Isolation and characterization of microsatellite loci in Pitcairnia albiflos (Bromeliaceae), an endemic bromeliad from the Atlantic Rainforest, and cross-amplification in other species

Eight microsatellite markers were isolated from Pitcairnia albiflos, an endangered endemic bromeliad species restricted to 'inselberg' rock outcrops in the state of Rio de Janeiro, Brazil. The number of alleles observed for each locus ranged from two to 12. Average observed and expected heterozygosities were 0.408 and 0.663, respectively. The cross-amplification test in 16 taxa suggests that the markers will be useful in numerous related bromeliad species. The loci will be used to study genetic structure and reproductive biology in fragmented inselberg populations and the origin and maintenance of barriers to gene flow between sympatric Pitcairnia species.     

Isolation and characterization of microsatellite loci in Pseudoplatystoma corruscans (Siluriformes: Pimelodidae) and cross‐species amplification

A total of five polymorphic microsatellites loci from Pseudoplatystoma corruscans were isolated and characterized. A population survey involving 43 specimens resolved a large number of alleles (range seven to eight among loci) and high observed heterozygosity (0.500–0.615), indicating its usefulness in population genetics studies. Cross‐species amplification was successful in four other Pimelodidae species.     

Characterization of microsatellite loci in Humboldt penguin (Spheniscus humboldti) and cross‐amplification in other penguin species

The Humboldt penguin (Spheniscus humboldti) was once very common throughout its range along the coast of Peru and Chile. Today, listed as endangered, it is crucial to gain an understanding of gene flow and levels of genetic variation between breeding colonies to protect this species effectively. We developed seven microsatellite primers to investigate gene flow and population structure among four colonies. Locus‐specific allelic diversity ranges from five to 11 alleles and observed heterozygosity ranges from 0.50 to 0.88. These markers cross‐amplify in eight penguin species over five genera.     

Characterization and PCR multiplexing of polymorphic microsatellite loci in cashew (Anacardium occidentale L.) and their cross‐species utilization

Cashew (Anacardium occidentale L.) is the most economically important tropical nut crop in the world, and yet there are no sequence tagged site (STS) markers available for its study. Here we use an automated, high‐throughput system to isolate cashew microsatellites from a non‐enriched genomic library blotted onto membranes at high density for screening. Sixty‐five sequences contained a microsatellite array, of which 21 proved polymorphic among a closely related seed garden population of 49 genotypes. Twelve markers were suitable for multiplex analysis. Of these, 10 amplified in all three related tropical tree species tested: Anacardium microcarpum, Anacardium pumilum and Anacardium nanum.     

Genetic relationships and variation in reproductive strategies in four closely related bromeliads adapted to neotropical 'inselbergs': Alcantarea glaziouana, A. regina, A. geniculata and A. imperialis (Bromeliaceae)

Background and Aims: Bromeliads (Bromeliaceae) adapted to rock outcrops or ‘inselbergs’in neotropical rain forests have been identified as suitableplant models for studying population divergence and speciationduring continental plant radiations. Little is known about geneticrelationships and variation in reproductive strategies withinand among inselberg-adapted species, yet knowledge of theseparameters is important for understanding divergence processesand for conservation planning. Methods: Nuclear microsatellites were used to assess the role of clonalreproduction, estimate genetic diversity and explore geneticrelationships and variation in reproductive strategies for atotal of 15 populations of four closely related Alcantarea inselbergspecies in south-eastern Brazil: A. glaziouana, A. regina, A.geniculata and A. imperialis. Key Results: Clonal propagation is frequent in coastal populations of A.glaziouana and A. regina, but absent in the high-altitude speciesA. geniculata and A. imperialis. Considerable variation in clonaldiversity, gene diversity (H_e), allelic richness, and Wright'sinbreeding coefficient (F_IS) exists within and between speciesof Alcantarea. A Bayesian analysis of coastal inselberg speciesindicated pronounced genetic structure. A neighbor-joining analysisgrouped populations of each species together with moderate bootstrapsupport, except for the high altitude species A. imperialis. Conclusions: The coastal inselberg species A. glaziouana and A. regina tendto propagate asexually via vegetative clonal growth, and bothreproductive strategies and breeding systems vary greatly betweenpopulations and species of Alcantarea. The microsatellite dataindicate a history of hybridization and reticulation involvingthe high-altitude species A. geniculata and A. imperialis inareas of co-occurrence. The results highlight the need to understandsimilarities and differences in reproductive strategies bothwithin and between related species for conservation planningand as a basis for understanding evolutionary processes in tropicalradiations.     

New polymorphic microsatellite loci,cross‐species amplification and PCR multiplexing in the black aphid,Aphis fabae Scopoli

Aphis fabae includes four morphological cryptic subspecies, which are mostly identified by their partially distinct secondary host range. To determine the extent of gene flow and isolation between these four taxa, we isolated and characterized 12 microsatellite loci from Aphis fabae fabae and tested cross‐species amplification of eight loci from the closely related species Aphis gossypii. Using eight previously described microsatellite loci, we have developed the polymerase chain reaction (PCR) multiplexing of 24 loci, which were separated in tree sets and five PCRs. These sets of microsatellite loci provide high throughput capacity for large‐scale population genetic studies at a minimum cost.     

Ten polymorphic autosomal microsatellite loci for the Eider duck Somateria mollissima and their cross‐species applicability among waterfowl species (Anatidae)

We describe the isolation and characterization of the first microsatellite loci specifically developed for the Common Eider duck, Somateria mollissima. Our 10 loci show Mendelian inheritance and no linkage disequilibrium between any pair of loci. In the Eider duck, we observed between two and 16 alleles per locus, an expected heterozygosity between 0.31 and 0.97, and an observed heterozygosity between 0.14 and 1.00. Most primers also yield reproducible results in several other anatid species. These loci comprise a set of autosomal molecular markers for various applications, from moderately polymorphic loci suitable for population studies to highly polymorphic loci for pedigree analysis in waterfowl.     

Characterization and cross‐species amplification of microsatellite loci in a Cyprinodon species flock

In this study, two new microsatellite loci from a library of Cyprinodon beltrani from Laguna Chichancanab, Mexico, were characterized. Additionally, cross‐species amplification with primer pairs developed for other Cyprinodon species was performed. The 11 markers show moderate to high levels of polymorphism (two to 33 alleles) in six species of the Cyprinodon flock from Laguna Chichancanab and in their sister species Cyprinodon artifrons. These loci were characterized for population genetic study to detect gene flow between the different endemic pupfish species.     

Isolation,characterization and cross‐species amplification of microsatellite DNA loci in the tropical American yam Dioscorea trifida

We developed microsatellite markers in American yam (Dioscorea trifida). A microsatellite sequence‐enriched genomic library was screened, and after sequencing, primers were designed for 20 microsatellites. Among these, eight primer pairs yielded amplification products that were both interpretable and polymorphic in 24 yam cultivars. The number of alleles per locus ranged from two to 13 and the overall expected heterozygosity was around 0.5. Six of the eight Dioscorea trifida microsatellite loci gave amplification products in other Dioscorea species.     

Isolation and cross‐species amplification of microsatellite loci from the fucoid seaweeds Fucus vesiculosus,F. serratus and Ascophyllum nodosum (Heterokontophyta,Fucaceae)

The Fucaceae is a family of brown seaweeds that dominate and frequently co‐occur on North Atlantic rocky shores. We developed nine polymorphic microsatellite markers for the fucoid seaweeds Fucus vesiculosus, F. serratus and Ascophyllum nodosum using a combined, enriched library. Six of these loci were polymorphic in at least two species, showing from two to eight alleles with heterozygosities ranging from 0.41 to 0.85. Loci were also tested on F. spiralis, revealing five polymorphic microsatellite loci in this species.     

New polymorphic microsatellite loci for different camel species

New microsatellite loci were screened and sequenced from the genomic DNA of male Camelus bactrianus. Among 32 loci, 23 were amplified in bactrian and dromedary species, 19 in llama and 20 in alpaca. The different species had similar fragment lengths per locus, with more striking similarities between bactrian and dromedary and between llama and alpaca, respectively. Seven loci had more than 10 alleles each, nine were monomorphic in all species, and one was monomorphic in Old World and polymorphic in New World camels. The results show that the informative microsatellite loci can be widely applied to several species.     

Development and cross‐species amplification of 18 microsatellite markers in the Sumatran tiger (Panthera tigris sumatrae)

Eighteen polymorphic microsatellite loci from the highly endangered Sumatran tiger (Panthera tigris sumatrae) were isolated and characterized. Upon polymerase chain reaction amplification, 16 of these markers produced a single, sharp band in all three tiger and 10 non‐tiger felid species examined. Of the two remaining loci, 6HDZ057 and 6HDZ635 failed to amplify genomic DNA from puma (Felis concolor) and cheetah (Acinonyx jubatus), respectively. The amplification of these markers across four genera is an indication of their usefulness for population genetics studies and conservation work in a wide range of felid species.     

Ten new microsatellite loci for the yellowhammer (Emberiza citrinella) and their cross‐species applicability among related taxa

We describe isolation and characterization of the first microsatellite loci specifically developed for a very common European passerine bird, the yellowhammer Emberiza citrinella. Nine out of our 10 loci are polymorphic within the species E. citrinella. Number of alleles ranged from two to 21 per locus and observed heterozygosity between 0.20 and 0.91. Four primer pairs also yielded reproducible results in other species of Emberizidae. These loci comprise a set of molecular markers for various applications, from moderately polymorphic loci suitable for population studies to highly polymorphic loci for pedigree analysis in Emberizidae.     

Isolation of microsatellite loci in green abalone (Haliotis fulgens) and cross‐species amplification in two other North American red (Haliotis rufescens) and pink (Haliotis corrugata) abalones

Microsatellite loci were isolated in Haliotis fulgens using a (CT)_n enriched‐genomic library. From 33 sequenced clones, 21 microsatellites regions were identified, 15 with the expected (CT)_n. Eight microsatellite loci were amplified, six of which were polymorphic with a range of three to 20 alleles, and five cross‐amplified in two other species (Haliotis rufescens and Haliotis corrugata). These microsatellites will be useful as population genetic markers in the three species.     

Isolation and characterization of polymorphic microsatellite loci from an EST library of turbot (Scophthalmus maximus) and cross‐species amplification

In the present study, we report 12 polymorphic microsatellite loci developed from a cDNA library from the turbot, Scophthalmus maximus. Observed and expected heterozygosities varied from 0.20 to 1.00 and from 0.18 to 0.78, respectively. No significant linkage disequilibrium between pairs of loci was found, but two loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction. Cross‐species amplifications of these microsatellites in five additional fish species revealed between five and 11 positive amplifications and between zero and four polymorphic loci per species.     

Characterization of microsatellite loci in silver carp (Hypophthalmichthys molitrix), and cross‐amplification in other cyprinid species

Captive populations of silver carp (Hypophthalmichthys molitrix), a major aquaculture species in Asia, would undoubtedly benefit from genetic monitoring and improvement programs. We report the isolation and preliminary characterization of 16 microsatellite loci derived from both conventional and microsatellite‐enriched libraries. Inheritance studies confirmed the allelic nature of observed polymorphisms at all loci, while identifying null alleles at two loci. These loci, having varying degrees of polymorphism, should provide useful markers for applied genetic studies. A high degree of cross‐amplification among 10 other cyprinid species suggests that these loci may have more widespread utility.     

Identification of microsatellite loci from Epimedium koreanum and cross‐species amplification in four species of Epimedium (Berberidaceae)

Nineteen polymorphic microsatellite markers were isolated and characterized from a trinucleotide enriched partial genomic library of Epimedium koreanum. The average allele number of these microsatellites was 5.9 per locus, ranging from two to 11. The observed heterozygosity (H_O) and expected heterozygosity (H_E) at the population level were 0.00–0.90 and 0.12–0.90, respectively. In addition, the results of cross‐species amplification of this set of microsatellite markers in four closely related Epimedium species, E. brevicornum, E. sagittatum, E. pubescens and E. wushanense, revealed that these microsatellite markers were useful for population genetic structure evaluation and genotype analysis of major Epimedium species that have been used as traditional Chinese medicines.     

New microsatellite loci for Carcharhinid sharks (Carcharhinus tilstoni and C. sorrah) and their cross‐amplification in other shark species

Twelve microsatellite DNA markers were isolated in the spot‐tail shark (Carcharhinus sorrah) and nine were isolated in Australian black‐tip shark (Carcharhinus tilstoni). These loci plus 18 others developed for sharks from the genera Negaprion, Ginglymostoma, Carcharodon and Isurus were tested for amplification success on four species of Carcharhinus (including C. sorrah and C. tilstoni) and four other species representing three diverse families. Cross‐amplification was most common within families. Five loci were subsequently tested for polymorphism on 50 C. sorrah and 60 C. tilstoni. The number of alleles per locus was two to 24 and the average heterozygosity was 0.54 (range 0.16–0.87) for C. sorrah and 0.64 (range 0.44–0.78) for C. tilstoni. These loci may be useful tools for genetic analyses of the Carcharhinidae.     

Isolation and characterization of polymorphic microsatellite loci from an EST‐library of red sea bream (Chrysophrys major) and cross‐species amplification

Microsatellite markers have been developed from a complementary DNA (cDNA) library of red sea bream, Chrysophrys major. Twenty‐eight microsatellites were selected for designing microsatellite primers, of which 11 gave working primer pairs. Observed and expected heterozygosities varied from 0.33 to 1.00 and from 0.38 to 0.83, respectively. Five additional fish species assessed for cross‐species amplification revealed between one and six positive amplifications and between 0 and 6 polymorphic loci per species.     

Isolation of polymorphic microsatellite loci from Eurasian woodcock (Scolopax rusticola) and their cross‐utility in related species

We isolated one trinucleotide and seven tetranucleotide microsatellite loci for the Eurasian woodcock (Scolopax rusticola). We describe polymerase chain reaction conditions and primers for the successful amplification of these loci and report the results obtained from their use in 42 specimens from two populations in Europe. The number of alleles per locus ranged from three to 15, observed heterozygosity was comprised between 0.11 and 1.00 and expected heterozygosity ranged between 0.10 and 0.91. Cross‐specific amplification experiments highlighted the potential usefulness of these molecular markers for the study of three related scolopacid waders.