Rochelle R. Beasley

Characterization of Microsatellite Loci for an Australian Epiphytic Orchid, Dendrobium calamiforme, Using Illumina Sequencing

Premise of the study: Microsatellite loci were developed for the epiphytic pencil orchid Dendrobium calamiforme for population genetic and phylogeographic investigation of this Australian taxon. Methods and Results: Nineteen microsatellite loci were identified from an Illumina paired-end shotgun library of D. calamiforme. Polymorphism and genetic diversity were assessed in 24 individuals from five populations separated by a maximum distance of ∼80 km. All loci were polymorphic with two to 14 alleles per locus, expected heterozygosity ranging from 0.486 to 0.902, and probability of identity values ranging from 0.018 to 0.380. Conclusions: These novel markers will serve as valuable tools for investigation of levels of genetic diversity as well as patterns of gene flow, genetic structure, and phylogeographic history.

Development of 28 polymorphic microsatellite markers for the endemic Azorean spider Sancus acoreensis (Araneae, Tetragnathidae)

We isolated and characterized a total of 28 microsatellite loci from Sancus acoreensis. Loci were screened in 26 individuals originating from seven (Flores, Faial, Pico, São Jorge, Terceira, São Miguel, and Santa Maria) out of the nine islands of the Azores. The number of alleles per locus ranged from 2 to 14, observed heterozygosity ranged from 0.040 to 0.708, and the probability of identity values ranged from 0.02 to 0.97. Sancus acoreensis is a Laurel forest specialist species, endemic to the Azores, and is facing a great extinction risk due to the severe fragmentation of its habitat. The newly developed microsatellite loci will aid in detecting signs of population bottlenecks and pinpoint the island populations that are facing the greatest risk of extinction. Sancus acoreensis (Araneae, Tetragnathidae) is an endemic Azorean species that inhabits the Laurel forest remnants within the Azores. It is facing a high risk of extinction due to the fragmentation and degradation of its habitat (Triantis et al. 2010). Using ecological indicators of risk, this species was found to be among the arthropod species mostly threatened. In order to assess the genetic diversity levels, and the population structure of this spider species throughout the Azores, we isolated and characterized 28 polymorphic microsatellites. Genomic DNA was extracted using a kit (NucleoSpin Tissue kit, Macherey–Nagel) from a single individual. An Illumina paired-end shotgun library was prepared by shearing 1 lg of DNA using a Covaris S220 and following the standard protocol of the Illumina TruSeq DNA Library Kit and using a multiplex identifier adaptor index. Illumina sequencing was conducted on the HiSeq with 100 bp paired-end reads. Five million of the resulting reads were analyzed with the program PAL_FINDER_v0.02.03 (Castoe et al. 2012) to extract those reads that contained di-, tri-, tetra-, penta-, and hexa-nucleotide microsatellites. Once Electronic supplementary material The online version of this article (doi:10.1007/s12686-013-9976-7) contains supplementary material, which is available to authorized users.

Development and characterization of twenty-five microsatellite markers for the longnose dace (Cyprinidae: Rhinichthys) using paired-end Illumina shotgun sequencing

We isolated and characterized a total of 48 microsatellite loci in Rhinichthys cataractae a widely distributed freshwater fish that may contain several cryptic species. Loci were screened in 24 individuals from several areas of British Columbia, Canada. The number of alleles per locus ranged from 5 to 24, observed heterozygosity ranged from 0.250 to 0.940, and the probability of identity ranged from 0.006 to 0.453. These new loci are being used for conducting investigations into the genetic structure, diversity, and speciation in populations of this exceptionally broadly-distributed North American freshwater fish.

Development and characterization of twenty-two polymorphic microsatellite markers for the leafcutter ant, Acromyrmex lundii, utilizing Illumina sequencing

We isolated and characterized a total of 22 microsatellite loci for the leafcutter ant, Acromyrmex lundii. The loci were screened for 24 individuals from southern Brazil and Uruguay. The number of alleles per locus ranged from 5 to 20, the observed heterozygosity ranged from 0.417 to 0.917, and the probability of identity values ranged from 0.011 to 0.38. These genetic markers will be useful for understanding the population and conservation biology of the leafcutter ant A. lundii and closely related species, and will provide novel insights into the evolutionary biology of social parasitism and leafcutter ant mating systems.

Patterns of amphibian infection prevalence across wetlands on the Savannah River Site, South Carolina, USA.

Amphibian diseases, such as chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd) and ranaviral disease caused by ranaviruses, are often linked to global amphibian population declines, yet the ecological dynamics of both pathogens are poorly understood. The goal of our study was to determine the baseline prevalence, pathogen loads, and co-infection rate of Bd and ranavirus across the Savannah River Site (SRS) in South Carolina, USA, a region with rich amphibian diversity and a history of amphibian-based research. We tested over 1000 individuals, encompassing 21 amphibian species from 11 wetlands for both Bd and ranavirus. The prevalence of Bd across individuals was 9.7%. Using wetland means, the mean (±SE) Bd prevalence was 7.9 ± 2.9%. Among toad species, Anaxyrus terrestris had 95 and 380% greater odds of being infected with Bd than Scaphiopus holbrookii and Gastrophryne carolinensis, respectively. Odds of Bd infection in adult A. terrestris and Lithobates sphenocephalus were 75 to 77% greater in metal-contaminated sites. The prevalence of ranavirus infections across all individuals was 37.4%. Mean wetland ranavirus prevalence was 29.8 ± 8.8% and was higher in post-metamorphic individuals than in aquatic larvae. Ambystoma tigrinum had 83 to 85% higher odds of ranavirus infection than A. opacum and A. talpoideum. We detected a 4.8% co-infection rate, with individuals positive for ranavirus having a 5% higher occurrence of Bd. In adult Anaxyrus terrestris, odds of Bd infection were 13% higher in ranavirus-positive animals and odds of co-infection were 23% higher in contaminated wetlands. Overall, we found the pathogen prevalence varied by wetland, species, and life stage.

Development and characterization of 30 novel microsatellite markers for Grant’s gazelle (Nanger granti)

We isolated and characterized a set of 30 novel microsatellite loci for Grant’s gazelle (Nanger granti). Loci were screened in 24 individuals from a population in Laikipia County, Kenya. The mean number of alleles per locus was 3.73 (range 1–10), and observed heterozygosity ranged from 0.00 to 0.870 (mean 0.404). The Grant’s gazelle is currently listed as a species of least concern by the IUCN, but declining numbers across a large part of its range are a cause for concern. These new loci will facilitate basic behavioral, ecological, and population genetic studies of a species facing declining populations.

Development of polymorphic microsatellite markers for a rare dragonfly, Cordulegaster sarracenia (Odonata: Cordulegastridae), with notes on population structure and genetic diversity

We isolated and characterized a total of 13 microsatellite loci from Cordulegaster sarracenia (Odonata: Cordulegastridae). Loci were screened in 24 individuals from Louisiana and Texas. Within C. sarracenia, the number of alleles per locus ranged from 0 to 5, and observed and expected heterozygosities ranged from 0.000 to 0.556 and 0.000 to 0.613, respectively. Overall differentiation among study populations was very high (FST = 0.423), suggesting significant geographic population structure with low diversity within populations. Twelve of the 13 primers amplified in C. sayi, C. diastatops, C. maculata, and C. obliqua and polymorphism levels are reported. These new genetic markers will provide tools for addressing a number of population genetic and demographic questions relating to conservation of this rare dragonfly species.

Development, Characterization, and Utility of 13 Polymorphic Microsatellite Loci in Praticolella (Gastropoda: Polygyridae) Species from South Texas, U.S.A.

Abstract: We developed and characterized 13 polymorphic microsatellite loci in South Texas species of Praticolella von Martens, 1892 (Gastropoda: Polygyridae), some of which have restricted distributions and can be difficult to identify using traditional shell characters. To make this genomic tool more broadly useful in these species, instead of characterizing loci in many individuals of a single species, we tested them across five populations of four different species. Twelve loci amplified in all four species tested, and eleven loci showed deviations from Hardy-Weinberg equilibrium. These loci will be valuable in assessing species identity and population genetic connectivity among South Texas Praticolella.

Development and characterization of 33 novel polymorphic microsatellite markers for the brown tree snake Boiga irregularis

BackgroundBoiga irregularis is a widespread invasive species on Guam and has led to extirpation of most of the island’s native avifauna. There are presently no microsatellite markers for this invasive species, hence we developed highly polymorphic microsatellite markers to allow for robust population genetic studies on Guam.FindingsWe isolated and characterized 33 microsatellite loci for the brown tree snake, B. irregularis. The loci were screened across 32 individuals from Guam. The number of alleles per locus ranged from three to ten, with an average of 4.62. The expected (He) and observed heterozygosity (Ho) ranged from 0.294 to 0.856 and from 0.031 to 0.813, with an average of 0.648 and 0.524, respectively. Significant deviations from Hardy–Weinberg equilibrium were detected at seven loci after Bonferoni correction. Probability of identity values ranged from 0.043 to 0.539.ConclusionsThese genetic markers are useful for understanding a suite of post-invasion population genetic parameters, sources of invasions, and effectiveness of management strategies for this invasive species.

Development of polymorphic microsatellite markers for the orange-breasted falcon (Falco deiroleucus)

We isolated and characterized a total of 24 microsatellite loci from the orange-breasted falcon (Falco deiroleucus). Loci were screened in 32 individuals currently maintained as a captive population: 13 wild-caught individuals from Panama and four from Belize, and the remaining 15 were first generation F1 offspring. The number of alleles per locus ranged from 2 to 9, observed heterozygosity ranged from 0.000 to 0.938, and the probability of identity values ranged from 0.075 to 0.604. These new loci will provide tools for identifying relatedness values among sampled individuals currently in captivity and for exploring genetic diversity levels and connectivity between populations in Central America.