phyloPipeR: An R Package for End-to-End Phylogenetic Reconstruction and Tree Comparison
No abstract available.
Read PDFBrowse Papers
Search the literature by keyword, topic, or author. Filter to articles with full text available.
3689 results
Insights into Convergent Evolution From Studying Amino Acid Patterns in Independent Lineages of Birds
Vocal learning, the ability to imitate sounds, is a complex convergent trait crucial for spoken language and observed in a few independent lineages of mammals and birds. While convergences in gene expression have been found …
Read PDFGenome-based reclassification of <i>Parabacteroides chartae</i> as a later heterotypic synonym of <i>Macellibacteroides fermentans</i>
Strain PK034 was isolated from a municipal wastewater treatment plant in Stillwater, OK, USA. A comparison of 16S rRNA gene sequences revealed ≥99.4% sequence similarity to the type strains of <i>Macellibacteroides fermentans</i> (isolated from an …
Read PDFGlobal diversity of the <i>Tylopilus alboater</i> complex (<i>Boletaceae</i>, <i>Boletales</i>): new genus and species, and typification of the name <i>Boletus alboater</i>
Recognition of <i>Tylopilus alboater</i> once relied heavily on the morphological features of the basidiomata, which resulted in considerable confusion due to morphological stasis and plasticity. In this study, we examined specimens morphologically identified as <i>T. …
Read PDFGenomic insights into Streptomyces albidoflavus SM254: tracing the putative signs of anti-Pseudogymnoascus destructans properties
White-nose syndrome, caused by the psychrophilic fungus Pseudogymnoascus destructans, has devastated bat populations across North America. Streptomyces albidoflavus SM254 was previously reported to exhibit antifungal activity against this pathogen, but no comprehensive genomic characterization has …
Read PDFPhylogenomics Unveils the Complex Evolution of Retroviruses in Birds
The rise of birds represents one of the major evolutionary transitions in the history of life. Yet, much remains obscure about the origins and diversification of viruses in birds. Endogenous retroviruses (ERVs), relics of past …
Read PDFGenome sequence of the marine alphaproteobacterium <i>Lentilitoribacter</i> sp. EG35 isolated from the temperate octocoral <i>Eunicella gazella</i>
We report the genome sequence of <i>Lentilitoribacter</i> sp. strain EG35 isolated from the octocoral <i>Eunicella gazella</i> sampled off the coast of Portugal. We reveal the coding potential for the biosynthesis of polyhydroxyalkanoates - biodegradable polyesters …
Read PDFCharacterizing semi-directed phylogenetic networks and their multi-rootable variants
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently, phylogenetic studies have started to focus on a special class of such …
Read PDFComparative analysis towards the identification of genome wide characteristics of a beneficial fungal endophyte
Fusarium solani strain K (FsK) is an endophytic fungus with a wide host range that protects its host plants against pathogens and environmental stresses. In this study, we performed de novo genome sequencing and annotation, …
Read PDFVariant Calling in the Goldilocks Zone: How Reference Genome Choice and Read Mapping Stringency Impact Heterozygosity Estimates and Phylogenetic Analyses
The increasing numbers of published reference genomes and affordability of whole genome resequencing have enabled multispecies population genomic and phylogenomic studies on non-model organisms, but they raise a new question for comparative genomics: what reference …
Read PDFReply to: Embracing the taxonomic and topological stability of phylogenomics
No abstract available.
Read PDFPhylogenomics of novel clones of <i>Aeromonas veronii</i> recovered from a freshwater lake reveals unique biosynthetic gene clusters
Aquatic ecosystems serve as crucial reservoirs for pathogens and antimicrobial resistance genes, thus presenting a significant global health risk. Here, we investigated the phylogenomics of <i>Aeromonas veronii</i> from Lake Wilcox in Ontario. Among the 11 …
Read PDFIdentification and characterization of RacX, a new broad-specificity amino acid racemase from a novel taxon within the order <i>Flavobacteriales</i>
Amino acid racemases are pivotal for d-amino acid (DAA) biosynthesis with wide-ranging biotechnological applications, yet their industrial deployment is hindered by narrow substrate specificity and instability. Here, we report the discovery of <i>Halocola ammonii</i> gen. …
Read PDFMitochondrial Phylogenomics of Scoliidae from China, with Evidence to Challenge the Former Placement of the <i>Colpa</i> Group
Scoliidae, also known as scarab hunters or flower wasps, are important in the biological control of scarabs and for pollination. Mitogenomic and phylogenetic studies are rare for this group. In this study, 10 mitochondrial genomes …
Read PDFGenome-Based Reclassification of <i>Streptococcus taoyuanensis</i> ST2<sup>T</sup> as a Later Heterotypic Synonym of <i>Streptococcus caecimuris</i> CLA-AV-18<sup>T</sup>
This study systematically evaluated the taxonomic relationship between <i>Streptococcus taoyuanensis</i> ST2<sup>T</sup> and <i>Streptococcus caecimuris</i> CLAAV18<sup>T</sup>. Comparative genomic analysis revealed a high 16S rRNA gene sequence similarity of 99.6%, with the two strains clustering closely in …
Read PDFReticulate evolutionary history underpins a revised generic circumscription of Paphiopedilum (Orchidaceae): insights from integrative phylogenomics and historical biogeography
BACKGROUND: The taxonomy of Paphiopedilum—a diverse group of slipper orchids—has long posed challenges due to high morphological variability and conflicting phylogenetic signals. Despite intensive research, a clear and stable infrageneric classification remains unresolved. RESULTS: We …
Read PDFReassessing the phylogenetic relationships of <i>Pseudosorghum</i> and Saccharinae (Poaceae) using plastome and nuclear ribosomal sequences
The sugarcane subtribe Saccharinae (Andropogoneae, Poaceae) was established in 1846, but its delimitation has long been debated. Moreover, the relationships among the genera of Saccharinae remain unclear, and there is no consensus on whether <i>Pseudosorghum</i>, …
Read PDFPhenotypic and genomic characterization of tigecycline heteroresistance in carbapenem-resistant <i>Klebsiella pneumoniae</i>
The presence of tigecycline heteroresistance in carbapenem-resistant <i>Klebsiella pneumoniae</i> (CRKP) can compromise the efficacy of antimicrobial therapy. This study aimed to investigate the phenotypic and genomic characteristics of Tgc-HR in CRKP clinical isolates. A total …
Read PDFCAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution
Phenotypic convergence is found across the tree of life, and morphological similarities in distantly related species are often presumed to have evolved independently. However, clarifying the origins of traits has recently highlighted the complex nature …
Read PDFPhylogenomic and metabolomic approaches to provide insight for species delimitation of cultivated <i>Ferula</i> species in Xinjiang, China
The genus <i>Ferula</i> is an important medicinal group within the Apiaceae family, valued globally for its health and culinary uses. Recently, it has gained significant attention because of its cultivation and use to meet growing …
Read PDF