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22 results for “Ambystoma salamanders”
Fig. 3 in Acute mortality in California tiger salamander (Ambystoma californiense) and Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) caused by Ribeiroia ondatrae (Class: Trematoda)
Fig. 3. Ribeiroia ondatrae cercaria from Planorbella sp. collected from Ellicott Pond in Ellicott Slough National Wildlife Refuge, Santa Cruz County, California, U.S.A.
Fig. 4 in Acute mortality in California tiger salamander (Ambystoma californiense) and Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) caused by Ribeiroia ondatrae (Class: Trematoda)
Fig. 4. Molecular phylogenetic analysis by Maximum Likelihood method based on the Hasegawa-Kishino-Yano plus G model with 500 bootstrap replications based on partial 28S rRNA gene sequences of Ribeiroia ondatrae metacercariae from California tiger salamanders (Ambystoma californiense), cercariae from Planorbella sp. and sequences of R. ondatrae publicly available in GenBank with Notocotylus attenuatus as an outgroup. Tree is drawn to scale with branch lengths measure in the number of substitutions per site. The analysis involved 13 nucleotide sequences. All positions with less than 95% site coverage were eliminated. There was a total of 1189 positions in the final dataset.
Fig. 2 in Acute mortality in California tiger salamander (Ambystoma californiense) and Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) caused by Ribeiroia ondatrae (Class: Trematoda)
Fig. 2. Photomicrograph of California tiger salamanders (Ambystoma californiense) in late-stage metamorphosis from a mortality event in the Ellicott Slough National Wildlife Refuge in Santa Cruz County, California, U.S.A. (A) Cross-section of dorsal tail showing widespread ulcerative dermatitis with superficial serocellular crust formation and intralesional metacercariae (asterisk) (H&E). (B) Metacercariae (asterisk) associated with mixed cellular to granulomatous inflammation widespread in the gills and subcutis (PAS). Inset: Encysted metacercariae are surrounded by mixed-cellular to granulomatous to infiltrate (H&E).
Fig. 1 in Acute mortality in California tiger salamander (Ambystoma californiense) and Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) caused by Ribeiroia ondatrae (Class: Trematoda)
Fig. 1. Gross photographs of ethanol-fixed salamanders in late-stage metamorphosis from a mortality event in the Ellicott Slough National Wildlife Refuge (ESNWR) in Santa Cruz County, California, U.S.A. showing integumentary lesions. (A) California tiger salamander (Ambystoma californiense) exhibiting an extensive roughening of the skin with multifocal ulceration around the eyes, gular fold, and dorsal tail (arrows). (B) Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) with ulceration and crust formation on the gular fold and base of the tail (arrow).
Data from: Cryptic sex? Estimates of genome exchange in unisexual mole salamanders (Ambystoma sp.)
Cryptic sex has been argued to explain the exceptional longevity of certain parthenogenetic vertebrate lineages, yet direct measurements of genetic exchange between sexual and apparently parthenogenetic forms are rare. Female unisexual mole salamanders (Ambystoma sp.) are the oldest known unisexual vertebrate lineage (~5 million years), and one hypothesis for their persistence is that allopolyploid female unisexuals periodically exchange haploid genomes 'genome exchange' during gynogenetic reproduction with males from sympatric sexual species. We test this hypothesis by using genome-specific microsatellite DNA markers to estimate the rates of genome exchange between sexual males and unisexual females in two ponds in NE Ohio. We also test the prediction that levels of gene flow should be higher for 'sympatric' (sexual males present) genomes in unisexuals compared to 'allopatric' (sexual males absent) unisexual genomes. We used a model testing framework in the coalescent-based program MIGRATE-N to compare models where unidirectional gene flow is present and absent between sexual species and unisexuals. As predicted, our results show higher levels of gene flow between sexuals and sympatric unisexual genomes compared to lower (likely artefactual) levels of gene flow between sexuals and allopatric unisexual genomes. Our results provide direct evidence that genome exchange between sexual and unisexual Ambystoma occurs and demonstrate that the magnitude depends on which sexual species are present. The relatively high levels of gene flow suggest that unisexuals must be at a selective advantage over sexual forms so as to avoid extinction due to genetic swamping through genome exchange.
Data from: The importance (or lack thereof) of niche divergence to the maintenance of a northern species complex: the case of the long-toed salamander (Ambystoma macrodactylum Baird)
The relative importance of ecological versus non-ecological factors for the origin and maintenance of species is an open question in evolutionary biology. Young lineages—such as the distinct genetic groups that make up the ranges of many northern species—represent an opportunity to study the importance of ecological divergence during the early stages of diversification. Yet, few studies have examined the extent of niche divergence between lineages in previously glaciated regions and the role of ecology in maintaining the contact zones between them. In this study, we used tests of niche overlap in combination with ecological niche models to explore the extent of niche divergence between lineages of the long-toed salamander (Ambystoma macrodactylum Baird) species complex and to determine whether contact zones correspond to (divergent) niche limits. We found limited evidence for niche divergence between the different long-toed salamander lineages, substantial overlap in the predicted distribution of suitable climatic space for all lineages and range limits that are independent of niche limits. These results raise questions as to the importance of ecological divergence to the development of this widespread species complex and highlight the potential for non-ecological factors to play a more important role in the maintenance of northern taxa.
Data from: Individual performance in relation to cytonuclear discordance in a northern contact zone between long-toed salamander (Ambystoma macrodactylum) lineages
Cytonuclear discordance in contact zones between related lineages is common, with mitochondrial clines often being displaced from clines in nuclear allele frequency. Proposed explanations for such a pattern include adaptive introgression of mtDNA or a neutral wake of mtDNA being left behind following hybrid zone movement. However, studies investigating these hypotheses are rare. Our previous survey of genetic variation in the long-toed salamander (Ambystoma macrodactylum) highlighted a potential case of cytonuclear discordance between two lineages in western Canada. Here, we use additional markers and samples to clarify the extent of this discordance. We simultaneously assess the feeding performance of individuals in a common environment to test for an association between mitotype and individual performance. The genetic results confirm a general pattern of cytonuclear discordance in the focal region. However, we also observed more limited introgression of a diagnostic nuclear marker. Intriguingly, although there were differences in individual performance associated with the transition between mitotypes, these differences were not fully explained by mitotype. Instead, the lowest performance was observed in individuals demonstrating the greatest mismatch between mtDNA and all nuclear markers, suggesting the potential for cytonuclear incompatibilities to be acting. These results highlight the complexity of understanding the causes and consequences of mtDNA introgression and cytonuclear discordance in contact zones.
Data from: A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)
The central-marginal hypothesis (CMH) predicts that population size, genetic diversity, and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core-to-edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size, and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core-to-edge genetic patterns. These results suggest that multiple processes may influence a species' distribution based on the heterogeneity of habitat across a species' range and that replicated sampling may be needed to accurately test the CMH. Our work also emphasizes the importance of identifying the geographic range core with methods other than using the Euclidean center on a map, which may help to explain discrepancies among other empirical tests of the CMH. Assessing core to edge population genetic patterns across an entire species' range accompanied with ENM can inform our general understanding of the mechanisms leading to species' geographic range limits.
Larval A. bishopi microsatellite data from: Metapopulation genetics of endangered reticulated flatwoods salamanders (Ambystoma bishopi) in a dynamic and fragmented landscape
<p>The dataset consists of 9 microsatellite markers used to analyze reticulated flatwoods salamanders' (<em>Ambystoma bishopi</em>) population structure on Eglin AFB. Samples came from various breeding ponds and allele sizes were scored using GeneMapper (GeneMapper v4.0; Applied Biosystems). Data was collected via allele scoring in GeneMapper by two independent researchers. Allele sizes for each individual have been re-formatted for various programs using the microsatellite Add-in in Excel as well as by using the GenAlEx extension in Excel. </p>
Data from: Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex
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Data from: The importance (or lack thereof) of niche divergence to the maintenance of a northern species complex: the case of the long-toed salamander (Ambystoma macrodactylum Baird)
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Data from: Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing
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Data from: A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)
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Data from: Cryptic sex? Estimates of genome exchange in unisexual mole salamanders (Ambystoma sp.)
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Data from: Individual performance in relation to cytonuclear discordance in a northern contact zone between long-toed salamander (Ambystoma macrodactylum) lineages
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Larval A. bishopi microsatellite data from: Metapopulation genetics of endangered reticulated flatwoods salamanders (Ambystoma bishopi) in a dynamic and fragmented landscape
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Data from: The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum)
BACKGROUND: Next-generation sequencing methods have contributed to rapid progress in the fields of genomics and population genetics. Using this high-throughput and cost-effective technology, a number of studies have estimated single nucleotide polymorphism (SNP) frequency by calculating the mean number of SNPs per unit sequence length (e.g., mean SNPs/kb). However, both read length and contig depth are highly variable and thus raise doubt about simple methods of SNP frequency estimation. RESULTS: We used 454 pyrosequencing to identify 2,980 putative SNPs in the eastern tiger salamander (Ambystoma tigrinum tigrinum) transcriptome, then constructed analytical models to estimate SNP frequency. The model which considered only contig length (i.e., the method employed in most published papers) was evaluated with very poor likelihood. Our most robust model considered read depth as well as contig length, and was 7.5 × 1055 times more likely than the length-only model. Using this novel modeling approach, we estimated SNP frequency in protein-coding (mRNA) and non-coding transcripts (e.g., small RNAs). We found little difference in SNP frequency in the contigs, but we found a trend of a higher frequency of SNPs in long contigs representing non-coding transcripts relative to protein-coding transcripts. These results support the hypothesis that long non-coding transcripts are less conserved than long protein-coding transcripts. CONCLUSIONS: A modeling approach (i.e., using multiple model construction and model selection approaches) can be a powerful tool for identifying selection on specific functional sequence groups by comparing the frequency and distribution of polymorphisms.
Data from: Evolutionary basis of mitonuclear discordance between sister species of mole salamanders (Ambystoma sp.)
Distinct genetic markers should show similar patterns of differentiation between species reflecting their common evolutionary histories yet there are increasing examples of differences in the biogeographic distribution of species-specific nuclear (nuDNA) and mitochondrial DNA (mtDNA) variants within and between species. Identifying the evolutionary processes that underlie these anomalous patterns of genetic differentiation is an important goal. Here we analyze the putative mitonuclear discordance observed between sister species of mole salamanders (Ambystoma barbouri and A. texanum) in which A. barbouri-specific mtDNA is found in animals located in the range of A. texanum. We test three hypotheses for this discordance (undetected range expansion, mtDNA introgression and hybridization) using nuDNA and mtDNA data analyzed with methods that varied in the parameters estimated and the timescales measured. Results from a Bayesian clustering technique (structure), bi-directional estimates of gene flow (migrate-n and IMa2), and phylogeny-based methods (*beast, bucky) all support the conclusion that the discordance is due to geographically restricted mtDNA introgression from A. barbouri into A. texanum. Limited data on species-specific tooth morphology match this conclusion. Significant differences in environmental conditions exist between sites where A. texanum with and without A. barbouri-like mtDNA occur, suggesting a possible role for selection in the process of introgression. Overall, our study provides a general example of the value of using complimentary analyses to make inferences of the directionality, time scale, and source of mtDNA introgression in animals.
Data from: The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum)
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Data from: Evolutionary basis of mitonuclear discordance between sister species of mole salamanders (Ambystoma sp.)
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