Isolation and characterization of microsatellite loci in the southern brown bandicoot (Isoodon obesulus), and their applicability to other marsupial species

The southern brown bandicoot (Isoodon obesulus) was once widely distributed throughout coastal regions of Australia, however, populations have now become fragmented and the number of individuals are declining rapidly. As a result, this species is now classified as endangered in New South Wales and requires management. We have developed eight microsatellite markers to investigate levels of genetic variation and subdivision among these isolated populations. These microsatellite markers show levels of variability ranging from four to eight alleles and observed heterozygosities of 0.353–0.938. These microsatellite markers are also suitable for similar population studies on other related marsupials.     

Genetic Divergence Detected by ISSR Markers and Characterization of Microsatellite Regions in Mytilus Mussels

The wide distribution of microsatellites in mussels of the Mytilus edulis complex (Mytilidae) enables the analysis of inter-simple-sequence repeat (ISSR) markers. The aim of this investigation was to assess genetic differentiation in six sampling localities distributed along the European Atlantic coast to expose the potential of these markers in genetic studies requiring the detection of low polymorphism and as a source of sequences for developing microsatellite markers. We detected low genetic structuring within each member of the Mytilus edulis complex. Nei and Li distances and AMOVA clustered the individuals studied into two groups. On the basis of these results two sampling localities coming from the M. edulis × M. galloprovincialis mosaic hybrid zone in Western Europe were assigned to one species. On the other hand, mussels of a sampling locality in the Baltic Sea were not significantly different from a pure M. edulis locality supporting an extensive introgression of M. edulis in these individuals. Finally, 148 microsatellites were found in the sequences of 51 ISSR markers, and two polymorphic microsatellite markers were developed.     

Identification and characterization of microsatellites for striped bass from repeat-enriched libraries

Striped bass (Morone saxatilis) is economically important in the US due to its value as an aquaculture species and in supporting commercial and recreational fisheries, especially those off the Atlantic coast and in the Gulf of Mexico. Modern strategies for managing fishery populations and aquaculture broodstocks employ the use of molecular genetic markers to identify individuals, assign parentage, and characterize population genetic structure and levels of inbreeding and migration. As part of a collaborative effort to utilize molecular genetic technologies in striped bass breeding programs we generated microsatellite markers for use in population genetic studies, broodstock selection and management strategies, and the construction of a genetic map. We developed 345 new microsatellite markers for striped bass, a subset (n=71) of which was characterized by genotyping samples from two striped bass broodstock populations to evaluate marker polymorphism, percent heterozygosity, Hardy–Weinberg equilibrium (HWE), linkage disequilibrium (LD) and utility for population genetic studies.     

Microsatellite markers for the large blue butterflies Maculinea nausithous and Maculinea alcon (Lepidoptera: Lycaenidae) and their amplification in other Maculinea species

We developed microsatellite markers for Maculinea nausithous and Maculinea alcon, two of five species of endangered large blue butterflies found in Europe. Two separate microsatellite libraries were constructed. Eleven markers were developed for M. nausithous and one for M. alcon. The primers were tested on both species as well as on the three other European Maculinea species. The number of alleles per locus ranged from two to 14. These markers will be useful tools for population genetic studies of Maculinea species.     

Isolation and characterization of polymorphic microsatellite markers in <Emphasis Type="Italic">Cupressus </Emphasis><Emphasis Type="Italic">chenggiana</Emphasis> S. Y. Hu (Cupressaceae)

Cupressus chenggiana S. Y. Hu (Cupressaceae) is an endemic and endangered conifer species in southwest China. In order to study the population genetics and design the effective conservation methods, we aimed to develop microsatellite primers for this species in the present study. We developed eight new microsatellite loci for this species through biotin capture method. Polymorphism of each locus was further assessed in 18 individuals from three geographically distant populations. The number of alleles per locus ranged from 6 to 11 with an average of 8.13. The observed and expected heterozygosities ranged from 0.219 to 0.296 and from 0.374 to 0.470, with averages of 0.254 and 0.417, respectively. We further found that three of nine microsatellite loci developed previously for another congeneric species showed polymorphic banding patters. We performed primer-crossing tests of these loci in the other two congeneric species which are closely related to C. chenggiana (C. gigantea and C. duclouxiana). These microsatellite markers would be effective for analyzing genetic diversity and population genetic structure of this species and its morphological differentiation with the close relatives.     

Fine‐scale Population Genetic Structure of Two Dioecious Indian Keystone Species,Ficus hispida and Ficus exasperata (Moraceae)

Although Ficus (Moraceae) is a keystone plant genus in the tropics, providing resources to many frugivorous vertebrates, its population genetic structure, which is an important determinant of its long‐term survival, has rarely been investigated. We examined the population genetic structure of two dioecious fig species (Ficus hispida and Ficus exasperata) in the Indian Western Ghats using co‐dominant nuclear microsatellite markers. We found high levels of microsatellite genetic diversity in both species. The regression slopes between genetic relationship coefficients (f_ij) and spatial distances were significantly negative in both species indicating that, on average, individuals in close spatial proximity were more likely to be related than individuals further apart. Mean parent–offspring distance (σ) calculated using these slopes was about 200 m in both species. This should be contrasted with the very long pollen dispersal distances documented for monoecious Ficus species. Nevertheless, overall population genetic diversity remained large suggesting immigrant gene flow. Further studies will be required to analyze broader scale patterns.     

Isolation and characterization of microsatellite loci of Lycopodium fordii Bak. (Lycopodiaceae, Pteridophyta)

Lycopodium fordii Bak. (Lycopodiaceae, Pteridophyta) is a gardening plant with a native, fragmentary distribution in Taiwan. In this study, we described the development of eleven microsatellite loci in L. fordii for genetic studies. These new markers were tested in 16 individuals of three populations. The number of alleles ranged from 1 to 5 and the expected heterozygosity from 0.41746 to 0.72222. Four of the nine polymorphic loci were significantly deviated from Hardy-Weinberg expectations due to the heterozygote deficiency. The microsatellite markers have also been proved as informative genetic markers for other 15 Lycopodium species.     

Microsatellite DNA loci from the typical halophyte <Emphasis Type="Italic">Thellungiella salsuginea</Emphasis> (Brassicaceae)

Thellungiella salsuginea (Brassiaceae) is a typical halophyte which can tolerate extreme cold, drought, and salinity. In order to understand the adaptive evolution of this species in the arid habitats, it is important to know its genetic structure. In this study, 17 polymorphic microsatellite loci were isolated and characterized from an enrichment genomic library of this species. We further assessed the polymorphisms of each locus in 18 individuals from nine geographically distant populations. The number of alleles per locus ranged from six to fourteen. The observed and expected heterozygosity ranged from 0.17 to 0.28 and 0.32 to 0.45, respectively. These markers have been crossly checked in another congeneric species, T. halophila. These microsatellite markers will be useful for investigating population genetics and adaptive evolution of this species and morphological divergence between and it and the closely related species.     

Development of 12 novel microsatellite loci in a traditional Chinese medicinal plant, Epimedium brevicornum and cross-amplification in other related taxa

A total of 12 polymorphic microsatellite loci were developed and characterized for a Chinese medicinal plant, Epimedium brevicornum (Berberidaceae). A genomic DNA enrichment protocol was used to isolate microsatellite loci and polymorphism was explored using 38 individuals from one natural population. The observed number of alleles ranged from 2–14. The ranges of observed and expected heterozygosity were 0.00–0.83 and 0.15–0.88, respectively. In addition, successful cross-species amplification of this set of microsatellite markers in other four medicinal Epimedium species suggested that they would provide a useful tool for the genetic and conservation studies of Epimedium species.     

Microsatellite loci in Bactris gasipaes (Arecaceae): their isolation and characterization

We constructed a microsatellite‐enriched genomic library for Bactris gasipaes, an economically important, domesticated palm. We developed 18 polymorphic microsatellite markers, and found an average of seven alleles per locus in a sample of 14 individuals selected from a germplasm bank. Cross‐species amplification was evaluated in six other Bactris species. The loci detected will permit population studies and germplasm characterization, and can be used for genetic analyses in related species.     

High variability and disomic segregation of microsatellites in the octoploid Fragaria virginiana Mill. (Rosaceae)

The objectives of the present study were to develop microsatellite markers for the wild strawberry, Fragaria virginiana, to evaluate segregation patterns of microsatellite alleles in this octoploid species, and assess genetic variability at microsatellite loci in a wild population. A genomic library was screened for microsatellite repeats and several PCR primers were designed and tested. We also tested the use of heterologous primers and found that F. virginiana primers amplified products in cultivated strawberry, Fragaria × ananassa Duch. and Fragaria chiloensis. Similarly, microsatellite loci developed from cultivated strawberry also successfully amplified F. virginiana loci. We investigated four microsatellite loci in detail, three developed from F. virginiana and one from cultivated strawberry. A survey of 100 individuals from a population of F. virginiana in Pennsylvania demonstrated high heterozygosities (H_e or gene diversity ranged from 0.80 to 0.88 per locus) and allelic diversity (12–17 alleles per locus), but individual plants had no more than two alleles per locus. Segregation patterns in parents and progeny of two controlled crosses at these four loci were consistent with disomic Mendelian inheritance. Together these findings suggest that the genome of F. virginiana is "highly diploidized" and at least a subset of microsatellite loci can be treated as codominant, diploid markers. Significant heterozygote deficiencies were found at three of the four loci for hermaphroditic individuals but for only one locus among females in this gynodioecious species.Communicated by J. Dvorak     

Isolation and characterization of microsatellite loci in the endangered freshwater fish <Emphasis Type="Italic">Pararasbora moltrechti</Emphasis> (Cyprinidae) using PCR-based isolation of microsatellite arrays (PIMA)

Pararasbora moltrechti (Cyprinidae) is an endangered freshwater fish with a scattered distribution in the central Taiwan. In order to undertake a conservation program for this species in Taiwan, it is essential to evaluate its genetic diversity and population structure. For this purpose, we described the development of eight microsatellite loci in P. moltrechti for genetic studies. These new molecular markers were tested in 36 individuals of the rare species. The number of alleles per locus ranged from 8 to 14. As the expected heterozygosity varied from 0.770 to 0.932, all microsatellite loci, however, were significantly deviated from Hardy–Weinberg expectations due to the heterozygote deficiency. Hung-Du Lin and Teh-Wang Lee contributed equally.     

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 of single sequence repeat markers for the ant Aphaenogaster senilis and cross-species amplification in A. iberica, A . gibbosa, A. subterranea and Messor maroccanus

Eight polymorphic microsatellite loci were isolated and characterized for Aphaenogaster senilis, a common ant species distributed in the Western Mediterranean. Characterization of 15 individuals form southern Spain showed moderate to high allelic diversity ranging from 2 to 9 alleles per locus. Cross-species tests on 10 individuals of A. iberica, A. gibbosa, A. subterranea and Messor maroccanus revealed successful amplification for most loci. This set of markers can be useful for population genetic studies and might even prove useful in other phylogenetically close species of the subfamily Myrmicinae.     

Ten polymorphic microsatellite markers for Scaphoideus titanus,the vector of flavescence dorée phytoplasma

The leafhopper Scaphoideus titanus is a vector of flavescence dorée phytoplasma, the causal agent of the most important grapevine yellow disease in European vineyards. Ten polymorphic microsatellite loci were developed from a genomic library enriched for AC and AG repeats. Levels of polymorphism were evaluated in 106 individuals from S. titanus European and American populations. An average of 16 alleles per locus was detected and the observed heterozygosity ranged from 0.141 to 0.813. Cross‐species amplification was successful in four other Cicadellidae species. These 10 microsatellites are valuable markers for population genetic and phylogeographical studies of S. titanus.     

Population genetic structure and distribution of introduced American mink (<Emphasis Type="Italic">Mustela vison</Emphasis>) in Spain,based on microsatellite variation

The population genetic structure of an invasive species in Spain, the American mink (Mustela vison), was investigated using microsatellite DNA markers. This semi-aquatic carnivore, originating from North America, was imported into Europe for fur farming since the beginning of the 20th century. Due to massive escapes, farm damages, deliberate releases and/or accidents, feral mink populations were established in the aquatic ecosystems of many European countries, including Spain. We genotyped 155 American mink originating from the Spanish regions Basque Country, Catalonia, Castilla-Leon, Aragon, Valencia and Galicia using 10 polymorphic microsatellite loci to highlight population genetic structure, distribution and dispersal. M. vison populations in Spain appear differentiated and not yet connected by gene flow. Bayesian clustering analyses and spatial analyses of molecular variance detected four inferred clusters, overall coinciding with the sampled geographical localities. Preliminary testing shows moderate to large estimated effective population sizes. Molecular analyses result useful to provide baseline data for further research on the evolution of invasive mink populations, as well as support local management strategies and indirectly benefit the conservation of threatened species in Spain, such as the endangered European mink (Mustela lutreola), and the polecat (Mustela putorius), which share the habitat with the American mink. This paper is dedicated to the memory of Xavier Domingo-Roura.     

Cross-species amplification of microsatellite markers in the invasive spiny-cheek crayfish (Orconectes limosus): Assessment and application

The North American spiny-cheek crayfish,Orconectes limosus (Cambaridae), endangered in its native range, is a widespread invasive species in European waters and conservationally important carrier of crayfish plague. However, its population structure is poorly known, and no informative genetic markers for the species are available. We tested cross-species transfer of microsatellite loci to spiny-cheek crayfish from 5 other crayfish species. Variability of 10 successfully amplifying loci derived from 4 species was then tested in 60 individuals ofO. limosus originating from 3 natural populations: the river Danube at Bogyiszló in Hungary, a pond in Stary Klíčov, and the brook Černovicky, both in the Czech Republic. The allele number within the populations ranged from 4 to 10 alleles per locus, while heterozygosity levels varied from 0.650 to 0.900 forHo and from 0.660 to 0.890 forHe. No linkage disequilibrium and no null alleles were detected. The selected markers are useful for assessing population structure, intraspecific variation, and paternity studies in spiny-cheek crayfish.     

Isolation and characterization of eight polymorphic microsatellite loci for the critically endangered Arenaria nevadensis (Caryophyllaceae)

We report on the isolation and characterization of eight microsatellite markers from enriched libraries for Arenaria nevadensis, one of the most critically endangered plant species in the Iberian Peninsula. These are the first microsatellite loci reported for Arenaria species. The number of alleles ranged from two to eight, and the expected heterozygosity from 0.067 to 0.873. These markers will be useful for characterizing the genetic diversity in A. nevadensis and understanding its population structure, and will provide important genetic data for the conservation and recovery of this species.     

Isolation and characterization of twelve novel microsatellite loci in the ark shell <Emphasis Type="Italic">Scapharca broughtonii</Emphasis>

Scapharca broughtonii is an over-exploited bivalve in China. In order to promote a conservation program for this species, it is necessary to evaluate its genetic diversity and population genetics. For this purpose, we isolated twelve novel polymorphic microsatellite markers and examined their allelic variation using 40 wild individuals collected from one locality along the Chinese coast. The number of alleles ranged from 2 to 22 per locus with the expected heterozygosities ranging from 0.444 to 0.944. These markers will be useful for the assessment of genetic variation for this species.     

Di‐ and tetranucleotide microsatellite markers for the Alpine newt (Triturus alpestris): characterization and cross‐priming in five congeners

We developed a set of di‐ and tetranucleotide microsatellite markers for the Alpine newt, Triturus alpestris. Polymorphism as detected in 39 individuals ranged from 3 to 32 alleles at a locus. Cross‐priming with samples of five other Triturus species showed extremely poor levels of cross‐species utility. Still, these markers are suitable for studies of inter‐ and intrapopulation genetic diversity in the focal species.