Population Genetic Structure of Pacific White Shrimp (<Emphasis Type="Italic">Litopenaeus vannamei</Emphasis>) from Mexico to Panama: Microsatellite DNA Variation

Genetic variation and population structure of wild white shrimp (Litopenaeus vannamei) from 4 geographic locations from Mexico to Panama were investigated using 5 microsatellite DNA loci. The genetic diversity between populations was indicated by the mean number of alleles per locus and mean observed heterozygosity, which ranged from 7.4 to 8.6 and from 0.241 to 0.388, respectively. Significant departures from Hardy-Weinberg equilibrium were found at most locations at each locus, with the exception Guatemala at Pvan0013, and were caused by high heterozygote deficiencies. Genetic differences between localities were detected by pairwise comparison based on allelic and genotypic frequencies, with the exception of locus Pvan1003. Significant pairwise F _ST values between locations and total F _ST showed that the white shrimp population is structured into subpopulations. However, population differentiation does not follow an isolation-by-distance model. Knowledge of the genetic diversity and structure of L.vannamei populations will be of interest for aquaculture and fisheries management to utilize and preserve aquatic biodiversity.     

Isolation and characterization of 14 polymorphic microsatellite markers for the blue and red shrimp, Aristeus antennatus (Crustacea, Decapoda)

Eighteen microsatellite loci were isolated and characterized from the blue and red shrimp, Aristeus antennatus Risso 1816, a commercially exploited marine crustacean widely distributed throughout the Mediterranean Sea and in the eastern Atlantic. Polymorphism was assessed in a population (n = 20) from the southwestern Sardinian seas; 14 loci resulted polymorphic and showed from three to 13 alleles. The observed heterozygosity ranged from 0.2 to 0.85. These microsatellites will be potentially useful for the study of A. antennatus population genetic structure.     

Histological,Physiological and Transcriptomic Analysis Reveal the Acute Alkalinity Stress of the Gill and Hepatopancreas of Litopenaeus vannamei

Marine Biotechnology - The pacific white shrimp (Litopenaeus vannamei)&nbsp;has gradually become a promising economic species in the development of saline-alkali water fishery. The study...     

Characterization of novel microsatellite loci for red clover (Trifolium pratense L.) from enriched genomic libraries

Twenty‐seven polymorphic microsatellite markers were isolated from red clover (Trifolium pratense). Allelic variability and cross‐species amplification were assessed on 24 red clover and eight white clover (Trifolium repens) genotypes. The number of alleles detected in red clover ranged from two to 25. Observed and expected heterozygosities were high with average values of 0.71 and 0.88, respectively. Five of the 27 loci were also successfully amplified from white clover, where two to 13 alleles were detected. These highly polymorphic microsatellite loci provide powerful tools for population genetic studies as well as for marker‐assisted selection in this important forage legume species.     

Microsatellite development suggests evidence of polyploidy in the social sponge-dwelling snapping shrimp Zuzalpheus brooksi

We isolated and characterized 33 novel, polymorphic microsatellite loci from the social sponge‐dwelling snapping shrimp Zuzalpheus brooksi. We screened all 33 loci in approximately 31 individuals from a population of Z. brooksi from the Florida Keys, USA and found an average of 16 alleles per locus. Approximately 25% of the loci showed more than two bands per individual, suggesting evidence of high gene duplication, or more likely, polyploidy, which is common in crustaceans. The 25 disomic loci had an observed heterozygosity of 0.57 (range = 0.03–1.00) and will be useful for studying the social organization in Zuzalpheus shrimp.     

Development of new microsatellite primers for green and white sturgeon

Sixty-eight primer sets for microsatellite loci were developed from microsatellite motif enriched genomic libraries of pooled DNA from the polyploid green and white sturgeon (Acipenser medirostris and A. transmontanus). Four individuals from each species were screened for polymorphism at these loci. Forty-eight loci amplified in both species, and some exhibited species-specific amplification for white or green sturgeon (8 and 12 loci, respectively). The number of alleles per locus ranged from one to 12. At least 68% of the green and 65% of the white sturgeon loci we developed are polysomic.     

Variable microsatellite markers for a snapping shrimp (Alpheus armillatus) species complex

Snapping shrimp (Alpheus) are an important ecological component of tropical marine systems and are excellent models for studies of phylogeography and behavioural ecology. Here, I describe 10 variable microsatellite loci for the Alpheus armillatus species complex of snapping shrimp. The primers were tested on 60 individuals representing three evolutionary lineages within the complex, and yielded three to 21 alleles. These loci will be effective tools in future studies on population genetics and mating behaviour in this complex.     

Juvenile white sturgeon (Acipenser transmontanus) habitat and distribution in the Lower Fraser River, downstream of Hope, BC, Canada

The primary objective of this study was to identify and characterize juvenile white sturgeon (Acipenser transmontanus) habitat in the Lower Fraser River downstream of Hope, BC, Canada. A secondary objective was to estimate the juvenile white sturgeon population in the Lower Fraser River. A total of 1867 white sturgeon was captured with gill nets at 26 sites in the Lower Fraser River. The greatest numbers of sturgeon were caught in three sloughs; all but three sturgeon were captured in the June to August period. These three sloughs all had water deeper than 5 m and current that was multidirectional. Turbidity ranged greatly from 1.5 NTU (Nephelometric Units) to 67.0 NTU and the substrate of most sites was fine sediments, fine sand, silt and clay. Stomach contents were mysid shrimp (Mysidacea), midge larvae (Chironomidae) and peamouth chub (Mylocheilus caurinus). We identified three of 26 sites with appreciable numbers of juvenile sturgeon, identified water quality parameters of these sites, identified any incidental species that might be prey and also determined that between 1985 and 1993 the juvenile white sturgeon population had declined.     

Stage-structured interactions between seasonal and permanent residents of an estuarine nekton community

Estuarine assemblages of fishes and natant decapod crustaceans (i.e. nekton) comprise both permanent resident species and juveniles of coastal marine species that use estuaries primarily as nurseries. In an attempt to understand how the young of marine species successfully invade communities of permanent estuarine residents we studied potential interactions between two of the most abundant decapod crustaceans in nekton assemblages of the southeastern United States. Three years of quantitative samples from an intertidal marsh on Sapelo Island, Georgia showed that densities of the resident daggerblade grass shrimp Palaemonetes pugio were reduced during the time that juvenile white shrimp Penaeus setiferus used the estuary as a nursery. Results of a field enclosure experiment showed that white shrimp had no significant lethal or sublethal effects on adult grass shrimp. However, they did reduce survival of both juvenile and larval grass shrimp in laboratory experiments, suggesting the potential importance of a stage-dependent predatorprey interaction between the two shrimp species. The mortality rate of young grass shrimp in the presence of white shrimp was unaffected by grass shrimp density, but larvae (2.6–3.0 mm) suffered higher mortalities than did juveniles (5.0–15.0 mm). We suggest that the vulnerability of grass shrimp to predation by white shrimp is related to their molting cycle. The window of vulnerability opens more often for younger grass shrimp because they molt more frequently. When combined with losses due to other predators and competitors, the impact of early white shrimp cohorts on grass shrimp larvae and juveniles may prevent the resident species from maintaining its population at high densities, thereby freeing resources in the nursery for subsequent cohorts of juvenile white shrimp.     

Antivibrio compounds produced by <Emphasis Type="Italic">Pseudomonas</Emphasis> sp. W3: characterisation and assessment of their safety to shrimps

In order to explore compounds naturallly inhibitory to shrimp pathogenic vibrios, a culture filtrate of Pseudomonas sp. W3 at a pH of 2 was extracted with ethyl acetate (EtOAc) to produce 82.15 mg/l of a yellow–brown extract (EtOAc-W3) that had MIC values of 225-450 μg/ml against the growth of 18 shrimp pathogenic Vibrio harveyi strains. The MIC of EtOAc-W3 against the most pathogenic strain PSU 2015 was 450 μg/ml and this strain had the lowest LD₅₀ (50% lethal dose) to pacific white shrimp (Litopenaeus vannamei, PL 21). At this MIC value, EtOAc-W3 in artificial sea water (ASW) killed strain PSU 2015; however in natural sea water, only a partial growth inhibition was observed. The toxicity to pacific white shrimp and antivibrio activity of the EtOAc-W3 were investigated by conducting an experiment with 4 sets; native control (commercial ASW), EtOAc-W3 control (MIC/10, 45 μg/ml), challenge (inoculation 6.0 × 10⁶ c.f.u./ml PSU 2015) and treatment (6.0 × 10⁶ c.f.u./ml PSU 2015 + 45 μg/ml EtOAc-W3). The same experiment was repeated by increasing the dose of EtOAc-W3 to 90 μg/ml (MIC/5). Both concentrations of EtOAc-W3 tested had no toxicity to postlarval shrimps. A significant decrease in shrimp mortality was observed over a 72 h period as approximately 80% of the shrimps died in each challenge set but only 63 and 23% died in the presence of 45 and 90 μg/ml EtOAc-W3. The major component of EtOAc-W3 was supposed to be 2-heptyl-4-quinolone (HHQ) by FAB-MS and ¹H-NMR analyses of the purified fraction.     

Characterization of microsatellite loci in the brown treecreeper (Climacteris picumnus) and cross‐species amplification in the white‐throated treecreeper (Cormobates leucophaeus)

Eight polymorphic microsatellite markers were developed for the brown treecreeper, Climacteris picumnus. The number of alleles ranged from three to 25 per locus with observed heterozygosities between 0.05 and 0.76. Seven of the eight primer pairs also amplified polymorphic microsatellite loci in the white‐throated treecreeper (Cormobates leucophaeus). These markers are likely to be useful for population genetic and parentage studies in any of the Australasian treecreepers (Climacteridae) and are the first genetic markers developed for any member of this passerine family.     

Characterization of microsatellite markers for the mangrove tree Avicennia germinans L. (Avicenniaceae)

We describe 10 primers for amplification of microsatellite loci for the mangrove, Avicennia germinans. Eight loci were isolated from a DNA sample from the Pacific coast of Baja California, Mexico and two loci were isolated from a DNA sample from the Atlantic coast of Bermuda. Polymorphism was investigated in a population from the Mexican Pacific coast (n = 15) and in four samples scattered throughout the range of the species. Total number of alleles for the species ranged from two to 10. Observed heterozygosity in the Mexican Pacific coast population ranged from 0.27 to 0.60, with two loci having fixed alleles.     

Isolation and characterization of tri‐ and tetra‐repeat microsatellite loci in the white‐spotted charr Salvelinus leucomaenis (Salmonidae)

Tri‐ and tetra‐motif repeat microsatellite marker loci were developed for the white‐spotted charr Salvelinus leucomaenis. The 454 pyrosequencing was used to discover repeat arrays, and eight microsatellite‐primer sets, available for the estimation of polymorphisms, were identified. The number of alleles in a wild population ranged from two to four and the observed and expected heterozygosities were 0·180–0·600 and 0·188–0·599, respectively.     

Population genetic structure of Penaeus monodon, in relation to monsoon current patterns in Southwest, East and Andaman coastal waters of India

The black tiger shrimp (Penaeus monodon), a commercially important penaeid species, is widely distributed across the Indo-Pacific region. Genetic diversity in P. monodon collected from eight geographical regions in Southwest, East and Andaman coastal waters of India (N = 418) was investigated using 10 polymorphic microsatellite loci. Average observed heterozygosity at sampled loci were high, ranging from 0.643 (Coromandel Coast) to 0.753 (South Andaman). Pairwise F_ST (ranged from 0.005 to 0.078) and R_ST (ranged from 0.005 to 0.171) estimates revealed surprisingly strong and statistically significant genetic structure among tiger shrimp populations. A synthetic map generated by multidimensional scaling shows an apparent cline in allele frequencies paralleling the roughly circular flow of surface currents in the Bay of Bengal. Significant heterozygote deficiencies were noted in most population samples at most loci. Andaman Island sites showed the highest diversity. Recognition of high genetic diversity and distinct population structuring of P. monodon in Indian seas has important implications for future domestication of this species in India, for two reasons: identification of the best wild founding stocks for aquaculture and, subsequently, the potential impacts of release of domesticates to the wild, either accidentally or deliberately (i.e. for stock enhancement).     

Characterization of microsatellite markers for the tanoak tree,Lithocarpus densiflorus

We describe the development of 19 primers for amplification of microsatellite loci for tanoak, Lithocarpus densiflorus (Hook. & Arn.). A population from Soquel State Demonstration Forest, Santa Cruz County, California (n = 20), and eight individuals from four additional coastal populations and one interior (Sierra Nevada) population were used to investigate polymorphism. The total number of alleles per locus ranged from two to 10. Observed heterozygosity in the Soquel population ranged from 0.05 to 0.70, with two loci being fixed.     

Isolation and characterization of 16 polymorphic microsatellite loci in the endemic Hawaiian damselfly Megalagrion xanthomelas (Odonata: Coenagrionidae)

Microsatellite loci have been isolated from two species of endemic Hawaiian damselflies, Megalagrion xanthomelas and M. eudytum, that are of conservation concern. Sixteen polymorphic loci were characterized in 32 M. xanthomelas from one population on Molokai and one on Hawaii Island. The total number of alleles per locus ranged from two to 16 and observed population heterozygosity ranged from 0.0 to 0.963. Eleven of these loci amplified successfully in M. eudytum as well. These loci will be used to further conservation efforts and infer genetic consequences of Pleistocene glaciations.     

Characterization of expressed sequence tag‐derived microsatellites from the kuruma prawn,Marsupenaeus japonicus

The kuruma prawn, Marsupenaeus japonicus, is a commercially important benthic marine crustacean in East Asia. Understanding the species’ population structures will be very important for its proper stock assessment and management strategy. Herein, 13 polymorphic microsatellite loci originating from expressed sequence tag libraries of M. japonicus were isolated and characterized. Number of alleles per locus ranged from two to 15, observed and expected heterozygosities ranged from 0.250 to 0.906 and from 0.310 to 0.932, respectively. The adequate level of variability within the population renders these microsatellite loci ideal markers for population genetic analysis of M. japonicus.     

Development and characterization of twelve polymorphic microsatellite loci in the threatened Red Hills salamander, Phaeognathus hubrichti

We isolated and characterized 12 microsatellite loci from the endangered Red Hills salamander, Phaeognathus hubrichti. Loci were screened in 24 individuals of P. hubrichti. The number of alleles per locus ranged from 2 to 16, observed heterozygosity ranged from 0.130 to 0.750, and the probability of identity values ranged from 0.012 to 0.778. These new loci provide tools for examining the population genetics of this federally threatened salamander.     

Characterization of 15 polymorphic microsatellite loci in an endangered tropical tree Hopea bilitonensis (Dipterocarpaceae) in Peninsular Malaysia

This study reports the isolation and characterization of 15 polymorphic microsatellite loci in an endangered tropical tree Hopea bilitonensis (Dipterocarpaceae). The primers were designed from a genomic library enriched for dinucleotide (CT) repeats and screened on 24 adult trees from a natural population. The number of alleles ranged from two to eight, and the observed heterozygosity ranged from 0.042 to 1.000. These loci will allow mating system and population analyses to be carried out in this species.     

Development of polymorphic EST-derived SSR markers for the shrimp, Fenneropenaeus chinensis

In our study, we evaluated simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) of Fenneropenaeus chinensis. Characteristics of 11 EST-SSR loci were investigated using 34 F. chinensis individuals. The number of alleles per locus ranged from 4 to 9. The observed heterozygosity ranged from 0.118 to 0.826, while the expected heterozygosity ranged from 0.623 to 0.847. Two loci (T2 and T12) conformed to the Hardy–Weinberg equilibrium. There was no LD observed between all pairs of EST-SSRs loci. The PIC values of 11 microsatellite loci were higher than 0.5. These loci and markers will be useful for population genetics and systemic evolution of F. chinensis.