Taiwan Fishery Research Institute

Kaohsiung, Taiwan

Taiwan Fishery Research Institute

Kaohsiung, Taiwan
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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 | Year: 2015

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.

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 | Year: 2012

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.

Lu H.-J.,National Taiwan Ocean University | Kang M.,Myriax Software Pty Ltd | Huang H.-H.,National Taiwan Ocean University | Lai C.-C.,Taiwan Fishery Research Institute | Wu L.-J.,Taiwan Fishery Research Institute
Fisheries Science | Year: 2011

To provide target strength (TS) information for estimating the body length of yellowfin tuna Thunnus albacares and its abundance around fish aggregating devices, TS was measured ex situ and in situ. In the ex situ TS measurements, two cameras synchronized with a 200 kHz echosounder were used to obtain the precise orientation of the yellowfin tuna under free swimming conditions. The ex situ TS (dB re 1 m 2)-fork length (FL, cm) regression was: TS = 27.06 log (FL) - 85.04. Ex situ TS was found to reach its maximum in the tilt angle range of -15° to -20° after excluding TS samples with insignificant correlation to the tilt angle. The angle between the vertebra and the swim bladder was approximately 25° according to X-ray images, supporting the above tilt range. The relationship between the swim bladder volume (V SB, ml) and the fork length was: V SB = 0.000213 FL 3. The results from the in situ TS measurements indicated that the tilt angle was highly concentrated between -10° and 15°. The results from a calculation using the ex situ TS-FL equation with the fork length from biological sampling agreed strongly with the average in situ TS. © 2011 The Japanese Society of Fisheries Science.

Lee M.-A.,National Taiwan Ocean University | Kuo Y.-C.,National Taiwan Ocean University | Chan J.-W.,Taiwan Ocean Research Institute | Chen Y.-K.,Taiwan Fishery Research Institute | Teng S.-Y.,National Taiwan Ocean University
Terrestrial, Atmospheric and Oceanic Sciences | Year: 2015

Long-term (1982-2012) advanced very-high-resolution radiometer (AVHRR) data collected at a resolution of 0.04° clearly indicated sea surface temperature (SST) warming and variations associated with El Niño and Southern Oscillation (ENSO) in the Taiwan Strait (TS) during the summer. From 1982-2012 the spatially averaged warming trend in the TS was 0.057°C y-1. However, during the last 10 years the warming phenomenon appears to have halted and a slight cooling rate (0.03°C y-1) was observed. The monthly SST transition from June-July became increasingly sharp. The first mode (70%) of the empirical orthogonal function (EOF) analysis indicated an SST warming trend. The warming occurred primarily in the eastern strait. The warming slowed down and considerable inter-annual variation occurred in the period after 1994. EOF results applied to the data between 1994-2012 showed that the first EOF mode (55%) revealed a warming pattern, whereas the second EOF mode (12%) revealed a pattern that explained the inter-annual variation in the SST, which was strongly correlated with the wind speed. Strong winds enhanced the upwelling along the China coast, eastern Taiwan Banks (TWB) and southern Peng-Hu Islands, whereas the SST in eastern TS increased because of increased warm water transport from the South China Sea. The inter-annual variation in the southwesterly wind could be affected by both ENSO and the background Pacific Decadal Oscillation (PDO) phase. The strongest upwelling in the TS tended to occur when ENSO and PDO were in phase associated with the southwesterly wind.

Hasegawa T.,Nagasaki University | Yeh H.-M.,Taiwan Fishery Research Institute | Chen J.-R.,Taiwan Fishery Research Institute | Kuo C.-L.,Taiwan Fishery Research Institute | And 2 more authors.
Ichthyological Research | Year: 2016

To investigate the early life history of Seriola dumerili, we first validated otolith daily increments using reared fish (11–51 days after hatching). Four larval and early-juvenile S. dumerili were collected in May and July 2015 around the Penghu Islands, Taiwan (23.45–23.70 °N, 119.40–119.70 °E), by surface larval net towing, but not from drifting seaweeds. Seriola dumerili were caught at the thermal front, and the total lengths and ages ranged 7.4–42.5 mm and 18–56 days, respectively. Our results indicate that the hatching dates of S. dumerili were April to June and larvae may have been accumulated in the frontal zone before the juvenile phase. © 2016 The Ichthyological Society of Japan

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) | Year: 2013

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.

Lee M.-A.,National Taiwan Ocean University | Wang Y.-C.,National Taiwan Ocean University | Chen Y.-K.,Taiwan Fishery Research Institute | Chen W.-Y.,Taiwan Fishery Research Institute | And 4 more authors.
Journal of Marine Science and Technology (Taiwan) | Year: 2013

This study investigated the relationships between assemblages of larval fish and hydrographic features in the East China Sea (ECS) and seas surrounding Taiwan during the summer of 2007. A survey was conducted from 2007 July 1 to 2007 July 11 in the ECS and from 2007 July 4 to 2007 July 16 in the waters surrounding Taiwan. A total of 12,670 larval fishes belonging to 95 families, 163 genes, and 189 species were identified. Engraulis japonicus and Sillago japonica were the 2 dominant species, accounting for 56.15% and 6.66% of the fish larvae samples. The cluster analysis results showed that the fish larval distribution patterns corresponded to hydrographic conditions. The results were also used to identify the following larval assemblages: the Kuroshio assemblage, coastal assemblage, Changjiang diluted water (CDW)/Yellow Sea mixed water assemblage, and Taiwan Strait water assemblage. The spatial distribution results showed a clear association between high abundances of larval fishes and shallow water areas near the ECS coast, and between low abundances and offshore Kuroshio water. The canonical correlation analysis results indicated that abundances of E. japonicus and S. japonica were strongly and positively correlated with chlorophyll a, but negatively correlated with salinity. These associations suggest that food sources and CDW might be crucial factors that determine the abundance and distribution of larval fishes during the summer.

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.
Biogeosciences | Year: 2014

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).

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 | Year: 2011

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.

Lee M.-A.,National Taiwan Ocean University | Chao M.-H.,National Taiwan Ocean University | Weng J.-S.,Taiwan Fishery Research Institute | Lan Y.-C.,Taiwan Fishery Research Institute | Lu H.-J.,National Taiwan Ocean University
Journal of Marine Science and Technology | Year: 2011

A 26-hr acoustic observation was carried out on board of the "Ocean Research II" in the Kuroshio waters at 123°09.027'E, 25°05.019'N from August 4 to 5,2007. Acoustic volume scattering strengths (SVs) were collected by a scientific echo sounder (EK500, 38 kHz) and diel variations of sound scattering layer were analyzed. The maximum SV of surface scattering layers (SSL) around 20-80 m was observed after dawn, and mean SVs of SSL in nighttime was about -68 dB, 8 dB higher than that of daytime. Two deep scattering layers (DSL) were found in daytime at depth of 400-500 m and 600-700 m, which resulted in mean SVs were about -72 dB and -78 dB, respectively. Two clear diel vertical movements were also detected from these two DSL. A part of these two DSL started to ascend at dusk with a speed of 2.9 (±2.1) and 3.8 (±2.8) cm/s, and stayed at 10 to 120 m at nighttime, while another part of these DSL remained in the deep layer during daytime. These two DSL started to descend at dawn with a speed of 2.0 (±1.1) to 4.0 (±3.8) cm/s, and then stayed at depth of 400∼500 m and 600∼700 m during daytime, respectively.

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