A giant anguilliform leptocephalus Thalassenchelys foliaceus Castle & Raju is a junior synonym of Congriscus maldivensis (Norman 1939)

A single specimen of giant leptocephalus Thalassenchelys foliaceus Castle & Raju 1975 was caught in subtropical waters of the western North Pacific Ocean. Mitochondrial coI gene sequence divergence between T. foliaceus and Congriscus maldivensis (Norman 1939) was 0·64 ± 0·27% (mean ± s.e. ), and the myomere and vertebral counts of these species were similar, indicating T. foliaceus is a junior synonym of C. maldivensis.     

DNA barcode and minibarcode identification of freshwater fishes from Cerrado headwater streams in Central Brazil

The extraordinary species diversity of the Neotropical freshwater fish fauna is world renown. Yet, despite rich species diversity, taxonomic and genetic resources for its Cerrado ichthyofauna remain poorly developed. We provide a reference library of 149 DNA barcodes for 39 species/lineages of Cerrado headwater stream fishes from the Brazilian Distrito Federal and nearby areas and test the utility of distance-based criteria, tree-based criteria and minibarcodes for specimen identification. Mean Kimura 2-parameter genetic distances within species to orders ranged 1·8–12·1%. However, mean intraspecific v. congeneric-interspecific distances (0·9–1·3%) overlapped extensively and distance-based barcoding failed to achieve correct identifications due to c. 4–12·1% error rates and 19·5% ambiguous identifications related to the presence of singletons. Overlap was reduced and best-match success rates improved drastically to 83·5% when Characidium barcodes representing potential misidentifications or undescribed species were removed. Tree-based monophyly criteria generally performed similarly to distance methods, correctly differentiating up to c. 85% of species/lineages despite neighbour-joining and Bayesian tree errors (random lineage-branching events, long-branch attraction). Five clusters (Ancistrus aguaboensis, Characidium spp., Eigenmannia trilineata, Hasemania hanseni and Hypostomus sp. 2) exhibited deep intraspecific divergences or para−/polyphyly and multiple Barcode Index Number assignments indicative of putative candidate species needing taxonomic re-examination. Sliding-window analyses also indicated that a 200 bp minibarcode region performed just as well at specimen identification as the entire barcode gene. Future DNA barcoding studies of Distrito Federal–Cerrado freshwater fishes will benefit from increased sampling coverage, as well as consideration of minibarcode targets for degraded samples and next-generation sequencing.     

Utilization of the exotic cladoceran Daphnia lumholtzi by juvenile fishes in an Illinois River floodplain lake

Daphnia lumholtzi comprises a substantial component of the zooplankton community during mid‐ to late‐summer in Lake Chautauqua, a floodplain lake along the Illinois River near Havana, Illinois. In order to quantify the utilization of D. lumholtzi by juvenile fishes, diet analyses were conducted for seven juvenile fish species collected from Lake Chautauqua during the 2001 annual drawdown period. Freshwater drum Aplodinotus grunniens and emerald shiner Notropis atherinoides demonstrated negative selectivity for D. lumholtzi relative to native zooplankton species whereas four species of fish (bluegill Lepomis macrochirus, white bass Morone chrysops, white crappie Pomoxis annularis and black crappie Pomoxis nigromaculatus) consumed substantial amounts of D. lumholtzi. Although selectivity values for D. lumholtzi varied among these fish species, positive selection for D. lumholtzi increased similarly among larger size classes of each fish species, and corresponded with ontogenetic shifts in diet. Mean body length of D. lumholtzi consumed by 20–69 mm L_T juvenile fishes ranged from 0·75 to 0·99 mm with a calculated total length range of 2·0–2·6 mm. Results from this study provide evidence that high abundances of D. lumholtzi in mid‐ to late‐summer provide an additional food source for several juvenile fish species during a time when abundances of large native cladoceran species (i.e. Daphnia) are low, and juvenile fishes are searching for larger prey associated with ontogenetic shifts from zooplankton to macroinvertebrates and fishes. Because zooplankton production is typically lower in rivers than in lakes, survivorship of juvenile fishes produced in floodplain lakes may be higher in riverine systems if they are not reliant on zooplankton as a primary food resource. Therefore, high abundances of D. lumholtzi may benefit juvenile fishes in managed floodplain lakes, such as Lake Chautauqua, by increasing growth and facilitating the transition from zooplanktivory to insectivory or piscivory.     

Integrative taxonomy of Peniculus,Metapeniculus, and Trifur (Siphonostomatoida: Pennellidae), copepod parasites of marine fishes from Chile: species delimitation analyses using DNA barcoding and morphological evidence

Pennellidae is a family of copepod parasites of widely distributed marine fishes. The pennellid species are usually morphologically differentiated by cephalothorax, neck, trunk, and abdomen shape. These characters, however, show high polymorphism and therefore using only this type of data, delimitation at species level of this genus is difficult. In this study, we explored the genetic distances calculated from sequences of a DNA barcoding marker (COI mt) (678 base pairs). We also explored the genetic distances of 25 Peniculus specimens associated within nine marine fish species, four Metapeniculus specimens associated within one marine fish species, and four Trifur specimens associated within one marine fish species. All specimens were collected in Antofagasta Bay, Chile and were calculated from sequences of a DNA barcoding marker (COI mt) (678 base pairs). The genetic distance among the Peniculus specimens was 0.95% from the different host species, the Metapeniculus specimens distance was 0.44% and the Trifur specimens was 2.25%. Genetic difference between Peniculus and Metapeniculus was 17.86% and Peniculus differ from T. tortuosus by 18.16%. We analysed the barcoding gene fragment using Bayesian Inference (BI) for phylogenetic reconstruction using three outgroups. Based on the phylogenetic analysis an ultrametric tree was built and a general mixed Yule-coalescent (bGMYC) model was conducted for species delimitation. Morphometrics analyses were made with Bayesian statistics. Mean and credibility limit (95%) for each parameter was calculated. Results show that based on morphology the individuals collected can be assigned to P. cf. fistula von Nordmann, 1832, Metapeniculus antofagastensis Castro-Romero & Baeza-Kuroki, 1985, and Trifur cf. tortuosus Wilson, 1917. High morphological polymorphism was observed for the lineage of Peniculus associated to several host species of marine fishes. Similar results were obtained for Trifur cf. tortuosus parasites on Chilean marine fishes.     

DNA barcoding of freshwater ichthyoplankton in the Neotropics as a tool for ecological monitoring

Quantifying and classifying ichthyoplankton is one of the most effective ways of monitoring the recruitment process in fishes. However, correctly identifying the fish based on morphological characters is extremely difficult, especially in the early stages of development. We examined ichthyoplankton from tributaries and reservoirs along the middle stretch of the Paranapanema River, one of the areas most impacted by hydroelectric projects in the Neotropics. Matching DNA sequences of the COI gene (628–648 bp) allowed us to identify 99.25% of 536 samples of eggs (293) and larvae (243) subjected to BOLD‐IDS similarity analysis with a species‐level threshold of 1.3%. The results revealed 37 species in 27 genera, 15 families and four orders, some 23.8% of documented fish species in the Paranapanema River. Molecular identification meant that we could include data from egg samples that accounted for about 30% of the species richness observed. The results in this study confirm the efficacy of DNA barcoding in identifying Neotropical ichthyoplankton and show how the data produced provide valuable information for preparing plans for conserving and managing inland waters.     

Sequence diversity at cytochrome oxidase 1 (Co-1) gene among sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish of Russia Far East with phylogenetic and taxonomic insights

Mitochondrial DNA (mtDNA) atCo-1 gene region was sequenced for 7 scorpion fish species (in total, 16 sequences of at least 552 bp) from the Far East of Russia and compared with 15 other sequences of Scorpaeniformes comprising altogether 29 scorpion-like fish sequences and two outgroup sequences (Cypriniformes). The analysis of the protein-codingCo-1 gene revealed statistically substantiated bias in the (T+C) ∶ (A+G) content, proving basic findings. The average scores ofp-distances for different scales of the evolutionary history atCo-1 gene revealed a clear pattern of increased nucleotide diversity at four different levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intraorder. The scores of averagep-distances for the compared fish groups were: (1) 1.00±0.20%, (2) 3.80±0.20%, (3) 12.40±1.20%, and (4) 18.00±0.38%, respectively (mean±SE). These data support the concept that speciation in the order Scorpaeniformes, in most cases, follows a geographic mode through accumulation of numerous small genetic changes over a long period of time. However, intraspecies diversity was surprisingly high among scorpionfish. Phylogenetic trees for 29 sequences of scorpionfish and 2 other fishes belonging to ray-finned fishes (Actinopterigii) were developed usingCo-1 gene and four different analytical approaches: Bayesian (BA), maximum likelihood (ML), neighbour-joining (NJ), and maximum parsimony (MP). The analysis revealed a monophyletic origin for the representatives of Cottidae, which is the principal scorpionfish family investigated (100, 96, 98% support level in our BA, MP, and NJ analyses). Similarly, the monophyletic origin of up to the three compared scorpion-like fish genera was supported by molecular phylogenetic data. Species identification on individual basis (barcoding tagging) was high. A few taxonomic complications arose during the analysis and they are discussed here in.     

Why are there so few freshwater fish species in most estuaries?

The freshwater fish assemblage in most estuaries is not as species rich as the marine assemblage in the same systems. Coupled with this differential richness is an apparent inability by most freshwater fish species to penetrate estuarine zones that are mesohaline (salinity: 5·0–17·9), polyhaline (salinity: 18·0–29·9) or euhaline (salinity: 30·0–39·9). The reason why mesohaline waters are avoided by most freshwater fishes is difficult to explain from a physiological perspective as many of these species would be isosmotic within this salinity range. Perhaps, a key to the poor penetration of estuarine waters by freshwater taxa is an inability to develop chloride cells in gill filament epithelia, as well as a lack of other osmoregulatory adaptations present in euryhaline fishes. Only a few freshwater fish species, especially some of those belonging to the family Cichlidae, have become fully euryhaline and have successfully occupied a wide range of estuaries, sometimes even dominating in hyperhaline systems (salinity 40+). Indeed, this review found that there are few fish species that can be termed holohaline (i.e. capable of occupying waters with a salinity range of 0–100+) and, of these taxa, there is a disproportionally high number of freshwater species (e.g. Cyprinodon variegatus, Oreochromis mossambicus and Sarotherodon melanotheron). Factors such as increased competition for food and higher predation rates by piscivorous fishes and birds may also play an important role in the low species richness and abundance of freshwater taxa in estuaries. Added to this is the relatively low species richness of freshwater fishes in river catchments when compared with the normally higher diversity of marine fish species for potential estuarine colonization from the adjacent coastal waters. The almost complete absence of freshwater fish larvae from the estuarine ichthyoplankton further reinforces the poor representation of this guild within these systems. An explanation as to why more freshwater fish species have not become euryhaline and occupied a wide range of estuaries similar to their marine counterparts is probably due to a combination of the above described factors, with physiological restrictions pertaining to limited salinity tolerances probably playing the most important role.     

Northernmost record of the little gulper shark Centrophorus uyato in the north‐eastern Atlantic Ocean,with taxonomical notes on Centrophorus zeehaani

A specimen of the little gulper shark Centrophorus uyato was collected in the Norwegian Sea off the coast of northern Norway, marking the northernmost record of the species in the eastern North Atlantic Ocean. Morphological characteristics collected from the specimen indicate a close relationship to the Australian species Centrophorus zeehaani. DNA barcoding analysis of the mitochondrial cytochrome oxidase subunit I (coI) gene for species of Centrophorus suggests conspecificity of C. uyato and C. zeehaani.     

DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf

We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo–West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes– Bayesian PTP (PTP–bPTP) and nucleotide-divergence-threshold (NDT) models), found 137 and 119 entities respectively. Overall, NDT method, neighbour-joining species tree and the prior taxonomic assessment provided similar results. Among the 54 families considered, only 10 (Ariommatidae, Ephippidae, Leiognathidae, Nemipteridae, Plotosidae, Pomacanthidae, Pomacentridae, Priacanthidae and Rachycentridae) showed the occurrence of molecular diagnostic pure characters. The DNA barcoding database developed during this study will help ichthyologists to identify and resolve the taxonomic ambiguities they may encounter with the fishes occurring in The Gulf and throughout the region.     

New tools (DNA barcoding), old hypothesis: the case of the taxonomic identity of the Argentine hakes (Actinopterygii: Merluccius)

The present study evaluated the possible occurrence of cryptic species among Merluccidae from Argentina by examining sequences of cytochrome c oxidase subunit I (coI) mtDNA. This approach can discriminate Merluccius hubbsi and Merluccius australis; specimens with morphological diagnostic characters of Merluccius patagonicus formed a cohesive cluster with M. hubbsi specimens. BIN analysis confirmed the effectiveness of barcoding within a global context.     

Interactions between gnathiid isopods,cleaner fish and other fishes on Lizard Island,Great Barrier Reef

The rate of emergence of micropredatory gnathiid isopods from the benthos, the proportion of emerging gnathiids potentially eaten by Labroides dimidiatus, and the volume of blood that gnathiids potentially remove from fishes (using gnathiid gut volume) were determined. The abundance (mean ±s.e .) of emerging gnathiids was 41·7 ± 6·9 m^?2 day^?1 and 4552 ± 2632 reef^?1 day^?1 (reefs 91–125 m²). The abundance of emerging gnathiids per fish on the reef was 4·9 ± 0·8 day^?1; but excluding the rarely infested pomacentrid fishes, it was 20·9 ± 3·8 day^?1. The abundance of emerging gnathiids per patch reef was 66 ± 17% of the number of gnathiids that all adult L. dimidiatus per reef eat daily while engaged in cleaning behaviour. If all infesting gnathiids subsequently fed on fish blood, their total gut volume per reef area would be 17·4 ± 5·6 mm³ m^?2 day^?1; and per fish on the reefs, it would be 2·3 ± 0·5 mm^?3 fish^?1 day^?1 and 10·3 ± 3·1 mm³ fish^?1 day^?1 (excluding pomacentrids). The total gut volume of gnathiids infesting caged (137 mm standard length, L_S) and removed from wild (100–150 mm L_S) Hemigymnus melapterus by L. dimidiatus was 26·4 ± 24·6 mm³ day^?1 and 53·0 ± 9·6 mm³ day^?1, respectively. Using H. melapterus (137 mm L_S, 83 g) as a model, gnathiids had the potential to remove, 0·07, 0·32, 0·82 and 1·63% of the total blood volume per day of each fish, excluding pomacentrids, caged H. melapterus and wild H. melapterus, respectively. In contrast, emerging gnathiids had the potential of removing 155% of the total blood volume of Acanthochromis polyacanthus (10·7 mm L_S, 0·038 g) juveniles. That L. dimidiatus eat more gnathiids per reef daily than were sampled with emergence traps suggests that cleaner fishes are an important source of mortality for gnathiids. Although the proportion of the total blood volume of fishes potentially removed by blood‐feeding gnathiids on a daily basis appeared to be low for fishes weighing 83 g, the cumulative effects of repeated infections on the health of such fish remains unknown; attacks on small juvenile fishes, may result in possibly lethal levels of blood loss.     

莱州湾春季鱼卵仔稚鱼群落结构和物种多样性

于2007—2010年春季(5月)利用大型浮游生物网对莱州湾海域位置相同的12个站位进行4个航次拖网调查,研究分析了该海域鱼卵仔稚鱼群落组成、优势种、空间分布及其多样性特征。结果表明:4个航次共获得鱼卵、仔稚鱼26种,隶属于6目16科24属,1种衔科鱼卵鉴定到科,另有1种鱼卵未能鉴定种类。鱼卵、仔稚鱼分布不均匀,莱州湾西部还湾底海域分布较多。斑鰶(Konosiruspunctatus)为该海域鱼卵的第一优势种;鳀(Engraulisjaponicus)在2007年和2008年作为仔稚鱼的第一优势种出现,而2009年和2010年仔稚鱼的第一优势种则是虾虎鱼。调查期间该海域鱼卵、仔稚鱼的均匀度指数和生物多样性指数变化趋势一致,均表现为从2007年开始随年代递减的趋势;种类数和丰富度指数则从2008年开始呈现随年代递减的趋势。2007—2010年4a鱼卵仔稚鱼聚类结果显示,2007年和2008年鱼卵仔稚鱼群落结构相似,与2009年和2010年均有差异。与1982年山东省近岸调查结果相比,莱州湾海域鱼卵仔稚鱼群落结构发生明显变化,斑鰶取代鳀成为第一优势种,小黄鱼等经济鱼类数量逐渐降低。     

Molecular approach to the identification of fish in the South China Sea

Background

DNA barcoding is one means of establishing a rapid, accurate, and cost-effective system for the identification of species. It involves the use of short, standard gene targets to create sequence profiles of known species against sequences of unknowns that can be matched and subsequently identified. The Fish Barcode of Life (FISH-BOL) campaign has the primary goal of gathering DNA barcode records for all the world''s fish species. As a contribution to FISH-BOL, we examined the degree to which DNA barcoding can discriminate marine fishes from the South China Sea.

Methodology/Principal Findings

DNA barcodes of cytochrome oxidase subunit I (COI) were characterized using 1336 specimens that belong to 242 species fishes from the South China Sea. All specimen provenance data (including digital specimen images and geospatial coordinates of collection localities) and collateral sequence information were assembled using Barcode of Life Data System (BOLD; www.barcodinglife.org). Small intraspecific and large interspecific differences create distinct genetic boundaries among most species. In addition, the efficiency of two mitochondrial genes, 16S rRNA (16S) and cytochrome b (cytb), and one nuclear ribosomal gene, 18S rRNA (18S), was also evaluated for a few select groups of species.

Conclusions/Significance

The present study provides evidence for the effectiveness of DNA barcoding as a tool for monitoring marine biodiversity. Open access data of fishes from the South China Sea can benefit relative applications in ecology and taxonomy.     

Effect of acclimation temperature on the upper thermal tolerance of Colorado River cutthroat trout Oncorhynchus clarkii pleuriticus: thermal limits of a North American salmonid

In an effort to explore the thermal limitations of Colorado River cutthroat trout Oncorhynchus clarkii pleuriticus, the critical thermal maxima (T_cmax) of 1+ year Lake Nanita strain O. c. pleuriticus were evaluated when acclimated to 10, 15 and 20° C. The mean ±s.d. T_cmax for O. c. pleuriticus acclimated to 10° C was 24·6 ± 2·0°C (n = 30), for 15° C‐acclimated fish was 26·9 ± 1·5° C (n = 23) and for 20° C‐acclimated fish was 29·4 ± 1·1° C (n = 28); these results showed a marked thermal acclimation effect (Q₁₀ = 1·20). Interestingly, there was a size effect within treatments, wherein the T_cmax of larger fish was significantly lower than that of smaller fish acclimated to the same temperature. The critical thermal tolerances of age 0 year O. c. pleuriticus were also evaluated from three separate populations: Lake Nanita, Trapper Creek and Carr Creek reared under ‘common‐garden’ conditions prior to thermal acclimation. The Trapper Creek population had significantly warmer T_cmax than the Lake Nanita population, but that of the Carr Creek fish had T_cmax similar to both Trapper Creek and Lake Nanita fish. A comparison of these O. c. pleuriticus T_cmax results with those of other stream‐dwelling salmonids suggested that O. c. pleuriticus are less resistant to rapid thermal fluctuations when acclimated to cold temperatures, but can tolerate similar temperatures when acclimated to warmer temperatures.     

The effects of environmental salinity on the growth and physiology of totoaba Totoaba macdonaldi and shortfin corvina Cynoscion parvipinnis

Totoaba Totoaba macdonaldi and shortfin corvina Cynoscion parvipinnis, were acclimated and reared together at salinities of 0, 2, 5, 10, 20 and 35 for 56 days. Initial overall mean ± s.d . body masses of 67·6 ± 7·1 g T. macdonaldi and 37·3 ± 3·1 g C. parvipinnis increased to final overall masses of 217·4 ± 30·3 and 96·5 ± 16·5 g, respectively, at the end of the study. Totoaba macdonaldi was not able to tolerate salinities of 0 and 2 and C. parvipinnis of 0. In contrast, both species had 100% survival at salinities ≥ 10. Somatic growth was highest not at natural seawater salinity of 35, but at 10. Plasma osmolality ranged from 172·5 to 417·0 mOsmol kg^?1 for T. macdonaldi and from 207·0 to 439·5 mOsmol kg^?1 for C. parvipinnis and varied in direct proportion to salinity. The estimated isosmotic salinities of T. macdonaldi and C. parvipinnis were 12·3 and 13·4, respectively. Cynoscion parvipinnis reared at two had significantly lower plasma lysozyme activity (95·0 Units ml^?1) than fish held at salinities from 5 to 35 (ranging from 215·0 to 355·0 Units ml^?1), but without clear trends over this range. Blood neutrophil oxidative radical production (NBT) (ranging from 3·9 to 6·7 mg ml^?1) had some significant differences among salinities, but these did not follow a clear pattern. For T. macdonaldi, neither lysozyme activity nor NBT was affected by salinity. Ash content of whole fishes varied directly and moisture content inversely, with salinity for both species.     

DNA barcoding is a useful tool for the identification of marine fishes from Japan

In this study, 229 DNA sequences of cytochrome oxidase subunit I gene (COI) from 158 marine fishes of Japan were employed to test the efficacy of species identification by DNA barcoding. The average genetic distance was 60-fold higher between species than within species, as Kimura two parameter (K2P) genetic distances averaged 17.6% among congeners and only 0.3% among conspecifics. There were no overlaps between intraspecific and interspecific K2P distances, and all sequences formed species units in the neighbor-joining dendrogram. Hybridization phenomena in two species (Kyphosus vaigiensis and Pterocaesio digramma) were also detected through searches in Barcode of Life Data Systems (BOLD). DNA barcoding provides a new way for fish identification.     

Comparative characteristics of the ichthyoplankton of lagoon lakes of the south-eastern part of Sakhalin

Ichthyoplankton surveys are made in lagoon water bodies of the south-eastern part of Sakhalin (the Vavai-Chibisan system of lakes, Lake Tunaicha, Lake Izmenchivoe) from April until November 2002–2007. Comparative characteristics of ichthyoplankton complexes in the ice-free period is given. In the investigated lagoon lakes, differences in the species composition of the ichthyoplankton by the number and time of appearance of the maxima of abundance of eggs and larvae are noted, and also related to morphological structure and hydrological conditions of water bodies. In lagoon lake Izmenchivoe with a salinity not less than 26‰, the eggs and larvae of marine fishes only takes place while, in Vavai-Chibisan lakes, that of freshwater fishes only takes place. In brackish lake Tunaicha, the lowest number of fish species reproduce. In the Vavai-Chibisan system and in Lake Izmenchivoe, one maximum of abundance of ichthyoplankton in June is recorded and, in Lake Tunaicha, two maxima (the highest in June and less expressed in August) are recorded. Irrespective of the species composition, the ichthyoplankton complexes of lagoon lakes have general traits determined by hydrological conditions of water bodies and by their general origin and geographic situation: prevalence of eggs and larvae of low boreal fish species, the maximum species diversity in the late spring-early summer, and decrease of abundance in cooler years.     

A three‐phase excess post‐exercise oxygen consumption in Atlantic salmon Salmo salar and its response to exercise training

The recovery of oxygen uptake to the standard metabolic rate (SMR) following exhaustive chasing exercise in Atlantic salmon Salmo salar parr occurred in three phases (rapid, plateau and slow). The initial recovery phase lasted 0·7 h and contributed 16% to the total excess post‐exercise oxygen consumption (EPOC). It was followed by a longer plateau phase that contributed 53% to the total EPOC. The slow recovery phase that completed recovery of SMR, which has not been reported previously, made a 31% contribution to the total EPOC. The plasticity of EPOC was demonstrated in exercise‐trained fish. Exercise training increased EPOC by 39% when compared with control fish (mean ± S.E., 877·7 ± 73·1 v . 629·2 ± 53·4 mg O₂ kg^?1, d.f. = 9, P <  0·05), with the duration of the plateau phase increasing by 38% (4·7 ± 0·58 v . 3·4 ± 0·16 h, d.f. = 9, P <  0·05) and the contribution of the slow phase to the total EPOC increasing by 80% (173·9 ± 23·9 v . 312·5 ± 50·4 mg O₂ kg^?1, d.f. = 9, P  < 0·05). As a result, the combination of the plateau and slow phases of exercise‐trained fish increased by 47% compared with control fish (756·6 ± 71·4 v . 513·6 ± 43·1 mg O₂ kg^?1; d.f. = 9, P  = 0·01). To substantiate the hypothesis that the plateau and slow recovery phase of EPOC was related to general metabolic recovery following exhaustive exercise, the time‐course for recovery of SMR was compared with previously published metabolite recovery profiles. The final phase of metabolic recovery was temporally associated with the final phases of gluconeogenesis, lactate oxidation and muscle intracellular pH regulation. Therefore, the plasticity of the latter phase of EPOC agreed with the known effects of exercise training in fishes.     

Identifying Fishes through DNA Barcodes and Microarrays

Background

International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.

Methodology/Principal Findings

This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.

Conclusions/Significance

Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.     

Larval fish variability in response to oceanographic features in a nearshore nursery area

The influence of oceanographic features on ichthyoplankton assemblages in the warm temperate nearshore region of Algoa Bay, South Africa, was assessed. The nearshore ichthyoplankton comprised 88 taxa from 34 families. Samples were collected at six stations between August 2010 and July 2012 using a plankton ring net of 750 mm diameter and 500 µm mesh aperture. The majority of larvae collected were in a preflexion stage, indicating the potential importance of the nearshore for newly hatched larvae. Engraulidae dominated the catch (38·4%), followed by Cynoglossidae (28·1%) and Sparidae (8·4%). Larval fish abundance was highest during austral spring and summer (September to February). Unique patterns in responses of each dominant fish species to oceanographic features in the nearshore indicate the sensitivity of the early developmental stage to environmental variables. Using generalized linear models, ichthyoplankton abundance responded positively to upwelling and when warm water plumes originating from an Agulhas Current meander entered Algoa Bay. Highest abundances of Engraulis encrasicolus and Sardinops sagax were observed during Agulhas Plume intrusions into Algoa Bay. When a mixed and stratified water column persisted in the nearshore region of Algoa Bay, larval fish abundance decreased. The nearshore region of Algoa Bay appears to serve as a favourable environment for the accumulation of ichthyoplankton.