Nine polymorphic microsatellite loci for the northern leopard frog (Rana pipiens)

We describe the cloning and characterization of nine microsatellite loci from the northern leopard frog. Seven loci consist of tetranucleotide repeats, one locus consists of a dinucleotide repeat and one locus consists of a GT repeat juxtaposed with a GATA repeat. In a sample of 36 frogs from a natural population, polymorphism at these loci ranged from two to 13 alleles per locus with expected heterozygosities ranging from 0.5 to 0.91. These loci will be useful to researchers since this species is used for a broad range of studies.     

Evolutionary history of the northern leopard frog: reconstruction of phylogeny, phylogeography, and historical changes in population demography from mitochondrial DNA

This study uses a combined methodological approach including phylogenetic, phylogeographic, and demographic analyses to understand the evolutionary history of the northern leopard frog, Rana pipiens. We tested hypotheses concerning how (or if) known geological events and key features of the species biology influenced the contemporary geographic and genetic distribution of R. pipiens. We assayed mitochondrial DNA variation from 389 individuals within 35 populations located throughout the species range. Our a priori expectations for patterns and processes influencing the current genetic structure of R. pipiens were supported by the data. However, our analyses revealed specific aspects of R. pipiens evolutionary history that were unexpected. The phylogenetic analysis indicated that R. pipiens is split into populations containing discrete eastern or western haplotypes, with the Mississippi River and Great Lakes region dividing the geographic ranges. Nested clade analysis indicated that the biological process most often invoked to explain the pattern of haplotype position is restricted gene flow with isolation by distance. Demographic analyses showed evidence of both historical bottlenecks and population expansions. Surprisingly, the genetic evidence indicated that the western haplotypes had significantly reduced levels of genetic diversity relative to the eastern haplotypes and that major range expansions occurred in both regions well before the most recent glacial retreat. This study provides a detailed history of how a widespread terrestrial vertebrate responded to episodic Pleistocene glacial events in North America. Moreover, this study illustrates how complementary methods of data analysis can be used to disentangle recent and ancient effects on the genetic structure of a species.     

Metamorphic changes in localization of sugars in skin of the leopard frog,Rana pipiens

A lectin histochemical study was carried out to determine the distribution of specific sugars in glycoconjugates within an important osmoregulatory organ, amphibian skin. Paraffin sections were made of Rana pipiens skin from dorsal and ventral regions of aquatic larvae in representative developmental stages as well as from several body regions of semiaquatic adult frogs. Sections were incubated with horseradish peroxidase (HRP)‐conjugated lectins, which bind to specific terminal sugar residues of glycoconjugates. Such sites were visualized by DAB‐H₂O₂. The following HRP‐lectins were used: UEA‐1 for α‐L ‐fucose, SBA for N‐acetyl‐D ‐galactosamine, WGA for N‐acetyl‐β‐D ‐glucosamine, PNA for β‐galactose, and Con A for α‐mannose. We found that lectin binding patterns in larvae change during metamorphic climax as the skin undergoes extensive histological remodeling; this results in adult skin with staining patterns that are specific for each lectin and are similar in all body regions. Such findings in R. pipiens provide additional insight into the localization of molecules involved in osmoregulation in amphibian skin. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.     

Directionality of phase locking in auditory nerve fibers of the leopard frog Rana pipiens pipiens

Summary A dorsal approach to the eighth nerve and free-field stimulation were used to investigate the effect of sound direction and intensity on phase locking in auditory nerve fibers of the leopard frog Rana pipiens pipiens.Tuning curves of 75 auditory neurons were analyzed (Fig. 2). Amphibian papillar neurons, but not basilar papillar neurons, exhibit significant phase locking to short tone bursts at the characteristic frequency (CF), the degree of phase locking (vector strength) decreasing with the neuron's CF (Figs. 3, 4 and 10E). Vector strength increases with sound pressure level to saturate about 20 dB above threshold, while the preferred firing phase is only slightly affected (Figs. 5 and 6).In contrast, sound direction hardly affects vector strength (Figs. 7, 8, 9A and 10A and C), but has a strong influence on the preferred firing phase (Figs. 7, 8, 9B and C, 10B and D): With respect to anterior tone presentation there are phase lags for ipsilateral and phase leads for posterior and contralateral presentation. Phase differences between both ears show a sinusoidal or cardioid/ovoidal directional characteristic; maximum differences are found with antero-lateral tone presentation (Fig. 11). The directionality of phase locking decreases with the neuron's CF (Fig. 10F) and only slightly changes with sound pressure level (Fig. 12). Thus, phase locking of amphibian papilla neurons can potentially provide intensity-independent information for sound localization.Abbreviations SPL sound pressure level - FTC frequency threshold curve - CF characteristic frequency - TF test frequency - VS vector strength - AP amphibian papilla - BP basilar papilla     

Microsatellite variation and fine-scale population structure in the wood frog (Rana sylvatica)

We investigated genetic population structure in wood frogs (Rana sylvatica) from a series of Prairie Pothole wetlands in the northern Great Plains. Amphibians are often thought to exist in demographic metapopulations, which require some movement between populations, yet genetic studies have revealed strong subdivision among populations, even at relatively fine scales (several km). Wood frogs are highly philopatric and studies of dispersal suggest that they may exhibit subdivision on a scale of approximately 1-2 km. We used microsatellites to examine population structure among 11 breeding assemblages separated by as little as 50 m up to approximately 5.5 km, plus one population separated from the others by 20 km. We found evidence for differentiation at the largest distances we examined and among a few neighbouring ponds, but most populations were strikingly similar in allele frequencies, suggesting high gene flow among all but the most distant populations. We hypothesize that the few significant differences among neighbouring populations at the finest scale may be a transient effect of extinction-recolonization founder events, driven by periodic drying of wetlands in this hydrologically dynamic landscape.     

RAPD marker estimation of genetic structure among isolated northern leopard frog populations in the south-western USA

Amphibians in the south-western United States are currently experiencing population declines. Causal explanations for these population changes as well as the implementation of sound management practices requires an understanding of the genetic structure of natural amphibian populations. To this end, we estimated genetic differences within and among seven isolated populations of northern leopard frogs, Rana pipiens , from Arizona and southern Utah using random amplified polymorphic DNA (RAPD) analyses. Fourteen arbitrarily designed primers detected 38 polymorphic loci in 85 individual frogs. Three types of population structure were observed in this study. (i) Two populations showed low genetic diversity ( D = 0.10 and 0.04) and may have been established by relatively recent events. (ii) Two were not genetically distinct and exhibited a high degree of within-population diversity ( D = 0.35). The possibility of gene flow between these populations is high due to their geographical proximity and their shared genetic structure. (iii) Three populations were genetically distinct from each other and the other populations, and exhibited intermediate within-population variation ( D = 0.19, 0.17, 0.14). Genetic distances among the seven populations ranged from 0.00 to 0.20, suggesting that some of these leopard frog populations are genetically distinct. Although based on relatively small samples, these data suggest that leopard frog populations in the south-west are likely to represent unique genetic entities worthy of conservation. The management implications of these results are that isolated leopard frog populations should be evaluated on an individual basis to best preserve them.     

History vs. current demography: explaining the genetic population structure of the common frog (Rana temporaria)

The amount of genetic variability at neutral marker loci is expected to decrease, and the degree of genetic differentiation among populations to increase, as a negative function of effective population size. We assessed the patterns of genetic variability and differentiation at seven microsatellite loci in the common frog (Rana temporaria) in a hierarchical sampling scheme involving three regions (208-885 km apart), three subregions within regions and nine populations (5-20 km apart) within subregions, and related the variability and differentiation estimates to variation in local population size estimates. Genetic variability within local populations decreased significantly with increasing latitude, as well as with decreasing population size and regional site occupancy (proportion of censured localities occupied). The positive relationship between population size and genetic variability estimates was evident also when the effect of latitude (cf. colonization history) was accounted for. Significant genetic differentiation was found at all hierarchical levels, and the degree of population differentiation tended to increase with increasing latitude. Isolation by distance was evident especially at the regional sampling level, and its strength increased significantly towards the north in concordance with decreasing census and marker-based neighbourhood size estimates. These results are in line with the conjecture that the influence of current demographic factors can override the influence of historical factors on species population genetic structure. Further, the observed reductions in genetic variability and increased degree of population differentiation towards the north are in line with theoretical and empirical treatments suggesting that effective population sizes decline towards the periphery of a species' range.     

Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population

Knowledge of the degree of temporal stability of population genetic structure and composition is important for understanding microevolutionary processes and addressing issues of human impact of natural populations. We know little about how representative single samples in time are to reflect population genetic constitution, and we explore the temporal genetic variability patterns over a 30-year period of annual sampling of a lake-resident brown trout (Salmo trutta) population, covering 37 consecutive cohorts and five generations. Levels of variation remain largely stable over this period, with no indication of substructuring within the lake. We detect genetic drift, however, and the genetically effective population size (N(e)) was assessed from allele-frequency shifts between consecutive cohorts using an unbiased estimator that accounts for the effect of overlapping generation. The overall mean N(e) is estimated as 74. We find indications that N(e) varies over time, but there is no obvious temporal trend. We also estimated N(e) using a one-sample approach based on linkage disequilibrium (LD) that does not account for the effect of overlapping generations. Combining one-sample estimates for all years gives an N(e) estimate of 76. This similarity between estimates may be coincidental or reflecting a general robustness of the LD approach to violations of the discrete generations assumption. In contrast to the observed genetic stability, body size and catch per effort have increased over the study period. Estimates of annual effective number of breeders (N(b)) correlated with catch per effort, suggesting that genetic monitoring can be used for detecting fluctuations in abundance.     

Directionality of the pressure-difference receiver ears in the northern leopard frog, Rana pipiens pipiens

We studied the directional response of the coupled-eardrum system in the northern leopard frog, Rana pipiens pipiens. Eardrum behavior closely approximates a linear time-invariant system, with a highly correlated input–output relationship between the eardrum pressure difference and the eardrum velocity. Variations in the eardrum transfer function at frequencies below 800 Hz indicate the existence of an extratympanic sound transmission pathway which can interfere with eardrum motions. The eardrum velocity was shown to shift in phase as a function of sound incident angle, which was a direct result of the phase-shift of the eardrum pressure difference. We used two laser-Doppler vibrometers to measure the interaural vibration time difference (IVTD) and the interaural vibration amplitude difference (IVAD) between the motions of the two eardrums. The coupled-eardrum system enhanced the IVTD and IVAD by a factor of 3 and 3 dB, respectively, when compared to an isolated-eardrum system of the same size. Our findings are consistent with the time-delay sensitivity of other coupled-eardrum systems such as those found in crickets and flies.     

Spatial and temporal population structure of sea trout at the Island of Gotland, Sweden, delineated from mitochondrial DNA

In a study of the genetic relationships among 879 anadromous brown trout Salmo trutta from 13 streams at the Island of Gotland, Sweden, using RFLP analysis of a mitochondrial DNA segment (NADH dehydrogenase-1 gene), six haplotypes were detected. Significant genetic divergence was observed among streams as well as between cohorts within streams. Approximately 8–9% of the total variation was due to differences between populations, and 4–5% was explained by differences between cohorts within populations. The female effective population size ( N _ef) was assessed from temporal haplotype frequency differences between consecutive cohorts; the estimated average N _ef over all populations was just below 30, suggesting that these populations were effectively quite small. With such small effective sizes the populations are expected to loose genetic variability quickly, but the observed levels do not appear particularly low. This indicates that female migration between streams occurs. The observed level of differentiation does not support the presumption that a particular pre-smolt migratory behaviour observed in Gotland streams, with large portions of fry leaving for the sea soon after hatching, results in a reduced homing ability. From a conservation management perspective the Gotland brown trout streams should be regarded as a population system where the vitality and survival of brown trout in one stream is dependent on the opportunity of contact and exchange of individuals from other streams.     

Morphology of neurons in the torus semicircularis of the northern leopard frog,Rana pipiens pipiens

The neuronal morphology of the torus semicircularis of the northern leopard frog, Rana pipiens pipiens, was examined in Golgi-impregnated material. Neurons in each of the five subdivisions of the torus semicircularis (Potter, '65a) have distinct morphologies which are characteristic of the subdivision. Laminar nucleus neurons are mostly multipolar with spherical or ovoidal somata and smooth dendrites oriented primarily parallel and perpendicular to the cell laminae. Principal nucleus neurons have variable soma shapes with short dendrites ( < 100 μm) radiating in all directions. In the magnocellular nucleus, there are three major cell types: neurons characterized by small, spherical-shaped somata, with short, thin, radiating dendrites and many varicosities; bi- or tripolar neurons with ovoidal somata, and long (100–200 μm) and smooth dendrites orienting primarily dorsoventrally and mediolaterally; and multipolar neurons with triangular-shaped somata and very long (200–350 μm) dendrites, which are either smooth or highly spiny. Neurons in the commissural nucleus are mostly multipolar cells with ovoidal somata and beaded dendrites projecting mostly dorsally and ventrally. The subependymal midline nucleus contains mostly uni- or bipolar neurons with small ovoidal somata and straight, spiny dendrites. In addition to revealing the morphological features of neurons in the torus, the counterstained material shows further cytoarchitectural organization of the principal nucleus, i.e., the presence of a circular lamellar organization. The functional significance of these anatomical features is discussed.     

The ebb and flow of antimicrobial skin peptides defends northern leopard frogs (Rana pipiens) against chytridiomycosis

Many amphibian species are threatened with extinction by the emerging infectious disease, chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis. This unprecedented global crisis threatens to reduce the biodiversity of the entire amphibian class. The fungus invades the skin and impairs the uptake and retention of essential ions leading to cardiac arrest. Antimicrobial peptides (AMPs) secreted into the mucus of some amphibians are thought to be an important defense against chytridiomycosis. However, little is known about the quantities of AMPs secreted under natural conditions, whether they are sufficient to protect against this pathogen, and how they interact with commensal microbes. To understand how defensive peptides and skin microbes may interact, it is essential to know the precise quantities of AMPs present under natural conditions. Using matrix‐assisted laser desorption time‐of‐flight mass spectrometry and growth inhibition assays, we show that northern leopard frogs (Rana pipiens) at rest constitutively release low amounts of AMPs that inhibit B. dendrobatidis in vitro, and AMP defenses are elevated following a simulated predator attack. Using a synthetic peptide analogue of brevinin‐1Pb as an external control, we quantified the amounts of four previously described AMPs (brevinin 1Pa, brevinin‐1Pb, brevinin‐1Pd, and ranatuerin‐2P) at several time points after secretion. Once secreted onto the skin, the peptides are most active for 15 min, and small quantities persist for at least 2 h. Taken together, our data suggest that small amounts of AMPs are rapidly available and quite stable on the skin of R. pipiens. They are effective inhibitors of B. dendrobatidis at these low constitutive concentrations but degrade within 2 h, protecting the integrity of the skin and commensal bacteria.     

Isolation and characterization of microsatellite markers in the lowland leopard frog (Rana yavapaiensis) and the relict leopard frog (R. onca), two declining frogs of the North American desert southwest

We characterized 15 microsatellite loci for the lowland leopard frog (Rana yavapaiensis) and the relict leopard frog (R. onca) for future studies of population genetic structure and relatedness. Analysis of 20 individuals from single populations of each species showed that all markers were polymorphic in at least one species. Observed and expected heterozygosities ranged from 0 to 0.94 and from 0.11 to 0.85, respectively, and there were three to 11 alleles per locus. No loci were in linkage disequilibrium, but six loci deviated significantly from Hardy-Weinberg equilibrium, and the presence of a null allele was detected in two of these loci.     

Effective population size associated with self-fertilization: lessons from temporal changes in allele frequencies in the selfing annual Medicago truncatula

Despite its significance in evolutionary and conservation biology, few estimates of effective population size (N(e)) are available in plant species. Self-fertilization is expected to affect N(e), through both its effect on homozygosity and population dynamics. Here, we estimated N(e) using temporal variation in allele frequencies for two contrasted populations of the selfing annual Medicago truncatula: a large and continuous population and a subdivided population. Estimated N(e) values were around 5-10% of the population census size suggesting that other factors than selfing must contribute to variation in allele frequencies. Further comparisons between monolocus allelic variation and changes in the multilocus genotypic composition of the populations show that the local dynamics of inbred lines can play an important role in the fluctuations of allele frequencies. Finally, comparing N(e) estimates and levels of genetic variation suggest that H(e) is a poor estimator of the contemporaneous variance effective population size.     

The genetic population structure and temporal genetic stability of gilthead sea bream Sparus aurata populations in the Aegean and Ionian Seas,using microsatellite DNA markers

We examined 662 gilthead sea bream Sparus aurata from wild samples of the species in the Aegean and Ionian Seas, using 20 EST-linked microsatellite markers, in three multiplex panels, as well as seven anonymous loci. Most of the markers were revealed to be highly polymorphic. We found low genetic differentiation between the sampling stations/areas with total F_ST 0.002 (P < 0.05). Based on comparison of five temporal samples, our results indicate genetic data consistency over time for all tested samples, pointing to stable populations, despite reported repeated escape events. Our results confirm the genetic population structure previously observed in these specific areas, using by far more markers than in previous studies in both coding and non-coding DNA loci. The limited genetic structure and the temporal genetic stability indicate neither major genetic differentiation of local populations by geographic isolation nor influence from anthropogenic factors. These results provide a baseline for future reference in any management programme of both wild and farmed population of S. aurata as well as of other aquaculture species with a potential introgression among farmed and wild populations.     

Long-term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout (Salmo trutta) populations

We examined the long-term temporal (1910s to 1990s) genetic variation at eight microsatellite DNA loci in brown trout (Salmo trutta L) collected from five anadromous populations in Denmark to assess the long-term stability of genetic composition and to estimate effective population sizes (Ne). Contemporary and historical samples consisted of tissue and archived scales, respectively. Pairwise thetaST estimates, a hierarchical analysis of molecular variance (amova) and multidimensional scaling analysis of pairwise genetic distances between samples revealed much closer genetic relationships among temporal samples from the same populations than among samples from different populations. Estimates of Ne, using a likelihood-based implementation of the temporal method, revealed Ne >or= 500 in two of three populations for which we have historical data. A third population in a small (3 km) river showed Ne >or= 300. Assuming a stepping-stone model of gene flow we considered the relative roles of gene flow, random genetic drift and selection to assess the possibilities for local adaptation. The requirements for local adaptation were fulfilled, but only adaptations resulting from strong selection were expected to occur at the level of individual populations. Adaptations resulting from weak selection were more likely to occur on a regional basis, i.e. encompassing several populations. Ne appears to have declined recently in at least one of the studied populations, and the documented recent declines of many other anadromous brown trout populations may affect the persistence of local adaptation.     

Effects of anthropogenic intermixing on the genetic structure of Dybowski's frog populations in northeast China

The Dybowski's frog (Rana dybowskii) is mainly distributed in northeast China and the Russian Far East. Its dried oviduct, or frog oil, has been used in traditional Chinese medicine for thousands of years. Frogs from different geographic regions exhibit variations in their body mass and oil productivity. As a result, farmers usually import high quality breeding stock from different areas to increase oviduct productivity. This practice could alter the genetic structure of the frog populations. We used 10 microsatellite loci to investigate the level of genetic variation for 10 frog populations in the context of human-mediated disturbance. The study populations comprised the following: the Hebei, Tieli, and Jiamusi populations from the Lesser Khingan Mountains; the Mudanjiang, Jilin, Jiaohe, and Huadian populations from the north central Changbai Mountains; and the Tonghua, Benxi, and Xiuyan populations from the southern Changbai Mountains. Our results showed that the 3 Lesser Khingan Mountain populations exhibited highly significant differentiation values (F_ST = 0.047–0.071, P < 0.001). In addition, the Tonghua population differentiated significantly from the other 6 populations of the Changbai Mountains (P < 0.001). The genetic differentiation coefficient (F_ST) and gene flow (N_em) estimates showed that the Benxi and Jiaohe populations had a high degree of genetic similarity despite being geographically separated by mountains and river systems. We obtained similar results for the Xiuyan and Tieli populations. Furthermore, the degree of gene flow between the Jiamusi and the north central Changbai Mountain populations was greater than that observed between the Jiamusi and the other Lesser Khingan Mountain populations. These results therefore suggest that the Benxi, Xiuyan, and Jiamusi populations have undergone substantial intermixing because of human-mediated relocation. Economic demands make completely stopping the geographical relocation of Dybowski's frog in northeast China virtually impossible. Consequently, effective management strategies are now a high priority to ensure that conservationists and local economies can work together to guarantee the long-term survival of this species. © 2013 The Wildlife Society.     

Inheritance of enzymes and blood proteins in the leopard frog,Rana pipiens: Three linkage groups established

Individuals from natural populations of the leopard frog, Rana pipiens, were analyzed for electrophoretic differences in blood proteins and enzymes from an amputated digit. The proteins examined represent products of 72 loci. Presumptive heterozygotes at multiple loci were selected for experimental crosses. Mendelian inheritance of 18 protein variations were demonstrated in the offspring. Tests for linkage or independent assortment were performed for 75 locus pairs. Three linkage groups were established. Linkage group 1 contains two loci, aconitase-1 (Acon1) and serum albumin (Alb), with a 19% recombination frequency between them. Linkage group 2 contains four loci, glyoxalase (Gly), acid phosphatase-1 (Ap1), acid phosphatase-2 (AP2), and esterase-5 (Est5). The data show the relationships Gly-21.1%-AP1-0%-AP2-6.3%-Est5, and Gly-25.6%-Est5. Linkage group 3 consists of four closely linked esterase loci. The data, Est1-5.1%-Est6, Est6-1.8%-Est10-1.9%-Est4 and Est6-3.0%-Est4, do not establish a complete order but suggest that Est10 is between Est4 and Est6. These results, with data demonstrating apparent independent assortment of 67 other locus pairs, provide a foundation for establishing the frog genetic map.The project was supported by Grant No. RR-00572 from the Division of Research Resources, National Institutes of Health. This paper is contribution No. C-87 from the Amphibian Facility, George W. Nace, Director.     

Integration and recovery processes contribute to the temporal selectivity of neurons in the midbrain of the northern leopard frog, Rana pipiens

This study examined the mechanisms underlying amplitude modulation selectivity in the anuran auditory midbrain. Single units were recorded extracellularly in the torus semicircularis of the northern leopard frog, Rana pipiens. Two physiologically distinct classes of neurons were identified, based on their response latencies and their selectivities to pulse repetition rates. Cells in one group had short response latencies (median = 31 ms) and responded best to pulse repetition rates below 40 Hz. Tuning to low amplitude modulation rates was largely determined by recovery processes and phasic response properties. Cells in the second group had much longer latencies (median=81 ms) and were generally selective for pulse repetition rates greater than 40-50 Hz. Sensitivity to higher amplitude modulation rates resulted from integration processes; these units only responded when a threshold number of pulses were presented at a minimum pulse density (amplitude modulation rate). At amplitude modulation rates above their best rate, their responses decreased, apparently due to inadequate recovery time between pulses.