Nuclear and mitochondrial DNA analyses reveal four genetically separated breeding units of the swordfish

Variants in the calmodulin gene intron 4 ( CaM ) and the mtDNA D-loop region ( D-loop ) detected by RFLP and nucleotide sequence analyses were used to investigate the global stock structure of the swordfish Xiphias gladius . Two alleles ( A and B ) were observed at the CaM locus among 8 samples (Mediterranean, Tarifa, four Atlantic areas, Indian and Pacific oceans) comprising 567 individuals. Genotype distributions at this locus within samples were in accordance with Hardy-Weinberg equilibrium. Significant differences in allele frequencies were observed between Mediterranean-Northwest Atlantic samples ( A =0·347–0·493) and those from tropical Atlantic and Indo-Pacific ( A =0·81–1). In the D-loop region, Alu I and Rsa I digestions detected 4 ( A - D ) and 8 ( A - H ) genotypes, respectively. The frequency of type C for Alu I was lower in Indo-Pacific samples (0·2) than Atlantic and Mediterranean samples (0·365–0·643). Frequency of type C for Rsa I increased from the Pacific (0·398) to the Northwest Atlantic (0·698) and Tarifa (0·949) samples, and the Mediterranean sample was fixed for type C . These samples were classified into three groups (Mediterranean-Tarifa, Atlantic and Indo-Pacific) using a heterogeneity test of mtDNA genotype distributions. Combined analysis of the CaM and D-loop loci indicated that there are at least four breeding units: Mediterranean, northwestern Atlantic, tropical to South Atlantic, and Indo-Pacific.     

Genetic analysis of fish genomes and populations: allozyme variation within and among Atlantic salmon from Downeast rivers of Maine

Analysis of genetic variation within and among samples of naturally produced Atlantic salmon ( n  = 372) from 7 Maine (U.S.A.) and one Canadian river were conducted based on 54 allozyme loci. Eight of the 54 loci proved polymorphic, and estimated heterozygosities ( H _S) based on all loci ranged from 0·012 to 0·026 (mean = 0·021, s . e . = 0·002). Only one of 56 tests revealed genotypic proportions that deviated significantly from Hardy–Weinberg expectations. Genetic distances ( D ) between samples ranged from 0·002 to 0·022. No obvious association existed between genetic and geographic distances. Cluster analysis of genetic distances revealed the Dennys River sample as the most differentiated when all samples were included in the analysis, though bootstrap support of the cluster analysis was generally weak. G ‐tests revealed significant differences in allele frequencies among samples at five of the polymorphic loci, and the G ‐value summed over all loci also indicated significant differences among samples. F _ST values indicated that 3·4% of the total genetic diversity was due to variability among samples, while 96·6% was due to variability within samples. These results indicate that the Atlantic salmon analyzed in this study had levels of genetic variability and differentiation among samples comparable to native populations from other areas collected across a similar geographic range.     

Phylogenetic relationships among Thunnus species inferred from rDNA ITS1 sequence

Intra and interspecific nucleotide sequence variation of rDNA first internal transcribed spacer (ITS1) was analysed using all eight species of the genus Thunnus plus two out‐group species within the same family, skipjack tuna Katsuwonus pelamis and striped bonito Sarda orientalis . Intraspecific nucleotide sequence variation in ITS1, including intra‐genomic variation, was low, ranging from 0·003 to 0·014 [Kimura's two parameter distance (K2P)], whereas variation between species within the genus Thunnus ranged from 0·009 to 0·05. The Atlantic and Pacific northern bluefin tunas Thunnus thynnus thynnus and Thunnus thynnus orientalis , recently proposed to be distinct species, were found to share nearly identical ITS1 sequences (mean K2P = 0·006) well within the range of intraspecific variation. The northern bluefin tuna appeared to be a sister group to albacore Thunnus alalunga , with all other Thunnus species in a distinct clade. The ITS1 phylogeny was consistent with mtDNA phylogeny in clustering the three tropical Thunnus species ( T. albacares , T. atlanticus and T. tonggol ). Southern bluefin Thunnus maccoyii and bigeye Thunnus obesus tunas showed a closer affinity to this tropical tuna group than to the northern bluefin tuna and albacore. The molecular data supported mitochondrial introgression between species and contradicted morphological subdivision of the genus into two subgenera Neothunnus and Thunnus .     

Molecular genetic assessment of bipolarity in the anchovy genus Engraulis

To test three hypotheses accounting for bipolar distributions in Engraulis , seven of eight taxa (except E. eurystole ) were surveyed with allozymes (34 loci) and 521 bp of the mitochondrial DNA cytochrome b gene. Both allozymes and mtDNA sequences revealed deep separations between New World and Old World anchovies with a mean allozyme genetic distance D  = 1·26 and net mtDNA sequence divergence d  = 15%. These values reflected separations of 5 to 10 million years. Contrary to previous phylogenetic hypotheses, which place north‐east Pacific E. mordax and south‐east Pacific E. ringens as sister taxa, the south‐west Atlantic E. anchoita and E. ringens are most closely related to each other. The north‐east Pacific E. mordax is the closest lineage to the Old World Engraulis , a group of taxa showing low divergences typical of population‐level separations (mean D  = 0·06; mean d  = 0·87%). Bipolarities of sister taxa in the east Atlantic and west Pacific reflect recent dispersals. Bipolarities in the east Pacific and west Atlantic represent paraphyletic taxa in lineages isolated since the Miocene. None of the bipolarities can be attributed to tectonic separations or competitive displacements from the tropics, but the latter situation should be re‐evaluated with comparisons to tropical anchovies of the New World.     

Age and growth of Mediterranean albacore

Estimated ages of 1136 individual albacore Thunnus alalunga (57–92 cm L F) from the Aegean and Ionian Sea ranged from 1⁺ to 9 years. Males grew faster and reached a greater size and age than females. No significant differences were found in the mean lengths at estimated ages between the two sampling areas. The von Bertalanffy growth model was fitted to mean lengths of estimated ages of individual fish and estimated growth parameters for the combined sexes were: L _∞=94·7 cm, K =0·258, to=–1·354 years. Significant differences were found when the Mediterranean albacore growth parameters were compared with those determined for Atlantic Ocean albacore. It is not possible to determine if the differences in growth rates for the two populations are phenotypic or genotypic at the present time.     

Genetic variation in skipjack tuna Katsuwonus pelamis(L.) using PCR‐RFLP analysis of the mitochondrial DNA D‐loop region

A high level of genetic diversity was observed in Katsuwonus pelamis populations from India ( h  = 0·952, ne  = 14·3) and Japan ( h  = 0·897, ne  = 8·9). The log‐likelihood ( G )‐based exact test revealed significant heterogeneity in the distribution of haplotypes between the two populations ( P  < 0·01, s . e . = 0·001). This result suggests that the two populations should now be treated as demographically independent and managed separately.     

Inter‐individual differences in rates of routine energy loss and growth in young‐of‐the‐year juvenile Atlantic cod

Inter‐individual differences in rates of routine (non‐feeding) metabolism and growth were evaluated in young‐of‐the‐year (YOY) juvenile Atlantic cod Gadus morhua . Rates of O₂ consumption, CO₂ production and ammonia (TAN) excretion were measured in 64, 25–43 mm standard length ( L _S) YOY growing at different rates (0·27–0·47 mm day⁻¹) in a common rearing tank. Parameter rates ( y ) increased allometrically ( y = a·M^b ) with increasing body mass ( M ) with b ‐values for O₂ production, CO₂ consumption and TAN excretion equal to 0·81, 0·89 and 0·56, respectively. In some cases, residuals from these regressions were significantly negatively correlated to fish growth rate. In no cases did residuals of parameter rates increase with increasing growth rate. These data suggest that, during unfed periods, relatively fast‐growing fish were more metabolically efficient than slower‐growing fish from the same cohort. The fish condition factor, derived from     , also significantly decreased with increasing growth rate. Results indicated differences in both the rates of routine energy loss and the patterns of growth allocation among YOY Atlantic cod. Since these physiological attributes were positively correlated with growth rate, they may be indicative of 'survivors' in field populations.     

Life‐history variation among local populations of Atlantic cod from the Norwegian Skagerrak coast

Small‐scale spatial variation in life history was found among genetically distinct local populations of Atlantic cod Gadus morhua from the Norwegian Skagerrak coast. Among populations, age at 50% maturity varied from 2·6 to 3·8 years, total ( L _T) length at 50% maturity from 35 to 60 cm, annual survival from 33 to 64%, mean L _T at age 4 years from 43 to 63 cm, and mean backcalculated L _T at age 1 year from 8 to 12 cm.     

Ontogenetic changes in temperature preference of Atlantic cod

Final thermal preferendum ( T ) experiments were conducted in a horizontal thermal gradient tank from the beginning of August 2001 to mid‐November 2001 using Atlantic cod Gadus morhua from 6·5 to 79·0 cm fork length ( L _F). The value of T varied significantly ( P  < 0·005) with L _F( T  = 7·23–0·054 L _F), with smaller (younger) fish choosing higher temperatures than larger (older) fish. The preferendum varied from 6·9° C for fish of 6·5 cm to 3·0° C for those of 79·0 cm. Experiments comparing fish positions in the gradient tank between thermal gradients of 0·5–11·0 and 4·5–14·5° C demonstrated that fish positions were determined by temperature selection instead of undesirable tank effects. This study is the first to demonstrate the effect of ontogeny on temperature preferences of a marine fish species.     

Regional differentiation of North American Atlantic salmon at allozyme loci

Allozyme variation was characterised by starch gel electrophoresis at 23 enzyme coding loci and one regulatory locus in Atlantic salmon from 53 rivers in Eastern Canada, encompassing the majority of the species' North American range. Variation among rivers was highly heterogeneous and eight of the 15 polymorphisms showed regionally restricted distributions. Nearest neighbour joining (NJ) analysis and multi‐dimensional scaling suggest six distinct regional groups; Labrador/Ungava, Gulf of Saint Lawrence, Newfoundland (excluding Gulf rivers), the Atlantic shore/Southern Uplands of Nova Scotia, the inner Bay of Fundy, and the outer Bay of Fundy. Approximately 25% of observed genetic variation was distributed among these regions with a weak though significant overall correlation of genetic and geographic distance (Mantel Test, r  = 0·255, P  = 0·005). Collectively, the rivers showed consistent divergence from European populations with strong bootstrap support for the two clusters across loci in the NJ analysis. Mean heterozygosity was 0·061 for both continental groups, but the European population showed more than twice the variation among populations. F _ST values were 0·076 and 0·176 for North America and Europe, respectively, with an overall F _ST of 0·330.     

Temporal stability of sea louse Lepeophtheirus salmonis Krøyer populations on Atlantic salmon Salmo salar L. of wild, farm and hybrid parentage

Atlantic salmon salmo salar smolts of wild, hybrid and farmed parentage were individually tagged then reared in a sea cage for 8 months. The fish were sampled three times during this period. On all occasions, farmed Atlantic salmon displayed the highest abundance and density of sea lice Lepeophtheirus salmonis , whilst no significant differences were observed between hybrid and wild Atlantic salmon. Percentage variation between the lowest and highest infected groups was as high as 175 and 144% for L. salmonis abundance and density respectively (sample 2). The temporal stability of interindividual sea lice infection levels was investigated pair‐wise between samples using correlation (sample 1 v . 2, 1 v . 3 and 2 v . 3). When calculated using sea louse abundance, correlations ranged from r ² = 0·11, P  < 0·01 to r ² = 0·39, P  < 0·001, but, when the effects of fish size were controlled for by converting abundance to density, all correlations were <  r ² = 0·1. Therefore, these data indicate that a fish's relative infection level in one sample was a weak predictor of its relative infection level in another sample. This suggests that identification of individual Atlantic salmon that display reduced susceptibility to sea lice, may be problematic.     

A new technique to gather 3‐D spatial information using a single camera

A new technique using a single camera and shadows to determine 3‐D spatial positions of fishes in the laboratory is described. The apparatus consisted of a large aquarium (2·0 × 1·5 × 0·4 m), a wide‐angle camera mounted above and two light sources to cast shadows to either side of the fish. Using image analysis and vector mathematics, aquarium objects were plotted within 1·5 cm of their actual location along the x ‐, y ‐ and z ‐axis. The technique was also successful in quantifying changes in 3‐D spatial pattern of juvenile fish, Atlantic cod Gadus morhua (7·4–8·6 cm standard length, L _S) and cohabitant piscivorous shorthorned sculpin Myoxocephalus scorpinus (12·0–25·8 cm L _S), at these same viewing fields. The new technique should have a wide application, largely because it is potentially less expensive, laborious and invasive than alternative methods for determining 3‐D positions of fishes.     

Differential population history in the migratory catfishes Brachyplatystoma flavicans and Pseudoplatystoma fasciatum(Pimelodidae) from the Bolivian Amazon assessed with nuclear and mitochondrial DNA markers

The catfishes Brachyplatystoma flavicans ( n  = 49) and Pseudoplatystoma fasciatum ( n  = 69) showed comparable low allozyme diversities ( H _e = 0·012 and 0·009–0·028, respectively), but contrasting PCR‐RFLP restriction site mitochondrial DNA diversities (three haplotypes: π = 0·034–0·092 and five haplotypes: π = 0·001–0·023, respectively) in the Rio Ichilo and Beni (Bolivia). Genetic homogeneity between samples was high for B. flavicans and lower for P. fasciatum . Based on mitochondrial diversity, both species probably experienced a historic population reduction but at different time scales.     

Growth variation in larval Makaira nigricans

The Atlantic blue marlin Makaira nigricans larvae were collected from Exuma Sound, Bahamas and the Straits of Florida over three summers (2000–2002). Sagittal otoliths were extracted and read under light microscopy to determine relationships between standard length ( L _S) and age for larvae from each year and location. Otolith growth trajectories were significantly different between locations: after the first 5–6 days of life, larvae from Exuma Sound grew significantly faster than larvae from the Straits of Florida. Exponential regression coefficients were similar among years for Exuma Sound larvae (mean instantaneous growth rate, G _L = 0·125), but differed between years for larvae from the Straits of Florida ( G _L = 0·086–0·089). Differences in larval growth rates between locations resulted in a 4–6 mm difference in L _S by day 15 of larval life. These differences in growth appeared to be unrelated to mean ambient water temperatures, and may have been caused by location‐specific differences in prey composition or availability. Alternatively, population‐specific differences in maternal condition may have contributed to these differences in early larval growth.     

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

The optimal management of the commercially important, but mostly over‐exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded F_ST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between‐ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17‐SNP panel was developed in Atlantic BFT by cross‐species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (F_ST = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.     

Interhabitat and instream movements of large Atlantic salmon parr in a Newfoundland watershed in winter

Radio‐telemetry was used to investigate movement of large, mainly mature male (80%) Atlantic salmon Salmo salar parr in Stoney River, Newfoundland during early winter (November; water temperature 6·0 ± 0·1° C) and mid‐winter (January to February; 0·8 ± 0·0° C). Site fidelity of parr in early winter was low. Parr moved between fluvial and lacustrine habitats and were active throughout the diel cycle. Parr caught in fluvial habitats in mid‐winter were smaller and younger than parr caught in early winter. Site fidelity of parr in mid‐winter was greater than in early winter. Parr in mid‐winter moved between fluvial and adjacent small lacustrine habitats, but avoided a larger pond inhabited by large piscivorous fishes. Instream movement rates in mid‐winter were lower than in early winter and occurred primarily during hours of darkness (dawn, dusk and night). Fluvial habitats were relatively stable and ice‐free throughout the study periods. These results suggested that large Atlantic salmon parr utilize a variety of habitats and remain active throughout the winter, even under stable environmental conditions.     

Mackerel icefish size and age differences and long‐term change at South Georgia and Shag Rocks

This study analysed the total length ( L _T)‐frequency distribution of mackerel icefish Champsocephalus gunnari at South Georgia and Shag Rocks from nine bottom trawl surveys at South Georgia and eight at Shag Rocks between 1987 and 2002. The estimated mean L _T of age‐classes 1+, 2+, 3+ and 4+ years during January were, respectively, 14·7, 23·5, 29·8 and 35·1 cm at South Georgia. Age‐classes 1+, 2+ and 3+ years were 18·3, 26·2 and 33·8 cm at Shag Rocks. The derived Bertalanffy growth parameters for South Georgia were: L _∞ = 51·7 cm, k  = 0·27 and t ₀ = −0·26. The mean L _T of each age‐class of C. gunnari at Shag Rocks was significantly larger than at South Georgia, equivalent to c . 5 months growth, although the annual growth in L _T was similar. This is further evidence that C. gunnari hatched earlier at Shag Rocks. At South Georgia, the mean L _T of age‐classes 1+ and 3+ years were correlated, and significantly decreased between 1987 and 2002, and were smaller following warmer summers. This decrease in the size of C. gunnari may be the result of reduced food availability linked to climate warming.     

Feeding preference and deterrence in rabbitfish Siganus fuscescens for the cyanobacterium Lyngbya majuscula in Moreton Bay, south‐east Queensland, Australia

Rabbitfish Siganus fuscescens preferences for Lyngbya majuscula collected from three bloom locations in Moreton Bay, Queensland, Australia, were tested along with a range of local plant species in the laboratory. Consumption of L. majuscula by fish did not differ between wild and captive‐bred fish ( P  = 0·152) but did differ between bloom location ( P  = 0·039). No relationship was found between consumption rates and lyngbyatoxin‐a concentration ( r ² = 0·035, P  = 0·814). No correlation existed between C : N and proportion of food consumed when all food types were analysed statistically, whereas a clear correlation was observed when L. majuscula was removed from the calculations. In simulated bloom conditions, fish avoided ingestion of L. majuscula by feeding through gaps in the L. majuscula coverage. Both wild and captive‐bred S. fuscescens showed a distinct feeding pattern in 10 day no‐choice feeding assays, with less L. majuscula being consumed than the preferred red alga Acanthophora spicifera . Lyngbya majuscula however, was consumed in equal quantities to A. spicifera by wild S. fuscescens when lyngbyatoxin‐a was not detectable. Wild fish probably do not preferentially feed on L. majuscula when secondary metabolites are present and are not severely impacted by large L. majuscula blooms in Moreton Bay. Furthermore, poor feeding performance in both captive‐bred and wild S. fuscescens suggests that they would exert little pressure as a top‐down control agent of toxic L. majuscula blooms within Moreton Bay.     

Phylogeography of the Turkish brown trout Salmo trutta L.: mitochondrial DNA PCR‐RFLP variation

In the present study, mitochondrial DNA polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) assay was used to assess the phylogenetic and phylogeographic relationships among 27 brown trout Salmo trutta populations from Turkey. The complete NADH 5/6 region and a second segment comprising the cytochrome b gene and D‐loop of mtDNA amplified by PCR were digested with six and five restriction enzymes, respectively. A total of 27 haplotypes were observed and divided into three major phylogenetic assemblages, namely Danubian (DA), Adriatic (AD) and a newly proposed Tigris (TI) lineage. The timing of the net nucleotide divergence between the major lineages along with the geological history of Turkey suggested pre‐Pleistocene isolation of the Turkish brown trout and provided evidence that Turkey could be considered as a centre of diversification for these lineages. The average haplotype diversity (0·1397) and the nucleotide diversity (0·000416) within populations were low in comparison to the observed interpopulation nucleotide diversity (0·021266). PCR‐RFLP analysis showed that most of the mtDNA sequence variation found in the Turkish brown trout populations was imputable to differences among lineages. On the other hand, there was also an obvious relationship between geographical distribution of the populations and their clustering. The present study showed that brown trout populations from Turkey are highly divergent and mainly have a unique genetic profile that could be used for conservation and management purposes.     

Population dynamics of fisheries stock enhancement

A comparative analysis was performed on sixteen morphometric characters, in three different juvenile sterlet Acipenser ruthenus L. populations. Specimens were collected from a wild population in the Serbian part of the Danube River ( n  = 46), from aquaculture stocks in the Czech Republic originating from Russia ( n  = 40), and aquaculture stocks in the Slovak Republic originating from Slovakian part of the Danube River ( n  = 28). Average values for total length were 29·9 ± 3·9 cm, 29·1 ± 3·7 cm and 27·3 ± 7·7 cm for Serbia, Czech Republic and Slovak Republic, respectively. Populations were compared using t ‐test and sequential Bonferroni correction for multiple comparisons was applied in order to determine significant differences between them. Results of analysis showed that all three populations differed in prebarbel length, interocular distance and maximum head width. Although all these characters are head‐related, head length itself was very uniform among all populations. The natural population from the Serbian part of the Danube River differed from the populations reared in aquaculture in seven morphometric characters. The two populations reared in aquaculture consistently showed lower morphological variability than the wild population, even though they had different genetic backgrounds (Russia and Slovakia). Future genetic studies will show if this tendency is caused by a reduction in genetic variability.