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PeerJ 2022The recent emergence of the pathogen () is associated with rapid population declines of salamanders in Europe and its arrival to new areas could cause dramatic negative...
The recent emergence of the pathogen () is associated with rapid population declines of salamanders in Europe and its arrival to new areas could cause dramatic negative effects on other amphibian populations and species. Amphibian species, present in areas with high amphibian diversity such as Mexico, could be highly threatened due to the arrival of , particularly salamander species which are more vulnerable to chytridiomycosis caused by this pathogen. Thus, immediate surveillance is needed as a strategy to efficiently contend with this emerging infectious disease. In this study, we analyzed 490 wild and captive amphibians from 48 species across 76 sites in the North, Central, and South of Mexico to evaluate the presence of . Amphibians were sampled in sites with variable degrees of amphibian richness and suitability for according to previous studies. From the 76 sampling sites, 10 of them were located in areas with high amphibian richness and potential moderate to high habitat suitability. We did not detect in any of the samples, and no signs of the disease were observed in any individual at the time of sampling. Our results suggest that has not yet arrived at the sampled sites or could be at low prevalence within populations with low occurrence probability. This is the first study that evaluates the presence of in different regions and amphibian species in Mexico, which is the second most diverse country in salamander species in the world. We highlight the risk and the importance of continuing surveillance of in Mexico and discuss control strategies to avoid the introduction and spread of in the country.
Topics: Animals; Mexico; Chytridiomycota; Amphibians; Batrachochytrium; Urodela
PubMed: 36213512
DOI: 10.7717/peerj.14117 -
Cold Spring Harbor Perspectives in... Aug 2015In amphibians, nerve cell size is highly correlated with genome size, and increases in genome and cell size cause a retardation of the rate of development of nervous (as... (Review)
Review
In amphibians, nerve cell size is highly correlated with genome size, and increases in genome and cell size cause a retardation of the rate of development of nervous (as well as nonnervous) tissue leading to secondary simplification. This yields an inverse relationship between genome and cell size on the one hand and morphological complexity of the tectum mesencephali as the main visual center, the size of the torus semicircularis as the main auditory center, the size of the amphibian papilla as an important peripheral auditory structure, and the size of the cerebellum as a major sensorimotor center. Nervous structures developing later (e.g., torus and cerebellum) are more affected by secondary simplification than those that develop earlier (e.g., the tectum). This effect is more prominent in salamanders and caecilians than in frogs owing to larger genome and cells sizes in the former two taxa. We hypothesize that because of intragenomic evolutionary processes, important differences in brain morphology can arise independently of specific environmental selection.
Topics: Amphibians; Animals; Brain; Genome
PubMed: 26261281
DOI: 10.1101/cshperspect.a019075 -
Viruses Nov 2011Although a variety of virus species can infect amphibians, diseases caused by ranaviruses ([RVs]; Iridoviridae) have become prominent, and are a major concern for... (Review)
Review
Although a variety of virus species can infect amphibians, diseases caused by ranaviruses ([RVs]; Iridoviridae) have become prominent, and are a major concern for biodiversity, agriculture and international trade. The relatively recent and rapid increase in prevalence of RV infections, the wide range of host species infected by RVs, the variability in host resistance among population of the same species and among different developmental stages, all suggest an important involvement of the amphibian immune system. Nevertheless, the roles of the immune system in the etiology of viral diseases in amphibians are still poorly investigated. We review here the current knowledge of antiviral immunity in amphibians, focusing on model species such as the frog Xenopus and the salamander (Ambystoma tigrinum), and on recent progress in generating tools to better understand how host immune defenses control RV infections, pathogenicity, and transmission.
Topics: Amphibian Proteins; Amphibians; Animals; DNA Virus Infections; Humans; Ranavirus; Urodela; Xenopus laevis
PubMed: 22163335
DOI: 10.3390/v3112065 -
BMC Ecology and Evolution Mar 2022The 16S mitochondrial rRNA gene is the most widely sequenced molecular marker in amphibian systematic studies, making it comparable to the universal CO1 barcode that is...
BACKGROUND
The 16S mitochondrial rRNA gene is the most widely sequenced molecular marker in amphibian systematic studies, making it comparable to the universal CO1 barcode that is more commonly used in other animal groups. However, studies employ different primer combinations that target different lengths/regions of the 16S gene ranging from complete gene sequences (~ 1500 bp) to short fragments (~ 500 bp), the latter of which is the most ubiquitously used. Sequences of different lengths are often concatenated, compared, and/or jointly analyzed to infer phylogenetic relationships, estimate genetic divergence (p-distances), and justify the recognition of new species (species delimitation), making the 16S gene region, by far, the most influential molecular marker in amphibian systematics. Despite their ubiquitous and multifarious use, no studies have ever been conducted to evaluate the congruence and performance among the different fragment lengths.
RESULTS
Using empirical data derived from both Sanger-based and genomic approaches, we show that full-length 16S sequences recover the most accurate phylogenetic relationships, highest branch support, lowest variation in genetic distances (pairwise p-distances), and best-scoring species delimitation partitions. In contrast, widely used short fragments produce inaccurate phylogenetic reconstructions, lower and more variable branch support, erratic genetic distances, and low-scoring species delimitation partitions, the numbers of which are vastly overestimated. The relatively poor performance of short 16S fragments is likely due to insufficient phylogenetic information content.
CONCLUSIONS
Taken together, our results demonstrate that short 16S fragments are unable to match the efficacy achieved by full-length sequences in terms of topological accuracy, heuristic branch support, genetic divergences, and species delimitation partitions, and thus, phylogenetic and taxonomic inferences that are predicated on short 16S fragments should be interpreted with caution. However, short 16S fragments can still be useful for species identification, rapid assessments, or definitively coupling complex life stages in natural history studies and faunal inventories. While the full 16S sequence performs best, it requires the use of several primer pairs that increases cost, time, and effort. As a compromise, our results demonstrate that practitioners should utilize medium-length primers in favor of the short-fragment primers because they have the potential to markedly improve phylogenetic inference and species delimitation without additional cost.
Topics: Amphibians; Animals; Genes, Mitochondrial; Phylogeny; RNA, Ribosomal; RNA, Ribosomal, 16S
PubMed: 35346025
DOI: 10.1186/s12862-022-01994-y -
Developmental Dynamics : An Official... Dec 2002Recent revisions in the Xenopus laevis fate map led to the designation of the rostral/caudal axis and reassignment of the dorsal/ventral axis (Lane and Smith [1999]... (Review)
Review
Recent revisions in the Xenopus laevis fate map led to the designation of the rostral/caudal axis and reassignment of the dorsal/ventral axis (Lane and Smith [1999] Development 126:423-434; Lane and Sheets [2000] Dev. Biol. 225:37-58). It is unprecedented to reassign primary embryonic axes after many years of research in a model system. In this review, we use insights about vertebrate development from anatomy and comparative embryology, as well as knowledge about gastrulation in frogs, to reexamine several traditional amphibian fate maps. We show that four extant maps contain information on the missing rostral/caudal axis. These maps support the revised map as well as the designation of the rostral/caudal axis and reassignment of the dorsal/ventral axes. To illustrate why it is important for researchers to use the revised map and nomenclature when thinking about frog and fish embryos, we present an example of alternative interpretations of "dorsalized" zebrafish mutations.
Topics: Amphibians; Animals; Body Patterning; Cell Lineage; Embryo, Nonmammalian; Gene Expression Regulation, Developmental; Models, Biological; Xenopus
PubMed: 12454921
DOI: 10.1002/dvdy.10182 -
Cold Spring Harbor Perspectives in... Jun 2011We review experiments in which somatic cell nuclei are transplanted singly to enucleated eggs (metaphase II) in amphibia and mammals and as multiple nuclei to the... (Review)
Review
We review experiments in which somatic cell nuclei are transplanted singly to enucleated eggs (metaphase II) in amphibia and mammals and as multiple nuclei to the germinal vesicle of amphibian oocytes (prophase I). These experiments have shown the totipotency of some somatic cell nuclei, as well as switches in cell type and changes in gene expression. Abnormalities of nuclear transplant embryo development increase greatly as nuclei are taken from progressively more differentiated donor cells. The molecular changes that accompany the reprogramming of transplanted nuclei help to indicate the mechanisms used by eggs and oocytes to reprogram gene expression. We discuss the importance of chromosomal protein exchange, of transcription factor supply, and of chromatin access in reprogramming.
Topics: Amphibians; Animals; Cell Dedifferentiation; Cell Differentiation; Cell Nucleus; Epigenesis, Genetic; Gene Expression Regulation, Developmental; Mammals; Mice; Nuclear Transfer Techniques; Oocytes; Xenopus
PubMed: 21555407
DOI: 10.1101/cshperspect.a002659 -
Infection and Immunity Mar 2022Amphibian populations have been declining around the world for more than five decades, and the losses continue. Although causes are complex, major contributors to these...
Amphibian populations have been declining around the world for more than five decades, and the losses continue. Although causes are complex, major contributors to these declines are two chytrid fungi, Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans, which both cause the disease termed chytridiomycosis. Previously, we showed that B. dendrobatidis impedes amphibian defenses by directly inhibiting lymphocytes and by release of soluble metabolites, including kynurenine (KYN), methylthioadenosine (MTA), and spermidine (SPD). Here, we show that B. salamandrivorans cells and cell-free supernatants also inhibit amphibian lymphocytes as well as a human T cell line. As we have shown for B. dendrobatidis, high-performance liquid chromatography (HPLC) and mass spectrometry revealed that KYN, MTA, and SPD are key metabolites found in the B. salamandrivorans supernatants. Production of inhibitory factors by B. salamandrivorans is limited to mature zoosporangia and can occur over a range of temperatures between 16°C and 26°C. Taken together, these results suggest that both pathogenic fungi have evolved similar mechanisms to inhibit lymphocytes in order to evade clearance by the amphibian immune system.
Topics: Animals; Humans; Amphibians; Batrachochytrium; Chytridiomycota; Kynurenine; Lymphocytes; Spermidine; Urodela
PubMed: 35130454
DOI: 10.1128/iai.00020-22 -
BMC Bioinformatics May 2020Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and...
BACKGROUND
Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not been extensively explored. We consider that the data of mitochondrial genomes in the NCBI database are a valuable alternative to generate a better understanding of the molecular dynamic of the repeat sequences in the amphibians.
RESULTS
This work presents the development of a strategy to identify and quantify the total amount of repeat sequences with lengths from 5 to 30 base pairs in the amphibian mitogenomes. The results show differences in the abundance of repeat sequences among amphibians and bias to specific genomic regions that are not easily associated with the classical amphibian ancestry.
CONCLUSIONS
Derived from these analyses, we show that great variability of the repeat sequences exists among amphibians, demonstrating that the mitogenomes of these organisms are dynamic.
Topics: Amphibians; Animals; DNA, Mitochondrial; Genome, Mitochondrial; Inverted Repeat Sequences; Repetitive Sequences, Nucleic Acid
PubMed: 32429835
DOI: 10.1186/s12859-020-3532-8 -
PloS One 2020In the last few years, DNA barcoding became an established method for species identification in biodiversity inventories and monitoring studies. Such studies depend on...
In the last few years, DNA barcoding became an established method for species identification in biodiversity inventories and monitoring studies. Such studies depend on the access to a comprehensive reference data base, covering all relevant taxa. Here we present a comprehensive DNA barcode inventory of all amphibian and reptile species native to Austria, except for the putatively extinct Vipera ursinii rakosiensis and Lissotriton helveticus, which has been only recently reported for the very western edge of Austria. A total of 194 DNA barcodes were generated in the framework of the Austrian Barcode of Life (ABOL) initiative. Species identification via DNA barcodes was successful for most species, except for the hybridogenetic species complex of water frogs (Pelophylax spp.) and the crested newts (Triturus spp.), in areas of sympatry. However, DNA barcoding also proved powerful in detecting deep conspecific lineages, e.g. within Natrix natrix or the wall lizard (Podarcis muralis), resulting in more than one Barcode Index Number (BIN) per species. Moreover, DNA barcodes revealed the presence of Natrix helvetica, which has been elevated to species level only recently, and genetic signatures of the Italian water frog Pelophylax bergeri in Western Austria for the first time. Comparison to previously published DNA barcoding data of European amphibians and reptiles corroborated the results of the Austrian data but also revealed certain peculiarities, underlining the particular strengths and in the case of the genus Pelophylax also the limitations of DNA barcoding. Consequently, DNA barcoding is not only powerful for species identification of all life stages of most Austrian amphibian and reptile species, but also for the detection of new species, the monitoring of gene flow or the presence of alien populations and/or species. Thus, DNA barcoding and the data generated in this study may serve both scientific and national or even transnational conservation purposes.
Topics: Amphibians; Animals; Austria; Biodiversity; DNA; DNA Barcoding, Taxonomic; Gene Library; Phylogeny; Reference Standards; Reptiles; Species Specificity
PubMed: 32163447
DOI: 10.1371/journal.pone.0229353 -
Vitamin A (retinoid) metabolism and actions: What we know and what we need to know about amphibians.Zoo Biology 2014Vitamin A status is an important consideration in the health of both wild and captive amphibians. Data concerning whole body vitamin A homeostasis in amphibians are... (Review)
Review
Vitamin A status is an important consideration in the health of both wild and captive amphibians. Data concerning whole body vitamin A homeostasis in amphibians are scarce, although these animals have been used as experimental models to study the actions of vitamin A in vision, limb regeneration and embryogenesis. The available data suggest that many aspects of vitamin A biology in amphibians are similar to the canonical characteristics of vitamin A metabolism and actions established in mammals. This is consistent with the evolutionary conservation of these important biological processes. Amphibians must obtain vitamin A in their diet, with captive animals being prone to vitamin A deficiency. There is still much to be learned about vitamin A biology in amphibians that can only be achieved through rigorous scientific research. Improved understanding of amphibian vitamin A biology will aid the conservation of endangered amphibians in the wild, as well as the successful maintenance of ex situ populations.
Topics: Amphibians; Animal Husbandry; Animal Nutritional Physiological Phenomena; Animals; Conservation of Natural Resources; Species Specificity; Vitamin A
PubMed: 24958673
DOI: 10.1002/zoo.21140