Isolation of 11 polymorphic tri- and tetranucleotide microsatellite loci in a North American sedge (Carex scoparia: Cyperaceae) and cross-species amplification in three additional Carex species

We report on the isolation and evaluation of 11 microsatellites from a widespread eastern North American wetland sedge, Carex scoparia. Loci exhibit 3-9 alleles over five populations and significant F(IS) (0.204-0.717) in most populations. All primers cross-amplify in at least two other species, and 10 cross-amplify in the more distantly related C. stipata. These markers will be used to examine population genetics and patterns of chromosomal diversification in this ecologically important sedge species and its relatives.     

Isolation and characterization of polymorphic microsatellite loci from Brandt's voles (Lasiopodomys brandtii)

Ten polymorphic microsatellite loci from Lasiopodomys brandtii have been isolated and characterized. Two to 11 alleles per locus were detected from 52 Brandt's voles samples collected from a single population. Expected heterozygosities ranged from 0.406 to 0.840. For the majority of loci observed heterozygosities were similar to or greater than the expected heterozygosity. One locus pair appeared to be in linkage disequilibrium. The microsatellite markers will enable the studies of genetic diversity, population structure and relatedness in this species, and perhaps in closely related species of vole.     

Isolation and characterization of microsatellite loci in the sand fly Phlebotomus papatasi (Diptera: Psychodidae)

Phlebotomus papatasi is a proven vector of Leishmania major which is one of the causative agents of cutaneous leishmaniasis in the Old World. Although it has a wide geographical range, its population structure is not yet well understood. In an effort to better understand the population dynamics of this vector, we developed a panel of di‐ and trinucleotide microsatellite markers, using a magnetic bead hybridization enrichment protocol. These microsatellite loci showed three to seven alleles with an expected heterozygosity range between 0.702 and 0.876. The level of polymorphisms found in this study suggests that these microsatellite loci can be used for population analysis of P. papatasi.     

Isolation and characterization of 11 microsatellite loci from Carex macrocephala (Cyperaceae)

Carex macrocephala (Cyperaceae) is a species of great conservation concern along the northwest coast of North America. Using a biotinylated-streptavidin bead protocol, we successfully isolated and characterized 11 microsatellite loci from a C. macrocephala genomic library. Although these loci are polymorphic, the scored populations exhibit a significant deficiency in heterozygosity. Carex macrocephala is a self-pollinating rhizomatously spreading sedge, consequently this may contribute to the observed patterns.     

Isolation and characterization of 18 new polymorphic microsatellite loci for the swordfish, Xiphias gladius

Eighteen microsatellite loci (13 di- and 5 tri-repeats) were isolated from swordfish and characterized in two populations from the Atlantic Ocean and Mediterranean Sea. The number of alleles per locus ranged from two to 29 and the observed heterozygosity from 0.302 to 0.953. All but one locus conformed to Hardy-Weinberg expectations and there was no evidence for linkage disequilibrium between loci.     

Isolation and characterization of microsatellite loci in the finless porpoise (Neophocaena phocaenoides)

Eight dinucleotide microsatellite loci were isolated from the finless porpoise (Neophocaena phocaenoides). Analysis of 30 individuals showed the number of alleles ranged from four to 21 with observed heterozygosity ranging from 0.300 to 0.833, and expected heterozygosity ranging from 0.437 to 0.932. Cross‐species amplification was tested in four other cetacean species. These microsatellite markers would be valuable tools for population genetic studies of finless porpoises and other cetacean species.     

Isolation, characterization and cross-amplification of polymorphic microsatellite loci in Laelia speciosa (Orchidaceae)

Laelia speciosa is an endangered epiphytic orchid endemic to central Mexico. Here, we report on the development of 14 perfect and imperfect microsatellite repeat loci for this species. Numbers of alleles ranged from two to 16 and levels of observed heterozygosities among the 14 loci ranged from 0.28 to 1.00 across two widely divergent populations. All loci were also tested for cross-amplification in four other Laelia species and other selected genera of the subtribe Laeliinae.     

Isolation and characterization of polymorphic tetranucleotide microsatellite loci in the Fire salamander Salamandra salamandra (Amphibia: Caudata)

Ten tetranucleotide and one dinucleotide polymorphic microsatellite loci were cloned and characterized for the Fire salamander (Salamandra salamandra) from 34 populations in Germany. A high genetic diversity (5–22 alleles per locus) and heterozygosity (40.6–95.2%) were observed for these markers. Chord distances for population comparisons of the western evolutionary recolonization lineage in the area near Cologne ranged from 0.139 to 0.366, whereas population comparisons between the western and eastern lineage ranged from 0.541 to 0.670. When compared with classical isolation methods, a sufficient number of polymorphic microsatellites can be obtained for the Fire salamander only from specially enriched sublibraries.     

Isolation and characterization of polymorphic microsatellite loci in the raccoon (Procyon lotor)

We report the isolation and characterization of 17 polymorphic microsatellite loci in the North American raccoon (Procyon lotor). These loci exhibit high levels of allelic diversity, with between four and 13 alleles per locus, and heterozygosity, with observed values of 0.500-1.000 in a sample of 20 individuals. All genotypes conformed to Hardy-Weinberg expectations and there were no instances of linkage disequilibrium detected.     

Isolation and characterization of microsatellite loci from Corydalis ambigua (Papaveraceae)

Primers for seven unlinked and highly polymorphic microsatellite loci were developed for Corydalis ambigua to investigate its mating system and population genetics. This species can be used to explore the impact of an alien bumblebee on plant reproduction. Genetic diversity and other population genetic parameters were estimated in two populations with and without the alien bumblebee. The number of alleles per locus ranged from 4 to 20, and observed heterozygosities ranged from 0.355 to 0.969. These markers can be applied to study mating systems and population genetics in C. ambigua.     

Isolation, characterization, and cross-amplification of polymorphic microsatellite loci in Guaiacum coulteri (Zygophyllaceae)

Guaiacum coulteri is a dry forest hardwood species of conservation concern endemic to the Pacific coast of Mexico. Fifteen microsatellite markers were developed which show high levels of polymorphism across two populations with the number of alleles ranging from four to 21. Most loci additionally exhibited consistent multiple banding patterns, indicating the likely polyploidy of this species. All loci were tested for cross-amplification with most found to amplify well across the genus Guaiacum, although amplification in other related genera of the Zygophyllaceae was limited.     

Isolation and characterization of polymorphic microsatellite loci in the Chagas’ disease vector Triatoma infestans (Hemiptera: Reduviidae)

Microsatellites were identified and characterized from Triatoma infestans, the principal vector of Chagas’ disease in the Southern Cone of South American countries. Ninety‐three microsatellite loci were isolated from partial genomic libraries, of which 30 were amplified and 10 were selected for genotyping. The degree of intrapopulation variation in these loci was determined using 34 specimens from the locality of Chancaní (Córdoba, Argentina). The number of alleles per locus ranged from five to 19 and the expected heterozygosity ranged from 0.608 to 0.941. The variability of these microsatellite markers provides a valuable molecular tool for population genetic studies in T. infestans.     

Isolation and characterization of polymorphic microsatellite loci in the gudgeon,Gobio gobio (Cyprinidae)

A total of seven polymorphic microsatellite loci from Gobio gobio were isolated and characterized. A preliminary population survey of 82 specimens from four populations, located in a downstream pollution gradient of cadmium and zinc, demonstrated the usefulness of these primers both in population genetic studies in general, as well as in evaluating the effects of anthropogenic pollution on genetic structure. Overall locus polymorphism ranged from two to 13 alleles. Observed heterozygosity per locus ranged from 0.39 to 0.73.     

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 polymorphic microsatellite loci in nurse shark (Ginglymostoma cirratum)

We report on the development of nine polymorphic microsatellite loci in nurse shark (Ginglymostoma cirratum) using a combination of enriched and unenriched subgenomic libraries. Based on the small percentage of positive clones in the unenriched library (0.4%) it appears that microsatellites are very scarce in nurse shark genomes. Numbers of alleles at polymorphic loci ranged from two to 15; observed heterozygosity ranged from 0.17 to 0.90. We expect these loci to be useful for studies of breeding structure and paternity.     

Isolation and characterization of microsatellite loci in the black rat snake (Elaphe obsoleta)

We obtained molecular markers useful for population level studies of the black rat snake (Elaphe obsoleta) by screening genomic DNA libraries enriched for dinucleotide, tetranucleotide, and pentanucleotide microsatellite repeats. Following sequencing of the positive clones, 11 pairs of primers were designed for polymorphic loci and their variability assessed in > 350 individuals from four populations in North America. The loci had between 9 and 40 alleles and observed heterozygosities ranged from 0.071 to 0.87. Some of these pairs of primers also successfully amplified DNA from two other snake species.     

Isolation and characterization of microsatellite loci in the flat‐headed bat (Tylonycteris pachypus)

Microsatellite loci were developed in the flat‐headed bat (Tylonycteris pachypus) from genomic DNA using an enriched library method. Nine loci were tested on 48 individuals sampled from Guangxi Province, China. The mean number of observed alleles per locus was 6.4 (range 4–12). Observed and expected heterozygosity values ranged from 0.24 to 0.83 and from 0.30 to 0.89, respectively. One locus revealed significant departure from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was detected between loci pairs. These markers will be used to examine genetic structure and parentage analysis in this species.     

Isolation and characterization of polymorphic microsatellite loci from Wilsonia backhousei (Convolvulaceae)

Wilsonia backhousei is a clonal saltmarsh plant restricted to the southern latitudes of Australasia and threatened in New South Wales. We have identified eight informative microsatellite loci in the species from (AG)_n‐ and (AC)_n‐enriched libraries. In 48 samples from two populations we detected an average of five alleles per locus (range 2–8, average H_E = 0.45), of which 72% were unique to one population or the other. Six of the eight loci were also amplifiable in Wilsonia rotundifolia under the same reaction conditions. The markers will be excellent tools for use in the management and conservation of both species.     

Twenty polymorphic microsatellite markers in the Asiatic lion (Panthera leo persica)

The Asiatic lion (Panthera leo persica) is driven to a single habitat in Gir forests in India for its survival. In order to devise adequate conservation and management strategies for this critically endangered species, it is important to characterize its genetic diversity and understand its population structure. Here we report twenty microsatellite loci, in addition to seven reported earlier, from the genome of a pure Asiatic lion. The microsatellite loci described here will provide potentially useful markers for the assessment of genetic variability in the only existing wild population of the Asiatic lions and other big cat species.     

Isolation and characterization of polymorphic microsatellite loci from Octodon degus

Quantifying genetic kinship and parentage is critical to understanding the adaptive consequences of sociality. To measure fitness in a species with variable group structure, we isolated 14 microsatellite loci from Octodon degus, a semi-fossorial rodent endemic to Chile. The number of alleles per locus ranged from four to 14. Thirteen loci were in Hardy-Weinberg proportions, with values of observed heterozygosity ranging from 0.550 to 0.950. These markers provide the basis for future studies of the direct fitness consequences of sociality in O. degus.