Kushima City, Miyazaki Prefecture, Kyushu, southern Japan over two seasons, autumn (September 2015) and spring (April 2016). A review of distributional records of Apocryptodon punctatus revealed that this population represents the southernmost record of the species in Japanese waters, and is isolated ca. 200 km south-southwest from the nearest point of the main range of the species along the Pacific coast of Japan. Publicising this population will help conserve it and its vulnerable habitat.

Convergent Aspects of Acoustic Communication in Darters, Sculpins, and Gobies.

Darters (Perciformes, Percidae), sculpins (Perciformes, Cottidae), and gobioids (Gobiiformes, Gobioidei) exhibit convergent life history traits, including a benthic lifestyle and a cavity nesting spawning mode. Soniferous species within these taxa produce pulsed and/or tonal sounds with peak frequencies below 200 Hz (with some exceptions), primarily in agonistic and/or reproductive contexts. The reduced or absent swim bladders found in these taxa limit or prevent both hearing enhancement via pressure sensitivity and acoustic amplification of the contracting sonic muscles, which are associated with the skull and pectoral girdle. While such anatomies constrain communication to low frequency channels, optimization of the S/N (signal-to-noise) ratio in low frequency channels is evident for some gobies, as measured by habitat soundscape frequency windows, nest cavity sound amplification, and audiograms. Similar S/N considerations are applicable to many darter and sculpin systems. This chapter reviews the currently documented diversity of sound production in darters, sculpins, and gobioids within a phylogenetic context, examines the efficacy of signal transmission from senders to receivers (sound production mechanisms, audiograms, and masking challenges), and evaluates the potential functional significance of sound attributes in relation to territorial and reproductive behaviours.

The complete mitogenome of the minute mudskipper, Periophthalmus minutus Eggert, 1935 (Perciformes: Gobiidae: Oxudercinae).

The mitogenome of an Australian sample of the mudskipper, Periophthalmus minutus, was recovered from partial sequencing using the MiSeq sequencer. This mudskipper has a mitogenome of 16,506 base pairs (55% A + T content) made up of two ribosomal subunit genes, 13 protein-coding genes, 22 transfer RNAs, and a 838 bp non-coding AT-rich region. This is the first sequenced mitogenome for the genus Periophthalmus and the fifth for the subfamily Oxudercinae.

Phylogeographical analysis of a cold-temperate freshwater fish, the Amur sleeper (Perccottus glenii) in the Amur and Liaohe River basins of Northeast Asia.

The Amur sleeper Perccottus glenii (Perciformes, Gobioidei, Odontobutidae) is well known as an invasive fish in the river basins of Eastern and Central Europe, but its genetic background is unavailable across its native habitats in northeast Asia. In this study, we used the mitochondrial cytochrome b gene by sampling 19 populations of P. glenii across its native distributional areas of Liaohe and Amur River basins to explore its evolutionary history. Phylogenetic analyses identified three major clades within P. glenii, among which Clade A and Clade B were co-distributed in the Liaohe and Amur River basins, and Clade C was restricted to the latter. Molecular dating showed that the splits of Clades A, B and C have happened in the late Early-early Middle Pleistocene and the most recent common ancestors of these clades have been presented in the late Middle-early Late Pleistocene. The P. glenii showed very high levels of genetic structure among populations (ΦST = 0.801), probably due to the characters of its life histories with very limited dispersal ability. The admixture of different clades in some populations of P. glenii probably reflects historical secondary contact. These findings indicate that Pleistocene climatic oscillation and river capture were major determinants for genetic variations and evolutionary history of the P. glenii.

Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies.

Gobioidei is one of the largest suborders of teleost fishes, with nearly 2000 extant species currently recognized. They have a worldwide distribution and show a spectacular variety in morphology, ecology, and behavior. Despite their importance, phylogenetic relationships among many groups of gobioids (including some of the major lineages) still remain poorly understood. In this study, we analyze sequence data of five molecular markers (two mitochondrial and three nuclear) averaging 6000 bp for 222 species of gobioids. Our study is the first to include both multiple nuclear and mitochondrial genes to reconstruct a comprehensive multilocus phylogeny of gobioids encompassing most major lineages representing the overall diversity of one of the most speciose vertebrate lineages. Two separate datasets are produced and used to specifically address the phylogenetic placement of Rhyacichthyidae and Odontobutidae, and the phylogenetic relationships among gobioid lineages. Our results strongly support that the initial split in the gobioid tree separated a clade containing Rhyacichthyidae+Odontobutidae as the sister group of all other lineages. The family Eleotrididae branches off the gobioid tree after the Rhyacichthyidae+Odontobutidae clade, followed by the Butidae as sister group to the Gobiidae. Additionally, several major monophyletic groups are confidently identified within the two major Gobiidae subclades, the gobiine-like gobiids and the gobionelline-like gobiids. Robustness of the phylogenetic trees inferred here is significantly higher than that of previous studies, hence our results provide the most compelling molecular phylogenetic hypothesis of Gobioidei thus far. For the first time, we provide a comprehensive sampling of European gobies that traditionally have been divided into "transverse" gobies and "sand gobies". We show that the European gobies cluster in three distinct lineages, the Pomatoschistus-, Aphia-, and Gobius-lineages. The former resolved within the gobionelline-like gobiids and the latter two within the gobiine-like gobiids. These findings have significant implications for our understanding of the phylogeographic origin of European gobies in the light of the closure of the Paratethys. A rogue taxon analysis identified Kraemeria as an unstable taxon decreasing support at the base of the gobiine-like gobiids. Removal of this rogue taxon significantly increased phylogenetic resolution in that part of the tree and revealed additional insights into early bursts of cladogenesis of the gobiine-like gobiids.

Peces criptobentónicos de arrecifes coralinos en el Parque Nacional Archipiélago de Los Roques, Caribe de Venezuela

Cryptobenthic coral reef fishes in Los Roques National Park, Caribbean of Venezuela. A significant portion of coral reef fish assemblages are composed of small cryptobenthic fishes, but these are poorly represented in regional fish characterization works. We characterized the cryptobenthic reef fish community associated with coral reef in Los Roques National Park during six week surveys. The study included 11 locations in which these fish were registered in transects of 10x2m. Specimens were collected using the suction method and a fine-mesh net. A total of 31 species of six families were collected (four Blenniidae, six Chaenopsidae, one Gobiesocidae, 12 Gobiidae, seven Labrisomidae and one Tripterygiidae). Six represented new records to the park, and Coralliozetus cardonae (Chaenopsidae) was a new record for Venezuela. The most important families were Gobiidae, Chaenopsidae and Labrisomidae. Cryptic fish assemblages changed with the reef environments, with a clear distribution pattern: some species were only observed in shallow areas of less than 5m depth, while in fringing and barrier reef areas, other species were present and differentially distributed between the reef crest and the seaward slope. These patterns probably are related to the close association that these small fish maintain with the benthos. Rev. Biol. Trop. 58 (1): 311-324. Epub 2010 March 01.

En los ambientes arrecifales, a pesar de que una proporción significativa de la ictiofauna está compuesta de pequeños peces criptobentónicos, estos están pobremente representados en los trabajos de caracterización regional. El objetivo de este estudio fue caracterizar la comunidad de estos peces asociados a diversos arrecifes coralinos en el Parque Nacional Archipiélago de Los Roques. El muestreo de seis semanas abarcó 11 localidades donde se censaron estos peces en franjas de 10x2m. Para la colecta de ejemplares se utilizó el método de succión y redes de mano. Se registraron 31 especies de seis familias (cuatro Blenniidae, seis Chaenopsidae, una Gobiesocidae, 12 Gobiidae, siete Labrisomidae y una Tripterygiidae), donde seis representaron nuevos registros para el parque, y Coralliozetus cardonae (Chaenopsidae) un nuevo registro para Venezuela. Las familias más importantes fueron Gobiidae y Chaenopsidae y Labrisomidae. Se observó un patrón de distribución de estos peces según los ambientes arrecifales: las especies de los bajos ambientes coralinos de profundidad menor a 5m, y las especies de los arrecifes franjeantes, que a su vez se distribuyeron diferencialmente entre la cresta arrecifal y el talud. Estos patrones probablemente se deben a la estrecha relación que estos peces mantienen con la comunidad arrecifal.