Population genetic structure and effective population size of ayu (Plecoglossus altivelis), an amphidromous fish

The temporal and spatial population genetic structure of ayu Plecoglossus altivelis (Salmoniformes: Plecoglossidae), an amphidromous fish, was examined using analysis of variation at six microsatellite DNA loci. Intracohort genetic diversities, as measured by the number of alleles and heterozygosity, were similar among six cohorts (2001–2006) within a population (Nezugaseki River), with the mean number of alleles per cohort ranging from 11·0 to 12·5 and the expected heterozygosity ranging from 0·74 to 0·77. Intrapopulational genetic diversities were also similar across the three studied populations along the 50 km coast, with the mean number of alleles and the expected heterozygosity ranging from 11·33 to 11·67 and from 0·75 to 0·76, respectively. The authors observed only one significant difference in pair-wise population differentiation ( F _ST-value) between the cohorts within a population and among three populations. Estimates of the effective population size ( N _e) based on maximum-likelihood method yielded small values (ranging from 94·8 to 135·5), whereas census population size ranged from c. 4800 to 24 000. As a result, the ratio of annual effective population sizes to census population size ( N _e/ N ) ranged from 0·004 to 0·023. These estimates of N _e/ N agree more closely with estimates for marine fishes than that of the larger estimates for freshwater fishes. The present study suggests that ayu which is highly fecund and shows low survival during the early life stages is also characterized by having low value of N _e/ N , similar to marine species with a pelagic life cycle.     

A comparison of genetic diversity levels in marine, freshwater, and anadromous fishes

Electrophoretic data were analysed from 49 species of freshwater fish, 57 species of marine fish, and seven anadromous species. For each species, at least 15 individuals had been assayed for at least 15 loci in two or more subpopulations. The results showed that while average total heterozygosity ( _T ) was approximately equal in freshwater and marine species (0·062 and 0·064 respectively), subpopulation heterozygosity ( _s ) was significantly less in the former group (0·046 and 0·059 respectively). Consequently the average degree of genetic subpopulation differentiation ( _ST ) was significantly greater for freshwater species (0·222 v. 0·062). On average, it is likely that marine subpopulations exchange between 10 and 100 times more migrants per generation than freshwater subpopulations, presumably because of the relative absence of barriers to dispersal in the marine environment. The reduced values of H_s in freshwater species are likely to reflect reduced effective subpopulation sizes relative to marine species. The few andromous species that have been analysed show intermediate levels of G_ST .     

The relationship of oocyte diameter and incubation temperature to incubation time in temperate freshwater fish species

Based on the analysis of six egg variables and incubation temperature of 65 temperate freshwater fish species, the possible relationships between oocyte diameter, incubation time and incubation temperature were reassessed and compared to the results obtained from marine fishes. Most freshwater species have eggs (mean ± s . d . 2·19 ± 1·52 mm) larger than marine species, that are chiefly demersal and develop stuck to various substrata, such as plants or rocks. A strong negative relationship was found between incubation time ( t , days) and incubation temperature ( T , ° C): t = 186·23e^{−0·197 T} ( r ²= 0·87). A strong dependence of incubation time on oocyte diameter ( Ø , mm) and incubation temperature was also found and was defined as: log₁₀ t = 3·002 + 0·599 log₁₀ Ø − 1·91 log₁₀ ( T + 2), which explained 92% of the variance of the data set. Five major groups of species were defined based on the principal component analysis (PCA) of four quantitative variables. There were two distinct groups of salmonids, displaying demersal and non-adhesive eggs with a long incubation time at low temperature, the eggs of which required a high number of degree-days. There was a large group of species possessing small, mostly demersal and adhesive eggs developing at high temperature during a short period of time, and requiring a low number of degree-days. Between these two extremes, there was a fourth group displaying intermediate values and a fifth group including three species with large, adhesive and demersal eggs incubating at high temperatures during a short period of time. The burbot Lota lota displayed an unusual combination of variables compared to the remaining species in the data set.     

Population structure of lake‐type and river‐type sockeye salmon in transboundary rivers of northern British Columbia

The population structure of 'lake‐type' and 'river‐type' sockeye salmon Oncorhynchus nerka , primarily in transboundary rivers in northern British Columbia, was examined with a survey of microsatellite variation. Variation at 14 microsatellite loci was surveyed from c . 3000 lake‐type and 3200 river‐type sockeye salmon from 47 populations in six river drainages in British Columbia. The mean F _ST for the 14 microsatellite loci and 47 populations was 0·068, and 0·034 over all river‐type populations. River‐type sockeye salmon were more genetically diverse than lake‐type sockeye salmon, with expected heterozygosity of river‐type sockeye salmon 0·72 and with an average 12·7 alleles observed per locus, whereas expected heterozygosity of lake‐type sockeye salmon was 0·65 with and average 10·5 alleles observed per locus. River drainage of origin was a significant unit of population structure. There was clear evidence of genetic differentiation among river‐type populations of sockeye salmon from different drainages over a broad geographic range in British Columbia.     

Genetic differentiation of freshwater and marine sticklebacks, (Gasterosteus aculeatus) of Eastern Europe

Electrophoretic variation of 13 presumptive enzymatic loci was studied in sticklebacks (Gasterosteus aculeatus) at 6 marine (Baltic) and 13 freshwater sites from Poland. Marine samples are significantly more variable (proportion of polymorphic loci, p # 0.38) than freshwater Samles (p # 0.12). Also the mean number of alleles per locus is significantly higher in the marine samples (n # 1.54) than in freshwater samples (n # 1.14). There is however no significant difference in values of mean heterozygosity between marine and freshwater sticklebacks. Some alleles are found in Baltic sticklebacks only, but all these occur in very low frequencies. Genetic distance between samples is low ranging from D = 0.000053 to 0.031410. However D is significant smaller between marine samples than between freshwater Samles. We suggest than this probaily is the result of larger genetic subdivision of freshwater populations. The low genetic divergence of marine and freshwater populations of the stickleback from poland might be expfained by the recent postglacial colonization of this area from a common refugium.     

Cloning and characterization of microsatellite loci in channel catfish, Ictalurus punctatus

Short tandem repeat (microsatellite) loci were cloned from the channel catfish, Ictalurus punctatus , genome for use as molecular markers for genetic improvement of this important agricultural species. Plasmid clones containing catfish genomic DNA inserts were identified, by hybridization with tandem repeat DNA probes, and sequenced using automated laser fluorescence. A feral population of catfish displayed levels of heterozygosity greater than 0·7 for 13 of 22 loci and heterozygosity greater than 0·5 for 20 of 22 loci. Allelic polymorphism ranged from three to 17 alleles per locus in the feral population. Populations of domestic, farm-raised catfish and a research strain displayed levels of heterozygosity similar to the feral population. Non-invasive tissue sampling provided abundant material for the polymerase chain reaction-based genotype assay. The microsatellite loci will be useful in the molecular characterization and genetic improvement of channel catfish populations.     

Isolation and characterization of 20 polymorphic microsatellite loci in the migratory freshwater fish Leporinus obtusidens (Characiformes: Anostomidae) using 454 shotgun pyrosequencing

Twenty polymorphic microsatellite markers were developed for the Neotropical fish Leporinus obtusidens using a next generation sequencing approach and tested in two other characifomes species, Schizodon platae and Prochilodus lineatus. Microsatellite loci alleles in L. obtusidens ranged between 2 and 20 alleles per locus (mean = 5·7), with expected heterozygosity values ranging from 0·097 to 0·956 (mean = 0·578) and observed heterozygosity values ranging from 0·000 to 0·800 (mean = 0·400) in a sample of 20 specimens from the lower Paraná River (Argentina). Most of these markers will be a valuable tool for captive breeding and stocking programmes, as well as for analyses of population connectivity and genetic structure in this broadly distributed Neotropical migratory fish.     

Enzyme polymorphism in the freshwater mussel species, Aspatharia pfeifferiana (Mollusca, Lamellibranchiata) from southern Africa

Gene products of 31 protein coding loci in Aspatharia pfeifferiana examined by horizontal starch gel electrophoresis revealed genetic variation at 10 (32.26%) of the loci studied. The mean number of alleles per locus was 1±39 (±0±11), and the average heterozygosity value was 0±074 (±0±026). Not only is this the first account of electrophoretic variants of this species, but also the results show that the species has less genetic variation than most other molluscs. Genetic variation compares favourably with values obtained for other invertebrate species and for fish from the same geographical region. A. pfeifferiana has sufficient variation to adapt to environmental changes or to be used in selection programmes. The results are useful for conservation stocking and it will undoubtedly aid in improving the systematics and phylogeny of freshwater clams in general.     

Reproductive biology of the endangered Oxleyan pygmy perch Nannoperca oxleyana Whitley

The reproductive biology of the Oxleyan pygmy perch Nannoperca oxleyana is described from simultaneous studies of wild populations in north-eastern New South Wales and mature fish held in aquaria. In the wild, 50% of males and females matured at total lengths of 24·0–25·9 and 28·0–29·9 mm, respectively. The species displays sexual dichromatism during the spawning season, with males developing more intense red and brown fin and body colouration, and black pelvic fins. Captive male broodfish displayed territoriality during the breeding season, closely guarding sites within artificial, plant-like substrata in which pairs of fish spawned adhesive eggs. Protracted serial spawning of wild and captive fish occurred from September to April and May at mean water temperatures ≥16·6° C and day length ≥10·7 h. Captive broodfish spawned on an average of 57% of days during the 256 day spawning period. Gonado-somatic indices averaged 0·7% for all ripe males and 4·1–4·2% for all ripe females collected. Mean total and batch fecundities of captive females were 1323 eggs per fish and 7·8 eggs per fish per day, respectively, and relative fecundity was 587 eggs g⁻¹ of body mass. Batch fecundity of wild females was estimated at 7·8 eggs per fish. The adaptive significance of this reproductive strategy in a harsh, variable environment is discussed.     

Twelve novel microsatellite loci from an endangered marine fish species golden pompano Trachinotus blochii

The golden pompano (Trachinotus blochii) is a marine fish species in tropical regions. No information about genetic variation and population structure of wild populations is available. A first set of 12 polymorphic microsatellites isolated from this species were characterized. The number of alleles ranged from 5 to 14 with an average of 8.0 alleles per locus. All 12 markers conformed to HWE and were in linkage equilibrium. These 12 microsatellite markers supply the first set of co-dominant DNA markers for studying population genetics of the species T. blochii.     

Population structure and phylogeography of Aphyocypris kikuchii (Oshima) based on mitochondrial DNA variation

Aphyocypris kikuchii is a cyprinid species endemic to northern and eastern Taiwan and is the only primary freshwater fish native east of the Coastal Mountain Range. In total, 92 individuals of A. kikuchii from seven populations in three regions of the island were surveyed for mitochondrial DNA (mtDNA) variation. High haplotype diversity ( h = 0·989) and low nucleotide diversity ( π = 0·009) of mtDNA were detected. Negative values of Tajima's D and unimodal mismatch distributions probably reflect a history of recent demographic expansions from small populations. Three major haplotype clusters displayed geographically non-overlapping distributions, indicating a long-term isolation between regions. Hierarchical analysis of molecular variance showed significant genetic structuring among populations ( Φ _ST= 0·66). Significant haplotype heterogeneity was also detected among populations within regions ( Φ _SC= 0·41, P < 0·001) and among regions ( Φ _CT= 0·43, P < 0·05). Molecular clock estimates of coalescence in the three major mtDNA lineages indicated coalescence in the most recent common ancestor c. 0·11–0·39 million years ago. Haplotypes of cluster B nested as interior nodes in the haplotype network, indicating that migrations from Shueilian (SL) populations to the northern region (cluster A) and to the eastern region (cluster C) may have occurred independently. Lineages A and B + C should be managed as two distinct evolutionarily significant units, while the northern, SL and southern groups should be managed as separate management units.     

Isolation and characterization of polymorphic microsatellite markers in the migratory freshwater fish Prochilodus costatus

We isolated six polymorphic microsatellite loci in the migratory freshwater fish Prochilodus costatus, which is an endemic species and important fisheries resource from São Francisco river basin, Brazil. We have evaluated the applicability of these loci to study genetic variation in wild population of this fish. Thus, based on the genotypes of 32–48 individuals, we detected two to 21 alleles per locus, observed and expected heterozygosities ranging from 0.19 to 0.89 and from 0.17 to 0.92, respectively. These polymorphic markers should provide efficient tools to study population genetic structure of this fish.     

Development and testing of 13 polymorphic microsatellite markers in Larimichthys polyactis (Sciaenidae) using 5' anchored PCR

Larimichthys polyactis is a commercially important marine fish species in southeast Asia. The population crashed due to overfishing in the 1970s, but has since recovered. We developed 13 novel polymorphic microsatellite markers in L. polyactis using 5' anchored PCR. The characteristics of these loci were estimated by analyzing a sample of 30 individuals. A total of 74 alleles were detected, with a mean of 5.7 alleles per locus. There were 2 to 12 alleles, 0.2760 to 0.8247 polymorphism information content, and 0.3214 to 1.000 observed and 0.3097 to 0.8567 expected heterozygosity per locus. The mean observed and expected heterozygosity was 0.6816 and 0.6724, respectively. Three loci deviated significantly from Hardy-Weinberg equilibrium after Bonferroni's correction, and no significant linkage disequilibrum between pairs of loci was found. This information will be useful for the analysis of population genetic diversity, and the management of this important fish resource.     

Genic diversity in Red River pupfish Cyprinodon rubrofluviatilis (Atheriniformes: Cyprinodontidae) and its implications for the conservation genetics of the species

Starch gel electrophoresis of proteins was used to study geographic variation at 26 gene loci in the Red River pupfish ( Cyprinodon rubrofluviatílís ), a species restricted to west Texas and Oklahoma. Marked differences were detected between populations in the Red and Brazos river drainages, with fixed or nearly fixed differences occurring at five gene loci. In addition, mean heterozygosity was uniformly high for the Red River form ( = 0·076–0·101) while samples of the Brazos River form were genetically depauperate ( =0·00–0·017). Introduced populations in the South Canadian and Colorado river drainages appear to have been derived from the Red River drainage. The presence of alleles diagnostic of the Red and Brazos river forms supports the suggestion from previous work that they may represent cryptic species. Regardless of taxonomy, however, the presence of two genetically distinct forms must be taken into consideration by those concerned with maintenance of biotic diversity.     

Fatty acid content of some freshwater fish of commercial importance from tropical lakes in the Ethiopian Rift Valley

Fifty samples of freshwater fish, representing eight tropical species, were collected from Ethiopian Rift Valley lakes in order to study the variation of lipids and fatty acids (FA) both within and between species. Most specimens (36 samples) were low in fat, ≥5% of dry weight (dw). Medium- (nine samples) and high-fat fish (five samples) contained ≤6% and >10% dw, respectively. The extent of variation was more pronounced in the herbivore Oreochromis niloticus than in the omnivorous (e.g. Barbus sp.) or carnivorous–piscivorous ( Clarias gariepinus ) fishes. Twenty-eight FA of various chain lengths and saturation levels were identified. Most FA were unsaturated and long-chained. The major individual FA were palmitic acid (16:0), stearic acid (18 : 0), oleic acid (18 : 1ω9) and docosahexaenoic acid (DHA) (22 : 6ω3). The ω3/ω6 ratio varied considerably (1·1–7·6) and O. niloticus from Lake Haiq was found to be superior in lipid quality to all the tropical fish species considered in this study. The data show that tropical freshwater fish are comparable to temperate freshwater fish as sources of polyunsaturated FA.     

Development and characterization of 32 microsatellite loci in the giant grouper Epinephelus lanceolatus (Serranidae)

An economically important marine fish species, the giant grouper Epinephelus lanceolatus (Serranidae) is widely cultured in Taiwan and costal areas of China. We isolated and characterized 32 polymorphic microsatellite loci from a CA-enriched genomic library of giant grouper. The number of alleles per locus ranged from 3 to 7, with a mean of 4.69. Observed and expected heterozygosities per locus varied from 0.387 to 1.000 and from 0.377 to 0.843, respectively. Six loci significantly deviated from Hardy-Weinberg equilibrium. After sequential Bonferroni's correction, only two loci showed deviation from Hardy-Weinberg equilibrium, and no linkage disequilibrium was found between any pair of loci. These microsatellites can be useful tools for the study of population genetics in the giant grouper.     

Loss of genetic variation in hatchery-reared Indian major carp, Catla catla

The hypothesis that effective population sizes are low in hatchery-reared catla ( Catla catla ) from Bangladesh, possibly leading to inbreeding and loss of variation, was tested. The study was based on analysis of seven microsatellite loci in three samples of hatchery-reared catla and four samples representing wild populations. Pair-wise estimates of genetic differentiation between samples were low between wild samples (θ ranging from 0·012 to 0·034), but high between hatchery samples (θ ranging from 0·153 to 0·185), suggesting strong genetic drift in hatcheries. Genetic variation, both in terms of expected heterozygosity and allelic richness, was significantly lower in hatchery samples than in samples of wild catla. Application of a method for reconstructing families among offspring without parental genetic data showed that the hatchery samples consisted of very few half- and full-sib families, whereas the wild samples consisted of a high number of families, suggesting that most individuals were unrelated. Finally, estimation of the effective number of parents ( N _b) in the largest sample of hatchery fish confirmed that effective population size was low ( N _b= 14·9 for multiallelic loci and N _b= 10·6 if alleles were pooled into two composite alleles). The results show that low effective population sizes leading to loss of variation and possibly inbreeding depression should be a matter of serious concern in aquaculture production of catla.     

Isolation and multiplex genotyping of polymorphic microsatellite DNA markers in the snakehead murrel, Channa striata

Seven polymorphic microsatellite loci were isolated and characterized for the snakehead murrel, Channa striata (Channidae), a valuable tropical freshwater fish species. Among 25 specimens collected from Kedah state in Malaysia, the number of alleles per locus ranged from 2 to 7. Observed and expected heterozygosities ranged from 0.120 to 0.880 and 0.117 to 0.698, respectively. A single locus (CS1-C07) was significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction. These novel markers would be useful for population genetic studies of the C. striata.     

Swimbladder volume and body density in an armoured benthic fish, the streaked gurnard

Body density of streaked gurnards Trigloporus lastoviza is anomalously low (mean 1·043 g ml⁻¹) for a benthic fish and overlaps with that of pelagic fish such as cod and lumpfish. It is clear that the heavy armour of gurnards is offset by buoyancy provided by the swimbladder. Swimbladder volume is a mean 3·88% of gurnard volume. Evidence is given to indicate that this is quite large for a marine teleost: data are also presented to show that the '5% of fish volume for marine fish, 7% for freshwater fish' rule for swimbladder volumes is unreliable.     

Circadian rhythms of demand-feeding and locomotor activity in rainbow trout

Under free-running conditions, most rainbow trout displayed circadian feeding rhythms, although the expression of circadian rhythmicity depended on the experimental condition: 16·7% of fish under constant dim light (LL dim), 66·1% under a 45 :45 min light-dark cycle (LD pulses), and 83·8% under constant light (LL). Under LD pulses, the period length of the free-running rhythms for feeding was significantly shorter (21·9 ± 0·7 h, n =8) than under LL (26·2 ± 0·3 h, n =10). Period length for locomotor activity under LL was 25·8 ± 0·6 h ( n =4). Under LD conditions, the daily demand-feeding profile was always confined to the light phase and chiefly composed of two main episodes, directly after lights on (light elicited) and in anticipation to lights off (endogenous). Contrasting to feeding, the diel locomotor activity profile varied remarkably: a diurnal activity pattern at the bottom, while a clearly nocturnal pattern at the surface. These results contribute to a better understanding of feeding and locomotor rhythms of rainbow trout, providing evidence for the existence of a biological clock involved in their circadian control. This finding contrasts with the previously recorded lack of an endogenous oscillator in the pineal organ driving the rhythmic secretion of melatonin, which suggests different locations from the pineal for the circadian pacemakers in this species.