Isolation and characterization of microsatellite markers for the heavily exploited rockfish Sebastes schlegeli, and cross-species amplification in four related Sebastes spp.

Here we report development and characterization of 14 polymorphic microsatellite loci from Sebastes schlegel. Polymorphism at these loci revealed from 3 to 23 alleles. The observed heterozygosity ranged from 0.34 to 1.00, and the expected heterozygosity ranged from 0.31 to 0.95. No linkage disequibrium was found. Two loci were significantly deviated from HWE (P < 0.01). The 14 loci were also surveyed in four other Sebastes species and 12 loci successfully amplified, where allelic diversity ranged from highly polymorphic to monomorphic. These results demonstrate these microsatellite markers can be used for the study of intra- and inter-specific genetic diversity.     

Characterization of microsatellite markers from capybaras,Hydrochoerus hydrochaeris (Rodentia: Hydrochoeridae)

Fourteen microsatellite loci were isolated from capybaras (Hydrochoerus hydrochaeris), which are large, diurnal social rodents that occur in the wet savannas of South America. Five of these loci were monomorphic. The remaining nine loci were polymorphic (two to seven alleles per locus), with observed levels of heterozygosity ranging from 0.063 to 0.800 (n = 17 animals). The latter loci provide a valuable tool for assessing patterns of parentage and kinship within capybara social groups.     

Development of new microsatellite loci and multiplex reactions for muskellunge (Esox masquinongy)

The muskellunge (Esox masquinongy) is a valued fisheries species throughout its native range. Numerous studies have documented performance and phenotypic differences among muskellunge populations, but genetic markers for assessment have been lacking. We characterized 14 microsatellite loci and developed five multiplex polymerase chain reactions. Successful amplification of northern pike (Esox lucius) was observed for seven loci. These microsatellites will be useful for analysing population structure, performance characteristics of propagated strains, and helping to develop and monitor hatchery management guidelines for muskellunge.     

Expulsion of miniature radio transmitters along with eggs of muskellunge and northern pike––a new method for locating critical spawning habitat

Identification and protection of critical spawning habitat for muskellunge Esox masquinongy and northern pike Esox lucius is important for preserving the reproductive potential of both species. In this study, we implanted miniature radio transmitters through the oviduct into the egg masses of female muskellunge and northern pike just prior to spawning. This non-surgical procedure was a novel approach for identifying spawning sites when transmitters were expelled with the eggs during egg deposition. Preliminary studies in three lakes showed that muskellunge and northern pike deposited many of the transmitters in likely spawning habitat. An inability to find eggs limited our validation of this method, but nevertheless, a relatively high proportion (70%) of northern pike larger than 690 mm (27.2 inches) expelled transmitters in a previously known spawning area in Willow Lake, Minnesota. Shoreline vegetation in that area consisted primarily of sedges Carex spp., and the adjacent water was shallow with substrate consisting of large mats of water bulrush Scirpus subterminalis. A lower proportion (50%) of muskellunge expelled transmitters in Elk Lake, Minnesota. Water depth at likely spawning sites averaged 1.1 m (3.6 feet) and vegetative cover was variable, but Chara spp. was common to most sites. In Moose Lake, Minnesota, containing sympatric populations of muskellunge and northern pike, 60% of muskellunge and 90% of pike expelled transmitters. Chara spp. beds were the predominant substrate where transmitters were expelled in Moose Lake, but the two species deposited transmitters on deepwater bars (3.7–5.2 m) in addition to shallow near-shore habitat. These results suggest more flexibility in depths used for spawning than typically reported for muskellunge and northern pike.     

Potential effects of spawning habitat changes on the segregation of northern pike (<Emphasis Type="Italic">Esox lucius</Emphasis>) and muskellunge (<Emphasis Type="Italic">E</Emphasis>. <Emphasis Type="Italic">masquinongy</Emphasis>) in the Upper St. Lawrence River

Changes in spawning habitat of northern pike (Esox lucius) may affect their segregation from and coexistence with the closely related muskellunge (E. masquinongy). We estimated the areal coverage of robust and shallow emergent vegetation in three shared-spawning bays in the Upper St. Lawrence River from aerial photographs taken from 1948 to 2003. Robust emergent vegetation (e.g., cattail) increased in coverage by 155–241% while shallow emergents (sedges) decreased by 46–96%. The loss of sedges, an important northern pike-spawning habitat, may facilitate greater spawning overlap in offshore-submersed aquatic vegetation within bay habitats used by muskellunge. Development rates and characteristics of northern pike and muskellunge eggs and larvae were compared to better understand the implications of greater spawning overlap. Northern pike eggs developed faster than muskellunge eggs at temperatures of 4.7–19°C, and adhesive eggs and the presence of adhesive papillae were present in both species. Equations were used to predict degree-day requirements for hatching and swim-up in three habitats (shallow emergents, bay, and offshore shoal) along a temperature gradient. Northern pike required more estimated degree days to reach hatching in bay and offshore shoal habitat relative to shallow emergent habitat due to cooler temperatures. Significant spawning overlap is known to occur within bay habitats, but poor success of northern pike in deep bay habitats and overall reductions in abundance are hypothesized to currently buffer muskellunge from potential negative interactions between these species. Guest editors: J. M. Farrell, C. Skov, M. Mingelbier, T. Margenau & J. E. Cooper International Pike Symposium: Merging Knowledge of Ecology, Biology, and Management for a Circumpolar Species     

Isolation and characterization of microsatellites in yellow perch (Perca flavescens)

A total of 45 microsatellite loci from yellow perch, Perca flavescens, were isolated and characterized. Among the 45 microsatellite loci, 32 had more than two alleles. A wild population of P. flavescens (n = 48) was used to examine the allele range of the microsatellite loci. Mendelian inheritance of alleles was confirmed by examining the amplified products in pair‐mated families. The number of alleles for the 32 polymorphic loci varied from two to 16, and observed heterozygosity ranged between 0.024 (YP79) and 0.979 (YP60). Cross‐species polymorphic amplification in four other Percidae species was successful for 22 loci.     

Dinucleotide microsatellite primers designed for a critically endangered primate,the black lion tamarin (Leontopithecus chrysopygus)

Black lion tamarin (BLT) monkeys (Leontopithecus chrysopygus) have suffered a severe reduction in their natural range and are consequently critically endangered. Because allozyme data showed very low levels of variation, it was not clear if these monkeys had much genetic diversity. We designed microsatellite primers for BLTs, and from them we identified nine polymorphic loci, seven of which were tested on golden lion tamarins (GLTs) (Leontopithecus rosalia). All of the seven polymorphic loci and two other monomorphic BLT loci were polymorphic in GLTs. The microsatellite markers identified here are directly applicable to ongoing lion tamarin population and conservation genetics studies.     

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.     

Comparison of mouth morphology and prey size selection among three esocid taxa

Aquatic organisms, especially fishes, exhibit exceptional diversity in mouth morphology and this variation has been shown to influence foraging patterns. We compared mouth morphology among muskellunge Esox masquinongy, northern pike Esox lucius and their hybrid, tiger muskellunge E. masquinongy x E. lucius. Head and mouth size among the three taxa were similar for juveniles (<400 mm total length), but diverged with increasing length, being greater for northern pike than muskellunge. Tiger muskellunge had a head and mouth size intermediate to the two, but more similar to northern pike than muskellunge. Morphological differences among taxa were related to data examining prey size selection in laboratory and field experiments. In the laboratory, northern pike selected prey that were smaller than their maximum mouth width (widest point between outside corners of mouth), tiger muskellunge selected larger prey, and muskellunge size-selection was intermediate between the other two taxa. Among the three esocids, muskellunge had the smallest increase in handling time with increasing prey body depth relative to predator mouth width. In a common garden field experiment in three lakes containing mainly deep-bodied prey, results generally followed morphological patterns, with northern pike selecting larger prey compared to muskellunge. Although morphology predicted most of the variation in greatest body depth of prey consumed, the best predictor of prey size was a model that included predator mouth width, taxon, and interaction. Information comparing prey size selection among esocid taxa is useful for understanding how to manage esocid populations based on system-specific prey characteristics and also for understanding how variations in morphological characteristics of apex predators can influence prey vulnerability and ecosystem structure.     

Microsatellite primers for the Western Pebble‐mound Mouse (Pseudomys chapmani) that show cross amplification for other species of Australian rodent

We describe 12 dinucleotide and one tetranucleotide microsatellite loci for the Western Pebble‐mound Mouse (Pseudomys chapmani) that can be amplified with the polymerase chain reaction. All primers produced clear and highly polymorphic amplification patterns containing between seven and 14 alleles and with high expected heterozygosities. The amplification of these primers across seven related conspecifics makes them useful for population genetic studies and conservation work in several of these species.     

Tetranucleotide microsatellite loci from the striped dolphin (Stenella coeruleoalba Meyen, 1833)

Five tetranucleotide microsatellite loci were isolated from the striped dolphin (Stenella coeruleoalba). Characterization of these loci revealed between three and 11 alleles at each locus and observed heterozygosity ranged from 0.192 to 0.775. All sets of primers amplified homologous loci when tested on four related species and showed polymorphisms in most locus–species combinations. A sixth microsatellite, which appeared to be monomorphic in the striped dolphin, was also shown to be polymorphic in three related species.     

Microsatellite markers for <Emphasis Type="Italic">Pseudopanax</Emphasis> trees and their cross-species amplification in the Araliaceae

In order to study hybridisation, taxonomic boundaries and phylogeography in the genus Pseudopanax (Araliaceae), we developed seven novel microsatellite loci from enriched genomic libraries of P. lessonii and P. crassifolius. These loci were characterised in 16 individuals from a single population of P. crassifolius, and displayed 2–11 alleles per locus. Observed heterozygosities ranged from 0.063 to 0.688. Most loci were polymorphic in the closely related Pseudopanax species, and several loci amplified widely across the Araliaceae.     

Isolation and characterisation of di and tri nucleotide microsatellite loci in Rosmarinus officinalis (Lamiaceae), using enriched genomic libraries

An enrichment protocol was used to isolate and characterise microsatellite loci in Rosmarinus officinalis, a Mediterranean chamephyte. Twelve microsatellite loci were characterised and amplified a total of 117 alleles in a sample of 30 individuals from one population, with an average of 9.75 alleles per locus. Observed heterozygosities ranged from 0.333 to 0.900. Cross-species transferability was also assayed in the two other species of the genus. The cumulated probabilities of exclusion for paternity and parentage of the 12 loci were of 0.999971 and 1, respectively, supporting the usefulness of these microsatellite loci for parentage analyses. Nine out of 12 microsatellite loci amplified in the two species and were polymorphic detecting a total of 49 and 45 in R. eriocalyx and R. tomentosus, respectively. Twenty-two alleles were exclusive of R. eriocalyx and 12 of R. tomentosus, additionally, three alleles were shared between these two species but were otherwise absent in the analysed individuals of R. officinalis. In total, this set of markers amplified 154 different microsatellite alleles, supporting their usefulness to conduct population genetic, reproductive biology and hybridisation studies in Rosmarinus.     

Isolation and characterization of polymorphic microsatellite loci for the study of paternity and population structure in the little penguin Eudyptula minor

We isolated and characterized eight novel microsatellite loci in the little penguin Eudyptula minor, using nonradioactive polymerase chain reaction‐based techniques to screen GA and GAAA repeats from enriched genomic DNA libraries. All eight loci were polymorphic and seven were variable in our main study population (mean H_E = 0.613, mean N_A = 7.14). Cross‐amplification using a microsatellite primer developed in Spheniscus demersus (African penguin) yielded one additional polymorphic locus. This locus combined with six of the little penguin loci is suitable for paternity assignment in little penguins (exclusion probability for seven unlinked loci = 0.993).     

Isolation of 22 new Haliaeetus microsatellite loci and their characterization in the critically endangered Madagascar fish‐eagle (Haliaeetus vociferoides) and three other Haliaeetus eagle species

We isolated a total of 22 microsatellite loci from two Haliaeetus species: the Madagascar fish‐eagle (Haliaeetus vociferoides) and the bald eagle (Haliaeetus leucocephalus). Five loci were monomorphic in both the Madagascar fish‐eagle (n = 24–43) and the bald eagle (n = 2–8) but were found to be polymorphic in other Haliaeetus species. Haliaeetus loci have proved useful for investigating gene flow in Haliaeetus and Aquila eagles. Ten loci were polymorphic in the critically endangered Madagascar fish‐eagle and will be used to investigate the genetic population structure and mating system in this species.     

Characterization of microsatellite loci in the dwarf eelgrass Zostera noltii (Zosteraceae) and cross‐reactivity with Z. japonica

Zostera noltii is an important species of eelgrass occurring along European, north African, Mediterranean, Black Sea and Azov Sea coasts. Nine microsatellite loci were developed and no linkage disequilibrium was observed. Cross‐amplification was observed for all loci (polymorphic) in Z. japonica; only four loci amplified (monomorphic) in Z. marina.     

Novel polymorphic microsatellite markers for paternity analysis in the red‐capped robin (Petroica goodenovii: Aves)

Seven microsatellite loci were isolated and characterized from the red‐capped robin Petroica goodenovii, using nonradioactive polymerase chain reaction (PCR)‐based techniques to screen an enriched genomic library. Five loci showed no evidence of null alleles and were variable [mean heterozygosity (H_E) = 0.440, mean number of alleles = 8]. Cross‐amplification using primers for microsatellites in Phylloscopus occipitalis and Emberiza schoeniclus yielded another two polymorphic loci. The combined set of five red‐capped robin and two cross‐amplified loci are suitable for paternity assignment (exclusion probability for seven unlinked loci = 0.9760).     

Cloning and characterization of novel microsatellite DNA markers for the grass rockfish,Sebastes rastrelliger,and cross‐species amplification in 10 related Sebastes spp

Here we report development and characterization of seven polymorphic loci derived from grass rockfish (Sebastes rastrelliger) genomic DNA phagemid libraries enriched for microsatellite motifs. Within grass rockfish, average allelic diversity was 11.3 alleles per locus and average heterozygosity was 0.73. The seven loci also were surveyed in 10 related species of Sebastes, where allelic diversity ranged from highly polymorphic to monomorphic. Deviations from Hardy–Weinberg were nonsignificant in all but one species/locus combination suggesting low occurrence of null alleles. Significant linkage disequilibrium was detected among three loci, but these events were limited to a single species in each case.     

Isolation and characterization of microsatellite loci in Ononis repens,Leguminosae

Ten polymorphic microsatellites were isolated from Ononis repens, using a microsatellite enrichment protocol and selective hybridization with a mixed synthetic dinucleotide repeat probe. Primers for DNA amplifications using polymerase chain reaction (PCR) were designed and synthesized. The loci amplified in both O. repens and O. spinosa. All 10 loci were polymorphic in each of four populations studied. These microsatellite markers will be useful for population genetic analysis and biodiversity studies of O. repens and O. spinosa.     

Isolation and characterisation of polymorphic microsatellite loci in the vulnerable spectacled flying fox, Pteropus conspicillatus

The spectacled flying fox, Pteropus conspicillatus, is listed as vulnerable in Australia and is under threat from numerous impacts. Primers to amplify eight co-dominant microsatellite loci were designed for Pteropus conspicillatus, based on an enriched genomic library. Four loci were monomorphic in this species while the remaining four loci were highly polymorphic with 16–23 alleles. Two of the four monomorphic loci were found to be polymorphic in Pteropus alecto, a closely related congener. All but one of the six polymorphic loci were in Hardy Weinberg equilibrium. Additionally, six microsatellite loci isolated for Pteropus rodricensis were tested against individuals of P. conspicillatus with all loci amplifying reliably. These loci will be used to investigate population genetic structure in the vulnerable spectacled flying fox.