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Genomic and transcriptomic data for the frog Platyplectrum ornatum
<p>The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms that drive or constrain genome size are poorly understood. Here we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog<b> (</b><i>Platyplectrum ornatum</i>) from Australia, and compare it to other published frog and vertebrate genomes to examine the forces driving reduction in genome size. At ~1.06 Gb, the <i>P. ornatum </i>genome is like that of birds, revealing four major mechanisms underlying TE dynamics: reduced abundance of all major classes of transposable elements (TEs); increased net deletion bias in TEs; drastic reduction in the lengths of introns; and expansion via gene duplication of the repertoire of TE-suppressing Piwi genes, accompanied by increased expression of piRNA-based TE-silencing pathway genes in germline cells. Transcriptome data from multiple tissues in both sexes corroborate these results and provide insight into sex-differentiation pathways in <i>Platyplectrum</i>. Genome skimming of two closely related frog species (<i>Lechriodus fletcheri </i>and <i>Limnodynastes fletcheri</i>) confirms a reduction in TEs as a major driver of genome reduction in <i>Platyplectrum</i> and supports a macroevolutionary scenario of small genome size in frogs driven by convergence in life history, especially rapid tadpole development and tadpole diet. The <i>P. ornatum</i> genome offers a model for future comparative studies on mechanisms of genome size reduction in amphibians and in vertebrates generally.</p>
Figure 1 in A redescription of the chigger Hannemania achalai Alzuet and Mauri, 1987 (Acariformes: Prostigmata: Leeuwenhoekiidae) in frogs from Sierra Grande, Cordoba, Argentina
Figure 1 Hannemania achalai Alzuet and Mauri, 1987 (larva): A – dorsal aspect of idiosoma, B – ventral aspect of idiosoma, C – ventral aspect of gnathosoma, D – dorsal aspect of gnathosoma, E – prodorsum showing scutum and eyes, F – palpal tarsus, G – palpal claw, H – lateral aspect of tarsus I.
Data from: Temperature dependent effects of cutaneous bacteria on a frog's tolerance of fungal infection
<p>Defense against pathogens is one of many benefits that bacteria provide to animal hosts. A clearer understanding of how changes in the environment affect the interactions between animals and their microbial benefactors is needed in order to predict the impact and dynamics of emerging animal diseases. Due to its dramatic effects on the physiology of animals and their pathogens, temperature may be a key variable modulating the level of protection that beneficial bacteria provide to their animal hosts. Here we investigate how temperature and the makeup of the skin microbial community impact the susceptibility of amphibian hosts to infection by <em>Batrachochytrium</em> <em>dendrobatidis</em>, one of two fungal pathogens known to cause the disease chytridiomycosis. To do this, we manipulated the skin bacterial communities of susceptible hosts, northern cricket frogs (<em>Acris</em> <em>crepitans</em>), prior to exposing these animals to <em>Batrachochytrium</em> <em>dendrobatidis</em> under two different ecologically relevant temperatures. Our manipulations included one treatment where antibiotics were used to reduce the skin bacterial community, one where the bacterial community was augmented with the antifungal bacterium, <em>Stenotrophomonas</em> <em>maltophilia</em>, and one in which the frog's skin bacterial community was left intact. We predicted that frogs with reduced skin bacterial communities would be more susceptible (i.e., less resistant to and/or tolerant of <em>Bd</em> infection), and frogs with skin bacterial communities augmented with the known antifungal bacterium would be less susceptible to <em>Bd</em> infection and chytridiomycosis. However, we also predicted that this interaction would be temperature-dependent. We found a strong effect of temperature but not of skin microbial treatment on the probability and intensity of infection in <em>Bd</em>-exposed frogs. Whether temperature impacted survival, however, differed among our skin microbial treatment groups, with animals having more <em>S</em>. <em>maltophilia</em> on their skin surviving longer at 14 but not at 26 °C. Our results suggest that temperature was the predominant factor influencing <em>Bd</em>'s ability to colonize the host (i.e., resistance) but that the composition of the cutaneous bacterial community was important in modulating the host's ability to survive (i.e., tolerate) a heavy <em>Bd</em> infection.</p>
FIGURE 6. A in A new species of Australian frog (Myobatrachidae: Uperoleia) from the New South Wales mid-north coast sandplains
FIGURE 6. A representative oscillogram (above) and spectrogram (below) of the advertisement call of Uperoleia mahonyi sp. nov., Oyster Cove, NSW. The x-axis is time in seconds.
Individual-based simulation model of annual movement paths for the Darwin's frog (R code and data)
<p>Desprition of the R code</p> <p>I constructed an individual-based simulation model that describes the movement path of an individual<em> Rhinoderma darwinii</em> through 3-month displacement steps. This model was primarily developed to evaluate the age-specific movement behaviour of Darwin's frogs, however, I also used it to provide better estimates (i.e. alleviating for movement censoring) of age-specific annual displacements in the species. I developed several variations of this model through a combination of different random walk sub-models for juveniles and adults: uncorrelated non-stationary random walks (NRW), correlated non-stationary random walks (CRW), and stationary random walks (SRW). The NRW and CRW were modelled as a first-order Markovian process where the location of an individual <em>i</em> in time<em> t</em> depends on its spatial location in <em>t </em>- 1. The NRW is unbiased, i.e., there is no preferred direction in each movement step. In contrast, the CRW includes persistence in the directionality of movement, so there is a correlation between successive step orientations. Finally, the SRW assumes that individuals have an activity centre to which all their spatial locations are related.</p> <p>Related data are provided (y.txt, x.txt and age.txt)</p>
Fig. 5 in A New Cascade Frog (Amphibia: Ranidae) From Laos And Vietnam
Fig. 5. Map illustrating the collecting localities of Rana khalam, new species, 1 = Xe Sap National Biodiversity Conservation Area, Kaleum District, Xe Kong Province, Laos, 16 04'10"N 106 58'45"E; 2 = Xe Sap National Biodiversity Conservation Area, Samoy District, Saravane Province, 16 08'40"N 106 56'50"E; 3 = Bach Ma National Park, Thua Thien-Hue Province, Hai Van mountain range, Vietnam, 16 10'33"N 107 48'23"E; 4 = Ba Na National Park, Danang Province, Hai Van mountain range, Vietnam, 16 08'15"N 107 55'47"E.
Fig. 2 in A New Cascade Frog (Amphibia: Ranidae) From Laos And Vietnam
Fig. 2. Male paratype of Rana khalam, new species, in life from Xe Sap National Biodiversity Conservation Area, Xe Kong Province, Laos.
Fig. 1 in A New Cascade Frog (Amphibia: Ranidae) From Laos And Vietnam
Fig. 1. Rana khalam, new species, male holotype (FMNH 258172) in preservative. A. dorsal view, B. ventrolateral surface showing band of round tubercles with fine, whitish spinules, C. palmar view of right hand, D. plantar view of left foot.
Fig. 3 in A New Cascade Frog (Amphibia: Ranidae) From Laos And Vietnam
Fig. 3. Female paratype of Rana khalam, new species, in life from Bach Ma National Park, Thua Thien-Hue Province, Vietnam.
Fig. 6 in A New Cascade Frog (Amphibia: Ranidae) From Laos And Vietnam
Fig. 6. Habitat of Rana khalam, new species, in Bach Ma National Park, Thua Thien-Hue Province, Vietnam.
Fig. 4 in A New Cascade Frog (Amphibia: Ranidae) From Laos And Vietnam
Fig. 4. Male paratype (ZISP 7245) of Rana khalam, new species, in life from Ba Na National Park, Danang Province, Vietnam, exhibiting pale night colouration.
Dataset for: The radiation continuum and the evolution of frog diversity
<p>Most of life's vast diversity of species and phenotypes is often attributed to adaptive radiation. Yet its contribution to species and phenotypic diversity of a major group has not been examined. Two key questions remain unresolved. First, what proportion of clades show macroevolutionary dynamics similar to adaptive radiations? Second, what proportion of overall species richness and phenotypic diversity do these adaptive-radiation-like clades contain? We address these questions with phylogenetic and morphological data for 1,226 frog species across 43 families (which represent >99% of all species). Less than half of frog families resembled adaptive radiations (with rapid diversification and morphological evolution). Yet, these adaptive-radiation-like clades encompassed ~75% of both morphological and species diversity, despite rapid rates in other clades (e.g., non-adaptive radiations). Overall, we support the importance of adaptive-radiation-like evolution for explaining diversity patterns and provide a framework for characterizing macroevolutionary dynamics and diversity patterns in other groups.</p>
Fig. 2 in A New Frog (Anura, Dicroglossidae), Related To Occidozyga Semipalmata Smith, 1927, From The Eastern Peninsula Of Sulawesi, Indonesia
Fig. 2. Occidozyga semipalmata from Lore Lindu, proximity of Kebun Kopi showing the flattened finger disks ornamented with a white bar. Photo by T. C. Wanger.
Fig. 3 in A New Frog (Anura, Dicroglossidae), Related To Occidozyga Semipalmata Smith, 1927, From The Eastern Peninsula Of Sulawesi, Indonesia
Fig. 3. Dorsal (A) and ventral (B) aspect of the female holotype (SVL 34.1 mm) of Occidozyga tompotika. Folds on the dorsum are partially an artifact from paper towel during preservation. Photo by D. T. Iskandar.
Fig. 1 in A New Frog (Anura, Dicroglossidae), Related To Occidozyga Semipalmata Smith, 1927, From The Eastern Peninsula Of Sulawesi, Indonesia
Fig. 1. Map of Sulawesi showing the distribution of Sulawesian Occidozyga. Legend: Circle, Occidozyga semipalmata; small circles denote localities with one or two specimens; Circle, Mount Lompobatang (the type locality); Star, Occidozyga tompotika; Inverted triangle, Occidozyga celebensis. Map modified from Google map.
Fig. 12. Oreophryne geislerorum, AMNH A 75042, SVL 26.3 in Systematics of Microhylid Frogs, Genus Oreophryne, from the North Coast Region of New Guinea
Fig. 12. Oreophryne geislerorum, AMNH A 75042, SVL 26.3, from Lae, Morobe Prov., Papua New Guinea (R. Zweifel photo).
Fig. 8 in Systematics of Microhylid Frogs, Genus Oreophryne, from the North Coast Region of New Guinea
Fig. 8. Audiospectrograms of calls of Oreophryne. A. O. biroi, UPNG 8134, Kowat, Adelbert Mtns., Madang Prov., Papua New Guinea, air 25.0°C; first 35 notes of a 67note call graphed with 59Hz and 300Hz filters. B. O. hypsiops, AMNH A83044, vicinity of Sempi, Madang Prov., Papua New Guinea, air 25.8°C; first 19 notes of a longer call graphed with 59Hz filter.
Fig. 11 in Systematics of Microhylid Frogs, Genus Oreophryne, from the North Coast Region of New Guinea
Fig. 11. Head width and tibia length ratios of Oreophryne geislerorum (crosses) and O. biroi (diamonds) compared. Solid diamonds represent specimens from Madang Prov., open diamonds specimens from East Sepik Prov.
Fig. 4 in Systematics of Microhylid Frogs, Genus Oreophryne, from the North Coast Region of New Guinea
Fig. 4. Regression of internarial span on snoutvent length in two samples of Oreophryne biroi from Papua New Guinea. Squares, specimens from Madang Prov.; crosses, specimens from East Sepik Prov.
Fig. 3 in Systematics of Microhylid Frogs, Genus Oreophryne, from the North Coast Region of New Guinea
Fig. 3. Regression of head width and eye diameter on snoutvent length in two samples of Oreophryne biroi from Papua New Guinea. Squares, specimens from Madang Prov.; crosses, specimens from East Sepik Prov.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.