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.     

Development of polymorphic microsatellite markers for the Steere's Liocichla (Liocichla steerii)

For the Steere's Liocichla (Liocichla steerii) we developed seven polymorphic microsatellite markers from a partial genomic library enriched for GATA, tetranucleotide repeats. Among the 27–28 individuals screened, allelic diversity ranged from six to 19 alleles per locus and the observed heterozygosity of each locus ranged from 0.250 to 0.889. All loci conformed to Hardy–Weinberg expectations except for two that appeared to be Z‐Iinked; such Z‐Iinked loci can be used in studies of male dispersal.     

Isolation and characterization of variable microsatellite loci in Lilium philadelphicum (Liliaceae)

Here we describe the characterization of six polymorphic microsatellite loci for Lilium philadelphicum (Liliaceae). Polymorphism levels ranged from 7 to 30 alleles per locus with a mean number of 15 alleles per locus. Observed heterozygosity (H_O) ranged from 0.17 to 0.82 and did not deviate from Hardy–Weinberg expectations in the three western Montana populations included in the analysis. These loci are proving useful in studying gene flow between populations of this species distributed across its range in North America.     

Characterization of 18 new microsatellite loci in Atlantic cod (Gadus morhua L.)

Eighteen new microsatellite loci consisting of 10 di‐, 5 tri‐, 2 tetra‐ and 1 heptanucleotide repeats are introduced for the Atlantic cod (Gadus morhua L.). All loci were co‐amplified in two polymerase chain reactions (plus two previously published microsatellites) and all products were typed clearly. The number of alleles per locus ranged from six (PGmo130) to 45 (PGmo76) and the observed heterozygosity ranged from 0.356 (PGmo130) to 0.957 (PGmo95). All loci except one followed Hardy–Weinberg expectations. Genetic linkage disequilibrium analysis between all pairs of loci did not yield any significant values.     

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.     

Polymorphic microsatellite DNA markers for the rhinoceros auklet (Cerorhinca monocerata)

Eight polymorphic microsatellite loci were isolated from the partial genomic library of the rhinoceros auklet Cerorhinca monocerata. The heterozygosities observed at the isolated loci using eight primer sets in 46 nestlings from one breeding colony in Japan ranged from 0.311 to 0.773, and all but one locus did not deviate from the Hardy–Weinberg expectations. Cross‐species amplification in the tufted puffin Fratercula cirrhata was successfully performed using six of the eight primer sets, indicating their applicability to this species.     

Isolation and characterization of microsatellite loci in the Alpine leaf beetle,Oreina elongata

For a study of local adaptations in the Alpine leaf beetle, Oreina elongata, we developed six microsatellite loci and screened them in 305 individuals from 13 populations. All markers were polymorphic with three to 15 alleles per locus. Average observed and expected heterozygosity values were 0.14 and 0.62, respectively. Four markers showed heterozygote deficiency and deviated significantly from Hardy–Weinberg expectations, indicating the presence of null alleles.     

New polymorphic microsatellite loci in two fish species: bluefin killifish (Lucania goodei) and yellow bullhead (Ameiurus natalis)

We identified four new polymorphic microsatellite loci in bluefin killifish (Lucania goodei) and five loci in yellow bullheads (Ameiurus natalis). We screened 400 killifish from 20 populations and 180 bullheads from nine populations, finding a high degree of polymorphism (nine to 54 alleles per locus; average expected heterozygosity 0.678–0.976). We found no evidence for linkage disequilibrium. Three of the loci found in bluefin killifish show heterozygote deficiency; the other loci do not deviate 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.     

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.     

Isolation and characterization of microsatellite markers from the Hypoptychus dybowskii (Pisces,Gasterosteiformes)

Hypoptychus dybowskii (Gasterosteiformes) exhibits allopaternal care frequently caused by various types of male reproductive tactics (sneaking, egg desertion and taking over). In order to understand this interesting reproductive system, we isolated microsatellites loci from H. dybowskii. Five microsatellites showed 2–10 alleles and expected heterozygosities ranged from 0.15 to 0.84. These were not significant deviations from Hardy–Weinberg expectations. These results suggest that these novel polymorphic loci should be useful for parentage analysis of H. dybowskii.     

Isolation and characterization of polymorphic microsatellite DNA markers in two shrew species,Sorex unguiculatus and S. caecutiens

We isolated six microsatellite markers from the partial genomic libraries of two Sorex shrews, S. unguiculatus and S. caecutiens, and examined their allelic variation. All loci showed high allelic variation ranging from 15 to 19 alleles and all but one locus conformed to Hardy–Weinberg expectations in the species where the loci were isolated. Cross-species amplifications showed that all primers derived from S. unguiculatus were useful for S. caecutiens, while among primer sets derived from S. caecutiens only one was useful for S. unguiculatus. Accordingly, at least five microsatellite markers were useful in S. caecutiens and three in S. unguiculatus.     

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.     

Isolation and characterization of microsatellite loci in the Bang's leaf‐nosed bat Hipposideros turpis

The Bang's leaf‐nose bat, Hipposideros turpis, is an endangered cave‐dwelling species inhabiting the southwesternmost islands of Japan. We isolated six dinucleotide microsatellite markers from the partial genomic library of the bat, and examined their allelic variation using a sample (N = 33) from the largest colony in Japan. All the loci showed a moderate allelic variation ranging from two to eight alleles, with the observed heterozygosities from 0.33 to 0.73, and conformed to Hardy–Weinberg expectations. The present microsatellite markers will be useful in assessing population genetic structure and gene flow among populations of this species.     

Development and characterization of 11 novel microsatellite loci for the roundscale spearfish Tetrapturus georgii and their cross‐species amplification among other istiophorid species

Eleven novel polymorphic microsatellite loci were developed and characterized for the recently validated roundscale spearfish Tetrapturus georgii. Characterization of these markers, based on 35 roundscale spearfish from the western North Atlantic, revealed two to 21 alleles per locus with an average expected heterozygosity (H_E) of 0·09–0·94, and all loci conformed to Hardy–Weinberg expectations. Cross‐amplification of these 11 loci against all other eight known istiophorid species indicates promising prospects for the utility of these markers for istiophorids in general.     

Isolation of polymorphic microsatellite loci in Crossosoma californicum (Crossosomataceae)

Crossosoma californicum (Crossosomataceae) is a rare shrub species endemic to the California Channel Islands. Previous studies based on allozymes revealed little genetic variability in this plant species. We have isolated 13 polymorphic microsatellite loci from C. californicum. These loci show intermediate levels of variability, averaging 4.2 alleles per locus and expected heterozygosity of 0.376. Two loci did not fit Hardy–Weinberg expectations with significant deficits of heterozygous genotypes consistent with the presence of null alleles or population subdivision.     

Novel microsatellite loci identified from the Australian eastern small‐eyed snake (Elapidae: Rhinocephalus nigrescens) and cross species amplification in the related genus Suta

A total of 15 microsatellite primers pairs were developed for the Australian small‐eyed snake Rhinoplocephalus nigrescens. Five primers were used to screen 93 individuals of R. nigrescens and were also tested against eight species of the closely related genus Suta. Allelic diversity in R. nigrescens was high in three loci (12–27) and there was high heterozygosity (0.58–0.82). Observed heterozygosity did not deviate from Hardy–Weinberg expectations for the five loci tested. These primers will be useful in studies of population genetics and mating systems of small‐eyed snakes and related species.     

PCR primers for microsatellite loci in the desert tortoise (Gopherus agassizii,Testudinidae)

The desert tortoise, Gopherus agassizii, is a threatened species native to the North American desert southwest and is recognized as having distinct Mojave and Sonoran populations. We identified six polymorphic microsatellite loci in the desert tortoise. All six loci were polymorphic in Sonoran samples. Five of the loci were variable in Mojave samples with varying degrees of amplification success. Two of the loci exhibited low allelic variation (2–3 alleles) while four were highly variable (8–27 alleles).     

Isolation and characterization of microsatellite markers in the South African abalone (Haliotis midae)

We report the isolation and characterization of 11 polymorphic microsatellite loci in the South African abalone Haliotis midae. These loci showed a range of five to 21 alleles per locus and observed heterozygosities ranging from 0.14 to 0.93 in a wild population of 32 individuals. All loci except four conformed to Hardy–Weinberg expectations and did not show linkage disequilibrium. The polymorphism exhibited at these loci indicate that they would be useful in determining levels of genetic variability in natural and commercial Haliotis midae populations as well as in parentage and Quantitative Trait Loci (QTL) analysis in hatchery reared abalone.     

Isolation and characterization of 27 polymorphic microsatellite loci for the common snook,Centropomus undecimalis

Here we describe 32 di‐, tri‐ and tetranucleotide microsatellite loci isolated by PIMA, a polymerase chain reaction (PCR)‐based procedure, for the common snook (Centropomus undecimalis). Five loci were monomorphic, and the remaining loci averaged 6.7 alleles per locus in a sample of 45 common snook. For polymorphic loci, expected heterozygosities ranged from 0.02 to 0.91 (mean = 0.538). Significant departures from Hardy–Weinberg equilibrium expectations occurred in two loci. Exact tests for genotype disequilibrium gave evidence for linkage at one pair of loci. Many cross‐species primer assays yielded PCR fragments of the expected size for 11 species of Centropomus and two species of the confamilial genus Lates.