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33 results for “Pseudacris”
Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris) – De novo reference transcriptome: Assemblerd contigs and gene annotations
<p>Assembled contigs (Trinity) and gene annotations (Trinotate) of a reference transcriptome for the Upland Chorus Frog, <em>Pseudacris feriarum</em>. Data to assemble the contigs were obtained by sequencing four tissue types: Brain, eyes, testis, and somatic (liver/heart/lung/skin/muscle). Raw reads are stored in the NCBI-SRA database (BioProject PRJNA723357).</p>
Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris) – De novo reference transcriptome raw data, contigs and gene annotations
<p>RNA-Seq raw data used in the assembly and annotation of a reference transcriptome for the Upland Chorus Frog, <em>Pseudacris feriarum</em>. Raw data were obtained by sequencing of four tissue types: Brain, eyes, testis, and somatic. Assembled contigs (Trinity) and gene annotations (Trinotate) are also provided.</p>
Data for the detection of the boreal chorus frog (Pseudacris maculata) using environmental DNA and call surveys at 180 ponds sampled in 2017-2018 in southeastern Québec, Canada
<p>The boreal chorus frog (<em>Pseudacris maculata</em>) is at risk of extinction in parts of its range in Canada. Our objectives were to quantify the influence of local and landscape characteristics on the occurrence of the species in wetlands in southern Québec. We hypothesized that site occupancy depends on local characteristics and landscape characteristics contributing to site connectivity. We developed an environmental DNA (eDNA) method to detect the species and compared the detection probability of this method to traditional call surveys. We collected water samples at a total of 180 sites (90 in 2017, 110 in 2018), whereas we surveyed a subset of 63 sites using both eDNA and call surveys in 2018. Site occupancy varied across years, but was higher in sites where the species had been previously detected during the last 12 years by other studies. Site occupancy did not vary with other local and landscape characteristics, in part due to an apparent decrease in the number of sites occupied by the species since the last 12 years. Detection probability via eDNA (0.81; 95% CI: [0.31; 0.98]) did not differ from that of call surveys (0.62; 95% CI: [0.25; 0.89]). To identify the optimal sampling period for the boreal chorus frog, future studies should estimate the detection probability of eDNA during the breeding season and the larval development period of the species.</p>
Using Anuran community diversity and Pseudacris crucifer to predict landscape quality across a land use gradient
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Data for the detection of the boreal chorus frog (Pseudacris maculata) using environmental DNA and call surveys at 180 ponds sampled in 2017-2018 in southeastern Québec, Canada
Open the record for dataset details and reuse information.
Data from: Contact zone dynamics during early stages of speciation in a chorus frog (Pseudacris crucifer)
Characterizing the genetic and behavioural consequences of contact between previously geographically isolated lineages provides insights into the mechanisms underlying diversification and ultimately speciation. The spring peeper (Pseudacris crucifer) is a widespread Nearctic chorus frog with six divergent mitochondrial DNA (mtDNA) lineages, many of which came into secondary contact during the Holocene. We examined genetics, morphology, advertisement calls and female preference for two lineages that began diverging in allopatry in the Pliocene and now overlap in southwestern Ontario, Canada. We found non-coincident clines in mtDNA and nuclear DNA, mirroring directionality of premating isolation barriers. We also found divergence in a range of traits between these two lineages, displacement in male call attributes and female preference for calls of their natal lineage in sympatry. Hybrids were morphologically distinct from both parental lineages, but hybrid male calls were acoustically intermediate. Female hybrids showed asymmetrical preference for Eastern male calls. These results considered together provide evidence of either unidirectional hybridization or selection against hybrids, potentially implying reproductive character displacement. Our work demonstrates the utility of integrated, multi-character approaches to understanding the processes of divergence and the nature of speciation.
Data from: Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing
The field of phylogenetics is changing rapidly with the application of high-throughput sequencing to non-model organisms. Cost-effective use of this technology for phylogenetic studies, which often include a relatively small portion of the genome but several taxa, requires strategies for genome partitioning and sequencing multiple individuals in parallel. In this study we estimated a multilocus phylogeny for the North American chorus frog genus Pseudacris using anonymous nuclear loci that were recently developed using a reduced representation library approach. We sequenced 27 nuclear loci and three mitochondrial loci for 44 individuals on 1/3 of an Illumina MiSeq run, obtaining 96.5% of the targeted amplicons at less than 20% of the cost of traditional Sanger sequencing. We found heterogeneity among gene trees, although four major clades (Trilling Frog, Fat Frog, crucifer, and West Coast) were consistently supported, and we resolved the relationships among these clades for the first time with strong support. We also found discordance between the mitochondrial and nuclear datasets that we attribute to mitochondrial introgression and a possible selective sweep. Bayesian concordance analysis in BUCKy and species tree analysis in *BEAST produced largely similar topologies, although we identify taxa that require additional investigation in order to clarify taxonomic and geographic range boundaries. Overall, we demonstrate the utility of a reduced representation library approach for marker development and parallel tagged sequencing on an Illumina MiSeq for phylogenetic studies of non-model organisms.
Data from: Hierarchical Hybrid Enrichment: multi-tiered genomic data collection across evolutionary scales, with application to chorus frogs (Pseudacris)
Determining the optimal targets of genomic sub-sampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for sub-sampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first we compare the benefits of target loci developed for deep- and shallow-scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography) and within a hybrid zone (population genomics). Specifically, we target evolutionary conserved loci that are appropriate for deep phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer longstanding evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels, we (a) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis-testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; (b) estimate the phylogeographic history of P. feriarum, which reveals five independent invasions of sympatry by this species to form replicated reinforcement contact zones with P. nigrita with ongoing gene flow into sympatry; and (c) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is much lower than previously found by microsatellite-based studies. We find that the hierarchical hybrid enrichment approach offers an efficient, multi-tiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales.
FIGURE 8 in A new North American chorus frog species (Amphibia: Hylidae: Pseudacris) from the south-central United States
FIGURE 8. Phylogeny of the trilling chorus frogs (clade within Pseudacris) based on Lemmon et al. (2007b). Also shown are within- and between-species average pairwise genetic distances (GTR+G+I corrected p-distances) for the 12S/ 16S mitochondrial region, expressed as percentages. Pseudacris maculata and P. clarkii are represented with a single branch because these species are not reciprocally monophyletic.
FIGURE 6 in A new North American chorus frog species (Amphibia: Hylidae: Pseudacris) from the south-central United States
FIGURE 6. Multivariate variation in morphology and advertisement calls within and among Pseudacris feriarum, P. fouquettei, P. m a c u l a t a, and P. nigrita along the first two principal component axes. Representatives of each species are enclosed by polygons. Analyses of morphological data were based on the nine variables in Fig. 7. Analyses of call data were based on the five variables in Fig. 5. Prior to analysis, morphological variables were averaged by population, such that each point on the graph represents a population. In contrast, points on the advertisement call graph represent individuals.
FIGURE 4 in A new North American chorus frog species (Amphibia: Hylidae: Pseudacris) from the south-central United States
FIGURE 4. Advertisement calls of Pseudacris nigrita (first row), P. fouquettei (second row), P. feriarum (third row), and P. maculata (fourth row). Individuals were recorded within ~2°C of each other at 11.6, 12.6, 13.8, and 11.7°C, respectively. Oscillograms (10 sec and 1.5 sec) are shown in columns A and B, spectrograms in column C, and power spectra in column D. Numbered calls in A indicate different individuals calling in sequence. A single call is represented in B–D. Units are as follows: amplitude (volts), time (seconds), and frequency (kilohertz).
FIGURE 1 in A new North American chorus frog species (Amphibia: Hylidae: Pseudacris) from the south-central United States
FIGURE 1. Distributions of Pseudacris feriarum, P. fouquettei, P. maculata, and P. nigrita in the southern United States based on genetic data (Lemmon et al. 2007b). Symbols indicate populations included in genetic analyses. The type locality of P. fouquettei is denoted with a star. Capital "C"s indicate populations analyzed for advertisement calls. Populations analyzed for morphometric data are not shown (see Appendix 1).
FIGURE 3 in A new North American chorus frog species (Amphibia: Hylidae: Pseudacris) from the south-central United States
FIGURE 3. Photographs of Pseudacris feriarum, P. fouquettei, P. maculata, and P. nigrita in life. Specimens are described with localities and museum numbers from left to right: P. nigrita: Calhoun Co., Florida TNHC 63211 and Barnwell Co., South Carolina TNHC 62205; P. fouquettei: Marion Co., Mississippi TNHC 63600 and Craighead Co., Arkansas TNHC 62259; P. feriarum: Calhoun Co., Florida TNHC 63319 and Johnson Co., North Carolina TNHC 63564; P. m a c u l a t a: Fillmore Co., Minnnesota TNHC 63612 and Douglas Co., Kansas TNHC 62378. Photos by EML except TNHC 63612 was photographed by Suzanne L. Collins.
FIG. 12 in Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States
FIG. 12. Oscillograms (first and second columns), spectrograms (third column), and power spectra (fourth column) of advertisement calls from (A) P. collinsorum (recorded at 10.28C) and (B) P. brachyphona (recorded at 12.68C). The second columns represent a single call extracted from those in the first column. In the case of P. collinsorum (A), two males were recorded while duetting and are identified with numbers.
FIG. 11 in Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States
FIG. 11. Live specimens of P. collinsorum (left, photo by EML) from Lawrence County, Alabama and P. brachyphona (right, photo by Suzanne Collins) from Harrison County, West Virginia. Specimens of P. collinsorum often lack a distinct dorsal coloration pattern. For a color version of this figure, please refer to the online version of this article.
FIG. 7 in Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States
FIG. 7. Response curves of variables with highest contribution (.10%) to the Northern (black line, dark gray shadow) and Southern (gray line, light gray shadow) clade SDMs. The solid lines represent average probability of occurrence based on ten model replicates, while shadowed areas equal to 6 standard deviation. The dotted line indicates a 50% occurrence probability, with environmental values above this threshold indicating suitable habitat. Each clade shows a peak of habitat suitability (.50% occurrence probability) at different values of each variable, suggesting ecological divergence.
FIG. 10 in Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States
FIG. 10. Dorsal and lateral views of type specimens of P. collinsorum (A– D) and P. brachyphona (E–H). (A–B) Male P. collinsorum from Hale County, Alabama (UF 190162). (C–D) Male P. collinsorum from Hale County, Alabama (UF 190167). (E–F) Female P. brachyphona from Preston County, West Virginia (NCSM 100109). (G–H) Male P. brachyphona from Preston County, West Virginia (NCSM 100110). Black bars equal to 1 cm. For a color version of this figure, please refer to the online version of this article.
FIG. 9 in Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States
FIG. 9. Differences in pulse rate (PR), number (PN), and dominant frequency peak (DFP) in acoustic signals recorded in P. brachyphona from Tennessee (TN) and Alabama (AL). Locality-specific distributions of PR, PN, and DFP (A–C). The thick bar in these boxplots represents mean value. Lower and upper edges of each box are 25th and 75th quantile, respectively, and lower and upper whiskers represent the minimum and maximum limits of the interquartile range. Outliers are represented as hollow points. Randomization tests (1,000 reps) were performed for each of these variables (D–E), yielding significant differences for PR and DFP between Tennessee and Alabama, but not for PN.
FIG. 5 in Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States
FIG. 5. Principal component analysis plot based on residuals from regressions of each morphometric variable against snout–vent length. Abbreviations for the labels on the PC loadings (arrows) are the same as in the text (see Materials and Methods). Convex hulls are shown for each clade.
FIG. 3 in Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States
FIG. 3. Genetic clustering based on 21,702 SNPs from AHE loci for P. brachyphona. (A) The Structure plot shows two genetic clusters: Northern (n ¼ 17, green) and Southern (n ¼ 16, blue) as observed in the map (B). The pie charts correspond to the proportion of admixture as estimated in Structure. A blue arrow marks the samples from Hale County, Alabama. Two individuals assigned to the Northern cluster showed introgression from P. feriarum (''out,'' gray). (C) The discriminant analysis of principal components (DAPC) required one discriminant function to explain 67.4% of the genetic variance. Lines at the bottom of the distributions represent one individual. The DAPC also shows two clusters in agreement with the Northern and Southern clusters from Structure. The location of the Tennessee River is shown.
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Allen Brain Atlas
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