A set of polymorphic dinucleotide and tetranucleotide microsatellite markers for the Indo-Pacific humpback dolphin (Sousa chinensis) and cross-amplification in other cetacean species

Eleven dinucleotide and five tetranucleotide polymorphic microsatellite loci were presented for the Indo-Pacific humpback dolphin Sousa chinensis, a species categorized as ‘data deficiency’ in the IUCN Red List. These markers were developed to allow future population studies, such as characterization of population structure and genetic diversity that are important for the species’ conservation. The number of alleles ranged from 2 to 9 with observed heterozygosity ranging from 0.167 to 0.917, and expected heterozygosity ranging from 0.159 to 0.913. Test of these loci in five additional cetacean species found that 10–13 loci have successful cross-amplifications.     

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).     

Development and characterization of microsatellite markers for Vriesea simplex (Bromeliaceae) and cross-amplification in other species of Bromeliaceae

Ten polymorphic microsatellite loci were isolated and characterized for Vriesea simplex epiphytic and endemic species from the Brazilian Atlantic Rainforest. The number of alleles per locus ranged from 2 to 16. The observed and expected heterozygosity ranged from 0.000 to 0.414 and 0.068 to 0.795, respectively. All loci departed significantly from Hardy–Weinberg equilibrium. Linkage disequilibrium was not detected in any pair of loci. Transferability of 10 loci was positive across ten other Bromeliaceae species. The loci will be used for studying population genetic structure, mating system variation, and the origin and maintenance of reproductive barriers to gene exchange among sympatric Vriesea species.     

Isolation and characterization of microsatellite markers for the heavily exploited rockfish Sebastes schlegeli, and cross-species amplification in four related Sebastes spp.

Here we report development and characterization of 14 polymorphic microsatellite loci from Sebastes schlegel. Polymorphism at these loci revealed from 3 to 23 alleles. The observed heterozygosity ranged from 0.34 to 1.00, and the expected heterozygosity ranged from 0.31 to 0.95. No linkage disequibrium was found. Two loci were significantly deviated from HWE (P < 0.01). The 14 loci were also surveyed in four other Sebastes species and 12 loci successfully amplified, where allelic diversity ranged from highly polymorphic to monomorphic. These results demonstrate these microsatellite markers can be used for the study of intra- and inter-specific genetic diversity.     

Isolation and characterization of eighteen polymorphic microsatellite loci in Schizopygopsis younghusbandi Regan and cross-amplification in three other schizothoracinae species

Eighteen polymorphic microsatellite loci were isolated from Schizopygopsis younghusbandi Regan and the characterization of these loci was assessed in 46 individuals collected from the Yarlung Tsangpo River in Tibet, China. The number of alleles per locus ranged from 2 to 14. The expected heterozygosity and Shannon-Wiener diversity index ranged from 0.022 to 0.879 and from 0.059 to 2.313, respectively. The cross-species amplification and applicability of these loci were tested in three other Schizothoracinae species belonging to Schizothorax and Oxygymnocypris. These loci will be useful for the evaluation of genetic diversity and population genetic structure in S. younghusbandi and other related species.     

Isolation and characterization of 16 microsatellite loci in the humbug damselfish, Dascyllus aruanus (family Pomacentridae)

Here we report on 16 microsatellite loci designed for the damselfish Dascyllus aruanus. All loci were tested on 98 individuals and were polymorphic (seven to 35 alleles). Expected heterozygosity ranged from 0.705 to 0.942. Six loci showed Hardy-Weinberg disequilibrium due to the occurrence of null alleles. Cross-species amplifications conducted within the genus Dascyllus (D. carneus, D. strasburgi, D. trimaculatus) lead to polymorphic fragments in 32 out of 48 tests. These 16 loci will enable future research into the behavioural ecology and population ecology of Dascyllus aruanus throughout the Indo-Pacific.     

Characterization and cross-amplification of 13 microsatellite loci in the northern pine processionary moth, Thaumetopoea pinivora (Lepidoptera: Notodontidae)

Thirteen polymorphic microsatellite loci were developed for the northern pine processionary moth (Thaumetopoea pinivora) and tested for cross-amplification in seven other species within the Thaumetopoea family. Number of alleles ranged from two to 10 when at least 28 individuals from one population were screened and one locus, Thapin06, appears to be sex linked. Expected heterozygosity ranged from 0.094 to 0.856 and observed heterozygosity ranged from 0.097 to 0.806. Amplification success varied between sister species, with two up to seven loci being successfully amplified. The described loci will be valuable for studying the population genetic structure and dispersal behaviour of this forest pest.     

Isolation and characterization of nine polymorphic microsatellite markers of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae)

Sebastiscus marmoratus is a typical sedentary fish and usually lives at the bottom of the coastal zone from Japan to the East China Sea. Next-generation sequencing platform was used to obtain microsatellite loci sequences of S. marmoratus, among which forty-eight perfect microsatellite repeats were suitable for primer design. Nine polymorphic microsatellite markers were exploited and characterized for it. The allele number of all polymorphic microsatellite markers ranged from 4 to 12. Expected and observed heterozygosity varied from 0.302 to 0.909 and from 0.190 to 0.625, respectively. In further studies, the genetic variation and population structure of this species would be investigated using these microsatellite loci.     

Development of microsatellite loci in the common reef starfish Linckia laevigata and Linckia multifora

We isolated seven polymorphic microsatellite loci from the coral reef starfish Linckia laevigata??a common coral reef sea star distributed widely in the Indo-Pacific. The number of alleles ranged from 4 to 13, with an average of 7.4. The ranges of observed and expected heterozygosities were 0.367/0.933 and 0.332/0.840 for L. laevigata and 0.182/0.818 and 0.329/0.697 for L. multifora, respectively. All of these markers can also be used in the sister species Linckia multifora. These microsatellite loci will be useful for population and conservation genetic studies in coral reef ecosystems.     

Development, characterization, segregation, and mapping of microsatellite markers for European hazelnut (Corylus avellana L.) from enriched genomic libraries and usefulness in genetic diversity studies

Eighty-six new microsatellite loci were developed for European hazelnut (Corylus avellana L.) by screening two genomic libraries enriched for dinucleotide repeats. The loci, 73 developed from a GA-enriched library and 13 from a CA-enriched library, showed a high level of polymorphism in 50 accessions. The number of alleles per locus ranged from five to 21, with a mean of 10.55. Mean values for expected heterozygosity, observed heterozygosity, and polymorphism information content were high, averaging 0.76, 0.69, and 0.73, respectively. In a mapping population, loci segregated 1:1, 1:2:1, and 1:1:1:1. Segregation distortion and null alleles were observed at some loci. Eighty-one of the 86 loci were assigned to linkage groups. A neighbor-joining dendrogram reflected great diversity among the 50 accessions and showed clustering by geographic origin.     

Microsatellite and mitochondrial haplotype diversity reveals population differentiation in the tiger shrimp (Penaeus monodon) in the Indo-Pacific region

The black tiger shrimp (Penaeus monodon) is an ecologically and economically important penaeid species and is widely distributed in the Indo-Pacific region. Here we investigated the genetic diversity of P. monodon (n = 355) from eight geographical regions by genotyping at 10 microsatellite loci. The average observed heterozygosity at various loci ranged from 0.638 to 0.743, indicating a high level of genetic variability in this region. Significant departures from Hardy-Weinberg equilibrium caused by heterozygote deficiency were recorded for most loci and populations. Pairwise F(ST) and R(ST) values revealed genetic differentiation among the populations. Evidence from the assignment test showed that the populations in the West Indian Ocean were unique, whereas other populations examined were partially admixed. In addition, the non-metric multidimensional scaling analysis indicated the presence of three geographic groups in the Indo-Pacific region, i.e. the African populations, a population from western Thailand and the remaining populations as a whole. We also sequenced and analysed the mitochondrial control region (mtCR) in these shrimp stocks to determine whether the nuclear and mitochondrial genomes show a similar pattern of genetic differentiation. A total of 262 haplotypes were identified, and nucleotide divergence among haplotypes ranged from 0.2% to 16.3%. Haplotype diversity was high in all populations, with a range from 0.969 to 1. Phylogenetic analysis using the mtCR data revealed that the West Indian Ocean populations were genetically differentiated from the West Pacific populations, consistent with the microsatellite data. These results should have implications for aquaculture management and conservation of aquatic diversity.     

Isolation and characterization of fifteen polymorphic microsatellite loci in the threatened freshwater mussel Solenaia oleivora (Bivalvia: Unionidae)

Freshwater mussels are among the most endangered fauna in the world, while little is known about their genetic diversity. We isolated 15 polymorphic microsatellite loci in a threatened freshwater mussel, Solenaia oleivora. The characteristics of these loci were tested with 46 individuals. The number of alleles per locus ranged from 2 to 15, and the PIC value ranged from 0.250 to 0.880. The observed and expected heterozygosity ranged from 0.167 to 0.929 and from 0.297 to 0.900, with an average of 0.562 and 0.647, respectively. Eight loci deviated significantly from Hardy–Weinberg equilibrium. These polymorphic microsatellites will be useful for the assessment of population genetic diversity and resource conservation of S. oleivora. Cross-species amplification demonstrated that six of 15 microsatellite loci amplified successfully in two other unionid species.     

PERMANENT GENETIC RESOURCES: Isolation, characterization and cross-species amplifications of microsatellite loci from Conradina (Lamiaceae)

We report the isolation of microsatellite loci from three species in the genus Conradina (Lamiaceae). To ensure their utility for multiple species, loci were screened for amplification and variability in all six Conradina species; 11 loci demonstrated high levels of amplification and polymorphism in most species. These 11 loci were characterized in 20 individuals from one population of Conradina brevifolia; alleles per locus ranged from five to 15, and observed heterozygosity ranged from 0.30 to 0.90. These microsatellites will be used to clarify species limits, detect interspecific hybridization, and understand the partitioning of genetic variation in each species of Conradina.     

Development of nine new microsatellite loci for the American beaver, Castor canadensis (Rodentia: Castoridae), and cross-species amplification in the European beaver, Castor fiber

We developed nine new nuclear dinucleotide microsatellite loci for Castor canadensis. All loci were polymorphic, except for one. The number of alleles ranged from two to four and from five to 12 in populations from Arizona and Wisconsin, respectively. Average heterozygosity ranged from 0.13 to 0.86 per locus. Since cross-species amplification in Castor fiber was successful only in four loci, we tested also nine recently published C. canadensis loci in the Eurasian species. Eight of the published loci amplified; however, three were monomorphic. The number of alleles was lower in C. fiber than in C. canadensis at all loci tested.     

Isolation and characterization of 14 polymorphic microsatellite loci in the ringneck snake <Emphasis Type="Italic">Diadophis punctatus</Emphasis> (Colubridae: Dipsadinae)

We constructed a genomic library and developed 14 polymorphic loci to assess species boundaries between previously described mtDNA lineages and to examine the genetic variability between populations of the ringneck snake Diadophis punctatus species complex. Polymorphism was investigated for these markers in 34 individuals from populations in southeastern Louisiana and southern Florida. The number of alleles ranged from 5 to 29, expected heterozygosity ranged from 0.816 to 0.962 and observed heterozygosity ranged from 0.452 to 0.889. These new loci provide the tools necessary to examine species boundaries, population genetics within species and to determine the conservation status of imperiled populations.     

Eight microsatellite markers for the San Esteban chuckwalla,Sauromalus varius

We characterize eight polymorphic microsatellite loci for the San Esteban chuckwalla, Sauromalus varius, which are being used as markers in a study of the genetic results from a decade of captive breeding in this endangered species. Observed heterozygosity estimates for S. varius ranged from 0.00 to 0.30, whereas expected heterozygosity estimates ranged from 0.06 to 0.58.     

Identification and characterization of eight microsatellite loci in Machilus pseudokobu (Lauraceae), an endemic species of the Bonin Islands

Eight microsatellite loci were identified and characterized for the endangered Machilus pseudokobu (Lauraceae), an endemic tree species of the Bonin Islands. The observed number of alleles at each locus ranged from 1 to 20 with an average of 6.2, and the expected heterozygosity ranged from 0.00 to 0.83 with an average of 0.47. All eight loci were screened in cross-amplification tests for two other endemic Machilus species that also inhabit the Bonin Islands. All loci were successfully amplified in these species.     

Isolation and characterization of microsatellite DNA markers from mangrove crab,Scylla paramamosain

The first five variable microsatellite DNA loci for mangrove crab, Scylla paramanosain, were developed. Allelic variation and other characteristics at these loci were examined in this species captured at the Urado Bay, Japan. The number of alleles per locus ranged from 24 to 44. The expected heterozygosity across loci ranged from 0.900 to 0.999 and probability of identity (P_I) ranged from 2.8 × 10^?3 to 1.7 × 10^?2. Therefore, these microsatellite markers could be useful for estimating effect of stock enhancement release and population genetic structure of mangrove crab.     

Characterization of 14 polymorphic microsatellite loci for the facultatively eusocial sweat bee Halictus rubicundus (Hymenoptera, Halictidae) and their variability in related species

Sweat bees display considerable variation in social organization and a few species, such as Halictus rubicundus, are even facultatively eusocial. Fourteen polymorphic, unlinked microsatellite loci were isolated from H. rubicundus and characterized in 45 females. The number of alleles per locus ranged from two to 18 (mean 10.1), observed heterozygosity ranged from 0.24 to 0.98 (mean 0.71) and expected heterozygosity ranged from 0.24 to 0.98 (mean 0.70). Six or more loci cross-amplified in four other sweat bees. These loci will be useful for the study of social evolution and population genetic structure in H. rubicundus and many other sweat bees.     

Genetic diversity and variation in wild populations of dark sleeper (Odontobutis potamophila) in China inferred with microsatellite markers

Twenty-one highly variable microsatellite loci were used to investigate the genetic diversity and variation of Odontobutis potamophila in China. A total of 160 samples from five wild populations (Dangtu, Sheyang, Yuyao, Minjiang and Donxishan) were genotyped. All of the 21 microsatellite loci tested in this study showed polymorphism. The number of allele per locus ranged from 5.05 to 9.90. Locus 87a of Minjiang population had a 259-bp characteristic allele. The average observed heterozygosity and expected heterozygosity ranged from 0.33 to 0.62 and from 0.40 to 0.70, respectively. The pair-wise F_ST tests and NJ trees of the five O. potamophlia populations revealed that Dangtu, Sheyang, Yuyao and Dongxishan were genetically close to one another and distinct from Minjiang. Far genetic distances were observed among populations from distant geographical areas. This result provided guide for the use of O. potamophila breeds and the protection of the species.