DNA barcoding Australia's fish species

Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups-dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus-were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species.     

Detritivory in two Amazonian fish species

In floodplain lakes of Central Amazon, the siluriform Liposarcus pardalis and the characiform Prochilodus nigricans consumed detritus with different compositions. Most of the diet of L. pardalis and P. nigricans was made of amorphous organic matter. The food ingested by L. pardalis had relatively higher organic matter (OM) (35–55%) and crude protein (10–19%) than that found in P. nigricans stomachs (10–20% and 2–5%, respectively). Both fish ingested higher quantities of OM and crude protein during the high-water season. The differences between the two species seem to be related to their ability to select different detrital components. Striking differences were also found in the digestibility rate of OM and protein between the two species. Prochilodus nigricans assimilated only 2·3% of its intake compared with 24% in L. pardalis .     

Comparative analysis of reproductive traits in 65 freshwater fish species: application to the domestication of new fish species

Based on an extensive literature search (1,000 references), the objectives of the present study were to establish a numerical clustering of temperate freshwater fish based on their reproductive traits and to evaluate whether it was possible to extrapolate zootechnical knowledge among species belonging to the same cluster. About 65 species were classified into ten homogeneous clusters from the analysis of 29 reproductive traits, among which the most important were temperature during spawning, egg incubation and larval rearing, degree-days for incubation, larval size upon hatching, spawning season, and parental care. From this typology, a rather regular continuum of reproductive clusters emerges with two obvious endpoints. Between these two extremes, species could be ordered chiefly according to temperature requirement, spawning season and parental care. In conclusion, this new typology, differing significantly from all others proposed earlier, may now serve as a possible framework to help enhancing the domestication of new species by comparison to species belonging to the same cluster.     

The distribution of an invasive fish species is highly affected by the presence of native fish species: evidence based on species distribution modelling

Topmouth gudgeon (Pseudorasbora parva) is one of the most invasive aquatic fish species in Europe and causes adverse effects to ecosystem structure and functioning. Knowledge and understanding of the species’ interactions with the environment and with native fish are important to stop and prevent the further spread of the species. Creating species distribution models is a useful technique to determine which factors influence the occurrence and abundance of a species. We applied three different modelling techniques: general additive models, random forests and fuzzy habitat suitability modelling (FHSM) to assess the habitat suitability of topmouth gudgeon. The former two techniques indicated that the abundance of native fish (i.e. biotic variables) was more important than environmental variables when determining the abundance of topmouth gudgeon in Flanders (Belgium). Bitterling (Rhodeus amarus), stone loach (Barbatula barbatula), three-spined stickleback (Gasterosteus aculeatus) and predator abundance were selected as the most important biotic variables and implemented in the FHSM to investigate species interactions. Depending on the preferred food source and spawning behaviour, either coexistence or interspecific competition can occur with bitterling, stone loach and three-spined stickleback. In contrast, the presence of predators clearly had a top down effect on topmouth gudgeon abundance. These findings could be applied as a biological control measure and implemented in conservation strategies in order to reduce the abundance of earlier established populations of topmouth gudgeon.     

DNA barcoding commercially important fish species of Turkey

DNA barcoding was used in the identification of 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. A total of 1765 DNA barcodes using a 654‐bp‐long fragment of the mitochondrial cytochrome c oxidase subunit I gene were generated for 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. These species belong to 70 genera, 40 families and 19 orders from class Actinopterygii, and all were associated with a distinct DNA barcode. Nine and 12 of the COI barcode clusters represent the first species records submitted to the BOLD and GenBank databases, respectively. All COI barcodes (except sequences of first species records) were matched with reference sequences of expected species, according to morphological identification. Average nucleotide frequencies of the data set were calculated as T = 29.7%, C = 28.2%, A = 23.6% and G = 18.6%. Average pairwise genetic distance among individuals were estimated as 0.32%, 9.62%, 17,90% and 22.40% for conspecific, congeneric, confamilial and within order, respectively. Kimura 2‐parameter genetic distance values were found to increase with taxonomic level. For most of the species analysed in our data set, there is a barcoding gap, and an overlap in the barcoding gap exists for only two genera. Neighbour‐joining trees were drawn based on DNA barcodes and all the specimens clustered in agreement with their taxonomic classification at species level. Results of this study supported DNA barcoding as an efficient molecular tool for a better monitoring, conservation and management of fisheries.     

Behavioural thermoregulation in two freshwater fish species

In the presence of a vertical thermal gradient, juvenile three‐spined sticklebacks Gasterosteus aculeatus and minnows Phoxinus phoxinus positioned themselves higher in the water column compared with adult conspecifics. This result was consistent regardless of whether age cohorts were tested separately or together. Furthermore, juveniles but not adult fishes positioned themselves higher in water column in the presence of a thermal gradient compared with those in the absence of a thermal gradient. Juvenile G. aculeatus and adult fish of both species did opt to position themselves higher in the water column in the hours immediately following a feeding event relative to their positions in the same gradient when they had not fed.     

Patterns of fish species richness in China's lakes

Aim To document the patterns of fish species richness and their possible causes in China's lakes at regional and national scales. Location Lakes across China. Methods We compiled data of fish species richness, limnological characteristics and climatic variables for 109 lakes across five regions of China: East region, Northeast region, Southwest region, North‐Northwest region, and the Tibetan Plateau. Correlation analyses, regression models and a general linear model were used to explore the patterns of fish species richness. Results At the national scale, lake altitude, energy availability (potential evapotranspiration, PET) and lake area explained 79.6% of the total variation of the lake fish species richness. The determinants of the fish richness pattern varied among physiographic regions. Lake area was the strongest predictor of fish species richness in the East and Southwest lakes, accounting for 22.2% and 82.9% of the variation, respectively. Annual PET explained 68.7% of the variation of fish richness in the Northeast lakes. Maximum depth, mineralization degree, and lake area explained 45.5% of the fish variation in the lakes of the North‐Northwest region. On the Tibetan Plateau, lake altitude was the first predictor variable, interpreting 32.2% of the variation. Main conclusions Lake altitude was the most important factor explaining the variation of fish species richness across China's lakes, and accounted for 74.5% of the variation. This may stem in part from the fact that the lakes investigated in our study span the largest altitudinal range anywhere in the world. The effects of the lake altitude on fish species richness can be separated into direct and indirect aspects due to its collinearity with PET. We also found that the fish diversity and its determinants were scale‐dependent. Fish species richness was probably energy‐determined in the cold region, while it was best predicted by the lake area in the relatively geologically old region. The independent variables we used only explained a small fraction of the variations in the lake fish species richness in East China and the Tibetan Plateau, which may be due to the effects of human activity and historical events, respectively.     

Comparison of muscle proteinase activity among fish species

The effects of temperature during storage, portion of muscle and growth stage of fish on the activity level of carp muscle acid (cathepsin D, EC 3.4.23.5), neutral and alkaline proteinases were examined. Icing storage, freezer storage and portion of muscle did not affect each proteinase activity (P less than 0.05), but acid proteinase activity was affected by growth stage (P less than 0.05) and the level decreased from small to large fish. The activity levels of three kinds of proteinases were compared among species (P less than 0.05) and the following order was obtained. Acid proteinase, white croaker = rainbow trout = carp greater than sardine = common mackerel, sardine greater than lizardfish, common mackerel = lizardfish. Neutral proteinase, rainbow trout greater than carp = white croaker greater than lizardfish = sardine = common mackerel. Alkaline proteinase, rainbow trout = sardine greater than white croaker = carp = common mackerel greater than lizardfish.     

Ganglioside pattern and thermal tolerance of fish species

The brain ganglioside pattern of taxonomically close and distant related fish species living at different temperatures and the mammalian pattern were compared. The results demonstrate correlations between body temperature and brain ganglioside pattern: the higher the body temperature of animals, the lower is the relative proportion of polysialogangliosides in their brain.     

Metallothionein levels in sperm of various fish species

In the present paper we determined low molecular heavy metal binding protein called metallothionein (MT) in fish spermatozoa sampled from four fish species ( Acipenser baerii, Acipenser ruthenus, Perca fluviatilis and Sander lucioperca ). The spermatozoa samples were analyzed with differential pulse voltammetry DPV (Brdicka reaction). The average content of MT in the fish sperm was 0.64 ± 0.55 μ m . The highest content of MT was determined in spermatozoa of S. lucioperca (0.96 ± 0.86 μ m ), followed by P. fluviatilis (0.88 ± 0.11 μ m ), A. ruthenus (0.57 ± 0.60 μ m ) and A. baerii (0.43 ± 0.25 μ m ). The differences in the content of MT was probably related to the differences in age and perhaps to the health status based on the environmental conditions in which the tested specimens developed while also other still unknown factors may have been involved.     

Implications of species loss in freshwater fish assemblages

Freshwater systems are vulnerable to pollution and species loss often ensues. Are there additional implications for assemblage structure? Here we use Berger‐Parker d. Simpson's I/D and Simpson's F to measure the ecological diversity of pristine and perturbed freshwater fish assemblages in Trinidad. West Indies, and Oklahoma. USA. Although the impacted sites typically had fewer species than expected, they could not be distinguished from unperturbed ones of equivalent richness. Changes in the evenness of these assemblages are thus driven by changes in richness. One practical outcome is that diversity indices may not provide independent verification of the detrimental consequences of pollution. The similarity in structure of naturally and anthropogenically impoverished assemblages provides no grounds for complacency, however, since it ignores the evolutionary history of the species concerned. On the basis of our results we suggest that species provenance may be important in tests of ecological function. Moreover, these investigations should replicate natural patterns of evenness as well as richness.     

Surveillance of fish species composition using environmental DNA

Prompt and accurate methods for assessing the species composition of given areas are indispensable in addressing the rapid loss of biodiversity. Here, we propose a method for the surveillance of fish species composition in freshwater using environmental DNA as species markers. First, the applicability of the method was demonstrated through aquarium experiments. DNA was extracted from 120?ml aquarium water, and the degenerated primers targeting the fish mitochondrial cytochrome b gene were used for amplification. PCR-amplified fragments were analysed by random cloning, and all species reared in the aquarium were detected. Next, this method was applied to natural freshwater environments. Water samples were collected from three sites in the Yura River, Japan; DNA was concentrated from 2?l of environmental water, and then amplified and cloned. Up to four species of fish were detected by sequencing 47 randomly selected clones from a single water sample. Overall, the results were consistent with previous knowledge of fish habitat utilisation. Using this method, the surveillance of fish species composition can be conducted less laboriously than with traditional methods.     

Vulnerability of sea hares to fish predators: importance of diet and fish species

Many sea hares (Opisthobranchia, Anaspidea) sequester secondary metabolites from their algal diets. Tests of the hypothesis that sequestered metabolites deter predators have yielded ambiguous results. We manipulated secondary metabolites in vivo by collecting the sea hare Stylocheilus striatus from different host algae, and by raising it in the laboratory on artificial diets containing or lacking secondary metabolites (malyngamides A and B). Sea hares were then offered to fish. Fish identity affected vulnerability of sea hares to predation far more than did diet history. Wrasses and bream ate most sea hares tasted; damselfishes, goatfishes, and other fishes rejected most. Diet history affected vulnerability of sea hares to wrasses in one of four experiments, and if data from all experiments were pooled, but the effect was modest. Diet history did not affect vulnerability of sea hares to other fish taxa. Despite several studies, evidence for diet-derived defenses against predators in sea hares remains equivocal.     

Trophic interactions between native and introduced fish species in a littoral fish community

The trophic interactions between 15 native and two introduced fish species, silverside Odontesthes bonariensis and rainbow trout Oncorhynchus mykiss, collected in a major fishery area at Lake Titicaca were explored by integrating traditional ecological knowledge and stable‐isotope analyses (SIA). SIA suggested the existence of six trophic groups in this fish community based on δ¹³C and δ¹⁵N signatures. This was supported by ecological evidence illustrating marked spatial segregation between groups, but a similar trophic level for most of the native groups. Based on Bayesian ellipse analyses, niche overlap appeared to occur between small O. bonariensis (<90 mm) and benthopelagic native species (31·6%), and between the native pelagic killifish Orestias ispi and large O. bonariensis (39%) or O. mykiss (19·7%). In addition, Bayesian mixing models suggested that O. ispi and epipelagic species are likely to be the main prey items for the two introduced fish species. This study reveals a trophic link between native and introduced fish species, and demonstrates the utility of combining both SIA and traditional ecological knowledge to understand trophic relationships between fish species with similar feeding habits.     

The host—parasite relationship of two copepod species and two fish species

A total of 2494 Menidia beryllina and 717 M. peninsulae (Atherinidae) were examined from the Pensacola Bay area for parasitic copepods. M. peninsulae was infested with Bomolochus concinnus (Bomolochidae) and Ergasilus marticatus (Ergasilidae) and had incidences (and intensities) of 12.3% (1.6) and 4.2% (1.3), respectively. Only seven M. peninsulae were infested with both species of parasites. M. beryllina was infested only with E. manicatus and showed different incidences (and intensities) in two areas: Mulatto Bayou, 13.2% (1.9); Catfish Basin, 53.0% (2.3). Fishes with parasites were significantly longer than fishes without parasites and the case of increasing number of parasites with increasing fish length was reinforced. B. concinnus is a warm water parasite on M. peninsulae while E. manicatus acts as a cold water parasite on M. peninsulae and a warm water parasite on M. beryllina . The parasites tended to be overdispersed on their hosts but at the same time showed evidence of negative intraspecific associations within a host. These data suggest intraspecific avoidance by the parasite but active acquisition by the host.