Isolation and characterization of microsatellite loci in the Caribbean sea fan coral, Gorgonia ventalina

Here we report primers for 10 microsatellite loci from the Caribbean sea fan coral, Gorgonia ventalina. Primers were tested on 237 genomic DNA extracts taken directly from tissue samples of G. ventalina. All loci were polymorphic with allelic richness ranging from 4 to 52. Expected heterozygosity ranged from 0.14 to 0.96. Preliminary data suggest that these microsatellites will be useful tools for studies of the population genetics of this important Caribbean coral species.     

Isolation and characterization of microsatellite loci in Symbiodinium B1/B184, the dinoflagellate symbiont of the Caribbean sea fan coral, Gorgonia ventalina

Here we report primers targeting 10 microsatellite loci of dinoflagellates in the genus Symbiodinium (clade B1/B184) symbiotic with the Caribbean sea fan coral, Gorgonia ventalina. Primers were tested on 12 Symbiodinium B1/B184 cultures, as well as 40 genomic DNA extracts of G. ventalina tissue samples. All loci were polymorphic with allelic richness ranging from 4-16. Gene diversity ranged from 0.15 to 0.91. These primers provide powerful tools for examining the fine-scale population structure and dynamics of Symbiodinium within a single host species.     

Range-wide population genetic structure of Symbiodinium associated with the Caribbean Sea fan coral, Gorgonia ventalina

Numerous marine invertebrates form endosymbiotic relationships with dinoflagellates of the genus Symbiodinium, yet few studies have examined the population structure of these symbionts. Here, we elucidate the population genetic structure of Symbiodinium harboured by the Caribbean octocoral Gorgonia ventalina throughout the entire range of the host. We used ten microsatellite loci to survey 35 localities spanning 3124 km across the Caribbean and Western Atlantic. Diversity of Symbiodinium haplotypes was low within colonies of G. ventalina but high among colonies. Despite high haplotypic diversity, significant evidence of clonal reproduction in Symbiodinium was detected, and most clones occurred within localities, not among them. Pairwise measures of F(ST) illustrated significant differentiation in 98% of comparisons between localities, suggesting low levels of gene flow. Clustering analyses identified six genetic groups whose distribution delimited four broad biogeographic regions. There was evidence of some connectivity among regions, corresponding with known geographic and oceanographic features. Fine-scale spatial surveys of G. ventalina colonies failed to detect differentiation among Symbiodinium at the metre scale. However, significant differentiation was observed among Symbiodinium hosted by sympatric G. ventalina colonies of different size/age classes. This cohort effect suggests that Symbiodinium may have an epidemic population structure, whereby G. ventalina recruits are infected by the locally predominant symbiont strain(s), which change over time.     

Characterization of Aspergillus sydowii (Thom et Church), a fungal pathogen of Caribbean sea fan corals

In the Caribbean, the fungus Aspergillus sydowii is currently causing an epizootic among sea fan corals (Gorgonia spp.). To elucidate potential factors that may have facilitated the emergence of this disease, we characterized and compared temperature requirements, susceptibility to coral crude extracts, and metabolic profiles of pathogenic (marine) and non-pathogenic (terrestrial) strains of A. sydowii. Growth of all A. sydowii strains were observed at all temperatures tested (22–36 °C) with an optimum of approximately 30 °C. Sea fan crude extracts inhibited growth of A. sydowii but were less effective at higher temperatures. Thus, temperature is likely to have a strong influence on the dynamics of the Gorgonia–Aspergillus interaction by promoting the growth of the pathogen while reducing the efficacy of host resistance. Metabolically, marine A. sydowii strains pathogenic to sea fans were distinct from non-pathogenic terrestrial strains.     

Range‐wide population genetic structure of the Caribbean sea fan coral,Gorgonia ventalina

The population structure of benthic marine organisms is of central relevance to the conservation and management of these often threatened species, as well as to the accurate understanding of their ecological and evolutionary dynamics. A growing body of evidence suggests that marine populations can be structured over short distances despite theoretically high dispersal potential. Yet the proposed mechanisms governing this structure vary, and existing empirical population genetic evidence is of insufficient taxonomic and geographic scope to allow for strong general inferences. Here, we describe the range‐wide population genetic structure of an ecologically important Caribbean octocoral, Gorgonia ventalina. Genetic differentiation was positively correlated with geographic distance and negatively correlated with oceanographically modelled dispersal probability throughout the range. Although we observed admixture across hundreds of kilometres, estimated dispersal was low, and populations were differentiated across distances <2 km. These results suggest that populations of G. ventalina may be evolutionarily coupled via gene flow but are largely demographically independent. Observed patterns of differentiation corroborate biogeographic breaks found in other taxa (e.g. an east/west divide near Puerto Rico), and also identify population divides not discussed in previous studies (e.g. the Yucatan Channel). High genotypic diversity and absence of clonemates indicate that sex is the primary reproductive mode for G. ventalina. A comparative analysis of the population structure of G. ventalina and its dinoflagellate symbiont, Symbiodinium, indicates that the dispersal of these symbiotic partners is not coupled, and symbiont transmission occurs horizontally.     

Isolation and characterization of microsatellite loci in the Caribbean gorgonian Pseudopterogorgia elisabethae

We report on the isolation and characterization of five polymorphic microsatellites in the gorgonian Pseudopterogorgia elisabethae from genomic DNA‐enriched libraries. Forty‐four microsatellites were screened from the libraries with the oligonucleotide probe (CA)₁₂. Five of the screened microsatellites were polymorphic. The levels of polymorphism found in 50 genotyped individuals from a single population suggest that microsatellites are useful tools for the study of genetic variation in gorgonians. These are the first microsatellite loci reported from any gorgonian species.     

Isolation and characterization of microsatellite loci in Eurycorymbus cavaleriei,a dioecious endemic tree species in China

Eleven dinucleotide microsatellites were developed and characterized for Eurycorymbus cavaleriei, a dioecious, rare and endemic tree species in China. A genomic DNA enrichment protocol was used to isolate microsatellite loci and polymorphism was explored using 30 trees from two natural populations. The observed heterozygosity (H_O) ranged from 0.379 to 0.931, with an average of 0.625. These markers provide powerful tools for the ongoing population and conservation genetics studies of E. cavaleriei.     

Isolation and characterization of microsatellite loci from rock shell, Thais clavigera

Imposex (superimposition of male genital organs on female phenotype) of the rock shell or whelk, Thais clavigera, shows typical evidence of endocrine disruption by organotin compounds within inter-tidal zones polluted by such compounds. It will be informative to see how low fertility caused by imposex of this species finally affects the genetic diversity of polluted populations. For future use in population genetic research of the rock shell, we report the isolation and characteristics of 11 highly polymorphic microsatellite markers with a mean of 11.7 alleles per locus. We observed heterozygosities of these sequences ranging from 0.43 to 0.95. These markers will be useful for future ecological genetic studies of rock shell.     

Globally panmictic population structure in the opportunistic fungal pathogen Aspergillus sydowii

Recent outbreaks of new diseases in many ecosystems are caused by novel pathogens, impaired host immunity, or changing environmental conditions. Identifying the source of emergent pathogens is critical for mitigating the impacts of diseases, and understanding the cause of their recent appearances. One ecosystem suffering outbreaks of disease in the past decades is coral reefs, where pathogens such as the fungus Aspergillus sydowii have caused catastrophic population declines in their hosts. Aspergillosis is one of the best-characterized coral diseases, yet the origin of this typically terrestrial fungus in marine systems remains unknown. We examined the genetic structure of a global sample of A. sydowii, including isolates from diseased corals, diseased humans, and environmental sources. Twelve microsatellite markers reveal a pattern of global panmixia among the fungal isolates. A single origin of the pathogen into marine systems seems unlikely given the lack of isolation by distance and lack of evidence for a recent bottleneck. A neighbour-joining phylogeny shows that sea fan isolates are interspersed with environmental isolates, suggesting there have been multiple introductions from land into the ocean. Overall, our results underscore that A. sydowii is a true opportunist, with a diversity of nonrelated isolates able to cause disease in corals. This study highlights the challenge in distinguishing between the role of environment in allowing opportunistic pathogens to increase and actual introductions of new pathogenic microorganisms for coral diseases.     

Microsatellite loci isolated from the Caribbean coral,Montastraea annularis

We report the isolation and characterization of seven microsatellite loci from the Caribbean reef‐building coral, Montastraea annularis. All loci are polymorphic with allele numbers ranging from five to 31 and observed heterozygosities from 0.17 to 0.89. These loci can be used in assessing gene flow patterns and diversity of this stony coral species both for local coral reef management purposes as well as for elucidating population connectivity within the greater Caribbean basin. These markers should also be applicable to other species of Montastraea and for resolving taxonomic relationships within the M. annularis species complex.     

Isolation and characterization of microsatellite loci in Merluccius australis and cross-species amplification

Eight novel and two heterologous microsatellite pairs of primers are presented for the Austral hake (Merluccius australis), representing the first microsatellite markers available for this species. Loci were characterized for 50 individuals from two populations in South America (Argentinean and Chilean coasts). All loci were polymorphic within M. australis (5 to 30 alleles per locus; observed heterozygosity between 0.320 and 0.840), and therefore useful for population genetic studies within the species. Cross-species transferability was tested for 100 individuals from four additional species within the Merluccius genus (M. albidus, M. bilinearis, M. gayi and M. hubbsi), and results indicate that most of these primers pairs will likely be useful for population genetic studies on Merluccius species.     

Isolation and characterization of variable microsatellite loci in Lilium philadelphicum (Liliaceae)

Here we describe the characterization of six polymorphic microsatellite loci for Lilium philadelphicum (Liliaceae). Polymorphism levels ranged from 7 to 30 alleles per locus with a mean number of 15 alleles per locus. Observed heterozygosity (H_O) ranged from 0.17 to 0.82 and did not deviate from Hardy–Weinberg expectations in the three western Montana populations included in the analysis. These loci are proving useful in studying gene flow between populations of this species distributed across its range in North America.     

Isolation and characterization of EST‐derived microsatellite loci from the fungal wheat pathogen Phaeosphaeria nodorum

Eleven polymorphic microsatellite loci and one minisatellite locus originating from expressed sequence tag (EST) libraries of Phaeosphaeria (syn. Stagonospora) nodorum were isolated and characterized. The satellite markers were used to genotype isolates from field populations collected in China, North America and South Africa. The number of alleles per locus ranged from two to 15. Genotype diversity ranged from 87.5 to 95.3 and gene diversity from 0.1 to 0.8. The variable levels of polymorphism within and among populations of P. nodorum renders these 12 satellite loci ideal markers for population genetic analysis of P. nodorum.     

Isolation and characterization of 49 polymorphic microsatellite loci in the ayu,Plecoglossus altivelis

A total of 49 novel polymorphic microsatellite markers in the ayu fish, Plecoglossus altivelis, were successfully isolated and characterized. The number of alleles per locus, observed heterozygosity, and expected heterozygosity ranged from two to 25 (11.3 on average), from 0.125 to 1.000 (0.648 on average), and from 0.123 to 0.957 (0.751 on average), respectively. These microsatellite markers will be useful for both studying population structure and identifying quantitative trait loci that control evolutionarily and economically important traits of ayu.     

Isolation and characterization of five microsatellite loci in an ectomycorrhizal fungus Laccaria laccata

Laccaria laccata is an early successional ectomycorrhizal fungus. We isolated five polymorphic microsatellite loci from L. laccata using a dual‐suppression polymerase chain reaction technique. The number of alleles per locus ranged from three to six. The observed and expected heterozygosities ranged from 0.269 to 0.462, and 0.249 to 0.775, respectively. These microsatellite markers would be valuable molecular tools for population genetic studies of L. laccata.     

Isolation and characterization of microsatellite loci from the barley scald pathogen,Rhynchosporium secalis

Fifteen primer pairs were designed for 14 polymorphic microsatellite loci, which were isolated and characterized from genomic libraries of Rhynchosporium secalis. Conditions for multiplexing and simultaneous genotyping of up to eight loci in a single run are described. The number of alleles per polymorphic locus ranged from two to 13 in populations from Switzerland and Australia. Genotypic diversity ranged from 61.5 to 66.7. Gene diversity ranged from 0.08 to 0.89 for individual polymorphic loci, with averages of 0.54 and 0.62 for the populations from Switzerland and Australia, respectively. Variable levels of polymorphism make these ideal markers for population genetic analyses.     

Isolation and characterization of polymorphic microsatellite loci in white truffle (Tuber magnatum)

Tuber spp. are fungi that establish symbiosis with several trees and shrubs. Some of these fungal species produce edible ascomata, also known as truffles, which are highly appreciated for their taste and odour. We isolated and characterized eight polymorphic microsatellite loci from Tuber magnatum, the finest white truffle species, and assessed their variability in 370 individuals collected from all over the species range of distribution. Although two to 18 alleles per locus were found, no heterozygous individuals were observed. The availability of simple sequence repeat loci provides valuable tools for assessment of the genetic structure and population dynamics in this species.     

Isolation and characterization of 16 microsatellite loci in the Great Tit Parus major

Six dinucleotide, three trinucleotide and seven tetranucleotide microsatellite loci developed for the great tit Parus major are presented. Thirty individual birds were screened at each locus. Loci were polymorphic (four to 19 alleles per locus). These markers provide a system to study paternity, genetic diversity in natural populations, gene flow, dispersal and inbreeding.     

Development of microsatellite markers for the Mediterranean gorgonian coral Corallium rubrum

Corallium rubrum, an endemic Mediterranean gorgonian coral, has undergone an intensive exploitation leading to the extinction of local commercial banks and changes in the structure and dynamics of coastal populations. Management and conservation of this species requires a better understanding of the genetic structuring and connectivity among populations. With this aim, seven microsatellite loci have been isolated. All loci were polymorphic with allele numbers ranging from five to 26 and observed heterozygosity ranging from 0.18 to 0.68. Significant deviations from Hardy–Weinberg expected genotype frequencies due to heterozygote deficiency were detected at all loci.