Characterization of 21 microsatellite marker loci in the Milne-Edwards’ Sifaka (Propithecus edwardsi)

Milne-Edwards’ Sifaka (Propithecus edwardsi) is a dark furred lemur with white flanks living in the southern region of the eastern rainforest belt of Madagascar. This species is endangered due to habitat destruction primarily from deforestation. Twenty-one polymorphic nuclear microsatellite loci were isolated from a genomic DNA derived from an individual from Ranomafana National Park, Madagascar. Population genetic parameters were estimated on 10 individuals each, from Andringitra National Park and the Vatoharana Forest in Ranomafana National Park.     

Characterization of 20 microsatellite marker loci in the red‐bellied brown lemur (Eulemur rubriventer)

Twenty nuclear microsatellite loci were isolated from a genomic DNA library derived from a free‐ranging red‐bellied brown lemur (Eulemur rubriventer), from the Ranomafana National Park, Madagascar. Population genetic parameters were estimated as baseline values from samples collected from populations harboured in the Ranomafana and Andringitra National Parks. The marker suite will be used in a future study on the population dynamics of this species.     

PERMANENT GENETIC RESOURCES: PCR primers for 100 microsatellites in red drum (Sciaenops ocellatus)

One hundred nuclear‐encoded microsatellites from a genomic library of red drum (Sciaenops ocellatus) were isolated and characterized. Eight microsatellites had tetranucleotide motifs; 92 had dinucleotide motifs. The average number of alleles per microsatellite (sample of 22–24 fish) was 17.7 (range = 2–30); gene diversity averaged 0.796 (range = 0.227–1.000). Following Bonferroni correction, genotype frequencies at 90 microsatellites did not deviate significantly from Hardy–Weinberg equilibrium expectations. Occurrence of null alleles was inferred at 15 microsatellites; alleles differing by only a single base were observed at 11 microsatellites. The microsatellites developed should prove useful for population‐genetic studies of ‘wild’ red drum and in construction of a genetic map.     

Multiplex PCR system applied for analysing microsatellite loci of Schlegel's black rockfish,Sebastes schlegeli

Two multiplex PCR amplifications were performed to analyse six microsatellite loci of Schlegel's black rockfish, Sebastes schlegeli, an important commercial fish in the northern part of Japan and an important species for the stock enhancement program in this area. We analysed 67 wild samples from Yamada Bay, Iwate Prefecture, Japan. The observed genotype frequencies agreed with the Hardy–Weinberg expectations at all loci, and the observed heterozygosities ranged from 0.072 to 0.897.     

Polymerase chain reaction primers for polymorphic microsatellite loci from the Korean sandfish,Arctoscopus japonicus

We developed 12 polymorphic microsatellite markers from Arctoscopus japonicus by screening an enriched genomic library using polymerase chain reaction (PCR) techniques. The average of alleles size was 16.2, and the average observed and expected heterozygosities were 0.59 and 0.78, respectively. The observed genotypic frequencies in five loci were significantly deviated from Hardy–Weinberg expectations. The high variability revealed in this study suggested that these microsatellite loci should provide useful markers for population genetics of A. japonicus.     

Microsatellite DNA markers for analysis of population structure in the sea urchin Centrostephanus rodgersii

We describe the development of 13 variable microsatellites developed to investigate population structure and dispersal in the sea urchin Centrostephanus rodgersii. This species is the dominant grazing herbivore in southeast Australian coastal waters and has the ability to modify benthic community structure. The microsatellites we identified showed a range of allele numbers (4–21) and expected heterozygosity (0.32–0.91) in two sampled populations. Contrary to previous findings in free‐spawning marine invertebrates, genotype proportions in neither population deviated significantly from Hardy–Weinberg expectations.     

Isolation of polymorphic microsatellite markers in the great tit (Parus major minor)

Six microsatellite loci were developed for a passerine bird, the great tit (Parus major), using two methods. These loci were polymorphic (3–8 alleles per locus) and exhibited expected heterozygosities from 0.45 to 0.77. At one locus the genotypic frequencies deviated significantly from Hardy–Weinberg expectations.     

Ten polymorphic tetranucleotide microsatellite markers isolated from the Anolis roquet series of Caribbean lizards

The Anolis roquet series of Caribbean lizards provides natural replicates with which to examine the role of historical contingency and ecological determinism in shaping evolutionary patterns. Here, we describe 10 polymorphic tetranucleotide microsatellites to facilitate studies on population differentiation and gene flow. All loci successfully amplified in several species from this series. Genotyping 96 individuals from two A. roquet populations demonstrated the markers’ suitability as population genetic markers: genetic diversity was high (9–22 alleles per locus); there were no instances of linkage disequilibrium; and, with one exception, all genotypic frequencies conformed to Hardy–Weinberg equilibrium expectations.     

hw‐quickcheck: an easy‐to‐use computer program for checking genotypes for agreement with Hardy–Weinberg expectations

Deviations from Hardy–Weinberg expectations are frequently a sign of genotyping error. hw‐quickcheck is an easy‐to‐use computer program for detecting departures from Hardy–Weinberg equilibrium. hw‐quickcheck uses exact tests for all of its calculations. These tests include a global test for heterozygote excess/deficiency and genotype‐specific tests.     

Isolation and characterization of microsatellite loci from Galápagos lava lizards (Microlophus spp.)

We describe the isolation of microsatellite loci from Galápagos lava lizards (Microlophus spp.) using an enriched genomic library. Twelve loci that are polymorphic among six populations from two species are described. Characterization of these loci in 20 individuals within one population (Isla Plaza Sur) showed seven to be polymorphic with 3–11 alleles. Heterozygosities within this population were high (0.32–0.90) and did not deviate from Hardy–Weinberg expectations. We suggest that these markers will be useful in studies of population differentiation within and among islands across the Galápagos archipelago.     

Isolation and characterization of microsatellite loci in Portunus pelagicus (Crustacea: Portunidae)

Seven dinucleotide and one tetranucleotide microsatellite loci were isolated and characterized, using routine protocols, from the blue swimmer crab, Portunus pelagicus. These loci will be useful for investigating the population structure of this broadly distributed and economically important portunid. In particular, all eight loci were polymorphic in P. pelagicus collected from throughout Australia. In addition, the genotype frequencies at each locus in each population sample were usually not significantly different from those expected under Hardy–Weinberg equilibrium conditions. Six of the eight loci also showed moderate to high levels of polymorphism in an undescribed species of Portunus from northern Australia.     

Significant deviations from Hardy-Weinberg equilibrium caused by low levels of microsatellite genotyping errors

Microsatellite genotyping from samples with varying quality can result in an uneven distribution of errors. Previous studies reporting error rates have focused on estimating the effects of both randomly distributed and locus‐specific errors. Sample‐specific errors, however, can also significantly affect results in population studies despite a large sample size. From two studies including six microsatellite markers genotyped from 272 sperm whale DNA samples, and 33 microsatellites genotyped from 213 bowhead whales, we investigated the effects of sample‐ and locus‐specific errors on calculations of Hardy–Weinberg equilibrium. The results of a jackknife analysis in these two studies identified seven individuals that were highly influential on estimates of Hardy–Weinberg equilibrium for six different markers. In each case, the influential individual was homozygous for a rare allele. Our results demonstrate that Hardy–Weinberg P values are very sensitive to homozygosity in rare alleles for single individuals, and that > 50% of these cases involved genotype errors likely due to low sample quality. This raises the possibility that even small, normal levels of laboratory errors can result in an overestimate of the degree to which markers are out of Hardy–Weinberg equilibrium and hence overestimate population structure. To avoid such bias, we recommend routine identification of influential individuals and multiple replications of those samples.     

Characterization of 10 microsatellite loci for the deep‐sea coral Lophelia pertusa (Linnaeus 1758)

The scleractinian coral, Lophelia pertusa, is distributed globally on continental slopes, mid‐oceanic ridges and in fjords. This species forms cold‐water reefs, which are associated with a diverse animal community. These communities are poorly understood but are currently under threat from human activities. Molecular markers are required to assess the spatial genetic population structure of this key species for management and conservation purposes. Ten polymorphic microsatellite loci were isolated for Lophelia pertusa using an enriched partial library technique. Nine loci showed significant differences from Hardy–Weinberg expected genotype frequencies, eight of which showed heterozygote deficiencies.     

Characterization of microsatellite markers for Couch's spadefoot toad (Scaphiopus couchii) and cross‐amplification in other species of the family Scaphiopodidae

I developed 12 di‐ and tetranucleotide microsatellite loci for Couch's spadefoot toad (Scaphiopus couchii). These loci have 3–37 alleles per locus and observed heterozygosities ranging from 0.157 to 0.941 among 85 individuals from four populations. Global and within‐population exact tests do not reveal departure from Hardy–Weinberg expectations and all loci pairs are in linkage equilibrium. These independent markers will be useful for studies of population structure and kinship in this commonly studied amphibian. Additionally, several of these loci may be applicable for studies of other North American toads of the family Scaphiopodidae.     

Microsatellite loci to assess genetic variation in Tor putitora

Seven polymorphic microsatellite DNA loci were identified in golden mahseer, Tor putitora, through cross‐species amplification. Thirty‐two primers developed for three cyprinid fishes were tested in the study. The genetic variation detected at each microsatellite locus in T. putitora specimens (n = 107), collected from three different rivers and one lake was assessed. The allele frequencies deviated significantly from that expected under Hardy–Weinberg equilibrium. The mean observed heterozygosity values ranged from 0.29 to 0.40. Significant genotype heterogeneity indicated that the samples were not drawn from the same gene pool. The results indicate that the identified microsatellite loci exhibit promise for use in fine scale population structure analyses of T. putitora.     

Isolation of polymorphic microsatellite markers from Hymeniacidon sinapium (Porifera: Demospongiae: Halichondrida)

Eight dinucleotide microsatellite markers were developed on Hymeniacidon sinapium (Porifera: Demospongiae), common littoral sponge around Japan, to investigate population genetic structure. Two to 10 alleles were identified in an analysis of 24 individuals of H. sinapium, with observed heterozygosity ranging from 0.04 to 0.83. All loci did not deviate from the Hardy–Weinberg expectations; however, significant linkage disequilibrium between Sinp126 and Sinp142 was found.     

Characterization of 20 microsatellite markers in the plowshare tortoise,Astrochelys yniphora

The plowshare tortoise, Astrochelys yniphora, or Angonoka is one of Madagascar’s land tortoises, living in the vicinity of Baly Bay bamboo scrub in northwest Madagascar. Primary threats to this endangered species are due to poaching for pet trade and the loss and fragmentation of its natural habitat. The number of wild Angonoka is estimated to be ~400. Twenty polymorphic nuclear microsatellite loci were isolated from a genomic DNA on individuals from Andrafiafaly in Baly Bay National Park, Madagascar. Results from this study will help for future studies of the social structure and population dynamics of this species as well as identification of confiscated individuals from the illegal pet trade.     

Isolation and characterization of ten microsatellite loci for Senegal sole (Solea senegalensis Kaup)

Senegal sole (Solea senegalensis Kaup) is a high‐value marine flatfish exploited in both fisheries and aquaculture. Here we describe the isolation of seven tetranucleotide and three dinucleotide polymorphic microsatellite loci. Characteristics of a captive broodstock and a wild population are described. Three loci displayed a significant departure from Hardy–Weinberg expectations in both populations, suggesting a substantial frequency of null alleles. The remaining seven loci were found to be in equilibrium in the wild population, whereas only four of them were in the cultured population. Cross‐species amplification was successful for three loci in other five flatfishes.     

Polymorphic tetranucleotide microsatellite loci in the Hwamei (Garrulax canorus canorus) (Timaliidae)

Eight polymorphic tetrarepeat (GATA)_n, microsatellite loci were isolated from a babbler, Hwamei (Garrulax canorus canorus). We evaluated the polymorphism of these microsatellite loci by genotyping 36–48 individuals from the Asian mainland. The number of alleles for each locus ranged from eight to 29. The heterozygosity was between 0.587 and 0.978. Except for one locus, genotype frequencies of these microsatellites did not significantly deviate from the Hardy–Weinberg expectation. These markers should be useful for monitoring potential hybridization between different Hwamei subspecies and provide new insights into the mating system and geographical differentiation of these birds.     

Characterization of 23 Tri‐ and tetranucleotide Microsatellite Loci in the Brown Tiger Prawn,Penaeus esculentus

Twenty‐three unique tri and tetra‐nucleotide microsatellites were isolated and characterized from the genome of the brown tiger prawn Penaeus esculentus. Nine of the 23 microsatellite loci were found to be polymorphic and were tested across a sample of wild caught Penaeus esculentus. Good fits to Hardy–Weinberg expectations were observed for six of the markers when tested in a population of at least 180 individuals. The total number of alleles for these six markers ranged from eight to 19, with an average total of 13. These values will make them useful for future stock identification and population genetics studies.