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opencc-by-4.0Mar 2020View details →

Re-scaffolded genome and supertranscriptome of the strawberry poison frog (Oophaga pumilio)

Re-scaffolded genome and SuperTranscriptome of Oophaga pumilio Supplementary data to the article: "Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)"

opencc-zeroJul 2020View details →

Data from: Chemical defenses shift with the seasonal vertical migration of a Panamanian poison frog

Dendrobatid poison frogs sequester lipophilic alkaloids from their arthropod prey to use as a form of chemical defense. Some dendrobatid frogs seasonally migrate between the leaf litter of the forest floor in the dry season to the canopy in the wet season, which may yield differences in prey (arthropods) and therefore alkaloid availability over space and time. Here, we document a seasonal vertical migration of Andinobates fulguritus (the yellow-bellied poison frog) from ground to canopy between dry and wet seasons. We observed turnover in alkaloid composition between seasons and found that dry season frogs contained a lower relative quantity of alkaloids; however, there was no change in alkaloid richness between seasons. The 77 alkaloids of 13 structural classes identified in this population appear to be derived mostly from mites and ants, though the two most common alkaloids were mite derived. Our observed shifts in defensive profiles are consistent with well-documented turnover in mite and ant communities between seasons and vertical strata. As climate change is expected to lengthen and strengthen dry seasons in many tropical regions, our results suggest that arboreal poison frogs forced to the ground for longer periods of time may see a shift in the abundance of alkaloids, possibly decreasing their defensive potential. This study provides further predictions for the wide-reaching effects of climate change, even as nuanced as charismatic poison frogs losing their poisons.

opencc-zeroDec 2015View details →

Data from: Poison frog color morphs express assortative mate preferences in allopatry but not sympatry

The concurrent divergence of mating traits and preferences is necessary for the evolution of reproductive isolation via sexual selection, and such coevolution has been demonstrated in diverse lineages. However, the extent to which assortative mate preferences are sufficient to drive reproductive isolation in nature is less clear. Natural contact zones between lineages divergent in traits and preferences provide exceptional opportunities for testing the predicted evolutionary consequences of such divergence. The strawberry poison frog (Oophaga pumilio) displays extreme color polymorphism in and around the young Bocas del Toro archipelago. In a transition zone between red and blue allopatric lineages, we asked whether female preferences diverged along with coloration, and whether any divergent preferences persist in a zone of sympatry. When choosing among red, blue and phenotypically intermediate males, females from monomorphic red and monomorphic blue populations both expressed assortative preferences. However, red, blue, and intermediate females from the contact zone all preferred red males, suggesting that divergent preferences may be insufficient to effect behavioral isolation. Our results highlight the complexity of behavioral isolation, and the need for studies that can reveal the circumstances under which divergent preferences do and do not contribute to speciation.

opencc-zeroMar 2020View details →

Genetic differentiation and overexploitation history of the critically endangered Lehmann's Poison Frog: Oophaga lehmanni

Species conservation with fragmented and endangered populations must be based on a prior and thorough knowledge of the structure and population dynamics. Oophaga lehmanni is a dendrobatid species endemic of Colombia and is restricted to its type locality. This species has a fragmented distribution and is considered as critically endangered mainly due to habitat destruction and overexploitation. Oophaga lehmanni exhibits phenotypic variation in the dorsal color pattern (red and yellow morphs). We reconstructed the overexploitation history that this species has faced in the last 40 years. In addition, we collected genetic and morphological data for the first time in natural populations to describe genetic diversity between and within populations, and to evaluate morphological and genetic differences between red and yellow morphs. Overexploitation data suggest that more than 80.000 (Min=60.047 - Max=102.236) frogs were extracted from the field in the last four decades, probably generating the local extirpation or population decline from the type locality. Genetic data showed reduced genetic diversity. Observed heterozygosity (mean±s.d.=0.599±0.165) is lower than expected (mean±s.d.=0.867± 0.082). We did not find differences in body size and heterozygosity between the two morphs; however, individuals analyzed were assigned to two genetic clusters, which corresponded to the O. lehmanni-yellow and O. lehmanni-red. In addition, FST (0.209) and Nei genetic distance (0.18) values indicated genetic differentiation between the two morphs; therefore, red and yellow morphs should be treated as independent management units. This information will help to define appropriate and long-term conservation units, as a useful tool to mitigate the extinction risk of this species.

opencc-zeroApr 2020View details →

The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts

Rough-skinned newts (Taricha granulosa) use tetrodotoxin (TTX) to block voltage-gated sodium (Nav) channels as a chemical defense against predation. Interestingly, newts exhibit extreme population-level variation in toxicity attributed to a coevolutionary arms race with TTX-resistant predatory snakes, but the source of TTX in newts is unknown. Here, we investigated whether symbiotic bacteria isolated from toxic newts could produce TTX. We characterized the skin-associated microbiota from a toxic and non-toxic population of newts and established pure cultures of isolated bacterial symbionts from toxic newts. We then screened bacterial culture media for TTX using LC-MS/MS and identified TTX-producing bacterial strains from four genera, including Aeromonas, Pseudomonas, Shewanella, and Sphingopyxis. Additionally, we sequenced the Nav channel gene family in toxic newts and found that newts expressed Nav channels with modified TTX binding sites, conferring extreme physiological resistance to TTX. This study highlights the complex interactions among adaptive physiology, animal-bacterial symbiosis, and ecological context.

opencc-zeroDec 2017View details →

Data from: Mate choice vs mate preference: inferences about color-assortative mating differ between field and lab assays of poison frog behavior

Co-divergence of mating traits and mate preferences can lead to behavioral isolation among lineages in early stages of speciation. However, mate preferences only limit gene flow when expressed as mate choice, and numerous factors might be more important than preferences in nature. In the extremely color polytypic strawberry poison frog (Oophaga pumilio), female mate preferences have co-diverged with color in most allopatric populations tested. Whether these lab-assayed preferences predict mating (gene flow) in the wild remains unclear. We observed courting pairs in a natural contact zone between red and blue lineages until oviposition or courtship termination. We found color-assortative mating in a disturbed habitat with high population density, but not in a secondary forest with lower density. Our results suggest color-assortative O. pumilio mate choice in the wild, but also mating patterns that do not match those predicted by lab-assayed preferences.

opencc-zeroMay 2020View details →

Data from: A ketocarotenoid-based color polymorphism in the Sira poison frog Ranitomeya sirensis indicates novel gene interactions underlying aposematic signal variation

The accumulation of red ketocarotenoids is an important component of coloration in many organisms, but the underlying mechanisms are poorly understood. In some organisms, ketocarotenoids are sequestered from the diet and can accumulate when enzymes responsible for carotenoid breakdown are disrupted. In other organisms, ketocarotenoids are formed endogenously from dietary precursors via oxidation reactions carried out by carotenoid ketolase enzymes. Here, we study the genetic basis of carotenoid coloration in an amphibian. We demonstrate that a red/yellow polymorphism in the dendrobatid poison frog Ranitomeya sirensis is due to the presence/absence of ketocarotenoids. Using whole-transcriptome sequencing of skins and livers, we found that a transcript encoding a cytochrome P450 enzyme (CYP3A80) is expressed 3.4-fold higher in livers of red frogs versus yellow. As CYP3A enzymes are known carotenoid ketolases in other organisms, our results point to CYP3A80 as a strong candidate for a carotenoid ketolase in amphibians. Furthermore, in red frogs, the transcript encoding the carotenoid cleavage enzyme BCO2 is expressed at a low level or as a splice variant lacking key catalytic amino acids. This suggests that BCO2 function may be disrupted in red frogs, providing a mechanism whereby the accumulation of ketocarotenoids and their dietary precursors may be enhanced.

opencc-zeroNov 2023View details →

Binding and sequestration of poison frog alkaloids by a plasma globulin

Alkaloids are important bioactive molecules throughout the natural world, and in many animals, they serve as a source of chemical defense against predation. Dendrobatid poison frogs bioaccumulate alkaloids from their diet to make themselves toxic or unpalatable to predators. Despite the proposed roles of plasma proteins as mediators of alkaloid trafficking and bioavailability, the responsible proteins have not been identified. We use chemical approaches to show that a ~50 kDa plasma protein is the principal alkaloid binding molecule in blood from poison frogs. Proteomic and biochemical studies establish this plasma protein to be liver-derived alkaloid-binding globulin (ABG) that is a member of the serine-protease inhibitor (serpin) family. In addition to alkaloid binding activity, ABG sequesters and regulates the bioavailability of "free" plasma alkaloids in vitro. Unexpectedly, ABG is not related to saxiphilin or albumin but instead exhibits sequence and structural homology to mammalian hormone carriers and amphibian biliverdin binding proteins. Alkaloid-binding globulin (ABG) represents a new small molecule binding functionality in serpin proteins, a novel mechanism of plasma alkaloid transport in poison frogs, and more broadly points towards serpins acting as tunable scaffolds for small molecule binding and transport across different organisms.

opencc-zeroDec 2023View details →

Supplementary material from: Deep divergences among inconspicuous clades of Epipedobates poison frogs

Poison frogs (Dendrobatidae) are famous for their aposematic species, having a combination of diverse color patterns and defensive skin toxins, yet most species in this family are inconspicuously colored and considered non-aposematic. Epipedobates is among the youngest genus-level clades of Dendrobatidae that includes both aposematic and inconspicuous species. Using Sanger-sequenced mitochondrial and nuclear markers, we demonstrate deep genetic divergences among inconspicuous species of Epipedobates but relatively shallow genetic divergences among conspicuous species. Our phylogenetic analysis includes broad geographic sampling of the inconspicuous lineages typically identified as E. boulengeri and E. espinosai, which reveals two putative new species, one in west-central Colombia (E. sp. 1) and the other in north-central Ecuador (E. aff. espinosai). We conclude that E. darwinwallacei is a junior subjective synonym of E. espinosai. We also clarify the geographic distributions of inconspicuous Epipedobates species including the widespread E. boulengeri. We provide a qualitative assessment of the phenotypic diversity in each nominal species, with a focus on the color and pattern of inconspicuous species. We conclude that Epipedobates contains eight known valid species, six of which are inconspicuous. A relaxed molecular clock analysis suggests that the most recent common ancestor of Epipedobates is ~11.1 million years old, which nearly doubles previous estimates. Last, genetic information points to a center of species diversity in the Chocó at the southwestern border of Colombia with Ecuador.

opencc-by-4.0Dec 2022View details →

Mechanism for SO2 poisoning of Cu-CHA during low temperature NH3-SCR

Dataset related to the article with the same title and authors: <a href="https://www.sciencedirect.com/science/article/pii/S0021951722005255">Mechanism for SO2 poisoning of Cu-CHA during low temperature NH3-SCR</a>   The zip file contain selected structures and a README.txt file with additional information.

opencc-by-4.0Mar 2022View details →

Poisonous and Edible Mushrooms in the Northeastern Region of Thailand

Mushroom dataset is divided into two parts: CNN and R-CNN. CNN will use an image size of 227x227 pixels, R-CNN will use an image of 300x300 pixels. Image data of mushrooms was collected in the northeastern region of Thailand. The mushroom datasets containing 2,000 images were divided into two sets: a poisonous mushroom set containing 527 images and an edible mushroom set containing 1,473 images. There are 5 species in all. Edible mushroom:  1. Amanita citrina.  2. Russula delica.  3. Phaeogyroporus portentosus. Poisonous mushroom:    1. Amanita phalloides.  2. Inocybe rimosa.  Format: JPEG, provided in .zip format Period covered: 13 July - 23th August 2020

opencc-zeroJun 2024View details →

Physiological state matching in a pair bonded poison frog

More than a century ago, Charles Darwin hypothesized that the empathy-like phenotype is a phylogenetically widespread phenomenon. This idea remains contentious, due to the challenges of empirically examining emotions, and few investigations among non-mammalian vertebrates. We provide support for Darwin's hypothesis by discovering partial evidence for the most ancestral form of empathy, emotional contagion (i.e., matching another individual's emotional state), in the pair bonding mimetic poison frog, Ranitomeya imitator. We found that male corticosterone, a physiological biomarker of stress, positively correlates with female partners in experimental and semi-natural conditions. This does not appear to coincide with behavioral state-matching. However, it is specific to female partners relative to familiar female non-partners, and is independent of effects that commonly confound studies on emotional contagion. Furthermore, this physiological state-matching is irrespective of partnership longevity or lifetime reproductive output. These results physiologically indicate socially selective emotional contagion in a monogamous amphibian, and paradigms that elicit coinciding neural and behavioral indicators and morphogenic co-variation are needed for further corroboration. Further studies on ancestral forms of empathy in non-mammalian vertebrates are warranted.

Fig. 78 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 78. Graphic summary of the proposed taxonomy of Dendrobatoidea.

Fig. 77 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 77. Graphic summary of the proposed higher-level taxonomy of Athesphatanura.

Fig. 45. Character 60 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 45. Character 60, dark lower lip line. State

Fig. 34. Character 49, pale paracloacal mark. State 1 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 34. Character 49, pale paracloacal mark. State 1, present (degranvillei, AMNH 90880).

Fig. 32. Character 30, tarsal fringe. State 1 in PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Fig. 32. Character 30, tarsal fringe. State 1, present (Megaelosia goeldii, AMNH 103950).