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Cerithioidea (Caenogastropoda: Gastropoda) represents a diverse superfamily of gastropods that inhabit marine, brackish, and freshwater environments worldwide. Despite this broad ecological distribution, their evolutionary history and phylogenetic relationships remain incompletely understood. Here, we report six …
Read PDFMembers of the genus <i>Rhizobium</i> are best known for nitrogen-fixing symbioses with legumes, yet their diversity and evolutionary roles in non-legume hosts remain poorly explored, particularly in arid ecosystems. We report the isolation and characterization …
Read PDF<h4>Background</h4>The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies- a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, …
Read PDFAnaerobic gut fungi (AGF, <i>Neocallimastigomycota</i>) represent a phylum of zoospore-producing fungi inhabiting the gastrointestinal tracts of herbivores. Twenty mammalian-affiliated genera (M-AGF) and two tortoise-affiliated genera (T-AGF) have been described so far. Here, we report on …
Read PDFWith the explosive growth of whole-genome datasets, accurate detection of orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods for identifying orthologous synteny face great limitations, particularly in scaling with varied polyploidy …
Read PDF<h4>Background and aims</h4>The evolution of mycoheterotrophy represents a major evolutionary transition that is likely to proceed through intermediate stages, such as initial and partial mycoheterotrophy. Cremastra aphylla, a predominantly leafless, fully mycoheterotrophic orchid, occasionally produces …
Read PDF<b>Background/Objectives:</b><i>Escherichia coli</i> (<i>E. coli</i>) spans commensal, intestinal pathogenic, and extraintestinal pathogenic lineages distributed across human, animal, and environmental reservoirs, yet the extent to which virulence architectures are shared across these compartments remains incompletely understood. Using …
Read PDFThe following Special Issue (SI) focuses on analyzing the structure, evolution, and diversity of mitochondrial genomes (mitogenomes) in predominantly aquatic animals, with two exceptions: semiaquatic lizards and the waterlily aphid [...].
Read PDFBACKGROUND: Hamamelidaceae, a family within the core eudicots and the order Saxifragales, represents a characteristic lineage of the East Asian flora and holds considerable ecological and economic importance. However, molecular phylogenetic studies based on single …
Read PDF<h4>Background</h4>The East Asia-eastern North America disjunction represents a classic biogeographic pattern, widely interpreted as a relic of Tertiary temperate forests that were widespread across the Northern Hemisphere. Although this pattern has been well-documented in woody …
Read PDF<h4>Premise</h4>We examined the African arid corridor (AAC) disjunction pattern of vascular plants between northeastern and southwestern Africa in the context of geological and climatic events since the late Miocene. We developed a phylogenetic and biogeographical …
Read PDFWhile some relationships in phylogenomic studies have remained stable since the Sanger sequencing era, many challenging nodes remain, even with genome-scale data. Incongruence or lack of resolution in the phylogenomic era is frequently attributed to …
Read PDF<i>Piper aduncum</i> L. has long been used in traditional medicine for its notable antimicrobial, anti-diarrheal, and anti-inflammatory properties. Flavonoids are recognized as the principal bioactive constituents of this plant, among which isoembigenin (IEGN) has been …
Read PDFUnderstanding gene flow between ploidy levels in polyploid complexes is essential for species delimitation and conservation. This study explores evolutionary dynamics in the polyploid complex Thymus sect. Mastichina (Lamiaceae), comprising three taxa: T. mastichina subsp. …
Read PDFSalamanders have large and complex genomes, hampering whole genome sequencing. However, reduced representation sequencing provides a feasible alternative to obtain genome-wide data. We present NewtCap: a sequence capture bait set that targets <i>c</i>. 7 k …
Read PDF<h4>Introduction</h4>The <i>Mycobacterium</i> "<i>Fortuitum-Vaccae</i>" clade (FVC) contains many rapid-growing species and is increasingly reported in human infections globally. However, the clade's taxonomic composition and the exact association with human infections remain to be explored.<h4>Methods</h4>In this study, …
Read PDFReconstructing the tree of life remains a central goal in biology. Early methods, which relied on small numbers of morphological or genetic characters, often yielded conflicting evolutionary histories, undermining confidence in the results. Investigations based …
Read PDFReticulate evolution (RE), involving hybridization and related processes, generates network-like rather than strictly bifurcating relationships among lineages and can obscure phylogenetic relationships. Detecting ancient hybridization is particularly challenging, as genomic signals may erode over time. …
Read PDFPlant phylogenetics has been revolutionised in the genomic era, with target capture acting as the primary workhorse of most recent research in the new field of phylogenomics. Target capture (aka Hyb-Seq) allows researchers to sequence …
Read PDFThe genus <i>Phyllosticta</i> comprises diverse plant-associated fungi, many of which are significant pathogens or endophytes with complex taxonomic histories. Traditional classification, reliant on morphology and host associations, has long been challenged by overlapping traits, necessitating …
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