DNA barcoding of marine teleost fishes (Teleostei) in Cebu, the Philippines, a biodiversity hotspot of the coral triangle.

A morphology-based barcoding library of market teleost fishes (Teleostei) in Cebu is built based on cytochrome c oxidase subunit I (COI) sequences and voucher specimens which aimed to establish a reliable reference of frequently traded fishes in the province, a biodiversity hotspot at the center of the Philippine archipelago. A total of 1721 specimens were collected from 18 fish markets and landing sites around the province, in which 538 specimens were sequenced belonging to 393 species from 229 genera, 86 families, and 37 orders. Most speciose families are coral reef or reef-related shallow-water species. Twelve species from 11 families are newly recorded in the Philippine waters, among which 7 species are deep-sea inhabitants, while 3 species have expanded their distribution range. Only 20 taxa could not be identified to the species level due to the difficulty in morphological examinations, absence of matched reference sequences in online databases, and/or problematic species awaiting further studies. This first comprehensive DNA barcoding survey of Cebu fishes can facilitate further taxonomic research as well as the conservation and management of fisheries in the Philippines.

Description of a new moray eel (Anguilliformes: Muraenidae) from the Philippines, with a preliminary assessment of genetic and morphological variations of the Uropterygius concolor species complex.

Uropterygius concolor Rüppell, the type species of the genus Uropterygius, is a small, uniformly brown moray considered to be widely distributed in the Indo-Pacific region. However, a recent study indicated that the real U. concolor is currently known only from the type locality in the Red Sea, and species recorded outside the Red Sea may represent a species complex that comprises several species. In this study, we assess the genetic and morphological variations of this species complex based on available data. Analyses of cytochrome c oxidase subunit I sequences revealed at least six distinct genetic lineages recognized under 'U. concolor'. After carefully comparing the morphologies, one of the lineages is described herein as a new species, Uropterygius mactanensis sp. nov., based on 21 specimens collected from Mactan Island, Cebu, Philippines. Another distinct lineage is considered to be a possibly undescribed species based on diagnostic morphological characters. Although the taxonomic status of junior synonyms of U. concolor and some lineages still remain unresolved, this study provides informative morphological characters (i.e., tail length, trunk length, vertebrae number, and arrangement of teeth) that can be used in future studies on this species complex.

A New Species of Parascorpaena Bleeker, 1876 (Teleostei: Scorpaenidae) from Taiwan.

A new species of scorpionfish, Poseidon's scorpionfish Parascorpaena poseidon, is described on the basis of ten specimens collected from southwestern Taiwanese waters ranging from Penghu to Chufongbi, Pingtung. The morphological and molecular analyses reveal the new species is clearly separated from the two similar species, P. aurita and P. mossambica. Parascorpaena poseidon is distinguished from congeners by the following combination of characters: three equal-sized suborbital spines without ridge; supraocular tentacle absent or very short; pectoral-fin rays 15-16 (usually 16); pored lateral-line scales 22-26 (usually 22-23); longitudinal scale rows 43-47; pre-dorsal-fin scale rows 2-3 (usually 3); 10-12 scale rows between 6th dorsal-fin spine base and lateral line; 10-12 scale rows between the last dorsal-fin spine base and lateral line; total gill rakers 15-16, gill rakers on hypobranchial 2-3; ratio of 11th and 12th dorsal-fin spine 60%-81% (mean 73%); blackish spots randomly distributed on all fins; absence of a distinct black blotch on spinous dorsal fin in male; body size relatively large.

Two New Moray Eels of Genera Diaphenchelys and Gymnothorax (Anguilliformes: Muraenidae) from Taiwan and the Philippines.

Two new moray eels of the genera Diaphenchelys and Gymnothorax from Taiwan and the Philippines are described. Diaphenchelys laimospila sp. nov. is described based on two specimens that represent the third species and a new geographic record of the genus. It can be distinguished from the other two congeners by the number of cephalic sensory pores, vertebral formula, morphometric measurements, and the coloration pattern. Gymnothorax pseudokidako sp. nov. is a muraenid with a dark brown body covered by pale snowflake-like blotches. It differs from the most similar species Gymnothorax kidako (Temminck and Schlegel) by having a relatively short tail (50.5-53.0% vs. 52.9-56.4% of TL), more dentary teeth (17-26 vs. 16-20), fewer total vertebrae (134-139 vs. 137-143), and the absence of white margin on anal fin (vs. prominent white margin). These two new species were also confirmed by molecular analyses, the mitochondrial COI gene (593 bp) for D. laimospila, and the nuclear EGR3 gene (767 bp) for G. pseudokidako.

DNA metabarcoding for dietary analysis of Holland's carp (Spinibarbus hollandi) to evaluate the threat to native fishes in Taiwan.

DNA metabarcoding analysis for gut contents has been shown to compensate the disadvantage of traditionally morphological identification and offer higher resolution of prey items in an efficient way. Holland's carp (Spinibarbus hollandi) is a freshwater fish native to southern and eastern Taiwan. In the past two decades, this species has been introduced as a sport fish into the river basins of northern and western Taiwan. The large body size and active predation make it a potential threat for native fishes, but which native species are preyed by Holland's carp remains unknown. In this study, the diet from the gut contents of Holland's carp from the Zhonggang River, an invaded basin, was examined using DNA metabarcoding from 51 individuals and by morphological examinations on 140 samples. Detritus of plants were found in 83.6% samples (117 individuals). Twenty fish species of seven families were identified by DNA metabarcoding, including species of all water layers. Taiwan torrent carp (Acrossocheilus paradoxus) and Rhinogobius spp. are the most common prey items. Based on the results of this study, Holland's carp is considered an opportunistic omnivore because of its diverse diet items, which is an important trait for successful invasive fish species. The population decline of Opsariichthys pachycephalus may not result from the invasion of Holland's carps. Nonetheless, the time lag between successful invasion and the samplings of this study may be a concern because the population size of O. pachycephalus may have declined and become difficult to prey. The Holland's carps consumed the least species in winter; nonetheless, the occurrence frequencies of preys among seasons were not significantly different probably because of limited temperature fluctuation. The smallest Holland's carps consumed the least prey species compared to other size categories, similar to the relationship of prey species number to size of invasive largemouth bass (Micropterus salmoides).

Amphidromous but endemic: Population connectivity of Rhinogobius gigas (Teleostei: Gobioidei).

Rhinogobius gigas is an amphidromous fish endemic to eastern Taiwan. Fishes with the diadromous behavior are expected to have a broader distribution range and higher genetic homogeneity despite that some amphidromous fishes with limited distribution are observed and R. gigas is an additional exception with a limited distribution range. Rhinogobius gigas has been documented to be retained inshore near the river plume with a short pelagic larval duration of 30-40 days, which may account for the endemism of this species. The short marine larval stage of R. gigas may imply a population genetic structure and the aim of the present study is to test whether the population genetic structure is present in R. gigas. To test the population genetic structure, fragments of mitochondrial displacement loop and cytochrome c oxidase subunit I were sequenced to provide molecular inference for genetic structure among populations. Sixty-nine haplotypes were identified among 191 R. gigas from 10 populations of eastern Taiwan and the mean haplotype and nucleotide diversities for all samples were 0.956 and 0.0024, respectively, implying a bottleneck followed by a recent population expansion further supported by Fu's Fs (-26.6; p < 0.001) and Tajima's D (-1.5; p = 0.037) values. The phylogenetic analysis revealed lack of genetic structure and the bush-like median joining network without commonly shared haplotypes supports the same scenario. The genetic homogeneity is probably due to the amphidromous life history providing the opportunity for passive larval transportation among the rivers through coastal currents in eastern Taiwan. The endemism to eastern Taiwan may be a consequence of complicated interactions among short pelagic larval duration, interspecific competition and coastal currents.

Rhodeus flaviventris, a new bitterling (Teleostei: Cyprinidae: Acheilognathinae) from China.

Rhodeus flaviventris, a new species, is described from the Le-An River, a tributary flowing into Poyang Lake in the Yangtze River basin, in Jiangxi Province, China. It is distinguished from all congeners by the combination of characters: branched dorsal-fin rays 9 (9-10); branched anal-fin rays 9 (9-10); longest simple rays of dorsal and anal fins thick and stiff; longitudinal scale series 33-34; transverse scale series 11 (10-12); pored scales 4-7; vertebrae 32-34; spindle-shaped eggs with major axis of 3.1-3.7 mm; color pattern of nuptial males (iris yellowish, belly yellow, central part of caudal fin orange, dorsal and anal fins with reddish-orange stripe).

A review of the genus Strophidon (Anguilliformes: Muraenidae), with description of a new species.

Strophidon McClelland is a muraenid genus with characteristic appearance of a very elongated body, a large mouth cleft and anteriorly placed eyes. The nomenclature and taxonomic history of species within Strophidon are contentious and its members are easily misidentified. In the present study, species of the genus Strophidon are revised based on morphological and molecular data, and five species are considered valid, including S. dawydoffi Prokofiev, S. dorsalis (Seale), S. sathete (Hamilton), S. ui Tanaka and a new species, S. tetraporus. Strophidon tetraporus sp. nov. is described based on 15 specimens from Indonesia, the Philippines, Taiwan and Vietnam with the unique characteristic of the constant presence of the fourth infraorbital pore among species of Strophidon. The intraspecific variation of vertebral formula within S. dorsalis is discussed based on molecular data. Muraena macrurus Bleeker and Thyrsoidea longissima Kaup are synonyms of S. sathete that can be distinguished from the most similar congener S. ui by a longer tail, smaller eyes and more inner maxillary and inner dentary teeth. A key to identify species of Strophidon is provided. The distribution and maximum size of each species are also re-evaluated.

Facultative amphidromy and pelagic larval duration plasticity of Rhinogobius formosanus (Teleostei, Gobioidei).

Rhinogobius formosanus Oshima, 1919 has long been considered an amphidromous goby. However, a landlocked population recently found in the Jingualiao Creek upstream of the Feitsui Reservoir in Taipei suggests that R. formosanus may complete its life in the river. This study aims to verify the habitat use of the landlocked population of R. formosanus collected from the Feitsui Reservoir and an amphidromous population collected in Malian Creek using otolith Sr:Ca ratio analysis. The hypothesis that early life history varies between the landlocked and migratory gobies was also tested. Genetic analyses show that the Feitsui Reservoir and Malian Creek populations are not genetically different. Rhinogobius formosanus from Malian Creek showed high-to-low otolith Sr:Ca ratios suggesting that these specimens spent a planktonic larval stage in the sea followed by a freshwater life at later stages. In contrast, R. formosanus from the Feitsui Reservoir showed constant lower otolith Sr:Ca ratios, implying a landlocked life history of fish in the creek upstream of the reservoir. In addition, the analysis of growth increments showed a longer pelagic larval duration for the fish in the Malian Creek (58.8 days) than those in the Feitsui Reservoir (38.8). Variation of pelagic larval duration in two genetically homogenous populations implies acclimatization to the reservoir by the landlocked gobies. This study shows that R. formosanus, like some other congeners, is capable of adapting to a freshwater landlocked environment in its early developmental stage and supports the hypothesis that landlocked populations may have a shorter pelagic larval duration.

Protective Evaluation of Compounds Extracted from Root of Rhodiola rosea L. against Methylglyoxal-Induced Toxicity in a Neuronal Cell Line.

Rhodiola rosea L. (R. rosea) is one of the most beneficial medicinal plants and it is studied as an adaptogen. This study aims to evaluate the neuroprotective activity of compounds extracted from the root of R. rosea against methylglyoxal (MG)-induced apoptosis in neuro-2A (N2A) cells. The root of R. rosea was extracted with ethanol and partitioned with water, ethyl acetate, and n-butanol fractions to evaluate acetylcholinesterase (AChE) inhibitory activity and neuroprotective activity. The ethyl acetate fraction exhibited the highest values of AChE inhibitory activity (49.2% ± 3%) and cell viability (50.7% ± 4.8%) for neuroprotection. The structure identification of the most potential fraction (ethyl acetate fraction) revealed 15 compounds, consisting of three tannins, five flavonoids, and seven phenolics by infrared spectroscopy, nuclear magnetic resonance, and mass spectroscopy. All compounds were evaluated for their neuroprotective activity. Salidroside had the most potential neuroprotective activity. Gallic acid and methyl gallate had potential cytotoxicity in N2A cells. This study showed that R. rosea might have potential neuroprotective activities.

Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters.

A background study is important for the conservation and stock management of a species. Terapon jarbua is a coastal Indo-Pacific species, sourced for human consumption. This study examined 134 samples from the central west and east coasts of Peninsular (West) Malaysia and East Malaysia. A 1446-bp concatenated dataset of mtDNA COI and Cyt b sequences was used in this study and 83 haplotypes were identified, of which 79 are unique haplotypes and four are shared haplotypes. Populations of T. jarbua in Malaysia are genetically heterogenous as shown by the high level of haplotype diversity ranging from 0.9167-0.9952, low nucleotide diversity ranging from 0.0288-0.3434, and high FST values (within population genetic variation). Population genetic structuring is not distinct as shown by the shared haplotypes between geographic populations and mixtures of haplotypes from different populations within the same genetic cluster. The gene flow patterns and population structuring observed among these regions are likely attributed to geographical distance, past historical events, allopatric speciation, dispersal ability and water currents. For instance, the mixture of haplotypes revealed an extraordinary migration ability of T. jarbua (>1200 km) via ancient river connectivity. The negative overall value of the neutrality test and a non-significant mismatch distribution are consistent with demographic expansion(s) in the past. The median-joining network concurred with the maximum likelihood haplotype tree with three major clades resolved. The scarcity of information on this species is an obstacle for future management and conservation purposes. Hence, this study aims to contribute information on the population structure, genetic diversity, and historical demography of T. jarbua in Malaysia.

DNA barcoding of coastal ray-finned fishes in Vietnam.

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding database of coastal ray-finned fishes in Vietnam. A total of 3,638 specimens were collected from fish landing sites in northern, central and southern Vietnam. Seven hundred and sixty-five COI sequences of ray-finned fishes were generated, belonging to 458 species, 273 genera, 113 families and 43 orders. A total of 59 species were newly recorded in Vietnam and sequences of six species were new to the Genbank and BOLD online databases. Only 32 species cannot be annotated to species level because difficulty in morphological identifications and their Kimura-2-Parameter (K2P) genetic distances to most similar sequences were more than 2%. Moreover, intra-specific genetic distances in some species are also higher than 2%, implying the existence of putative cryptic species. The mean K2P genetic distances within species, genera, families, orders and classes were 0.34%, 12.14%, 17.39%, 21.42%, and 24.80, respectively. Species compositions are quite different with only 16 common species among northern, central and southern Vietnam. This may attribute to multiple habitats and environmental factors across the 3,260 km Vietnamese coastline. Our results confirmed that DNA barcoding is an efficient and reliable tool for coastal fish identification in Vietnam, and also established a reliable DNA barcode reference library for these fishes. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in Vietnam.

Revalidation of a moray eel, Gymnothorax mucifer Snyder, 1904 (Teleostei: Anguilliformes: Muraenidae), with a revised distribution.

Gymnothorax mucifer Snyder, 1904 has been synonymized with G. kidako (Temminck Schlegel, 1846) since 2000. Examination of material from Hawaii (type locality) and Taiwan reveal that G. mucifer is a valid species based on morphological and molecular data. It can be distinguished from G. kidako by a plainly colored lower jaw (vs. mottled), white margin of the anal fin replaced by serial pale blotches posteriorly on the tail (vs. white margin continuous to tip of tail), more dentary teeth (17-27 vs. 16-20), and fewer total vertebrae (130-141 vs. 140-143). In the present study, a redescription of G. mucifer is provided, and the distribution of G. mucifer and G. kidako is reevaluated.

Pelagic larval duration, growth rate, and population genetic structure of the tidepool snake moray Uropterygius micropterus around the southern Ryukyu Islands, Taiwan, and the central Philippines.

The relationships between pelagic larval duration (PLD) and geographic distribution patterns or population genetic structures of fishes remain obscure and highly variable among species. To further understand the early life history of the tidepool snake moray Uropterygius micropterus and the potential relationship between PLD and population genetic structure of this species, otolith microstructure and population genetics based on concatenated mtDNA sequence (cytochrome b and cytochrome oxidase subunit I, 1,336 bp) were analyzed for 195 specimens collected from eight locations around the southern Ryukyu Islands, Taiwan, and the central Philippines. Eels with longer PLD and lower otolith growth rates were observed at relatively higher latitudes with lower water temperatures (54.6 ± 7.7 days and 1.28 ± 0.16 µm day-1 on Ishigaki Island, Japan, vs. 43.9 ± 4.9 days and 1.60 ± 0.19 µm day-1 on Badian, the Philippines), suggesting that leptocephali grew faster and had shortened pelagic periods in warmer waters. Meanwhile, the eels along the southwest coast of Taiwan had relatively longer PLD (57.9 ± 10.5 days), which might be associated with the more complex ocean current systems compared to their counterparts collected along the east coast of Taiwan (52.6 ± 8.0 days). However, the southwestern and eastern Taiwan groups had similar otolith growth rates (1.33 ± 0.19 µm day-1 vs. 1.36 ± 0.16 µm day-1). Despite the intergroup variation in PLD, genetic analysis revealed fluent gene flow among the tidepool snake morays in the study regions, implying that intraspecies PLD variation had a weak effect on genetic structure. The leptocephalus stage might have ensured the widespread gene flow among the study areas and leptocephalus growth was likely influenced by regional water temperature.

Sinorhodeus microlepis, a new genus and species of bitterling from China (Teleostei: Cyprinidae: Acheilognathinae).

A new genus and species, Sinorhodeus microlepis gen. et sp. nov., is described from a tributary of the Yangtze River, in Chongqing City, China. Sinorhodeus gen. nov. can be distinguished from four closely related genera, Paratanakia, Pseudorhodeus, Rhodeus, and Tanakia, by the following combination of characters: pharyngeal teeth 0,0,4-4,0,0, longitudinal scales 41-46, white spots on dorsal-fin rays absent, a black blotch on dorsal fin in juvenile absent, and less developed wing-like yolk sac projections in larvae. Phylogenetic analysis of one mitochondrial gene and six nuclear genes supports the establishment of the new genus.

The complete mitochondrial genome sequence of Nemateleotris decora (gobiiformes, gobiidae).

We determined the mitochondrial genome (mitogenome) sequence of Nemateleotris decora by using a long polymerase chain reaction (PCR) method and next-generation sequence (NGS) technology. The total length of N. decora mitogenome is 16 502 bp, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a non-coding control region. The overall base composition of N. decora is 25.22% for A, 25.90% for T, 30.69% for G, and 18.19% for C. Our results showed the complete mitogenome is a good marker for the phylogenetic study.

Smilosicyopus leprurus (Teleostei: Gobiidae) is a Fin-eater.

Ying-Tzu Lu, Min-Yun Liu, You He, and Te-Yu Liao (2016) Smilosicyopus leprurus is a small goby distributed in the Ishigaki Island and Taiwan. Hobbyists found S. leprurus attacked on the caudal fin of fishes kept together. In this study we investigate whether this fin-eating behavior occurs in the field and whether S. leprurus can be considered a fin-eater. Behavior observation in a tank showed S. leprurus snapped off a piece of fins and swallowed. Among S. leprurus preserved immediately after capture, a fin fragment and a few scales were recovered in the gut of a specimen and DNA barcoding shows the fin fragment belonging to Sicyopterus japonicas. The fin-eating behavior of S. leprurus occurs in captivity and in the wild. In addition, the 3D renderings of oral jaws of S. leprurus were provided. Oral teeth are numerous and arranged in close proximity to each other all together like a bladed dentition, which may provide the capability to shear the fin of its prey. The present study shows S. leprurus a fin-eater despite not feeding exclusively on fins.

Population structure of Hirundichthys oxycephalus in the northwestern Pacific inferred from mitochondrial cytochrome oxidase I gene.

BACKGROUND: Hirundichthys oxycephalus is an important flyingfish resource in eastern Taiwan and northwestern Japan. A substantial catch decline in Taiwan has caused serious concerns on stock status of the fish, prompting the government to impose a set of regulations on flyingfish egg fishery since 2008. However, the regulations were set in a precautionary manner, without considering the fundamental understanding of the population genetic structure. This study aims to investigate the population genetic structure of H. oxycephalus in the region based on mtDNA cytochrome oxidase I (COI) gene and to thus provide scientific information for sustainable management of theresource. RESULTS: Tissue samples (156) from six localities of eastern Taiwan and western Japan were collected, and 616 bpof mtDNA COI gene were sequenced. Seventy haplotypes were determined, and the haplotype diversity and nucleotide diversity were estimated as 0.93% and 0.57%, respectively. Results of various statistical analyses suggested that the genetic differentiations among the six localities were small and most variation occurred within populations, indicating a high gene flow in the region with undergoing population expansion. Although the study showed that the fishes were genetically divided into two groups, the support was low and the separation was not geologically evident. CONCLUSIONS: Thestudy revealed two groups of H.oxycephalus inthe northwestern Pacific Ocean. However, due to high gene flow, an association of either group to a spatial distribution was not observed, and so the two groups may be considered as one population. Thus, the results favored the conclusion that H. oxycephalus from eastern Taiwan and western Japan belong to the same population and, consequently, that the management unit of the current regulations only covering eastern Taiwan does not match the spatial structure of the population. Rather, the results suggest that joint efforts from countries within the population boundary are necessary to maintain a sustainable exploitation.

Phylogeographical analysis on Squalidus argentatus recapitulates historical landscapes and drainage evolution on the island of Taiwan and mainland China.

Phylogeographical analyses on Squalidus argentatus samples from thirteen localities within mainland China and Taiwan were conducted for biogeographic studies, as their dispersal strictly depends on geological evolution of the landmasses. A total of 95 haplotypes were genotyped for mtDNA cyt b gene in 160 specimens from nine river systems. Relatively high levels of haplotype diversity (h = 0.984) and low levels of nucleotide diversity (π = 0.020) were detected in S. argentatus. Two major phylogenetic haplotype groups, A and B, were revealed via phylogenetic analysis. The degree of intergroup divergence (3.96%) indicates that these groups diverged about 4.55 myr (million years) ago. Haplotype network and population analyses indicated significant genetic structure (F(ST) = 0.775), largely concordant with the geographical location of the populations. According to SAMOVA analysis, we divided these populations into four units: Yangtze-Pearl, Qiantang-Minjiang, Jiulong-Beijiang and Taiwan groups. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots indicated a significant population expansion for lineage A and B, approximately dated 0.35 and 0.04 myr ago, respectively. We found strong geographical organization of the haplotype clades across different geographic scales that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow.