Characterization of polymorphic microsatellite loci in Castelnau's Antshrike,Thamnophilus cryptoleucus (Aves: Thamnophilidae)

In order to study the biogeography and population genetic structure of the obligate river‐island species Thamnophilus cryptoleucus (Thamnophilidae) we isolated four microsatellite loci. Number of alleles ranged from six to 11, heterozygosities from 60% to 89%, and individual populations were found in Hardy–Weinberg equilibrium. Cross‐species amplification of the loci was tested in eight species of the family Thamnophilidae and all loci successfully amplified in five or more related species.     

Primers from the orders Osteoglossiform and Siluriform detect polymorphic microsatellite loci in sun-catfish, Horabagrus brachysoma (Teleostei: Bagridae)

Horabagrus brachysoma (sun‐catfish, Bagridae, Siluriformes) is a valuable ornamental and food fish. The stock structure of H. brachysoma, necessary to conserve its declining natural populations, is not known. Twenty‐five primers developed for four fish species belonging to the orders Siluriform (3) and Osteoglossiform (1) were tested and eight primers amplified microsatellite loci in H. brachysoma. The results demonstrate that cross‐priming between fish species belonging to different families and even to different orders can yield microsatellite loci. Five of eight primers each amplified two loci. However, the loci that had repeat motifs after sequencing were considered only for genotyping. Finally, eight loci were polymorphic with hree to seven alleles. Individual fish genotype data (n = 42; 21 each in two rivers) at each locus was analysed. Significant genetic heterogeneity was detected at six loci. The identified loci exhibited potential for use in population genetics application in H. brachysoma.     

Development and characterization of the first microsatellite markers in the mangrove species Pelliciera rhizophorae Triana & Planchon

Pelliciera rhizophorae is a unique Neotropical mangrove species belonging to Pelliciera genus. We isolated eight microsatellite loci from this species. All loci were polymorphic and showed three to nine alleles per locus in Colombian Pacific and Caribbean populations. Polymorphic information content ranged from 0.46 to 0.69. Two loci (PeRh‐14 and PeRh‐19) showed null alleles on the Caribbean coast, which suggest genetic differentiation between Pacific and Caribbean populations of P. rhizophorae. Development of these microsatellite loci constitutes a new molecular tool to carry out studies in the genome of the species and to evaluate its population dynamics.     

Isolation and characterization of 149 novel microsatellite DNA markers for striped bass,Morone saxatilis,and cross‐species amplification in white bass,Morone chrysops,and their hybrid

To support detailed genetic analysis of striped bass (Morone saxatilis) and white bass (Morone chrysops), we isolated 153 microsatellite loci from repeat‐enriched striped bass DNA libraries. Of these, 147 markers amplified in striped bass (average 4.7 alleles per locus) and 133 in white bass (average 2.2 alleles per locus). One hundred twenty‐two markers amplified in their hybrid. Development of new microsatellite markers will facilitate evaluations of genetic structure in wild populations and will support pedigree analysis and linkage mapping for selective breeding.     

Identification of microsatellite loci in Collinsia verna (Veronicaceae)

We developed eight polymorphic microsatellite loci for Collinsia verna (Veronicaceae). In a sample of 18–35 individuals from a single population, we found two to 15 alleles per locus (mean 8.3). We also tested these loci for cross‐amplification in all 22 species in the tribe Collinseae. Overall, more than half the species in the tribe amplified one microsatellite while three species most closely related to C. verna (Collinsia violacea, Collinsia parviflora and Collinsia grandiflora) amplified multiple microsatellite loci. These microsatellite loci will be used in future studies of mating system in this tribe and other quantitative genetic and population genetic studies.     

Characterization of novel microsatellite loci for red clover (Trifolium pratense L.) from enriched genomic libraries

Twenty‐seven polymorphic microsatellite markers were isolated from red clover (Trifolium pratense). Allelic variability and cross‐species amplification were assessed on 24 red clover and eight white clover (Trifolium repens) genotypes. The number of alleles detected in red clover ranged from two to 25. Observed and expected heterozygosities were high with average values of 0.71 and 0.88, respectively. Five of the 27 loci were also successfully amplified from white clover, where two to 13 alleles were detected. These highly polymorphic microsatellite loci provide powerful tools for population genetic studies as well as for marker‐assisted selection in this important forage legume species.     

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.     

Characterization of microsatellite loci in the brown treecreeper (Climacteris picumnus) and cross‐species amplification in the white‐throated treecreeper (Cormobates leucophaeus)

Eight polymorphic microsatellite markers were developed for the brown treecreeper, Climacteris picumnus. The number of alleles ranged from three to 25 per locus with observed heterozygosities between 0.05 and 0.76. Seven of the eight primer pairs also amplified polymorphic microsatellite loci in the white‐throated treecreeper (Cormobates leucophaeus). These markers are likely to be useful for population genetic and parentage studies in any of the Australasian treecreepers (Climacteridae) and are the first genetic markers developed for any member of this passerine family.     

Identification and characterization of nuclear microsatellite loci in the aquatic moss Platyhypnidium riparioides (Brachytheciaceae)

Eight microsatellite loci from the aquatic moss Platyhypnidium riparioides were identified using the method of microsatellite‐enriched libraries. Polymorphism was assessed in a sample of four populations of 20 individuals each from four streams of the Meuse hydrographic basin in southern Belgium. The markers amplified three to seven alleles per locus. Comparison of observed and expected heterozygosities as well as F‐statistics (F_ST = 0.62) reveals a significant genetic differentiation among populations. These markers will be useful for further investigation of population genetic structure and diversity at different nested spatial scales.     

Characterization of eight new microsatellite loci in the invading maritime pine bast scale Matsucoccus feytaudi (Hemiptera: Coccoidea: Margarodidae)

The bast scale Matsucoccus feytaudi is a specific pest of maritime pine that is endemic in the Iberian Peninsula and southwestern France, and invasive in southeastern France, Italy and Corsica where it causes heavy damages. We developed eight microsatellite polymorphic markers using an enrichment protocol in order to study the invasion pathways and infer the genetic diversity of the populations. All loci could be successfully amplified with no evidence of null alleles. Cross‐species amplifications failed to amplify the congeneric Matsucoccus josephi.     

Development of microsatellite markers for the neotropical tree species Dipteryx alata (Fabaceae)

? Premise of the study: Microsatellite markers were developed for the population genetic analyses of the neotropical tree Dipteryx alata (Fabaceae). ? Methods and Results: Microsatellites were developed from a genomic shotgun library. Polymorphism at each microsatellite loci was analyzed based on 94 individuals from three populations. Eight loci amplified successfully and presented one to 10 alleles, and expected heterozygosities ranged from 0.097 to 0.862. Four loci also amplified in Pterodon emarginatus and presented similar polymorphism. ? Conclusion: The eight microsatellite primer pairs are potentially suitable for population genetic studies and successfully amplified in another Fabaceae species.     

Ten microsatellite loci for the small red‐eyed damselfly Erythromma viridulum (Charpentier)

The small red‐eyed damselfly, Erythromma viridulum (Charpentier), is the first recorded example of a migrant damselfly establishing colonies in the British Isles. To examine the population genetic structure of E. viridulum, a partial genomic library enriched for CA microsatellite loci was constructed. Of the 42 loci tested, 19 amplified spurious bands and 13 were monomorphic, leaving 10 polymorphic loci that resolved distinct alleles within the expected size range. The number of alleles ranged between two (LIST14‐021, LIST14‐40) and eight (LIST14‐002). Observed and expected heterozygosities varied between 0.000–0.698 and 0.045–0.688, respectively.     

Microsatellite markers isolated from barn swallows (Hirundo rustica)

Fifteen polymorphic microsatellite DNA loci were isolated from barn swallow (Hirundo rustica) and optimized for future studies of radiation‐induced mutations in populations from Ukraine. The loci were screened for variability among 25 individuals from two populations. The primers amplified loci with relatively high numbers of alleles ranging from five to 32 alleles per locus and polymorphic information content from 0.481 to 0.951. Observed heterozygosity varied from 0.458 to 0.960. None of the loci showed deviations from Hardy–Weinberg equilibrium in either population.     

Microsatellite analysis of non-migratory colonies of Apis mellifera iberica from south-eastern Spain

Forty‐five unmanaged honeybee colonies from the south‐east of the Iberian Peninsula (Apis mellifera iberica) were selected for analysing their genetic structure using eight microsatellite loci. These colonies were not subjected to management for queen replacement, rearing or migratory movements and previous studies showed that they had mitochondrial DNA (mtDNA) of African origin. Six of the microsatellite loci show intermediate levels of polymorphism with a total number of alleles detected per locus ranging from 4 to 10. Microsatellite data relate these Iberian populations to the African A. m. intermissa, although the presence of some alleles and the observed heterozygosity are characteristic of the European A. m. mellifera, thus corroborating the postulated hybrid origin of A. m. iberica. The results suggest that no recent introgression from Africa has happened and that the populations of A. m. iberica are differentiated in many demes.     

Clonal diversity and genetic differentiation revealed by SSR markers in wild Vaccinium macrocarpon and Vaccinium oxycoccos

American cranberry (Vaccinium macrocarpon) is a perennial, woody plant species, native to North American bogs and wetlands. Cranberries represent one of the few agriculturally important native plants in which wild gene pools are still readily available within the undeveloped wetlands of the northern US and Canada. Earlier studies have reported low genetic variation in V. macrocarpon at the species and population level. However, in this study, we characterised 229 individuals of wild V. macrocarpon and V. oxycoccos (small cranberry) from Wisconsin and 22 accessions using microsatellite markers and observed substantial genetic variation and differentiation within and among populations and species. While V. macrocarpon was analysed using 108 alleles from 11 microsatellite loci revealing 42 unique genotypes, V. oxycoccos was analysed using 156 alleles from eight loci revealing 28 unique genotypes. There were a total of 182 alleles found in both species combined with 156 of those alleles present in V. oxycoccos and 84 alleles found in V. macrocarpon. All eight loci possessed species‐specific alleles with V. oxycoccos possessing 98 private alleles versus 26 private alleles found V. macrocarpon, and 58 alleles were found in common between both species. Our data will be valuable not only for future wild cranberry diversity and population genetics research, but for other cranberry breeding and genetics studies.     

High inbreeding and low connectivity among Ambystoma texanum populations in fragmented Ohio forests

Habitat loss and fragmentation negatively impact the size and diversity of many natural populations. Woodland amphibians require connected aquatic and terrestrial habitats to complete their life cycle, and often rely on metapopulation structure for long‐term persistence. Wetland loss and deforestation fragment amphibian populations, which may result in population isolation and its negative effects. The aim of this research was to analyze the population genetic structure of small‐mouthed salamanders (Ambystoma texanum) in western Ohio, where agriculture is now the dominant land use. Salamander tail tissue was collected from eight breeding pools. Three pools occur in the same forest; the other five are in forest patches at distances ranging from 250 m to 20 km from one another. Eight microsatellite loci were amplified by PCR and genotyped for allele size. Observed heterozygosities were lower than expected in all sampled populations; the two most isolated sites (Ha1, Ha2) had the highest inbreeding coefficients. Ha2 also had the lowest mean number of alleles and was found to be genetically differentiated from populations to which our data analysis indicates it was historically connected by gene flow. The most distant site (Ha1) had the highest number of private alleles and showed genetic differentiation from other populations both historically and currently. Geographic distance between pools was strongly correlated with the number of private alleles in a population. The results suggest that population isolation results in decreased genetic diversity and that a breakdown of metapopulation structure due to landscape change may contribute to differentiation between once‐connected populations.     

Isolation and characterization of polymorphic microsatellite loci in Asiatic sand sedge,Carex kobomugi Ohwi (Cyperaceae)

Fourteen polymorphic microsatellite loci were isolated from Asiatic sand sedge, Carex kobomugi Ohwi (Cyperaceae), a clonal perennial herb predominant in sandy coast vegetation in Japan. Polymorphism was surveyed for 24 ramets within a single population and for eight distinct individuals from six populations. Within a population, between two and eight alleles were found per locus, and expected heterozygosity ranged from 0.041 to 0.720. Among populations, a higher level of polymorphism was observed. The microsatellite loci were shown to be useful for the study of spatial genetic structure at fine scale and genetic differentiation among populations.     

Microsatellite markers for Ceiba pentandra (Bombacaceae), an endangered tree species of the Amazon forest

From a genomic library enriched for AG/TC repeats, eight polymorphic microsatellite markers were developed for Ceiba pentandra, a pan‐tropical forest tree. Polymorphism was evaluated using a panel of 74 adult trees. Using automated fluorescence detection, a total of 112 alleles was detected with an average of 14 alleles per locus. All microsatellite loci showed very high levels of genetic information content, with expected heterozygosity ranging from 0.814 to 0.895. These microsatellite markers represent a powerful tool to investigate refined questions of mating systems, gene flow, family structure and population dynamics in natural populations of C. pentandra.     

Microsatellite DNA markers for the Stable Fly,Stomoxys calcitrans (Diptera: Muscidae)

Eight polymorphic microsatellite markers have been isolated from a microsatellite‐enriched DNA library from the Stable Fly, Stomoxys calcitrans. These loci exhibited four to 15 alleles per locus and an expected heterozygosity ranging from 0.19 to 0.84 in the three populations studied from La Réunion island (Indian Ocean). They should therefore be valuable for studying genetic diversity and population structure. Cross‐species amplification of these eight loci in the closely allied species Stomoxys niger niger was successful for four of these loci, one of which was monomorphic and one of which strongly departed from Hardy–Weinberg expectations.     

Isolation and characterization of 11 microsatellite markers from Sagittaria latifolia (Alismataceae)

We developed 11 microsatellite loci for Sagittaria latifolia, an aquatic plant common to wetlands of North America. From an (AG)-enriched library, we identified 66 unique microsatellite sequences for which primers could be designed. Twenty-two loci reliably amplified a clear single band of expected size, and 11 loci were scoreable and polymorphic. For these 11 loci, we genotyped a monoecious and a dioecious population, yielding four to 14 alleles per locus. Three loci exhibited significant linkage disequilibrium leaving eight independent variable loci. Eight loci also amplified in four other Sagittaria species. These microsatellite loci will be useful to compare genetic structure among monoecious and dioecious populations of S. latifolia.