RESUMO
Most described species have not been explicitly included in phylogenetic trees-a problem named the Darwinian shortfall-owing to a lack of molecular and/or morphological data, thus hampering the explicit incorporation of evolution into large-scale biodiversity analyses. We investigate potential drivers of the Darwinian shortfall in tetrapods, a group in which at least one-third of described species still lack phylogenetic data, thus necessitating the imputation of their evolutionary relationships in fully sampled phylogenies. We show that the number of preserved specimens in scientific collections is the main driver of phylogenetic knowledge accumulation, highlighting the major role of biological collections in unveiling novel biodiversity data and the importance of continued sampling efforts to reduce knowledge gaps. Additionally, large-bodied and wide-ranged species, as well as terrestrial and aquatic amphibians and reptiles, are phylogenetically better known. Future efforts should prioritize phylogenetic research on organisms that are narrow-ranged, small-bodied and underrepresented in scientific collections, such as fossorial species. Addressing the Darwinian shortfall will be imperative for advancing our understanding of evolutionary drivers shaping biodiversity patterns and implementing comprehensive conservation strategies.
Assuntos
Biodiversidade , Evolução Biológica , Filogenia , Vertebrados , Animais , Vertebrados/genética , Vertebrados/classificação , Anfíbios/genética , Anfíbios/classificação , Répteis/classificação , Répteis/genéticaRESUMO
Disintegrins comprise a family of small proteins that bind to and alter the physiological function of integrins, especially integrins that mediate platelet aggregation in blood. Here, we report a lysine-glycine-aspartic acid (KGD) disintegrin-like motif present in a 15-amino acid residue peptide identified in a cDNA library of the amphibian Hypsiboas punctatus skin. The original peptide sequence was used as a template from which five new analogs were designed, chemically synthesized by solid phase, and tested for disintegrin activity and tridimensional structural studies using NMR spectroscopy. The original amphibian peptide had no effect on integrin-mediated responses. Nevertheless, derived peptide analogs inhibited integrin-mediated platelet function, including platelet spreading on fibrinogen.
Assuntos
Desintegrinas , Peptídeos , Anfíbios/genética , Anfíbios/metabolismo , Animais , DNA Complementar/genética , Desintegrinas/química , Desintegrinas/genética , Desintegrinas/farmacologia , Peptídeos/química , Peptídeos/genética , Peptídeos/farmacologia , Agregação Plaquetária/fisiologiaRESUMO
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.
Assuntos
Anfíbios/genética , DNA Mitocondrial/química , Genoma Mitocondrial , Animais , Sequências Repetidas Invertidas , Sequências Repetitivas de Ácido NucleicoRESUMO
Amphibians are the focus of a recent debate and public attention owing to the global decline in their populations worldwide. Amphibians are one of the most threatened and poorly known groups of vertebrates in several geographic areas, even though they play a central role in their own ecosystems. At different levels, amphibians make their contribution to proper ecosystem functioning. They act as regulators of the food web and nutrient cycling, and they also provide several valuable ecosystem services, e.g., as a food source and as animal models for lab research. In this sense, it seems clear that the maintenance of amphibian diversity should be one of the major goals for the several countries where their population decline is observed. However, we are still struggling with the very first step of this process, i.e., the correct identification of the amphibian species diversity. Over the past few decades, research on molecular identification of amphibians using DNA barcoding has encountered some difficulties related to high variability in the mitochondrial genome of amphibians, and a research gap is noticeable in the literature. We herein evaluated both COI and 16S rRNA mitochondrial genes for the molecular identification of frogs and tadpoles in a large fragment of the South American Atlantic Rainforest in Rio de Janeiro, Brazil. Our results suggest that both COI and 16S rRNA are informative markers for the molecular identification of the amphibian specimens with all specimens unambiguously identified at the species level. We also made publicly available 12 new sequences of Atlantic Rainforest amphibian species for the first time, and we discussed some conservation issues related to amphibians within the Atlantic Rainforest domains in the state of Rio de Janeiro, Brazil.
Assuntos
Anfíbios/genética , Conservação dos Recursos Naturais , Floresta Úmida , Animais , Oceano Atlântico , Larva/genética , Biologia Molecular , RNA Ribossômico 16S/genética , América do SulRESUMO
A number of hypotheses about compensatory mechanisms that allow ectothermic animals to cope with the latitudinal decrease in ambient temperature ( TA) have been proposed during the last century. One of these hypotheses, the 'metabolic homeostasis' hypothesis (MHH), states that species should show the highest thermal sensitivity of the metabolic rate ( Q10-SMR) at the colder end of the range of TAs they usually experience in nature. This way, species should be able to minimize maintenance costs during the colder hours of the day, but quickly take advantage of increases in TA during the warmer parts of the day. Here, we created a dataset that includes Q10-SMR values for 58 amphibian species, assessed at four thermal ranges, to evaluate three predictions derived from the MHH. In line with this hypothesis, we found that: (i) Q10-SMR values tended to be positively correlated with latitude when measured at lower TAs, but negative correlated with latitude when measured at higher TAs, (ii) Q10-SMR measured at lower TAs were higher in temperate species, whereas Q10-SMR measured at higher TAs were higher in tropical species, and (iii) the experimental TA at which Q10-SMR was maximal for each species decreased with latitude. This is the first study to our knowledge showing that the relationship between Q10-SMR and latitude in ectotherms changes with the TA at which Q10-SMR is assessed, as predicted from an adaptive hypothesis. This article is part of the theme issue 'Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen'.
Assuntos
Anfíbios/metabolismo , Anfíbios/classificação , Anfíbios/genética , Animais , Mudança Climática , Ecossistema , Homeostase , Oxigênio/metabolismo , Filogenia , TemperaturaRESUMO
In the frog genus Pseudis, previous works found a sex-linked heteromorphism of the PcP190 satellite DNA in the nucleolus organizer region (NOR)-bearing chromosome pairs of Pseudis bolbodactyla and Pseudis tocantins, which possess a ZZ/ZW sex determination system. A pericentromeric inversion was inferred to have occurred during W chromosome evolution, moving a chromosomal cluster enriched by the PcP190 from the short arm (as observed in P. bolbodactyla) to the NOR-bearing long arm (as observed in P. tocantins). However, whether such an inversion happened in P. tocantins or in the common ancestor of Pseudis fusca and P. tocantins remained unclear. To assess this question, we mapped PcP190 in the karyotype of P. fusca from three distinct localities. Southern blotting was used to compare males and females. The mitochondrial H1 fragment (which contains the 12S ribosomal RNA (rRNA), tRNAval, and 16S rRNA genes) and cytochrome b gene were partially sequenced, and a species tree was inferred to guide our analysis. Pseudis fusca specimens were placed together as the sister group of P. tocantins, but based on genetic distance, one of the analyzed populations is probably an undescribed species. A cluster of PcP190, located in the long arm of chromosome 7, is sex linked in this putative new species but not in the remaining P. fusca. We could infer that the pericentromeric inversion that moved the PcP190 site to the NOR-bearing chromosome arm (long arm) occurred in the common ancestor of P. fusca, the putative undescribed species, and P. tocantins.
Assuntos
Anfíbios/genética , DNA Satélite , Evolução Molecular , Cromossomos Sexuais/genética , Anfíbios/classificação , Animais , Citocromos b/genética , Feminino , Masculino , Filogenia , RNA Ribossômico/genéticaRESUMO
Amphibian secretion is an important source of bioactive molecules that naturally protect the skin against noxious microorganisms. Collectively called antimicrobial peptides (AMPs), these molecules have a wide spectrum of action, targeting viruses, bacteria and fungi. Like many membrane and secreted proteins, AMPs have cleavable signal sequences that mediate and translocate the nascent polypeptide chains into the endoplasmic reticulum. Although it is accepted that the signal peptides (SPs) are simple and interchangeable, there is neither sequence nor structure that is conserved among all gene families. They derived from a common ancestor but developed different traits as they adapt to distinct environmental pressures. The aim of this study was to provide anoverview of the diversity of SPs of the frog, taking into account reported cDNA sequences and the evolutionary relationship among them. We analysed more than 2000 records that reported the relative abundance, diversity and evolutionary divergence based on the peptide signals of frog AMPs. We conclude that the physical properties of the sequence are more important than the specific peptidesin AMP SPs. Since there is significant overlapping among related genera, differences in secretion from different peptide types should be regulated by additional levels, such as posttranscriptional modifications or 5-UTR sequences.
Assuntos
Proteínas de Anfíbios/genética , Anfíbios/genética , Antibacterianos/metabolismo , Peptídeos Catiônicos Antimicrobianos/genética , Bactérias/metabolismo , Sinais Direcionadores de Proteínas/genética , Pele/metabolismo , Proteínas de Anfíbios/metabolismo , Anfíbios/metabolismo , Animais , Peptídeos Catiônicos Antimicrobianos/metabolismoRESUMO
Rapid environmental change in highly biodiverse tropical regions demands efficient biomonitoring programmes. While existing metrics of species diversity and community composition rely on encounter-based survey data, eDNA recently emerged as alternative approach. Costs and ecological value of eDNA-based methods have rarely been evaluated in tropical regions, where high species richness is accompanied by high functional diversity (e.g., the use of different microhabitats by different species and life stages). We first tested whether estimation of tropical frogs' community structure derived from eDNA data is compatible with expert field assessments. Next, we evaluated whether eDNA is a financially viable solution for biodiversity monitoring in tropical regions. We applied eDNA metabarcoding to investigate frog species occurrence in five ponds in the Chiquitano dry forest region in Bolivia and compared our data with a simultaneous visual and audio encounter survey (VAES). We found that taxon lists and community structure generated with eDNA and VAES correspond closely, and most deviations are attributable to different species' life histories. Cost efficiency of eDNA surveys was mostly influenced by the richness of local fauna and the number of surveyed sites: VAES may be less costly in low-diversity regions, but eDNA quickly becomes more cost-efficient in high-diversity regions with many sites sampled. The results highlight that eDNA is suitable for large-scale biodiversity surveys in high-diversity areas if life history is considered, and certain precautions in sampling, genetic analyses and data interpretation are taken. We anticipate that spatially extensive, standardized eDNA biodiversity surveys will quickly emerge in the future.
Assuntos
Anfíbios/classificação , Anfíbios/genética , Biota , Código de Barras de DNA Taxonômico/métodos , Metagenômica/métodos , Animais , Bolívia , Custos e Análise de Custo , Código de Barras de DNA Taxonômico/economia , Metagenômica/economia , Clima TropicalRESUMO
Chytridiomycosis, due to the fungus Batrachochytrium dendrobatidis (Bd), has been associated with the alarming decline and extinction crisis of amphibians worldwide. Because conservation programs are implemented locally, it is essential to understand how the complex interactions among host species, climate and human activities contribute to Bd occurrence at regional scales. Using weighted phylogenetic regressions and model selection, we investigated geographic patterns of Bd occurrence along a latitudinal gradient of 1500 km within a biodiversity hot spot in Chile (1845 individuals sampled from 253 sites and representing 24 species), and its association with climatic, socio-demographic and economic variables. Analyses show that Bd prevalence decreases with latitude although it has increased by almost 10% between 2008 and 2013, possibly reflecting an ongoing spread of Bd following the introduction of Xenopus laevis. Occurrence of Bd was higher in regions with high gross domestic product (particularly near developed centers) and with a high variability in rainfall regimes, whereas models including other bioclimatic or geographic variables, including temperature, exhibited substantially lower fit and virtually no support based on Akaike weights. In addition, Bd prevalence exhibited a strong phylogenetic signal, with five species having high numbers of infected individuals and higher prevalence than the average of 13.3% across all species. Taken together, our results highlight that Bd in Chile might still be spreading south, facilitated by a subset of species that seem to play an important epidemiological role maintaining this pathogen in the communities, in combination with climatic and human factors affecting the availability and quality of amphibian breeding sites. This information may be employed to design conservation strategies and mitigate the impacts of Bd in the biodiversity hot spot of southern Chile, and similar studies may prove useful to disentangle the role of different factors contributing to the emergence and spread of this catastrophic disease.
Assuntos
Anfíbios/microbiologia , Biodiversidade , Micoses/veterinária , Filogenia , Anfíbios/genética , Anfíbios/crescimento & desenvolvimento , Animais , Chile , Quitridiomicetos , Humanos , Dinâmica Populacional , ReproduçãoRESUMO
Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species. Here, we provide new PCR conditions and tested new primers that increase the efficiency of barcode recovery in amphibians. We found that a low extension temperature for PCR cycles significantly improves the efficiency of amplification for all combinations of primers. Combining low PCR extension temperature and primers AnF1 + AnR1, we were able to recover COI sequences for 100% of the species analysed (N = 161), encompassing ~15% of the species known from Brazil (representing 77 genera and 23 families), which is an important improvement over previous studies. The preliminary assessment of species diversity suggested that number of species might be underestimated by about 25%. We conclude that DNA barcoding is an efficient, simple, and standardized protocol for identifying cryptic diversity in amphibians and advocate for its use in biodiversity inventories and across widespread populations within known species.