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10 results for “Aneides”
Data from: Levels of sex steroids in plethodontid salamanders: A comparative study within the genus Aneides
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Aneides vagrans toes
<p>This dataset, R code, and model output are intended to be Open Access data/analysis tools created to analyze blood concentrations in the toes of wandering salamanders, <em>Aneides vagrans</em>. This data and analysis are for a manuscript submitted for consideration of publication by Journal of Morphology, and we hope the reviewers will find it easy to access and interpret. If not, we can always delete this entry and re-upload the data/analyses as the reviewers see fit, generating a new Zenodo dataset and DOI to be included in the final publication. </p>
Data from: An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the arboreal salamander (Aneides lugubris)
Background: Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to the California floristic province. We used multi-locus data to reconstruct the evolutionary history of A. lugubris and to discover the geographic location of major genetic breaks within the species. We also used species distribution modeling and comparative phylogeography to better understand the environmental factors that have shaped the genetic history of A. lugubris. Results: We found six major mitochondrial clades in A. lugubris. Nuclear loci supported the existence of at least three genetically distinct groups, corresponding to populations north of the San Francisco Bay and in the Sierra Nevada, in the Santa Cruz Mountains, and in the central coast and southern California. All of the genetic breaks in mitochondrial and nuclear loci corresponded to regions where historical barriers to dispersal have been observed in other species. Geologic or water barriers likely were the most important factors restricting gene flow among clades. Climatic unsuitability during glacial maximum may have contributed to the isolation of the mitochondrial clades in the central coast and southern California. A projection of our species distribution model to a future scenario with a moderate amount of climate change suggests that most of the range of A. lugubris will remain climatically suitable, but climatic conditions in the Sierra Nevada and low elevation areas in Southern California are likely to deteriorate. Conclusions: Aneides lugubris contains substantial cryptic genetic diversity as a result of historical isolation of populations. At least two (and perhaps three) evolutionarily significant units in A. lugubris merit protection; all six mitochondrial clades should be considered as management units within the species.
FIG. 1 in A New Green Salamander in the Southern Appalachians: Evolutionary History of Aneides aeneus and Implications for Management and Conservation with the Description of a Cryptic Microendemic Species
FIG. 1. Population structuring in Aneides aeneus (Castaneides) as identified using 12 microsatellite loci and TESS. (A) Results of running TESS assuming the number of populations (K) ranges from two through six. Each column represents an individual, and the colors in each bar indicate the population each individual is assigned to. The height and color of each bar represents the admixture proportion for that individual. Results for a single run are shown. (B) Representation of best-fit (K ¼ 4) TESS results in geographic space. Samples are shown as pie charts, with colors corresponding to the populations identified in A, and the fractions corresponding to each sample's admixture proportions.
FIG. 4 in A New Green Salamander in the Southern Appalachians: Evolutionary History of Aneides aeneus and Implications for Management and Conservation with the Description of a Cryptic Microendemic Species
FIG. 4. Images representing Aneides aeneus (A) and A. caryaensis (B). Aneides caryaensis is characterized by smaller and less connected lichen-like patches of bright green to yellowish-green pigment.
FIG. 3 in A New Green Salamander in the Southern Appalachians: Evolutionary History of Aneides aeneus and Implications for Management and Conservation with the Description of a Cryptic Microendemic Species
FIG. 3. Nuclear phylogenies as estimated by (A) SVDquartets and (B) RAxML. Filled circles denote nodes with support values.95%, empty circles denote nodes with support values.90%, and all other nodal support values are indicated as text. Numbered/colored circles enclosing monophyletic groups in the trees indicate species as identified by PTP when applied to the best tree identified by RAxML. Support for these species are as follows: 1) 44%, 2) 82%, 3) 50%. Low support values for the HNG are due to zero branch lengths (see Fig. S4; see Data Accessibility). Corresponding circles are similarly shown on the tree inferred by SVDquartets. However, PTP was not applied to this phylogeny as SVDquartets does not yet infer branch lengths. See Data Accessibility for tree files.
FIG. 2 in A New Green Salamander in the Southern Appalachians: Evolutionary History of Aneides aeneus and Implications for Management and Conservation with the Description of a Cryptic Microendemic Species
FIG. 2. Mitochondrial phylogenetic lineages within Aneides aeneus (Castaneides). (A) Localities of samples used in the mitochondrial phylogenetic analysis. The type locality (Nickajack Cave) is in Tennessee, at the border with Alabama; specimens from this vicinity are nested in the southern Appalachian clade. Red stars are locations used in the nuclear phylogenetic reconstruction. (B) Bayesian consensus tree of Cytochrome b and 12S rDNA sequences as produced by BEAST 2. Node labels represent posterior probabilities for the four main lineage splits within A. aeneus (Castaneides). Outgroup contains one voucher specimen each of A. hardii and A. flavipunctatus, obtained from GenBank. Numbered stars indicate clades identified by PTP to comprise unique species across the majority of the posterior distribution. Support values for clades are as follows: 1) 59%, 2) 91%, 3) 71%, 4) 93%. See Data Accessibility for tree file.
FIG. 5 in A New Green Salamander in the Southern Appalachians: Evolutionary History of Aneides aeneus and Implications for Management and Conservation with the Description of a Cryptic Microendemic Species
FIG. 5. Results of Principal Components Analysis (PCA) and Linear Discriminant Analysis (LDA) using 14 morphological characters. For both analyses, data were normalized where possible and necessary (longest toe, 5th toe log-transformed; adpressed limbs converted to absolute value and then log-transformed). (A) PCA with points and normal data ellipses colored by species. (B) Density plot of prediction accuracy by LDA across 1,000 permutations of samples for the training and prediction sets.
External morphology measurements of several species of the plethodontid genus Aneides
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Data from: An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the arboreal salamander (Aneides lugubris)
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