Tetranucleotide microsatellite loci from the black bear (Ursus americanus)

We describe primers and polymerase chain reaction conditions to amplify 21 tetranucleotide microsatellite DNA loci in black bears (Ursus americanus). We tested primers using individuals from two populations, one each in Georgia and Florida. Among individuals from Georgia (n = 29), primer pairs yielded an average of 2.9 alleles (range, one to four) and an average observed heterozygosity (H_O) of 0.50 (range, 0.00 to 0.79). Among individuals from Florida (n = 19), primer pairs yielded an average of 5.7 alleles (range, one to 14) and an H_O of 0.55 (range, 0.00 to 1.00). A comparison of previously developed markers with individuals from Georgia suggests that bear populations in Georgia and Florida have reduced allelic diversity relative to other populations.     

Microsatellite markers for the Mexican spotted owl (Strix occidentalis lucida)

A genomic cosmid library was used to develop seven highly polymorphic microsatellite markers for the Mexican spotted owl (Strix occidentalis lucida). These are the first reported microsatellite markers derived from this species. The cloned and sequenced repeat motifs include a triplet repeat of (AAT)_n, two tetranucleotide repeats of (GATA)_n, a tetranucleotide repeat of (ATCC)_n, a compound repeat of (GA)_n(GATA)_n and the two pentanucleotide repeats (AGAAT)_n and (ATTTT)_n. The microsatellites described represent six presumably independent loci with the two pentanucleotide repeats having originated from a single cosmid. Primer pairs allow locus‐specific amplification of each marker from Mexican spotted owl genomic DNA.     

Selected di- and tetranucleotide microsatellites from chromosomes 7, 12, 14, and Y in various Eurasian populations

Microsatellite polymorphisms of nine Eurasian populations (>1200 chromosomes) were analyzed for the following loci: i) intronic (gt) _n stretches of three T cell receptor (TCR) B loci on chromosome 7 (TCRBV6S1, TCRBV6S3, TCRBV6S7); ii) an intergenic (gt) _n repeat in the region between the TCRDV3 and TCRAJ61 elements on chromosome 14; iii) two tetranucleotide simple repeats (D12S66, D12S67), not linked to known genes on chromosome 12; iv) a Y-chromosomal (gata) _n polymorphism (DYS19). In general, allele frequencies and heterozygosity rates were similar, but specific alleles were missing in one or more populations. Distinct DYS19 alleles predominated in particular cohorts. Different allele frequencies were observed for the TCR loci in European and Asian populations. Tetranucleotide polymorphisms were distributed normally, whereas TCR alleles displayed bimodal frequency profiles. For TCRBV6S1 and TCRBV6S7, this profile reflects a diallelic protein polymorphism that correlates exactly with the length of the intronic repeats.     

Characterization of 24 microsatellite loci in delta smelt, Hypomesus transpacificus, and their cross-species amplification in two other smelt species of the Osmeridae family

We characterized 24 polymorphic tetranucleotide microsatellite loci for delta smelt (Hypomesus transpacificus) endemic to the San Francisco Bay Estuary, CA, USA. Screening of samples (n = 30) yielded two to 26 alleles per locus with observed levels of heterozygosity ranging from 0.17 to 1.0. Only one locus deviated from Hardy–Weinberg equilibrium, suggesting these individuals originate from a single panmictic population. Linkage disequilibrium was found in two pairs of loci after excluding the locus out of Hardy–Weinberg equilibrium. Twenty‐two primer pairs cross‐amplified in wakasagi smelt (Hypomesus nipponensis), and 15 primer pairs cross‐amplified in longfin smelt (Spirinchus thaleichthys).     

Highly polymorphic tetranucleotide microsatellite loci for the eastern Canary Island lizard,Gallotia atlantica

We describe 10 polymorphic tetranucleotide microsatellite loci from the eastern Canary Island lacertid lizard, Gallotia atlantica. Loci were isolated from a partial genomic library that had been enriched for AAAG repeat sequence. All loci were highly polymorphic (eight alleles or more) with observed heterozygosities from 0.75 to 1.00. At least four loci were successfully amplified and polymorphic in the Gran Canarian lacertid, Gallotia stehlini. These loci will be used to examine correlations between patterns of gene flow and recent volcanism on the island of Lanzarote.     

Development and characterization of seven novel di‐, tri‐, and tetranucleotide microsatellite markers in Atka mackerel (Pleurogrammus monopterygius)

We describe the enrichment for and characterization of seven Pleurogrammus monopterygius microsatellite loci. We used (GACA)₄ as an oligonucleotide enrichment probe and screened 484 clones from the enriched library. The seven microsatellite loci include five tetranucleotide, one dinucleotide, and one trinucleotide motif. These markers can potentially be useful tools for use in population genetics studies, parentage analyses, and examining other life history questions.     

Isolation of microsatellite loci from the common buzzard,Buteo buteo (Aves: Accipitridae)

We isolated 56 common buzzard (Buteo buteo) microsatellite loci from (AC)_n‐ and (AAAG)_n‐enriched genomic libraries. Eleven loci were tested on 90 individuals from Eastern Westphalia in Germany, yielding two to 17 alleles per locus (average 5.7) and expected heterozygosities ranging from 0.11 to 0.93 (average 0.53). These highly variable microsatellite markers provide a powerful means for investigating population genetic diversity in the common buzzard, a little‐understood aspect of this widespread species.     

Isolation and characterization of novel microsatellite loci for the short‐beaked common dolphin (Delphinus delphis) and cross‐amplification in other cetacean species

Seven tetranucleotide and three dinucleotide microsatellite loci were isolated from the short‐beaked common dolphin (Delphinus delphis). Number of alleles and observed heterozygosity ranged from three to twelve (mean 8.4) and from 0.087 to 0.978 (mean 0.741), respectively. All loci were tested in four other odontocete species and showed polymorphisms in most locus–species combinations. This panel of nuclear markers will be useful for the investigation of population ecology and social interactions in common dolphins and other cetacean species.     

Characterization of 16 highly variable tetranucleotide microsatellite loci for Oregon chub (Oregonichthys crameri) and cross amplification in Umpqua chub (O. kalawatseti)

We describe the isolation and development of 16 polymorphic tetranucleotide microsatellite loci for the endangered Oregon chub (Oregonichthys crameri). Two loci appear to be duplicated. For the remaining 14 loci, we observed between three and 19 alleles per locus in a sample of 42 fish. Thirteen of these loci were also polymorphic in the closely related Umpqua chub (O. kalawatseti). These loci will aid in our understanding of the molecular ecology and conservation of these two species.     

Microsatellite loci isolation in the endangered Gran Canarian blue chaffinch (Fringilla teydea polatzeki) and their utility in closely related taxa

The blue chaffinch, Fringilla teydea, is an endemic species of the Canary Islands. This species is formed by two subspecies: The Teneriffean blue chaffinch (F. t. teydea), and the endangered Gran Canarian blue chaffinch, (F. t. polatzeki). Here we report the isolation and characterization of nine tetranucleotide microsatellites (AAAG and AAAT) from the Gran Canarian subspecies, using an enrichment protocol. An average of 7.8 alleles per locus and an average observed heterozygosity of 0.773 were found (n = 28). The loci were tested for their ability to cross amplify in the Teneriffean subspecies and in the common chaffinch (Fringilla coelebs). These microsatellites will be used to manage a captive breeding programme for the endangered Gran Canarian subspecies.     

Development of microsatellite DNA loci from the wood stork (Aves,Ciconiidae, Mycteria americana)

We isolated 11 polymorphic microsatellite loci for wood stork (Mycteria americana). Polymerase chain reaction (PCR) primers and conditions are described for the amplification of five dinucleotide, one trinucleotide and five tetranucleotide microsatellite loci. The PCR primers were tested on two wood stork populations, Fazenda Ipiranga, Mato Grosso, Brazil (n = 11) and Tamiami West, Everglades, Florida, USA (n = 20). The primers yielded two to four alleles per locus, an observed heterozygosity of 0.0–0.727 and a polymorphic information content of 0.048–0.604. The low level of polymorphism for these markers is consistent with previous studies of this species.     

Isolation of additional polymorphic tri‐ and tetranucleotide microsatellite loci for the giant Australian cuttlefish (Sepia apama)

We isolated 10 polymorphic microsatellite loci for the giant Australian cuttlefish, Sepia apama, from a genomic library enriched for (AAC)_n and (AAAG)_n repetitive elements. In the nine loci that reliably amplified, the number of alleles ranged from four to 12 per locus with observed heterozygosity ranging from 0.343 to 0.926. These and a previously developed set of six loci will be useful for analysis of genetic structure of populations and determining input to a massive seasonal breeding aggregation in northern Spencer Gulf, Australia.     

Isolation of polymorphic tetranucleotide microsatellite markers for the ornate nursery frog Cophixalus ornatus

We have isolated 18 polymorphic microsatellite loci for Cophixalus ornatus from genomic libraries enriched for (AAAG)_n, (AACC)_n and (AAGG)_n repetitive elements. The number of alleles ranges from five to 22 per locus with the observed heterozygosity ranging from 0.10 to 0.92. These markers will be useful for the analysis of population structure in C. ornatus and testing alternative models of speciation.     

Polymorphic microsatellite loci in the European subterranean termite,Reticulitermes santonensis Feytaud

We report on the identification and characterization of two dinucleotide, two trinucleotide and eight tetranucleotide microsatellite DNA loci isolated from the European subterranean termite Reticulitermes santonensis. We tested the loci on 51–92 individuals from 46 colonies from different regions of France. Eleven loci were polymorphic with 2–8 alleles per locus and low observed heterozygosities (0.10–0.48). We also tested the loci on 17–20 individuals from 10 colonies in the closely related North American species R. flavipes and found significantly more alleles (2–9 alleles per locus) and higher observed heterozygosities (0.15–0.80) than in R. santonensis. The lower observed heterozygosities in R. santonensis are consistent with higher levels of inbreeding in these colonies due to the presence of numerous inbred replacement reproductives.     

Tetranucleotide microsatellite loci from eastern bluebirds Sialia sialis

We describe primers and polymerase chain reaction (PCR) conditions to amplify 18 tetranucleotide microsatellite DNA loci in eastern bluebirds (Sialia sialis). The primers were tested using individuals from two study sites in Georgia and South Carolina. Among individuals from the Georgia population (n = 23), the primer pairs developed in this study yielded an average of 6.6 alleles per locus (range 2–12), an average observed heterozygosity of 0.56 (range 0.24–0.96) and an average polymorphic information content of 0.65 (range 0.3–0.86). Among individuals from the South Carolina population (n = 19), the primer pairs yielded an average of 5.8 alleles per locus (range 2–9), an average observed heterozygosity of 0.56 (range 0.05–0.86) and an average polymorphic information content of 0.63 (range 0.29–0.83).     

Characterization,multiplex conditions,and cross‐species utility of tetranucleotide microsatellite loci for Blanchard's cricket frog (Acris crepitans blanchardi)

We have isolated and characterized 17 tetranucleotide microsatellite loci for Blanchard's cricket frog (Acris crepitans blanchardi), an anuran common in the central USA. Sixteen loci were organized into four multiplex amplification reactions. These loci were highly polymorphic when screened in 55 individuals from two distant populations, with 11–48 alleles per locus (average = 24.8). Observed and expected heterozygosities ranged from 0.18 to 0.97 and from 0.17 to 0.96, respectively. Nine loci were also polymorphic in Acris crepitans crepitans, with seven polymorphic in Acris gryllus. Five loci amplified in all three taxa. These loci will be useful for population‐ and species‐level investigations of this widespread group.     

Isolation of highly polymorphic autosomal microsatellite loci and a sex‐linked locus from sugarbirds

We describe the isolation of six tetranucleotide microsatellites from the Cape sugarbird (Promerops cafer) using an enrichment protocol. All loci were highly variable with number of alleles ranging from nine to 26 and values of observed heterozygosity ranging from 0.534 to 0.931. All loci were in Hardy–Weinberg equilibrium with the exception of Pro66 and Pro86. Further analysis of Pro86 indicated it was Z‐linked. All loci amplified and were variable in the congeneric Gurneys sugarbird (Promerops gurneyi). These loci will be used in mating system and phylogeographic studies of Cape sugarbirds in South Africa.     

Highly polymorphic microsatellite loci for the Gran Canarian skink (Chalcides sexlineatus) and their applicability in other Canarian Chalcides

The scincid lizard Chalcides sexlineatus is endemic to the island of Gran Canaria, within which it shows a pronounced phylogeographical pattern. Understanding the maintenance of this pattern requires knowledge of nuclear DNA structuring. Eleven polymorphic tetranucleotide microsatellite loci were isolated from a library constructed from genomic DNA enriched for AAAG repeat sequence. The number of alleles per locus ranged from 12 to 19, and expected heterozygosities spanned from 0.738 to 0.933 (n = 30). The majority of these could be cross‐amplified in other endemic Canarian Chalcides. The loci will be used to investigate gene flow between the principal mitochondrial clades within C. sexlineatus.     

Nine new tetranucleotide microsatellite markers for the fire‐bellied toad (Bombina bombina)

We describe nine new polymorphic tetranucleotide microsatellite loci isolated from the fire‐bellied toad (Bombina bombina). The relative yield of new loci was higher than described in previous studies in amphibians: out of 12 loci initially evaluated, nine were polymorphic and amplifying reliably. Number of alleles ranged from four to 10 and observed heterozygosities from 0.47 to 0.91. Seven loci were polymorphic also in Bombina variegata and five in Bombina orientalis. Enrichment protocols yielding long flanking regions potentially overcome difficulties (i.e, low yield of reliable loci relative to number of clones screened) which have been reported in microsatellite development in anurans.     

Ten microsatellite loci for the strawberry poison frog (Oophaga pumilio)

We describe primers and PCR conditions to amplify nine new tetranucleotide loci and one new dinucleotide locus isolated from the strawberry poison frog (Oophaga pumilio). In 21 individuals from Costa Rica, the number of alleles ranged from 4 to 16, observed heterozygosities from 40 to 100%, and polymorphic information content ranged from 0.60 to 0.90 per locus. Evidence for linkage disequilibrium was found only between two loci, but this pattern was not found in other populations tested. All primer pairs cross-amplified in Oophaga vicentei from Panama.