Ten polymorphic STR loci in the cosmopolitan reef coral, Pocillopora damicornis

We report the development of 10 polymorphic molecular markers containing short tandem repeats in the cosmopolitan reef-building coral, Pocillopora damicornis, an important model species for coral health, physiology, ecology, and genetics. The availability of polymorphic DNA markers in P. damicornis can act as impetus for investigations into inheritance and population genetics, as well as novel investigations into host-symbiont ecology and evolution. Coral bleaching and gene flow studies performed with these markers can have direct conservation implications.     

Seascape and life-history traits do not predict self-recruitment in a coral reef fish

The persistence and resilience of many coral reef species are dependent on rates of connectivity among sub-populations. However, despite increasing research efforts, the spatial scale of larval dispersal remains unpredictable for most marine metapopulations. Here, we assess patterns of larval dispersal in the angelfish Centropyge bicolor in Kimbe Bay, Papua New Guinea, using parentage and sibling reconstruction analyses based on 23 microsatellite DNA loci. We found that, contrary to previous findings in this system, self-recruitment (SR) was virtually absent at both the reef (0.4–0.5% at 0.15 km²) and the lagoon scale (0.6–0.8% at approx. 700 km²). While approximately 25% of the collected juveniles were identified as potential siblings, the majority of sibling pairs were sampled from separate reefs. Integrating our findings with earlier research from the same system suggests that geographical setting and life-history traits alone are not suitable predictors of SR and that high levels of localized recruitment are not universal in coral reef fishes.     

Development and characterization of 16 polymorphic microsatellite loci in the Tibet endemic fish Glyptosternum maculatum

Sixteen novel polymorphic microsatellite loci were developed and characterized in Glyptosternum maculatum, an endemic fish inhabiting the Yarlung Zangbo River valley, Tibet, China. These loci were developed after the enrichment of microsatellite-containing genomic DNA fragments with a subtractive hybridization protocol. The polymorphism of these loci was analysed with 36 individuals representing a geographical population. The number of alleles found at these loci ranged from 3 to 10. The observed heterozygosity and expected heterozygosity ranged from 0 to 1 and from 0.31 to 0.75, respectively. These microsatellite loci will certainly facilitate the determination of the genetic structure of G. maculatum and the conservation of its genetic resource.     

Eleven polymorphic microsatellite loci in a coral reef fish,Pterapogon kauderni

We describe the isolation and characterization of 11 polymorphic tetranucleotide microsatellite loci from a male mouthbrooding coral reef fish, the Banggai cardinalfish Pterapogon kauderni. In a sample of 37 fish from a natural population, polymorphism at these loci ranged from two to 15 alleles, with expected heterozygosities ranging from 0.107 to 0.928, enabling high‐resolution genetic studies of this coral reef fish.     

Development of polymorphic microsatellite markers for the fungal tree pathogen Cryphonectria eucalypti

Polymorphic microsatellite DNA markers were developed from a single spore isolate of Cryphonectria eucalypti collected from a Eucalyptus stem canker in South Africa. Markers were obtained using the enrichment technique known as fast isolation by AFLPs of sequences containing repeats (FIASCO). Ten polymorphic markers were isolated, of which, two were discarded due to their high polymorphism in the flanking region. The mean number of alleles produced by the remaining eight markers from 20 isolates was 7.25, and alleles per locus ranged from four to 12. The markers will be used to study populations of C. eucalypti.     

Identifying the minimum number of microsatellite loci needed to assess population genetic structure: A case study in fly culturing

Small, isolated populations are constantly threatened by loss of genetic diversity due to drift. Such situations are found, for instance, in laboratory culturing. In guarding against diversity loss, monitoring of potential changes in population structure is paramount; this monitoring is most often achieved using microsatellite markers, which can be costly in terms of time and money when many loci are scored in large numbers of individuals. Here, we present a case study reducing the number of microsatellites to the minimum necessary to correctly detect the population structure of two Drosophila nigrosparsa populations. The number of loci was gradually reduced from 11 to 1, using the Allelic Richness (AR) and Private Allelic Richness (PAR) as criteria for locus removal. The effect of each reduction step was evaluated by the number of genetic clusters detectable from the data and by the allocation of individuals to the clusters; in the latter, excluding ambiguous individuals was tested to reduce the rate of incorrect assignments. We demonstrate that more than 95% of the individuals can still be correctly assigned when using eight loci and that the major population structure is still visible when using two highly polymorphic loci. The differences between sorting the loci by AR and PAR were negligible. The method presented here will most efficiently reduce genotyping costs when small sets of loci (“core sets”) for long-time use in large-scale population screenings are compiled.     

Isolation by distance and vicariance drive genetic structure of a coral reef fish in the Pacific Ocean

We studied the genetic diversity of a coral reef fish species to investigate the origin of the differentiation. A total of 727 Acanthurus triostegus collected from 15 locations throughout the Pacific were analyzed for 20 polymorphic loci. The genetic structure showed limited internal disequilibrium within each population; 3.7% of the loci showed significant Hardy-Weinberg disequilibrium, mostly associated with Adh*, and we subsequently removed this locus from further analysis of geographic pattern. The genetic structure of A. triostegus throughout the tropical Pacific Ocean revealed a strong geographic pattern. Overall, there was significant population differentiation (multilocus F(ST) = 0.199), which was geographically structured according to bootstraps of neighbor-joining analysis on Nei's unbiased genetic distances and AMOVA analysis. The genetic structure revealed five geographic groups in the Pacific Ocean: western Pacific (Guam, Philippines, Palau, and Great Barrier Reef); central Pacific (Solomons, New Caledonia, and Fiji); and three groups made up of the eastern populations, namely Hawaiian Archipelago (north), Marquesas (equatorial), and southern French Polynesia (south) that incorporates Clipperton Island located in the northeastern Pacific. In addition, heterozygosity values were found to be geographically structured with higher values grouped within Polynesian and Clipperton populations, which exhibited lower population size. Finally, the genetic differentiation (F(ST)) was significantly correlated with geographic distance when populations from the Hawaiian and Marquesas archipelagos were separated from all the other locations. These results show that patterns of differentiation vary within the same species according to the spatial scale, with one group probably issued from vicariance, whereas the other followed a pattern of isolation by distance. The geographic pattern for A. triostegus emphasizes the diversity of the evolutionary processes that lead to the present genetic structure with some being more influential in certain areas or according to a particular spatial scale.     

PERMANENT GENETIC RESOURCES: A set of 12 microsatellite loci for genetic studies of Leishmania braziliensis

Twelve microsatellite loci of Leishmania braziliensis were examined, nine of which were developed in this work. Fifty‐six Leishmania braziliensis were genotyped with these microsatellite loci. The 12 loci studied were polymorphic with the number of alleles ranging from five to 19, with a mean of 9.7 ± 4.1 and the observed heterozygosity averaging 0.425 ± 0.202. The important heterozygote deficits we observed (F_IS = 0.41, P value = 0.004) appear incompatible with the heterozygote excess expected in clonal diploids. This last result could revive the clonality/sexuality debate regarding Leishmania. This work validates the potential use of these microsatellites for population genetics analysis.     

Emergent patterns of population genetic structure for a coral reef community

What shapes variation in genetic structure within a community of codistributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the archipelago's stepping stone configuration, isolation by distance was the least common type of genetic structure, detected in four species. Regional structuring (i.e. division of sites into genetically and spatially distinct regions) was most common, detected in 20 species and nearly in all endemics and habitat specialists. Seven species displayed chaotic (spatially unordered) structuring, and all were nonendemic generalist species. Chaotic structure also associated with relatively high global F_ST. Pelagic larval duration (PLD) was not a strong predictor of variation in population structure (R² = 0.22), but accounting for higher F_ST values of chaotic and invertebrate species, compared to regionally structured and fish species, doubled the power of PLD to explain variation in global F_ST (adjusted R² = 0.50). Multivariate correlation of eight species traits to six genetic traits highlighted dispersal ability, taxonomy (i.e. fish vs. invertebrate) and habitat specialization as strongest influences on genetics, but otherwise left much variation in genetic traits unexplained. Considering that the study design controlled for many sampling and geographical factors, the extreme interspecific variation in spatial genetic patterns observed for Hawaìi marine species may be generated by demographic variability due to species‐specific abundance and migration patterns and/or seascape and historical factors.     

New polymorphic microsatellite loci for population studies in the European anchovy, Engraulis encrasicolus (L.)

Eleven microsatellite loci were developed in the European anchovy, Engraulis encrasicolus, and tested in samples from two geographically distant populations (Atlantic and Mediterranean Sea). Number of alleles ranged from eight to 28 and observed heterozygosity from 0.440 to 0.920. There was no evidence of linkage disequilibrium, although two loci are indeed linked. All loci were in Hardy-Weinberg equilibrium, except for one locus in the Atlantic and two loci in the Mediterranean sample. These three loci plus two more showed evidence for null alleles.     

Isolation and characterization of polymorphic microsatellite loci for the horn fly, Haematobia irritans (L.) (Diptera: Muscidae)

The horn fly, Haematobia irritans (L.) (Diptera: Muscidae), is a cosmopolitan livestock pest that has caused a great negative impact on the animal production sector throughout the world. Here, we describe 10 polymorphic microsatellite loci isolated from H. irritans. The number of alleles found ranged from two to eight per locus and the expected heterozygosity from 0.1421 to 0.7702. These loci are potentially useful for the fine-scale genetic characterization of horn fly populations and provide fundamental information for pest management and planning of control programs.     

Isolation and characterization of polymorphic microsatellite loci for the invasive plant Cytisus scoparius

Scotch broom (Cytisus scoparius) is a serious weed of natural and pastoral ecosystems and is invasive in many countries worldwide. Eight polymorphic microsatellite loci were developed and characterized for this species. The number of alleles per locus ranged from five to 23. The range of observed heterozygosity was between 0.207 and 0.928. These microsatellite markers will be useful tools for studies of population genetics in the native and invasive range of this species.     

Isolation and characterization of polymorphic microsatellite loci in the boll weevil,Anthonomus grandis Boheman (Coleoptera: Curculionidae)

The boll weevil (Anthonomus grandis Boheman) is a major insect pest of cotton in North America. Dispersal activity poses a threat to ongoing eradication efforts in the US, but little is known about the frequency of long‐distance migration. Nuclear molecular markers are needed to assess gene flow in relation to geographical distance. A biotin‐enrichment strategy was employed to develop microsatellite markers for the boll weevil. Of 23 loci isolated, 14 were polymorphic with three to 10 alleles per locus. Twelve of the polymorphic loci showed Mendelian inheritance and are likely to be useful in population genetics studies.     

Environmental gradients predict the genetic population structure of a coral reef fish in the Red Sea

The relatively recent fields of terrestrial landscape and marine seascape genetics seek to identify the influence of biophysical habitat features on the spatial genetic structure of populations or individuals. Over the last few years, there has been accumulating evidence for the effect of environmental heterogeneity on patterns of gene flow and connectivity in marine systems. Here, we investigate the population genetic patterns of an anemonefish, Amphiprion bicinctus, along the Saudi Arabian coast of the Red Sea. We collected nearly one thousand samples from 19 locations, spanning approximately 1500 km, and genotyped them at 38 microsatellite loci. Patterns of gene flow appeared to follow a stepping‐stone model along the northern and central Red Sea, which was disrupted by a distinct genetic break at a latitude of approximately 19°N. The Red Sea is characterized by pronounced environmental gradients along its axis, roughly separating the northern and central from the southern basin. Using mean chlorophyll‐a concentrations as a proxy for this gradient, we ran tests of isolation by distance (IBD, R² = 0.52) and isolation by environment (IBE, R² = 0.64), as well as combined models using partial Mantel tests and multiple matrix regression with randomization (MMRR). We found that genetic structure across our sampling sites may be best explained by a combined model of IBD and IBE (Mantel: R² = 0.71, MMRR: R² = 0.86). Our results highlight the potential key role of environmental patchiness in shaping patterns of gene flow in species with pelagic larval dispersal. We support growing calls for the integration of biophysical habitat characteristics into future studies of population genetic structure.     

Polymerase chain reaction primers for polymorphic microsatellite loci from the Korean sandfish,Arctoscopus japonicus

We developed 12 polymorphic microsatellite markers from Arctoscopus japonicus by screening an enriched genomic library using polymerase chain reaction (PCR) techniques. The average of alleles size was 16.2, and the average observed and expected heterozygosities were 0.59 and 0.78, respectively. The observed genotypic frequencies in five loci were significantly deviated from Hardy–Weinberg expectations. The high variability revealed in this study suggested that these microsatellite loci should provide useful markers for population genetics of A. japonicus.     

Development and characterization of microsatellite loci in Mormon crickets (Anabrus simplex,Orthoptera, Tettigoniidae)

Anabrus simplex is an economically significant crop pest in the western United States and is a model organism for studying the influence of sex role reversal on sperm allocation and utilization patterns and population genetics. We isolated seven polymorphic microsatellite loci in Anabrus simplex, and within population allele numbers ranged from 10 to 25. High polymorphism is not unusual for Orthopteran insects, although observed heterozygosities ranged from 0.24 to 0.91 and were lower than expected heterozygosities, suggesting null alleles. These microsatellites will greatly facilitate studies of postcopulatory reproductive isolation in nuptial gift‐giving insects and historical phylogenetics in the Rocky Mountains.     

Ten new highly polymorphic microsatellite loci in the blood clam Scapharca broughtonii

Ten novel microsatellite loci were isolated from blood clam Scapharca broughtonii, and the polymorphisms were examined to estimate genetic variability. The genetic variabilities varied depending on the locus. The number of alleles ranged from 11 to 23, and the observed and expected heterozygosities ranged from 0.63 to 0.93 and 0.66 to 0.95, respectively. Four loci showed significant Hardy–Weinberg disequilibrium at P < 0.05 level. The high variabilities revealed in this study suggest that microsatellites should prove useful for various genetic investigations.     

Ten polymorphic microsatellite loci in the giant scallop (Mizuhopecten yessoensis)

Ten novel microsatellite loci were isolated from giant scallop Mizuhopecten yessoensis, and the polymorphisms were examined to estimate genetic variability. The genetic variabilities varied depending on the locus. The number of alleles ranged from two to 17, and the observed and expected heterozygosities ranged from 0.17 to 0.99 and 0.33 to 0.90, respectively. Six loci showed significant Hardy–Weinberg disequilibrium. The high variabilities revealed in this study suggest that microsatellites should prove useful for various genetic investigations.