Decreased genetic diversity and a reduced effective population size in cultured silver-lipped pearl oysters (Pinctada maxima)

Before selection programmes for aquaculture species can commence, a fundamental knowledge of how the culture process affects genetic diversity is requisite. “South Sea” pearl production, through the culture of the silver-lipped pearl oyster, Pinctada maxima, stands to gain substantially from genetic selection. Aquaculture techniques for P. maxima have progressed vastly, to a point where the majority of current operations are based on hatchery-propagated stock; however, there has been no investigation on how the culture process is affecting the genetic diversity of this species. To address this deficiency, we investigated the genetic diversity and effective population sizes (N_e) in three wild and five hatchery-produced P. maxima populations. Using six microsatellite DNA markers, cultured populations exhibited low N_e (3.5–9.2) and reduced allelic richness (29–44%) compared with their wild progenitors. Observed heterozygosities were not affected greatly, however, an increased mean pairwise genetic relatedness was observed in all cultured populations. The practice of mass spawning was identified as a major factor in the reduction of diversity, although diversity was not necessarily maintained when a more controlled spawning approach was utilised. Pedigree reconstructions revealed genetic diversity and N_e is affected by large skews in full-sib family representations (up to 40% from a single family, in a cohort using 28 broodstock), and could be due to differential survival rates amongst communally reared families. In order to maximise future selective breeding efforts, further research should be directed towards identifying critical stages of the culture process in which genetic diversity is lost.     

Phenotypic indicators for cultured pearl size improvement in the black‐lipped pearl oyster (Pinctada margaritifera): towards selection for the recipient growth performance

The black‐lipped pearl oyster, Pinctada margaritifera, is the most important farmed species in French Polynesia and the basis of the most valuable export industry. Mass production of black pearls relies on a surgical operation requiring tissue from a donor pearl oyster to be grafted, together with a nucleus made of shell, into the gonad of a recipient oyster. Improving pearl size through family selection remains one of the main challenges for future aquaculture development. This study analyses the relative contribution of donor and recipient oysters to pearl size. To this end, hatchery‐produced donor oysters of two batches, large and small (based on shell height), were used to supply grafts for recipients, which were then monitored individually for their growth performance by recording shell height, width, and thickness, and total live weight (flesh + shells) every 6 months (four biometric measurement times) over 20 months of culture. Pearls issued from the two batches of donors showed no significant differences in nacre weight or thickness. In contrast, recipient oyster shell height and total weight were increasingly positively correlated with these pearl size parameters over the culture period, becoming significant at 8 months post‐grafting. Potential therefore exists to use shell height and oyster weight as phenotypic indicators for selective breeding of recipient oysters with high growth performance to increase pearl size in P. margaritifera.     

Genetic structure of brown trout,Salmo trutta,populations from differently sized tributaries of Lake Mjøsa in south‐east Norway

This study was based on genotyping eight microsatellite loci of 463 brown trout, Salmo trutta L., sampled in nine differently sized tributaries in three areas on the eastern shore of Lake Mjøsa, south‐eastern Norway. The populations were genetically structured, and Mantel's test showed that genetic distance correlated positively with geographical distance. Temporal differentiation F_ST over a 2‐year period was estimated in five streams and was non‐significant after Bonferroni correction. Effective population size N_e was positively correlated with the habitat length available from the lake (0.3–22 km) and negatively with the number of full sib pairs in the sample. There was no correlation between N_e and genetic diversity, and private alleles were recorded in three medium‐sized streams, but not in the largest two. The importance of small spawning and nursery streams for the maintenance of genetic diversity of brown trout was demonstrated.     

Genetic diversity and population structure of a giant freshwater prawn (Macrobrachium rosenbergii) breeding nucleus in China

The giant freshwater prawn breeding programme in China has been carried out as a closed nucleus from 2006. The programme aimed to improve the harvest body weight and pond survival and has achieved remarkable progress. In this study, the genetic diversity and population structure of the giant freshwater prawn breeding nucleus was analysed. Pedigree completeness, the status of genetic diversity, inbreeding accumulation and effective population size of the breeding nucleus were analysed according to the pedigree record. From 2006 to 2014, a total of 107,941 individuals with 555 males and 967 females in nine generations were included in the analyses. Pedigree completeness index in six generations was at least 0.92. After performing eight selections, the genetic diversity decreased by 3%, 67% of which was caused by random genetic drift. After performing 2 years’ selection, the inbreeding level began to show a marked upward trend. The regression of the average rate of inbreeding and the average rate of co‐ancestry was 0.0041 and 0.0051 from 2006 to 2014. The effective population size calculated from the above two parameters was 122 and 98 respectively. The effective population size is still within the recommended level for a population to continue the genetic improvement programme, but below the level required (500) for retaining the evolutionary potential. To restrain the increasing level of inbreeding and maintain effective population size, measures are required to develop a breeding programme which integrates management of genetic variability and selection.     

Effects of glycopeptides on development,growth and non‐specific immunity of pearl oyster Pinctada fucata (Gould)

The effects of glycopeptides, prepared from pearl oyster Pinctada fucata, on embryonic development, larval and juvenile growth and adult non‐specific immunity of P. fucata were investigated in this study. Glycopeptides had a pronounced stimulatory effect on embryonic development and larval and juvenile growth of P. fucata. enhancing with increased glycopeptide concentrations. All of haemocytes, phagocytosis, aggregation, serum microbiostatic activity and bacteriocidal activity all showed significant increases after 60‐day feeding, relative to unfed controls. The major conclusion is that glycopeptides had a pronounced stimulatory effect on the non‐specific immunity of pearl oysters.     

Census and effective population sizes of white‐spotted charr (Salvelinus leucomaenis) in a fragmented landscape

Several habitat models have been proposed to predict population size for stream fishes and to guide habitat assessment and monitoring techniques. However, most models do not incorporate the potential advantage of molecular genetic markers. We conducted a field survey and microsatellite DNA analyses to quantify the relationships among genetic diversity, census/effective population size and habitat variables in fragmented populations of white‐spotted charr (Salvelinus leucomaenis). The census population size significantly increased with the stream length, the number of pools and a pool‐riffle sequence index, a proxy for channel‐unit habitat type complexity within reaches. Population density was correlated with the pool‐riffle sequence index only. Genetic diversity and effective population size were not correlated with the habitat variables or census population size. There was a lack of isolation‐by‐distance population structure in the studied populations. Our results suggest that stream length and the number of pools within reaches associated with habitat complexity are the habitat variables that explain the majority of variation in population size of white‐spotted charr. Our findings provide further evidence that census population size per se is a poor indicator of the inclusive genetic diversity within populations in a fragmented landscape.     

Growth of wild pearl oysters <Emphasis Type="Italic">Pinctada fucata,Pinctada margaritifera</Emphasis> and <Emphasis Type="Italic">Pinctada sugillata</Emphasis> (Bivalvia: Pteriidae) in Taiwan

In order to understand growth features of pearl oysters in the genus Pinctada, i.e. Pinctada fucata, Pinctada margaritifera, and Pinctada sugillata in Taiwan, a total of 3062 wild individuals of these species from juvenile to adult were collected monthyly from March 2001 to April 2002 in Jukeng, Pingtung County, south-west Taiwan. Quantitative measurements of live oysters were conducted for shell height (SH), shell length (SL), shell width (SW), hinge length (HL), and wet weight (WW). Different cohorts were identified through multiple length frequency analysis on SH of P. fucata and P. margaritifera, and growth curves with seasonal variation were estimated for these species. Pinctada fucata in Taiwan had a different seasonal growth pattern from the Japanese population, but had similar growth rates during the high growth period. The growth rate of P. margaritifera in Taiwan was slower than in French Polynesia, the Solomon Islands, and the Red Sea. Comparisons of morphological growth features among the three species show large differences in the SW-related features. Pinctada fucata in Taiwan had larger SW than in Japan and Korea. The differences in growth rates and morphological features suggested that the wild Taiwanese oysters may retain genetically pristine characteristics, thus genetic conservation might be urgently needed.     

Climate‐driven population dynamics of a North American freshwater fish,Ictalurus furcatus: inference from the mitochondrial control region sequence data

Abstract – Using the Bayesian coalescent methodology and mitochondrial control region sequence data, the present study reconstructs the dynamics of effective population size of a temperature‐driven seasonal migratory North American freshwater fish, Ictalurus furcatus, during the last glacial cycle. The trend in effective population size is directly associated with the trend in surface air temperature; it is inversely associated with the accumulation of ice sheets in North America during the contemporary period. The long‐term decrease in effective population size during the cold period followed by rebound during the warmer period could be explained by this species’ preference for relatively warmer temperatures for its optimal growth and survival.     

Effect of different dietary microalgae combinations on growth and survival of black‐lip pearl oyster (Pinctada margaritifera) larvae and the feasibility of replacing microalgae with a dietary lipid emulsion

A 10‐day experiment was performed to examine different mono, binary and ternary dietary combinations on survival and growth of D‐shaped and umbone black‐lip pearl oyster, Pinctada margaritifera, larvae. The three tropical microalgae species were the flagellate Isochrysis galbana clone T. Iso (CS‐177) and diatoms Chaetoceros calcitrans (CS‐178) and Chaetoceros muelleri (CS‐176) which were fed to D‐shaped and umbone larvae at a density of 7000 and 14 000 cells mL^?1, respectively. A second experiment was performed to investigate the feasibility of replacing T. Iso with a lipid emulsion for both D‐shaped and umbone larvae for 10 and 12 days, respectively. The treatments included only T. Iso, unfed and lipid emulsion to substitute T. Iso at levels of 10% (LIP10), 30% (LIP30) and 100% (LIP100). In the first experiment, results showed that a monospecific diet of T. Iso led to significantly higher (P < 0.05) survival and growth of D‐shaped larvae than all the other treatments. Meanwhile, D‐shaped larval survival was significantly lower when only fed C. calcitrans as well as growth for those fed C. calcitrans or in combination with C. muelleri. However, for umbone larvae, survival and growth were significantly higher when fed a binary combination of T. Iso and C. muelleri or the ternary combination of T. Iso, C. muelleri and C. calcitrans compared with all other treatments. For the second experiment, results showed that with increasing lipid emulsion replacement, survival of both D‐shaped and umbone larvae significantly decreased (P < 0.05); however, the LIP100 treatment was not significantly different (P > 0.05) from the unfed treatment. For D‐shaped larvae, no significant growth difference was detected (P > 0.05) between the T. Iso and LIP10 fed treatments while for umbone larvae, the T. Iso, LIP10 and LIP30 were not significantly different (P > 005). These results indicate that microalgae combinations appear more necessary for later staged P. margaritifera larvae. In addition, the use of a lipid emulsion appeared to provide some nutrition to the larvae, although more research should be conducted to improve the use of such replacements.     

First‐year survival of North East Atlantic mackerel (Scomber scombrus) from 1998 to 2012 appears to be driven by availability of Calanus,a preferred copepod prey

Mackerel (Scomber scombrus) is one of the ecologically and economically most important fish species in the Atlantic. Its recruitment has, for unknown reasons, been exceptional from 1998 to 2012. The majority (75%) of the survivors in the first winter were found north of an oceanographic division at approximately 52°N, despite the fact that mackerel spawns over a wide range of latitudes. Multivariate time series modelling of survivor abundance in the north revealed a significant correlation with the abundance of copepodites (stage I–IV) of Calanus sp. in the spawning season (April to June). The copepodites were a mix of C. helgolandicus (dominating) and C. finmarchicus. The growth of mackerel larvae is known to be positively related to the availability of nauplii and copopodites of preferred prey species, namely, large calanoid copepod species such as Calanus. The statistical relationship between mackerel survivors and abundance of Calanus, therefore, most likely, reflected a causal relationship: high availability of Calanus probably reduced starvation, stage‐specific predation and cannibalism (owing to prey switching). The effects of other abundant, but less preferred zooplankton taxa, (Acartia sp., Branchiopoda spp. and Echinodermata spp. larvae), as well as stock size, temperature and wind‐induced turbulence were not found to be significant. However, stock size was retained in the final model because of a significant interaction with Calanus in oceanic areas west of the North European continental shelf. This was suggested to be a consequence of a density driven expansion of the spawning area that increased the overlap between early life stages of mackerel and food (Calanus) in new areas.