Eleven microsatellite markers for the eastern gray squirrel (Sciurus carolinensis) and their utility in eastern fox squirrels (Sciurus niger) and red squirrels (Tamiasciurus hudsonicus)

The eastern gray squirrel (Sciurus carolinensis) often serves as a model organism for investigations of wildlife ecology. The authors developed 11 polymorphic microsatellite markers to facilitate future research questions. The number of alleles per locus ranged from three to ten and observed heterozygosities ranged from 0.143 to 0.786. Interspecific screening revealed that several loci were polymorphic in Sciurus niger (eight loci) and Tamiasciurus hudsonicus (four loci). These markers will aid in investigations of movements, social structure and mating tactics of eastern gray squirrel populations.     

Development and multiplex genotyping of eighteen novel microsatellite markers for a threatened saltmarsh bird Epthianura albifrons (Meliphagidae)

Using 454 pyrosequencing and multiplex genotyping we developed 18 novel microsatellite loci in Epthianura albifrons (Jardine & Selby, 1828), a small passerine threatened by loss of coastal saltmarsh. We also tested the utility of 21 previously-developed microsatellite loci from two con-familial species, however these were weakly polymorphic in E. albifrons. The 18 loci developed for E. albifrons were polymorphic with a mean of 17.1 (±2.6SE) alleles per locus. The 18 new microsatellites will be useful tools for measuring gene flow in the Endangered population of E. albifrons.     

Characterisation of microsatellite markers for the granite endemic Kunzea pulchella (Lindl.) A. S. George (Myrtaceae) identified using next generation sequencing

A set of 11 polymorphic microsatellite loci were developed for Kunzea pulchella, a plant species endemic to granite outcrops in Western Australia. Genomic sequences were obtained from next generation (454) sequencing. A total of 20 microsatellite markers were then chosen for amplification and genotyping trials in individuals across the species range. Eleven of these loci were selected for analysis based on amplification and genotyping success. All were polymorphic with 4–10 alleles per locus (mean = 5.9). Expected and observed heterozygosity ranged from 0.29 to 0.92 averaging 0.606 and 0.690 respectively. Loci were in Hardy–Weinberg equilibrium (P < 0.05) except for two which showed evidence for null alleles. Linkage disequilibrium was evident in three loci pair combinations. These polymorphic microsatellite markers will be valuable for analysis of population genetic structure and connectivity in K. pulchella.     

Isolation of microsatellites using 454-sequencing for the grassland shrub Pimelea spinescens (Thymelaeaceae)

Ten microsatellite loci were developed for the grassland shrub Pimelea spinescens. Locus amplification varied between the two subspecies. For P. spinescens subsp. spinescens, nine loci amplified and were polymorphic. Number of alleles per locus ranged from two to eleven (average?=?5.7) and expected heterozygosity ranged from 0.103 to 0.782. For P. spinescens subsp. pubiflora, seven loci amplified, of which only three were polymorphic. For polymorphic loci, number of alleles ranged from four to seven (average?=?5.3) and expected heterozygosity ranged from 0.381 to 0.783. These loci will be used to investigate population genetic structure, assisting management of this endangered species.     

Development of microsatellite markers for Shorea platyclados (Dipterocarpaceae)

Nine polymorphic microsatellite markers were isolated and characterized in Shorea platyclados (Dipterocarpaceae) using CT-enriched library method. The polymorphism of the microsatellite loci was analyzed by screening 98 samples from a natural population. The number of alleles per locus ranged from 4 to 12, with an average of 8.22 per locus, and the observed heterozygosity ranged from 0.204 to 0.888 (average 0.562). These microsatellite loci will be useful for population genetic studies on S. platyclados and adding genetic information for hill dipterocarps.     

Isolation, via 454 sequencing, characterization and transferability of microsatellites for Grevillea thelemanniana subsp. thelemanniana and cross-species amplification in the Grevillea thelemanniana complex (Proteaceae)

A set of 12 polymorphic microsatellite markers were developed for Grevillea thelemanniana subsp. thelemanniana, a rare and threatened shrub, endemic to southwest Western Australia. Genomic sequences were obtained from next generation (454) sequencing in the target species. Primer pairs for a total of 30 microsatellite loci were designed from these of which 13 were successfully amplified in 25 individuals from Kenwick Nature Reserve, Perth. Twelve loci were polymorphic with observed heterozygosity ranging from 0.12 to 0.6 and the number of alleles per locus ranged from 2 to 8. These markers were trialed in all species within the G. thelemanniana species complex. Amplification success and level of polymorphism varied among loci and taxa, but most (96 %) were successful. These loci will be useful in understanding the genetic variation, molecular ecology and phylogenetic relationships in the G. thelemanniana complex.     

Isolation and characterization of 14 microsatellite loci for Chinese catfish Silurus asotus

Silurus asotus is a high commercially valuable aquaculture fish in some regions of China. In this survey, the first set of 14 polymorphic microsatellite loci for S. asotus was developed and characterized. The number of alleles per locus ranged from 9 to 15 and the observed and expected heterozygosities ranged from 0.593 to 0.931 and from 0.833 to 0.926, respectively. Four loci were found deviated from HWE in the sampled population after Bonferroni correction. These microsatellite loci will be useful for revealing population structure, and conservation genetics of S. asotus.     

Isolation and characterization of polymorphic microsatellite loci in the migratory freshwater fish Prochilodus lineatus (Characiformes: Prochilodontidae)

Thirteen new polymorphic microsatellite loci were developed and tested in 57 individuals from three locations along the Paraná River. All loci were polymorphic, with 2–22 alleles per locus. Cross-species amplifications were successful for all loci in four other Prochilodus species, suggesting that these microsatellites will be useful for investigation of genetic variation and structure in Prochilodus populations.     

Characterization of nine polymorphic microsatellite loci for the calcareous sponge Paraleucilla magna Klautau et al. 2004 introduced to the Mediterranean Sea

Nine polymorphic microsatellite markers are described for the calcareous sponge Paraleucilla magna. Microsatellite were isolated from a genomic library enriched for AC₁₅, AG₁₅, CAA₁₀ and GATA₇ repeats. The microsatellite motifs were perfect, imperfect, and compound. The polymorphism of the microsatellite loci was screened in a total of 35 individuals from two populations: western Mediterranean (Blanes, NE Spain) and Atlantic Ocean (Rio de Janeiro, Brazil). All loci were polymorphic and the number of alleles per locus ranged from 2 to 9 with an average of ca. 5 alleles per locus. Significant genetic differentiation was observed between populations. These markers have been used successfully for analysing population structure at short spatial and temporal scales, and are promising for assessing the historic pathways of the introduction of this exotic sponge, which risks to become invasive in the Mediterranean. These are the first microsatellites developed for any calcareous sponge.     

Isolation and characterization of novel microsatellite loci in Vaccinium arctostaphylos L

For the first time, this study has described the characterization of 25 novel polymorphic microsatellite loci from a repeat-enriched genomic library of V. arctostaphylos using a modified FIASCO method. Polymorphism of each locus was assessed in 64 individuals of the Vaccinium. The average allele number of the microsatellites, observed (H_O) and expected (H_E) heterozygosities were 5.88, 0.85 and 0.67 per locus, respectively. The polymorphic information content (PIC) value and inbreeding coefficient (F) ranged from 0.26 to 0.87 and ?0.72 to 0.03, respectively. Ten of the twenty-five loci showed significant departures from Hardy–Weinberg equilibrium. These microsatellite loci could be useful to study genetic diversity and population structure of V.arctostaphylos.     

Isolation of 13 polymorphic microsatellite loci for slimy sculpin (Cottus cognatus)

Our research on slimy sculpins (Cottus cognatus), a benthic, freshwater fish, requires highly polymorphic genetic markers, and microsatellite loci developed for other Cottus species were insufficient for our needs. We therefore developed 13 polymorphic microsatellite loci from C. cognatus libraries enriched for tri- and tetranucleotide repeats. These loci had 2–22 alleles and observed heterozygosities ranging from 0.36 to 0.86 in a sample of 47 individuals from one population. There was no evidence of linkage disequilibrium; however, one locus had a putative null allele. Twelve loci also worked for mottled sculpin (Cottus bairdi) but only eight were polymorphic in a sample of seven individuals.     

Isolation and characterization of microsatellite loci for a hyper-rare cliff endemic, Erigeron lemmonii, and a more widespread congener, Erigeron arisolius (Asteraceae)

We identified eight novel polymorphic microsatellite loci in Erigeron lemmonii and nine novel polymorphic microsatellite loci in Erigeron arisolius. Of these, three loci developed for E. arisolius cross-amplified E. lemmonii DNA and four loci developed for E. lemmonii cross-amplified E. arisolius DNA. This set of 17 loci will be used to analyze patterns of genetic structure in populations of these two Erigeron species in southeastern Arizona with the ultimate goal of comparing patterns of genetic structure within a hyper-rare cliff endemic (E. lemmonii) to those of a more widespread congener (E. arisolius).     

Isolation and characterization of nine microsatellite loci in a Malagasy endemic rodent, Eliurus carletoni (Rodentia: Nesomyinae)

We developed microsatellite markers for the recently described forest rodent, Eliurus carletoni, from an enriched genomic library. Nine loci composed of four dinucleotide, one trinucleotide, one tetranucleotide and three compound repeats were isolated and characterized using two wild populations. One locus was found to be monomorphic. For the polymorphic loci, the average number of alleles per locus was 7.13 and 8.38 for each population. Mean expected and observed heterozygosities were high (i.e. 0.76 and 0.80). Tests for linkage disequilibrium were not significant across all locus pairs. One locus tested significant for null alleles, but only one population exhibited a significant deviation from the Hardy–Weinberg Equilibrium (HWE) at this locus. All remaining loci show no evidence of departure from HWE. Overall, we identified eight polymorphic loci that may be used in conservation and population genetics studies of E. carletoni.     

Isolation and characterisation of ten microsatellite markers for the tetraploid Stypandra glauca R.Br. (Hemerocallidaceae) identified using next generation sequencing

Ten polymorphic microsatellite loci were developed for the tetraploid plant species Stypandra glauca which is common on granite outcrops in Western Australia. Amplification and genotyping trials were conducted on 48 individuals from two sampling localities. All 10 loci revealed multi-banding patterns with up to 4 bands visible in individuals consistent with tetraploidy. The number of alleles per locus ranged from 6 to 32 (mean = 12.5). The proportion of observed heterozygotes at each locus ranged from 0.32 to 0.98 (mean = 0.73). These polymorphic microsatellite markers will facilitate further analysis of population genetic structure and connectivity in Stypandra glauca.     

Development and characterization of 10 polymorphic microsatellite loci for the blue shark, Prionace glauca, and their cross shark-species amplification

Ten polymorphic nuclear microsatellite loci were developed from a microsatellite enriched genomic library of the blue shark, Prionace glauca. The utility of these markers for genetic studies of this globally distributed, heavily exploited, oceanic predator was assessed by screening 120 specimens sampled from six locations throughout the species’ range. Both moderately and highly polymorphic marker loci were identified. Three to 35 alleles were found to be segregating per locus (mean 10.1) with observed heterozygosities ranging from 24 to 91%. Evaluation of the cross-species amplification of these markers across 18 additional shark species indicates that these microsatellites are potentially useful for genetic studies of other species of conservation concern.     

Polymorphic microsatellite markers in the long-spined sea urchin Diadema setosum

We developed twenty polymorphic microsatellite markers for the long-spined sea urchin Diadema setosum by screening microsatellite enriched library, and characterized their polymorphism using two populations of 45 individuals. The number of alleles per locus ranged from 4 to 17, and the observed and expected heterozygosity varied from 0.0714 to 1.000 and 0.6655 to 0.9321, respectively. Twelve loci conformed to the Hardy–Weinberg equilibrium after Bonferroni correction. These polymorphic microsatellite markers will facilitate studies of population genetics and connectivity in D. setosum.     

Development and characterization of 15 polymorphic microsatellite loci in Sonneratia alba (Lythraceae) using next-generation sequencing

A set of 15 new microsatellite loci was developed and characterized for the widespread mangrove tree species Sonneratia alba (Lythraceae) by using next-generation sequencing. Forty-eight S. alba samples from seven populations in the Indo-West Pacific region were genotyped; all loci were polymorphic, with the number of alleles ranging from three to eight. The mean observed heterozygosity per locus was 0.21 for a population from Sabah, Malaysia. No null allele or significant linkage disequilibrium was detected, indicating the robustness of the markers. Only one locus (SA103) showed deviation from Hardy?CWeinberg equilibrium. As characterization of these microsatellite loci was done with samples covering most of the species?? distribution range, the markers can be applied to genetic diversity studies over the broad geographical range of the species.     

Development and characterization of microsatellite loci for eastern red and hoary bats (Lasiurus borealis and L. cinereus)

We developed ten dinucleotide and four tetranucleotide microsatellite markers for two species of tree bats from the family Vespertilionidae that are experiencing high mortality at wind energy facilities. Eleven of these loci were polymorphic in eastern red bats (Lasiurus borealis), whereas nine loci were polymorphic in hoary bats (Lasiurus cinereus). The number of alleles per locus ranged from 2 to 29 (mean = 14 alleles) and observed heterozygosity was generally high (mean 0.754, range 0.125–0.979). This set of microsatellite markers will be useful for studying population structure of these bats as part of a larger effort to understand the potential impacts of wind energy development on their populations.     

Characterization of 10 polymorphic microsatellite loci in the South American lizard Liolaemus fitzingerii with cross-amplification in L. chehuachekenk

We describe the characterization of ten polymorphic microsatellite loci from the Liolaemus fitzingerii species complex with cross-amplification for nine of the 10 loci in L. chehuachekenk. The number of alleles within L. fitzingerii ranged from 7 to 24 and the observed heterozygosity ranged from 0.311 to 0.956 for 45 individuals. Nine of the ten loci conformed to Hardy?CWeinberg equilibrium and we did not detect linkage disequilibrium between loci in L. fitzingerii. Cross-species amplification in L. chehuachekenk was successful for nine of the ten loci with polymorphisms detected for each successfully amplified locus. These microsatellite loci are the first developed for the Eulaemus clade of the genus, and will aid in both ongoing and future studies focusing on gene flow, historical divergence and population structure within the Liolaemus fitzingerii species complex.     

Isolation via 454 sequencing,and characterisation of microsatellite markers for the Pilbara endemic Acacia atkinsiana (Fabaceae)

We isolated 11 new polymorphic microsatellite markers from Acacia atkinsiana, a plant species endemic to the Pilbara region in Western Australia. Next generation (454) sequencing was used to identify 28 microsatellite markers that were trialled in individuals across the species range. Characterisation of 11 of these loci in 24 individuals from a single population yielded between two and nine alleles per locus, and observed heterozygosity ranged from 0.042 to 0.958. Four loci that amplified in A. atkinsiana were also successfully amplified and polymorphic in Acacia ancistrocarpa. These loci will be valuable for assessing population genetic structure in A. atkinsiana and identifying seed sources for rehabilitation of disturbed sites.