Characterization of microsatellite loci in two closely related Lissotriton newt species

We have developed eight di- and tetranucleotide Lissotriton microsatellite markers. Eight loci were polymorphic in the palmate newt Lissotriton helveticus and six were polymorphic in the smooth newt L. vulgaris. Polymorphism detected in 33 and 37 individuals per species ranged from 3 to 15 alleles. These markers are suitable for the investigation of population structure, genetic variation and taxonomic identification in the two focal species, and may also be of use in other Lissotriton–Triturus species.     

Microsatellite markers for the endangered Roanoke logperch, Percina rex (Percidae) and their potential utility for other darter species

The Roanoke logperch (Percina rex Jordan and Evermann), an endangered fish, occurs in only six watersheds in the Roanoke and Chowan river drainages of Virginia, USA. The species’ population genetic structure is poorly known. We developed 16 microsatellite markers that were reliably scorable and polymorphic P. rex. Markers were also screened in seven other darter species of the genus Percina. Most markers exhibited successful amplification and polymorphism in several species. These markers may therefore prove useful for population genetic studies in other darters, a diverse but highly imperiled group.     

Isolation of polymorphic tetranucleotide microsatellite markers for the little greenbul (Andropadus virens)

Thirteen polymorphic microsatellite markers have been developed for the little greenbul, Andropadus virens. The number of alleles range from two to 15 per locus with the observed heterozygosity ranging from 0.15 to 0.92. Eight sets of primers also amplify in closely related species, Andropadus laterostris and Andropadus tephrolaemus. These markers will be useful for analysis of questions concerning population genetic structure and models of speciation.     

Isolation and characterization of novel microsatellite markers for Cymodocea serrulata (Cymodoceaceae), a seagrass distributed widely in the Indo‐Pacific region

Cymodocea serrulata is a tropical seagrass species distributed widely in the Indo‐Pacific region. We developed 16 novel microsatellite (simple sequence repeat) markers for C. serrulata using next‐generation sequencing for use in genetic studies. The applicability of these markers was attested by genotyping of 40 individuals collected from a natural population in the Philippines. Of the 16 loci, 15 showed polymorphism. For the 15 polymorphic markers, the number of alleles per locus ranged from two to seven, and the observed and expected heterozygosities ranged from 0.131–1.000 and 0.124–0.788, respectively. These markers are useful tools for elucidating genetic diversity, connectivity, and structure in this foundational coastal species.     

Microsatellite loci for euglossine bees (Hymenoptera: Apidae)

The Neotropical Euglossini (Hymenoptera: Apidae) are important pollinators of many flowering plants, particularly orchids. Lack of highly polymorphic genetic markers for euglossine species has limited the study of their social organization and inbreeding. We therefore developed microsatellite markers for two species, Eulaema nigrita (11 loci) and Euglossa cordata (nine loci), most of which were highly polymorphic in the source species and in a range of related euglossine bees.     

Microsatellite DNA primers for the endangered vermilion darter,Etheostoma chermocki,and cross‐species amplification in other darters (Percidae: Etheostoma)

The endangered vermilion darter (Etheostoma chermocki) is endemic to the Black Warrior River system in the Mobile Basin in Alabama. Restoration and conservation of this species require an understanding of its population genetic structure, which can be characterized using microsatellite DNA. Nine microsatellite loci were developed; eight loci were polymorphic. Although observed heterozygosity was lower than expected heterozygosity in most polymorphic loci, only one locus showed significant deviation from Hardy–Weinberg equilibrium. These nine markers were tested in an additional 24 species of Etheostoma and appear to have sufficient allelic variation to be useful in studies of population genetic structure.     

Isolation and characterization of nine polymorphic microsatellite loci from the desert locust,Schistocerca gregaria

Because of the scarcity of polymorphic genetic markers, only a few genetic studies on the population structure of the desert locust, Schistocerca gregaria, have been carried out. We isolated and characterized nine polymorphic dinucleotide microsatellite loci. These markers were evaluated using individuals from Niger and Senegal. Seven of these microsatellite markers are also applicable to the nongregarious subspecies Schistocerca gregaria flaviventris. Cross‐species applicability was limited to one of the loci in the sister species S. americana and in the locust Locusta migratoria.     

Development and characterization of EST‐SSR markers for the genus Rhododendron section Brachycalyx (Ericaceae)

Simple sequence repeat (SSR) markers were developed from expressed sequence tags (ESTs) for Rhododendron section Brachycalyx in order to elucidate its evolutionary processes and reproductive ecology. Nineteen polymorphic EST‐SSR markers were developed from EST libraries of R. amagianum and R. hyugaense. Polymorphisms for these markers were assessed using four species of section Brachycalyx. The number of alleles ranged from 1 to 14, and the observed and expected heterozygosity ranged from 0.000 to 0.931 and 0.000 to 0.904, respectively. The EST‐SSR markers developed in this study will be useful for elucidating population genetic structure and breeding systems in section Brachycalyx.     

Isolation of polymorphic microsatellite loci from the European anchovy,Engraulis encrasicolus

The European anchovy (Engraulis encrasicolus L., Engraulidae) is a widely spread fish resource which is overexploited along its area of distribution. A proper knowledge of the population genetic structure of this fish species is crucial to allow a sustainable management of fishery stocks. We developed five polymorphic microsatellite loci (expected heterozygosity per locus ranging from 0.46 to 0.97) for E. encrasicolus. These genetic markers can be applied to define the population genetic structure of European anchovy.     

Characterization and cross-species amplification of microsatellites from the endangered Hawksbill turtle (Eretmochelys imbricate)

Twelve novel polymorphic microsatellites were isolated from the endangered Hawksbill turtle (Eretmochelys imbricate). Eight of 12 markers were used to study genetic diversity of two sea turtle species: E. imbricate and green sea turtle (C. mydas). In E. imbricate, the average allele number of the eight microsatellites was 6.25/locus with a range of 3–13. The average expected and observed heterozygosity was 0.66 and 0.63 respectively. In C. mydas, the average allele number of the eight markers was 11.63/locus. The observed heterozyosity (0.68) was lower than the expected heterozyosity (0.79). Most of 12 microsatellites amplified specific and polymorphic PCR products in other six turtle species. Hence, the developed microsatellites would facilitate studies on genetic diversity and population structure of E. imbricate and other marine turtle species.     

Polymorphic microsatellite markers for the Socotran endemic herb Begonia socotrana

Six polymorphic microsatellite markers have been developed to examine population structure and outcrossing rates in the narrow‐range endemic Begonia socotrana. Only two of the markers amplify products in its recently discovered sister species B. samhaensis. All of the loci amplify in winter‐flowering Begonia hybrids derived from B. socotrana, revealing little polymorphism and demonstrating the narrow genetic base of the material used in their production.     

Isolation and characterization of polymorphic microsatellite loci in the field vole,Microtus agrestis,and their cross‐utility in the common vole,Microtus arvalis

We developed nine polymorphic microsatellite loci for the field vole, Microtus agrestis. The number of alleles ranged from five to 15 and observed heterozygosities ranged from 0.40 to 1.00. We also tested the microsatellite loci for amplification and polymorphism in the congeneric species Microtus arvalis. Five of the nine loci were successfully analysed in this species. The microsatellite markers will be employed in studies of reproductive success and fine‐scale spatial genetic structure.     

Development of nuclear microsatellite markers for the Japanese conifers Tsuga diversifolia and T. sieboldii (Pinaceae)

Nuclear microsatellite markers were developed for the two Tsuga species native to the Japanese Archipelago, Tsuga diversifolia and T. sieboldii, and a population with genetic affinities to T. diversifolia on Ulleung Island, Korea. Tsuga diversifolia and T. sieboldii are widespread dominant trees of temperate and subalpine forests in Japan but to date no genetic markers have been developed for these species. Fifteen polymorphic loci were developed and characterized, of which 14 are reliably amplified in each taxon. Across both species and the Ulleung Island population, the number of alleles per locus ranged from 3 to 26 (average = 13.93) and observed heterozygosity ranged from 0.005 to 0.935 (average = 0.535). In addition, all 15 loci were successfully amplified in a single accession of the Chinese species, T. chinensis. These markers will be useful for investigating the species’ biogeography, range‐wide genetic diversity, conservation genetic issues and potential for hybridisation.     

Development and characterization of microsatellite markers in Eucommia ulmoides Oliver (Eucommiaceae)

Twenty‐three microsatellite markers were developed from an AC‐enriched genomic library of Eucommia ulmoides, an economically important tree species for both herbal medicine and organic chemical industry in China. Nineteen microsatellite loci were found polymorphic by testing 36 individuals from 10 populations, with two to 14 alleles per locus. The expected heterozygosity ranged from 0.054 to 0.874. This set of microsatellite markers has provided a useful tool for the ongoing efforts in studying population genetic structure of E. ulmoides.     

Development of microsatellite markers for Diaphanosoma dubium (Crustacea,Cladocera) and application to seasonal population dynamics

Diaphanosoma, the “tropical Daphnia”, is common and ubiquitous in South China. Like other ctenopods, Diaphanosoma has a reproductive mode similar to Daphnia’s, but its resting eggs are rarely observed and lack an ephippium. With limited dispersal and reduced buffer effect from resting egg banks, Diaphanosoma is expected to have a population genetic structure different from that of temperate Daphnia. To facilitate genetic comparison, we developed microsatellite markers using next-generation sequencing for the most common species in tropical and subtropical East Asia, Diaphanosoma dubium. Thirty-one polymorphic microsatellite markers were obtained, and 29 of them were efficient for the congeneric species D. excisum, D. orghidani, D. mongolianum and D. chankensis. The markers allowed intra- and interspecific genetic analysis, including population structure, hybridization and introgression. We used 11 selected microsatellite markers to analyze spatial and temporal heterogeneity of genetic diversity in four (sub)tropical D. dubium populations from two large reservoirs and two temporary ponds. In contrast to temperate Cladocera, higher genetic diversity in summer rather than in spring suggested weak contribution from resting eggs in spring. Clustering of DAPC and STRUCTURE analyses indicated a clear-cut genetic structure in the four populations. Variation partitioning revealed that water storage and depth were key factors in genetic differentiation. Within large reservoirs, we detected backward (reversing time) gene flow from resting egg banks. We conclude that resting eggs have an effective contribution to the genetic diversity in large water bodies during growing seasons and that large water bodies can host higher genetic diversity in summer due to environmental heterogeneity and high carrying capacity. Spatial and temporal heterogeneity of genetic diversity detected by our microsatellite markers showed the newly developed markers can be applied for further study of populations of D. dubium and other species of Diaphanosoma at a contemporary scale.

     

Application of microsatellite markers developed for arvicoline species in a population genetic study of the root vole <Emphasis Type="Italic">Microtus oeconomus</Emphasis>

Using a root vole Microtus oeconomus (Pallas, 1776) population in NE Poland we applied 31 microsatellite markers previously developed for root voles and closely related species, with the aim to improve the population genetic tools in this species. Here we present 16 polymorphic microsatellite markers grouped into four sets suitable for simultaneous amplification and genetically sex identification in M. oeconomus. The number of alleles per locus in 227 individuals varied from 7 to 26 with a low frequency of null alleles, expected heterozygosity ranged from 0.758 to 0.927, and observed heterozygosity from 0.722 to 0.947. Two loci showed significant deviation from Hardy-Weinberg equilibrium (p<0.05) and all loci showed independent inheritance. We expect these markers to be useful for studies of genetic population structure and kinship of M. oeconomus populations.     

Development of polymorphic simple sequence repeat markers for Pisolithus microcarpus

Six polymorphic simple sequence repeat (SSR) markers were developed for the ectomycorrhizal fungus Pisolithus microcarpus. A polymerase chain reaction (PCR)‐based technique was used in which random amplified polymorphic DNA (RAPD) fingerprints were probed with labelled SSR oligonucleotides by southern hybridization. The number of alleles per locus ranged from two to nine with expected heterozygosity values from 0.33 to 0.76. These loci will be potentially useful for genetic structure and gene flow studies of P. microcarpus populations. Cross‐species amplification with Pisolithus albus isolates at all loci was also observed.     

Development of twelve polymorphic microsatellite loci in polyploid endangered Omphalogramma vincaeflora Franch. (Primulaceae)

A total of twelve polymorphic microsatellite loci were developed from polyploid endangered species, Omphalogramma vincaeflora (Primulaceae). These loci were screened for variability among 45 individuals from three populations in China. The primers amplified loci with allele number ranging from 3 to 9, with an average of 4.25 per locus. Polymorphism information content ranged from 0.23 to 0.86. Nei’s genetic diversity ranged from 0.34 to 0.86. These primers provide an opportunity to use polymorphic DNA markers to study the population genetic structure and its breeding system in this species.     

Development of new polymorphic microsatellite markers for the New World screw‐worm Cochliomyia hominivorax (Diptera: Calliphoridae)

In this report, we describe the development of seven new polymorphic microsatellite markers for Cochliomyia hominivorax, a parasitic insect pest of primary agricultural and veterinary importance throughout the Neotropics. The number of alleles found ranged from 3 to 13 per locus, with the expected heterozygosity ranging from 0.4220 to 0.9045. The across‐taxa amplification of some of these new microsatellite loci was successful in four additional Calliphoridae species. In combination with the 10 polymorphic microsatellite markers previously described, the markers developed here should provide a high resolution for assessing the fine‐scale genetic structure of New World screw‐worms.