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Chen W.Y.,Taiwan Fishery Research Institute | Chen W.Y.,National Taiwan Ocean University | Lee M.A.,National Taiwan Ocean University | Lan K.W.,National Taiwan Ocean University | And 2 more authors.

A total of 8459 larval fish were collected from the southern East China Sea during the winter northeasterly monsoon season and the summer southwesterly monsoon season of 2008. The larvae comprised 184 species belonging to 105 families and 162 genera. The abundance in terms of CPUE (number of individuals/1000 m3) of the larvae was approximately 6 times higher during the southwesterly monsoon season than it was during the northeasterly monsoon season. The primary environmental factors affecting the larval abundance were water temperature during the northeasterly monsoon season, and food availability during the southwesterly monsoon season. Three larval fish assemblages were recognized: inshore assemblage, offshore assemblage, and summer coastal assemblage. The distribution and species composition of the larvae in the assemblages reflected the hydrographic conditions and water currents resulting from the seasonal monsoons. © 2014 Author(s). Source

Wang Y.-C.,National Taiwan Ocean University | Chen W.-Y.,National Taiwan Ocean University | Chen W.-Y.,Taiwan Fishery Research Institute | Chang Y.,National Cheng Kung University | Lee M.-A.,National Taiwan Ocean University
Journal of Marine Science and Technology (Taiwan)

The study of ichthyoplankton community associated with oceanic features on the continental shelf of southern East China Sea (ECS) was conducted in early winter from 2006 to 2009. The species composition of the ichthyoplankton and its spatial distribution was classified and compared with oceanic front. A total number of 1,809 fish larvae individuals were sampled from 5 field surveys, and represented 76 families and 137 species. Using the Bray-Curtis dissimilarity, the abundance of species found to exceed 0.5% of the total sample from 36 stations were classified into four groups: China Coastal Group, Mixed Shelf Group, Taiwan Strait Group, and Kuroshio Group. The shallow water species Sebastiscus marmoratus dominated the China Coastal Group, while the Mixed Shelf Group was dominated by Saurida spp., Trichiurus lepturus, and Bregmaceros spp. The Taiwan Strait Group was dominated by Engraulis japonicus and Benthosema pterotum. The dominant species in the Kuroshio Group was found to include Sigmops gracile and unidentified Myctophid larvae. The spatial distribution of the ichthyoplankton community groups was superimposed on a thermal front map of the study area. This clearly revealed that the China Coastal Front could be the boundary which separated the China Coastal Group on the west and the Mixed Shelf Group on the east. In addition, ichthyoplankton were found to increase in abundance and diversity in the region close to the Kuroshio Front. Source

Liu S.-Y.V.,Academia Sinica, Taiwan | Chan C.-L.C.,Academia Sinica, Taiwan | Hsieh H.J.,Taiwan Fishery Research Institute | Fontana S.,Academia Sinica, Taiwan | And 4 more authors.
Marine Biology

Based on only a handful of mitochondrial and nuclear loci, the phylogenetic relationships within the genus Acropora have been unclear. However, with the new sequencing technology of massively parallel sequencing (MPS), the inter-specific relationships within Acropora may be resolved. We performed multiplex sequencing of the mitochondrial genome of eleven Acropora species representing different groups using the Illumina Solexa platform. Mitochondrial genomes were sequenced from long PCR-amplified templates ligated with different index sequences (~9 kbp) and analyzed using the mitochondrial genome of Acropora tenuis as a reference. A total of 75 million read outputs in one Illumina lane were obtained, with mapping results having coverage up to 44,000-fold. Assembly results of multiplex samples confirmed with Sanger sequencing produced <0.03 % error. Aligning the eleven mitochondrial genomes with the reference sequence revealed only 110 phylogenetically informative sites over the mitochondrial genome. The largest pairwise genetic distance observed was in the putative control region (0.022). A comparison of two phylogenetic trees based on the whole mitochondrial genome and control region showed that the former tree produces a higher resolution of phylogenetic relationships. In this study, we demonstrated the first case of sequencing cnidarian mitochondrial genomes by using multiplex MPS and applying it in a phylogenomic analyses. © 2015, Springer-Verlag Berlin Heidelberg. Source

Wei N.V.,Academia Sinica, Taiwan | Wei N.V.,National Taiwan University | Hsieh H.J.,Taiwan Fishery Research Institute | Dai C.-F.,National Taiwan University | And 5 more authors.
Zoological Studies

Hybridization was proposed as being an important source of evolutionary novelty in broadcast-spawning reef-building corals. In addition, hybridization was hypothesized to be more frequent at the periphery of species' ranges and in marginal habitats. We tested the potential for hybridization in 2 ways: observations of the time of spawning and non-choice interspecific fertilization experiments of 4 sympatric Acropora species in a non-reefal coral assemblage at Chinwan Inner Bay (CIB), Penghu Is., Taiwan. We found that colonies of more than 1 species rarely released gametes at the same time, thus limiting the opportunities for cross-fertilization in the wild. On the few occasions when different species released gametes in synchrony, interspecific fertilization in experimental crosses was uniformly low (the proportion of eggs fertilized ranged 0%-4.58% with a mode of 0%), and interspecific-crossed embryos ceased development and died within 12 h after initially being fertilized. Ecological and experimental analyses indicated that reproductive isolation exists in these 4 Acropora species even though they have the opportunities to spawn synchronously, suggesting that hybridization is not very frequent in this marginal coral habitat at CIB. Source

Ku S.-Y.,Academia Sinica, Taiwan | Lu H.-J.,Academia Sinica, Taiwan | Lu H.-J.,National Taiwan Ocean University | Tseng C.-T.,National Taiwan Ocean University | And 2 more authors.
Journal of Marine Science and Technology

1D sequence homologous alignment tool, like FastA (FASTALL) [8] or BLAST (Basic Local Alignment Search Tool) [1], has been widely used in bioinformatics field and perform elegant and fast searching for the sequences developed from the same kinds of species. In other word, it can classify through determining the homologous similarity which is not totally similar in sequences of protein sequences, structure or nucleotide sequences. An approach is proposed in this paper called AA-FAST (abbreviation for Acoustics Alphabet-FAST) which takes advantage of alignment tool and significant sequence encoding method. In this experiment, it could not only determine 4 fish species with similar size and shape but also the motion of them with identical alignment matrix. Besides, it shows that the position containing higher similarity encoding sequence fragment is related to the position of specific fish species and the acoustic features of specific fish species. Other purpose of this paper is to demonstrate how a bioinformatics tool could be applied to the acoustic field. Source

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