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.     

Isolation and characterization of microsatellite loci in Aspergillus sydowii, a pathogen of Caribbean sea fan corals

Here we report on nine microsatellite loci designed for Aspergillus sydowii, a widely distributed soil saprobe that is also the pathogenic agent of aspergillosis in Caribbean sea fan corals. Primers were tested on 20 A. sydowii isolates from the Caribbean, 17 from diseased sea fans and three from environmental sources. All loci were polymorphic and exhibited varying degrees of allelic diversity (three to nine alleles). Gene diversity (expected heterozygosity) ranged from 0.353 to 0.821. These primers will enable future research into the epidemiology of A. sydowii as an emergent infectious disease.     

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.     

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.     

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 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.     

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 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 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.     

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.     

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 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.     

Isolation and characterization of microsatellite loci in the invasive Alliaria petiolata (Brassicaceae)

Eight novel polymorphic microsatellite loci are presented for garlic mustard (Alliaria petiolata, Brassicaceae) a European herb that is a serious invader of North American deciduous forests. The microsatellites will be useful tools to analyse pathways of introduction of garlic mustard, as well as its evolutionary potential in the invasive range.     

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 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 microsatellite loci in Babylonia areolata and cross-species amplification in Babylonia formosae habei

Nine novel microsatellite primer pairs were presented for Babylonia areolata, representing the first microsatellite markers available for this genus. Levels of polymorphism were variable with 2 to 11 alleles per locus and expected heterozygosities ranging from 0.073 to 0.907 in 27 individuals of the population from which the loci were isolated. We found significant heterozygote deficit at one locus that might be attributable to null alleles. We were successful at cross-amplifying six loci in the congeneric B. formosae habei. These markers are therefore potentially useful for conservation studies, population structure assessment, ecological analyses and linkage map construction.     

Isolation and characterization of polymorphic microsatellite DNA markers in the sea squirt Halocynthia roretzi

The sea squirt Halocynthia roretzi is an important marine food resource species that is found in the waters around Korea. We describe the isolation and characterization of 13 new polymorphic microsatellite loci in 96 sea squirt samples that were collected from the marine environment of Samcheok on the east coast of Korea. The number of alleles that were observed for each locus ranged from six to 32, and the value of expected and observed heterozygosities was 0.504-0.922 and 0.396-0.813, respectively. These markers will be useful tools for future population studies.     

Isolation and characterization of microsatellite DNA loci in the toad‐headed lizards,Phrynocephalus przewalskii complex

To assess mechanisms of hybridization and speciation, we isolated and characterized 12 dinucleotide microsatellite DNA loci for the toad‐headed lizards, Phrynocephalus przewalskii complex. A total of 48 specimens were examined and all loci were polymorphic with seven to 25 alleles per locus. The observed and expected heterozygosities ranged from 0.282 to 0.946 and 0.400 to 0.937, respectively. These loci are therefore suitable for a wide range of population level studies within the P. przewalskii complex.