Geographic structure in the Southern Ocean circumpolar brittle star Ophionotus victoriae (Ophiuridae) revealed from mtDNA and single‐nucleotide polymorphism data

Marine systems have traditionally been thought of as “open” with few barriers to gene flow. In particular, many marine organisms in the Southern Ocean purportedly possess circumpolar distributions that have rarely been well verified. Here, we use the highly abundant and endemic Southern Ocean brittle star Ophionotus victoriae to examine genetic structure and determine whether barriers to gene flow have existed around the Antarctic continent. Ophionotus victoriae possesses feeding planktotrophic larvae with presumed high dispersal capability, but a previous study revealed genetic structure along the Antarctic Peninsula. To test the extent of genetic differentiation within O. victoriae, we sampled from the Ross Sea through the eastern Weddell Sea. Whereas two mitochondrial DNA markers (16S rDNA and COI) were employed to allow comparison to earlier work, a 2b‐RAD single‐nucleotide polymorphism (SNP) approach allowed sampling of loci across the genome. Mitochondrial data from 414 individuals suggested three major lineages, but 2b‐RAD data generated 1,999 biallelic loci that identified four geographically distinct groups from 89 samples. Given the greater resolution by SNP data, O. victoriae can be divided into geographically distinct populations likely representing multiple species. Specific historical scenarios that explain current population structure were examined with approximate Bayesian computation (ABC) analyses. Although the Bransfield Strait region shows high diversity possibly due to mixing, our results suggest that within the recent past, dispersal processes due to strong currents such as the Antarctic Circumpolar Current have not overcome genetic subdivision presumably due to historical isolation, questioning the idea of large open circumpolar populations in the Southern Ocean.     

Isolation and characterization of polymorphic microsatellite loci from a dinucleotide-enriched genomic library of obscure puffer (Takifugu obscurus) and cross-species amplification

Obscure puffer (Takifugu obscurus) is an anadromous fish species in China. Here, we reported 10 polymorphic microsatellite loci isolated from a dinucleotide-enriched genomic library of T. obscurus. The number of alleles, observed and expected heterozygosity per locus in 30 individuals ranged from four to 10, from 0.57 to 0.86 and from 0.68 to 0.90, respectively. Three loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium between pairs of loci was found. Cross-species amplification of these microsatellite loci in additional three fish species was performed. These polymorphic microsatellite loci would be useful for investigating genetic population structure and construction of genetic linkage map in T. obscurus.     

Isolation and characterization of microsatellite loci in Hexagrammos otakii based on 2b-RAD method

In this study, we isolated 20 novel microsatellites loci associated with the growth of Hexagrammos otakii (Fat greenling) by using 2b-RAD sequencing method. The characteristics of 20 microsatellite loci were amplified in 105 H. otakii individuals which came from four different groups and tested by Capillary electrophoresis. The number of allele of the 20 microsatellite loci ranged from 8 to 26 with an average of 19.95. PIC value ranged from 0.1659 to 0.9227 with an average of 0.7555. Observed and expected heterozygosity varied from 0.0667 to 0.8571 and from 0.1710 to 0.9314, respectively. Highly polymorphic characteristics were observed in each microsatellite loci of the study except HO6. Further research showed that 10 microsatellite loci had transferability in Hexagrammos agrammus. In this study, high polymorphism and genetic diversity using the 15 polymorphic microsatellite loci suggest that they are suitable for investigating the fine-scale population structure, genetic relationship and further evaluating the artificial reproduction strategy of H. otakii.     

Isolation and characterization of microsatellite loci in Pratt’s Leaf-nosed Bat (<Emphasis Type="Italic">Hipposideros pratti</Emphasis>) and cross-species amplification in closely related taxa

We developed nine microsatellite loci using an enriched library method from the genomic DNA of Pratt’s leaf-nosed bat (Hipposideros pratti). These loci were tested on 96 individuals sampled from Sichuan Province, China. The number of alleles per locus varied from 4 to 14. The expected and observed heterozygosity values ranged from 0.513 to 0.886 and from 0.375 to 0.966, respectively. Three microsatellite loci departed significantly from Hardy–Weinberg equilibrium (HWE). No linkage disequilibrium was found. These microsatellite loci will be used in studies of conservation genetics in this species.     

Isolation and characterization of polymorphic microsatellite loci from black sea bass (Centropristis striata) and cross-species amplification

Black sea bass (Centropristis striata) is an economically important serranid species. A number of 39 microsatellite loci were isolated from two enriched genomic library of C. striata. Eleven of these loci were polymorphic in a test population with alleles per locus ranging from 3 to 8, and observed and expected heterozygosities per locus from 0.26 to 1.00 and from 0.61 to 0.84, respectively. Four loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium was found between pairs of loci. Cross-species amplification of these polymorphic microsatellite loci was performed in additional two related species. These polymorphic microsatellite loci would be useful for investigating genetic resource of C. striata and other related species.     

New microsatellite resources for groupers (Serranidae)

We characterized nine microsatellite loci and identified an additional 60 genomic regions containing microsatellites in the red hind grouper, Epinephelus guttatus. The nine loci were highly polymorphic, and primers designed from red hind genomic DNA produced a strong amplification product in a test panel of 16 other groupers in the genera Epinephelus and Mycteroperca collected from across the world. Most of the amplified regions were homologous to the red hind locus and a well‐defined microsatellite repeat was generally evident. The nine loci, together with the 60 uncharacterized microsatellite‐containing regions, provide a powerful tool for ecological and evolutionary studies in groupers.     

Isolation and characterization of microsatellite loci in the Pacific pleasure oyster,Crassostrea corteziensis,and their cross‐species amplification in four other oyster species

Microsatellite loci were isolated in Crassostrea corteziensis using (GT)_n, (CT)_n and (CTGT)_n‐enriched genomic libraries. Within each of 45 sequenced clones, an average of three microsatellite regions (156 total) were observed. Thirty‐three primers were designed, from which 11 microsatellite loci amplified. Ten of those were polymorphic, with a range of two to 30 alleles. Three loci were not in Hardy–Weinberg equilibrium, and linkage disequilibrium was found for six pairs of loci. These microsatellite loci will be further tested for segregation distortions and null alleles to establish a set for population genetic studies of the species in the Northwest coasts of Mexico, and for optimization of aquaculture development. Seven of the microsatellite loci cross‐amplified in Crassostrea palmula, a sympatric species, and will be useful in further genetic studies.     

Isolation and characterization of polymorphic microsatellite loci from black snapper Sebastodes fuscescens (Houttuyn)

Black snapper Sebastodes fuscescens (Houttuyn) is an economocally important species. Fourty-five microsatellite loci were isolated from an enriched genomic library of S. fuscescens. Ten of these loci were polymorphic in a test population with alleles per locus ranging from 2 to 5, and observed and expected heterozygosities per locus from 0.21 to 1.00 and from 0.19 to 0.86, respectively. Three loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium was found between pairs of loci. These polymorphic microsatellite loci would be useful for investigating genetic diversity of S. fuscescens and other related species.     

PRIMER NOTE. Using the incomplete genome of the ectomycorrhizal fungus Amanita bisporigera to identify molecular polymorphisms in the related Amanita phalloides

We describe the cross‐genomic isolation of 13 single nucleotide polymorphisms (SNPs) and one variable microsatellite from five loci for the death cap mushroom Amanita phalloides. Microsatellite repeats were identified by searching the partial Amanita bisporigera genome. Flanking primers were designed for 25 of these microsatellite loci and tested for cross‐amplification in A. phalloides. One locus contained an interrupted, compound microsatellite, and four loci contained one to six SNPs. These results demonstrate the usefulness of even an incomplete genome to identify molecular markers for population studies in nonmodel organisms.     

Microsatellite DNA loci for Western Hemlock [Tsuga heterophylla (Raf.) Sarg]

Polymorphic microsatellite loci were developed for Western Hemlock [Tsuga heterophylla (Raf.) Sarg], a prominent forest tree species in Western North America. Microsatellite‐enriched libraries were screened for (CA)_n dinucleotide repeats from which 33 positive clones were sequenced. Polymerase chain reaction (PCR) primers for 16 microsatellite loci were prepared and tested against DNA from unrelated Western Hemlock trees. The 12 most informative microsatellite loci are reported here. From four to 22 alleles per locus were observed, with an average expected heterozygousity of 0.799.     

Isolation and Characterization of Twenty Microsatellite Loci in Japanese Sea Cucumber (Stichopus japonicus)

Twenty microsatellite markers were first developed from the Japanese sea cucumber Stichopus japonicus using an enrichment protocol. Of the 20 microsatellite loci, 19 loci were polymorphic in the population examined. At these polymorphic loci, the number of alleles per locus varied from 2 to 15, and the observed heterozygosities ranged from 0.03 to 0.97, which is considerably higher than those previously found for allozymes. The high variability of the microsatellite markers identified in this study will make them excellent tools for genetic analyses of S. japonicus.     

Isolation and characterisation of di and tri nucleotide microsatellite loci in Rosmarinus officinalis (Lamiaceae), using enriched genomic libraries

An enrichment protocol was used to isolate and characterise microsatellite loci in Rosmarinus officinalis, a Mediterranean chamephyte. Twelve microsatellite loci were characterised and amplified a total of 117 alleles in a sample of 30 individuals from one population, with an average of 9.75 alleles per locus. Observed heterozygosities ranged from 0.333 to 0.900. Cross-species transferability was also assayed in the two other species of the genus. The cumulated probabilities of exclusion for paternity and parentage of the 12 loci were of 0.999971 and 1, respectively, supporting the usefulness of these microsatellite loci for parentage analyses. Nine out of 12 microsatellite loci amplified in the two species and were polymorphic detecting a total of 49 and 45 in R. eriocalyx and R. tomentosus, respectively. Twenty-two alleles were exclusive of R. eriocalyx and 12 of R. tomentosus, additionally, three alleles were shared between these two species but were otherwise absent in the analysed individuals of R. officinalis. In total, this set of markers amplified 154 different microsatellite alleles, supporting their usefulness to conduct population genetic, reproductive biology and hybridisation studies in Rosmarinus.     

Twelve polymorphic microsatellite loci from a dinucleotide-enriched genomic library of Japanese Spanish mackerel (Scomberomorus niphonius)

In the study, 34 microsatellite loci were isolated from a dinucleotide-enriched genomic library of Japanese Spanish mackerel (Scomberomorus niphonius). And 12 microsatellite loci were found to be polymorphic between 3 and 8 alleles. The number of observed and expected heterozygosity per locus in 23 individuals ranged from 0.6087 to 1.0000 and 0.8908 to 0.9773, respectively. Two loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction analysis and there was no significant linkage disequilibrium found between pairs of loci. As a result, 12 microsatellite loci probably located on different chromosome pairs and these polymorphic microsatellite loci should provide sufficient level of genetic diversity to investigate the fine-scale population structure and evaluate the breeding strategy in S. niphonius. The authors Shi-Chao Xing and Gen-Bo Xu contributed equally.     

Isolation and characterization of polymorphic microsatellite loci from fat greenling (Hexagrammos otakii)

Fat greenling (Hexagrammos otakii) is an economocally important marine fish species. Thirtyfive microsatellite loci were isolated from two enriched genomic library of Hexagrammos otakii. Ten of these loci were polymorphic in a test population with alleles per locus ranging from two to six, and observed and expected heterozygosities per locus from 0.2581 to 1.0000 and from 0.2892 to 0.7726, respectively. Four loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium was found between pairs of loci. These polymorphic microsatellite loci would be useful for investigating genetic diversity of Hexagrammos otakii.     

Isolation and characterization of 10 polymorphic microsatellite loci from small yellow croaker (Pseudosciaena polyactis)

Small yellow croaker (Pseudosciaena polyactis) is an economically important marine fish species. About 43 microsatellite loci were isolated from two enriched genomic library of Pseudosciaena polyactis. Ten of these loci were polymorphic in a test population with alleles per locus ranging from two to six, and observed and expected heterozygosities per locus from 0.3750 to 0.8750 and from 0.3112 to 0.8121, respectively. No loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium was found between pairs of loci. These polymorphic microsatellite loci would be useful for investigating genetic diversity of Pseudosciaena polyactis.     

Polymorphic microsatellite markers for studies of Aedes aegypti (Diptera: Culicidae), the vector of dengue and yellow fever

A significant challenge to population genetic studies of the dengue vector, Aedes aegypti, has been the lack of polymorphic microsatellite loci. In an effort to develop useful markers, we evaluated the genetic variation at 17 microsatellite loci identified in the A. aegypti genome. Nine loci with at least five alleles were identified in field‐collected specimens from Thailand. An additional two loci carried five alleles if samples from an A. aegypti laboratory colony were included. Our results greatly increase the number of highly variable markers available for the study of the genetics and the population structure of this medically important species.     

Isolation and characterisation of polymorphic microsatellite loci in the vulnerable spectacled flying fox, Pteropus conspicillatus

The spectacled flying fox, Pteropus conspicillatus, is listed as vulnerable in Australia and is under threat from numerous impacts. Primers to amplify eight co-dominant microsatellite loci were designed for Pteropus conspicillatus, based on an enriched genomic library. Four loci were monomorphic in this species while the remaining four loci were highly polymorphic with 16–23 alleles. Two of the four monomorphic loci were found to be polymorphic in Pteropus alecto, a closely related congener. All but one of the six polymorphic loci were in Hardy Weinberg equilibrium. Additionally, six microsatellite loci isolated for Pteropus rodricensis were tested against individuals of P. conspicillatus with all loci amplifying reliably. These loci will be used to investigate population genetic structure in the vulnerable spectacled flying fox.     

Microsatellite loci for Australian agamid lizards

We characterize 15 microsatellite loci from two microsatellite libraries developed from the Australian agamid lizards Amphibolurus muricatus and Ctenophorus pictus. All loci were tested for amplification in four other agamids: Ctenophorus fordi, Ctenophorus decresii, Chlamydosaurus kingii, and Physignathus lesueurii. These loci were highly polymorphic within and across species, with nine to 12 loci amplifying for each species tested.