Acute noise is harmful on the anti-predator behaviour of commercially important juvenile coral reef fishes.

Fish stock enhancement has been utilised in Taiwan for more than 30 years, yet the impacts of anthropogenic noise on the enhancement programs remain unknown. Anthropogenic noise can induce physiological and behavioural changes in many marine fishes. Therefore, we investigated the effects of acute boat noise (from stock enhancement release sites) and chronic noise (from aquaculture processes) on the anti-predator behaviour in three juvenile reef fishes: Epinephelus coioides, Amphiprion ocellaris and Neoglyphidodon melas. We exposed fish to aquaculture noise, boat noise and a combination of both, followed by a predator scare and documented kinematic variables (response latency, response distance, response speed and response duration). For the grouper E. coioides, their response latency decreased in the presence of acute noise, while their response duration increased in the presence of both chronic and acute noise. Among the anemonefish A. ocellaris, all variables remained unaffected by chronic noise, whereas acute noise increased the response distance and response speed. In the case of the black damselfish N. melas, chronic noise decreased the response speed, while acute noise decreased the response latency and response duration. Our results indicate that acute noise had a stronger influence on anti-predator behaviour than chronic noise. This study suggests that acute noise levels at restocking release sites can impact anti-predator behaviour in fishes, potentially altering fitness and likelihood of survival. Such negative effects and interspecific differences must be considered when restocking fish populations.

Comparative transcriptome analysis of skin color-associated genes in leopard coral grouper (Plectropomus leopardus).

BACKGROUND: The leopard coral grouper (Plectropomus leopardus) is an important economic species in East Asia-Pacific countries. To meet the market demand, leopard coral grouper is facing overfishing and their population is rapidly declining. With the improvement of the artificial propagation technique, the leopard coral grouper has been successfully cultured by Fisheries Research Institute in Taiwan. However, the skin color of farmed individuals is often lacking bright redness. As such, the market price of farmed individuals is lower than wild-type. RESULTS: To understand the genetic mechanisms of skin coloration in leopard coral grouper, we compared leopard coral grouper with different skin colors through transcriptome analysis. Six cDNA libraries generated from wild-caught leopard coral grouper with different skin colors were characterized by using the Illumina platform. Reference-guided de novo transcriptome data of leopard coral grouper obtained 24,700 transcripts, and 1,089 differentially expressed genes (DEGs) were found between red and brown skin color individuals. The results showed that nine candidate DEGs (epha2, sema6d, acsl4, slc7a5, hipk1, nol6, timp2, slc25a42, and kdf1) significantly associated with skin color were detected by using comparative transcriptome analysis and quantitative real-time polymerase chain reaction (qRT-PCR). CONCLUSIONS: The findings may provide genetic information for further skin color research, and to boost the market price of farmed leopard coral grouper by selective breeding.

The influence of tourism-based provisioning on fish behavior and benthic composition.

Distribution of non-natural food (provisioning) to attract fish, though popular in coral reef tourism, has often been discouraged due to its assumed adverse effects on fish health and behavior. However, the effects of provisioning on community structure, anti-predator, and foraging behavior of teleost fishes, as well as their potential to indirectly affect benthic organisms, are not yet clear. Here, we compared fish composition, wariness, foraging behavior of herbivorous fishes, and the benthic cover between provisioned and control sites. We found significant differences in fish abundance, species number, and composition at some locations, but not all. Although most provisioned herbivorous fish did not reduce their biting rates of benthic algae, provisioned sites still had higher coverage of green macroalgae. Our results dispute widely held presumptions on the effects of tourism-based provisioning on the ecology and behavior of teleost fishes, as well as the benthic cover. These findings suggest that while regulation of provisioning is necessary to manage and mitigate any deleterious outcomes, when moderated and monitored, it could still provide an educationally beneficial tool for coral reef ecotourism.

Complete mitochondrial genome of the palemargin grouper Epinephelus bontoides (Pisces: Perciformes).

The complete mitogenome of the palemargin grouper, Epinephelus bontoides, was presented in this study. This mitochondrial genome consists of 16 903 bp, follow the typical gene arrangement with 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region (CR). The overall base composition was A, 28.7%; G, 16.1%; C, 28.0%; and T, 27.2%. The control region was 1200 bp in length, which located between tRNAPro and tRNAPhe, rich in A + T (69.2%) content. Based on the Neighbor-Joining (NJ) tree, E. bontoides was grouped with E. trimaculatus, E. quoyanus, E. areolatus, and E. bleekeri, and then combined with E. merra formed a clade. This complete mitogenome of E. bontoides can provide essential phylogenetic information of Epinephelus.

DNA barcoding reveals that the common cupped oyster in Taiwan is the Portuguese oyster Crassostrea angulata (Ostreoida; Ostreidae), not C. gigas.

The Pacific cupped oyster, Crassostrea gigas, is one of the major aquacultural shellfish species that has been introduced to Europe and America from its native source in the West Pacific. In Taiwan, the cultivated cupped oysters along the west coast have been identified as C. gigas for over centuries; however, several molecular phylogenetic studies have cast doubt upon the existence of this species in Taiwan and adjacent waters. Indeed, our analyses of mitochondrial cytochrome oxidase I (COI) sequences from 313 Crassostrea collected from 12 locations along Taiwanese and southern Chinese coastlines confirm that all samples were the Portuguese oyster, C. angulata, rather than C. gigas. Multiple lines of evidence, including haplotypic and nucleotide diversity of the COI gene, demographic history, and population genetics, suggest that Taiwanese C. angulata is unique, probably experienced a sudden population expansion after the Last Glacial Maxima around 20,000 years ago, and has a significantly limited genetic connectivity across the Taiwan Strait. Our study applies an extended sampling and DNA barcoding to confirm the absence of C. gigas in natural and cultivated populations in Taiwan and southern China, where we only found C. angulata. We highlight the importance of conserving the gene pool of the C. angulata population in Taiwan, particularly considering the current threats by large-scale environmental disturbances such as marine pollution, habitat destruction, and climate change.

The complete mitochondrial genome of Conus tulipa (Neogastropoda: Conidae).

The complete mitogenome sequence of the cone snail Conus tulipa (Linnaeus, 1758) has been sequenced by next-generation sequencing method. The assembled mitogenome is 16,599 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition of C. tulipa is 28.7% A, 15.2% C, 18.4% G and 37.7% T. It shows 81.1% identity to the cone snail C. consors, 78.5% to C. borgesi and 77.5% to C. textile. Using the 13 protein-coding genes and 2 ribosomal RNA genes of C. tulipa in this study, together with 18 other closely species, we constructed the species phylogenetic tree to verify the accuracy and utility of new determined mitogenome sequence. The complete mitogenome of the C. tulipa provides an essential and important DNA molecular data for further phylogeography and evolutionary analysis for cone snail phylogeny.

Complete mitochondrial genome of the sixblotch hind Cephalopholis sexmaculata (Pisces: Perciformes).

The complete mitogenome of the sixblotch hind, Cephalopholis sexmaculata was presented in this study. This mitochondrial genome consists of 16,589 bp, with 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a noncoding control region (CR), and its gene arrangement is identical to most vertebrates. The overall base composition of the heavy strand is A, 29.35%; G, 16.08%; C, 28.56%; and T, 26.01%. The COI gene started with GTG codon and the ATP6 gene started with CTG codon. The complete mitogenomic data may provide informative for further phylogenetic approach of species of Cephalopholis and related genera belong to the Epinephelidae groupers.

Spatial Patterns and Environmental Settings of Non-reefal Coral Communities Across the Tropic of Cancer in the Penghu Archipelago (Pescadores), Taiwan.

Hernyi Justin Hsieh, Colin Kou-Chang Wen, Yuan-Chao Huang, Kao-Sung Chen, Chang-Feng Dai, and Chaolun Allen Chen (2016) Non-reefal coral communities occurring at the edges of scleractinian coral distribution ranges normally show a sharp gradient in the composition of coral species. Environmental and biological factors such as sea surface temperature (SST), competition with other benthos, and human disturbances might play roles in shaping the structure of coral communities. The Penghu Archipelago is located on the east side of Taiwan Strait straddling the Tropic of Cancer and hosts non-reefal coral communities. In this study, benthic surveys throughout the Penghu Archipelago were conducted and potential environmental and biological factors that shape coral species distributions were inferred by multivariate analyses. A total of 103 species representing 28 genera of scleractinian corals were recorded. Three major ecological sectors (northeast, south, and inner) were defined based on a canonical analysis of the principal coordinates of scleractinian species composition. Correlation analyses showed that scleractinians in the south and northeast sectors were strongly influenced by SST-related variables. In contrast, the coral communities in inner sector were mainly affect by turbidity or nutrition, which supposed come from human activities. Distance-based redundancy analysis showed that benthos, except soft corals, hardly interacted with scleractinian coral distributions. Our study demonstrated a distinct coral species assemblage among different islands across the Tropic of Cancer in the Penghu Archipelago. Natural and human-derived environmental factors both showed a strong correlation with coral species distribution. It's clear that either natural and human-derived factors influenced coral composition in Penghu archipelago.

Mitochondrial DNA sequence of Conus textile (Neogastropoda: Conidae).

The cone snail Conus textile belongs to the family Conidae. It is a kind of molluscivorous species. The complete mitochondrial DNA sequence was constructed by next-generation sequencing in this study. The mitogenome of C. textile is 15,765 bp in length, including 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 1 control region. The base composition was 27.3% A, 37.9% T, 15.7% C and 19.1% G. The phylogenetic tree of C. textile with the other 6 Conus species and 15 Neogastropoda sea snails was built. It provides fundamental data for further research of phylogeny and biogeography with this genus.

The complete mitochondrial genome of Conus capitaneus (Neogastropoda: Conidae).

The complete mitochondrial genome sequence of cone snail Conus capitaneus, a kind of worm-hunting sea snails, was performed by next-generation sequencing. The mitogenome is 15,829 bp in length, including 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes (12S and 16S rRNA) and 1 control region. It has an overall base composition of A (25.6%), T (36.6%), C (16.3%) and G (21.5%). It shows 79.8% identity with C. tribblei, which also belongs to worm-hunting sea snail. The phylogenetic analysis was conducted with 21 closely related species to assess their phylogenetic relationship. The complete mitogenome of the C. capitaneus provides important DNA molecular data for further phylogeography.

The complete mitochondrial genome of Conus striatus (Neogastropoda: Conidae).

Conus striatus is a kind of piscivorous cone snail. We have sequenced it by next generation sequencing method. We used de novo assembly and reference mapping methods to assemble mitogenome. The mitochondrial genome is 15,738 bp, containing 13 protein coding genes, 22 transfer RNAs and 2 ribosomal RNAs genes. The overall base composition of C. striatus is 25.9% for A, 16.3% for C, 20.8% for G and 38.6% for T. The phylogenetic analysis was conducted with 18 related species and confirmed the classification status. The complete mitogenome of the C. striatus provides an essential and important DNA molecular data for further phylogeography and evolutionary analysis for cone snail phylogeny.