The use of molecular data for documenting biodiversity has become more common over time as larger datasets can be generated faster. Nevertheless, studies addressing phenotypical data have not become as common. As a collateral effect, many samples used in molecular studies are assigned to a species without checking phenomic characters of the vouchers. Correct specific assignment is paramount for any biological hypothesis. A recent review of Phyzelaphryninae, while producing interesting results, has not specified how some vouchers used in molecular analyses were assigned to each species. Using new sequences from fresh material collected in Southern Bahia, we re-identify Adelophryne specimens based on molecular and morphological grounds. This new taxonomic understanding clarifies the phylogenetic position of A. pachydactyla and highlights a more parsimonious explanation for the evolution of a morphological character-the reduction of a phalange on Finger IV-within Adelophryne.
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http://dx.doi.org/10.11646/zootaxa.4444.5.5 | DOI Listing |
NAR Genom Bioinform
March 2025
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
Evaluating the accuracy of protein-coding sequences in genome annotations is a challenging problem for which there is no broadly applicable solution. In this manuscript, we introduce PSAURON (Protein Sequence Assessment Using a Reference ORF Network), a novel software tool developed to help assess the quality of protein-coding gene annotations. Utilizing a machine learning model trained on a diverse dataset from over 1000 plant and animal genomes, PSAURON assigns a score to coding DNA or protein sequence that reflects the likelihood that the sequence is a genuine protein-coding region.
View Article and Find Full Text PDFEcol Evol
January 2025
Unit of Evolutionary Biology/Systematic Zoology Institute for Biochemistry and Biology, University of Potsdam Potsdam Germany.
Genomics is an invaluable tool for conservation, particularly for endangered species impacted by wildlife trafficking. This study uses genomic data to provide new insights to aid conservation and management of endangered species, using as a case study the Yellow cardinal (), a bird endemic to southern South America severely affected by illegal trade and the transformation of its natural habitat. We explore population structure within the Yellow cardinal, delimiting management units and describing connectivity among them.
View Article and Find Full Text PDFProbiotics Antimicrob Proteins
January 2025
Home Economic Department, Faculty of Women for Arts Science and Education, Ain Shams University, Cairo, Egypt.
High-fat diet (HFD) consumption disrupts the gut microbiome, instigating metabolic disturbance, brain pathology, and cognitive decline via the gut-brain axis. Probiotic and prebiotic supplementation have been found to improve gut microbiome health, suggesting they could be effective in managing neurodegenerative disorders. This study explored the potential benefits of the probiotic strain Lactobacillus plantarum 20174 (L.
View Article and Find Full Text PDFGenetics
January 2025
Dept. of Genetics, Stanford University, Stanford CA 94305-5120, USA.
The Candida Genome Database (CGD; www.candidagenome.org) is unique in being both a model organism database and a fungal pathogen database.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada.
Spectra of the weakly bound H2O-O2 dimer are studied in the region of the H2O ν2 band using a tunable quantum cascade laser to probe a pulsed supersonic slit jet expansion. These are the first gas-phase infrared spectra of H2O-O2 and among only a few such results for O2-containing complexes. Almost 100 infrared lines are assigned based on the ground state combination differences from the microwave spectrum of H2O-O2.
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