phylogenetics / evolution

Segment-dependent phylogenetic resolution reveals geographic and host sampling gaps in Oropouche virus genomes

This study analyzes phylogenetic resolution differences among Oropouche virus genome segments and identifies sampling biases in publicly available sequences.

HERACLES for fast and accurate likelihood-based reconstruction of massive lineages

HERACLES improves lineage reconstruction accuracy and scalability by optimizing cell coordinates in hyperbolic space using a composite likelihood model of CRISPR editing.

Polyphyletic origins and lineage-specific expansion of chemosensory systems in phylum Actinomycetota

This study investigates the evolutionary distribution of chemosensory systems in Actinomycetota, finding lineage-specific retention and expansion, with TCS playing a dominant role in regulatory networks.

Ok-k-mer: Selecting k-mer length ensembles for calculating genomic distance

Ok-k-mer selects optimal k-mer length ensembles to improve genomic distance estimation by maximizing correlation with phylogenetic branch distances.

Tracing the Evolutionary Histories of Human Cholinergic Proteins Across Eukaryotes: A Comparative Phylogenomic Study

This study traces the evolutionary histories of human cholinergic proteins across eukaryotes using phylogenomic analysis, revealing heterogeneous patterns and phylogenetic relationships.

QRAFT: Scaling coalescent-based species tree inference to one million taxa

QRAFT efficiently infers species trees for up to a million taxa using coalescent-based methods, outperforming existing tools in speed and memory usage.

Rates of molecular and morphological evolution are uncoupled across the eukaryote Tree of Life

The paper investigates correlations between molecular and morphological evolutionary rates across eukaryotes and finds little evidence of a link, suggesting differing evolutionary dynamics at genomic and phenotypic levels.

Integrative identification of Tetratostichococcus sp. CCAH0201 (Trebouxiophyceae, Chlorophyta) from Rhizophora leaves in the Can Gio Mangrove Forest, Vietnam

The paper identifies a microalgal strain from mangrove leaves using molecular markers and phylogenetic analysis, placing it closely related to Tetratostichococcus jenerensis.

QUANTA: A quantum annealing framework for species tree estimation using weighted quartet amalgamation

QUANTA uses quantum annealing to improve species tree estimation from multi-locus data, achieving comparable accuracy to classical methods with significant speedup.

A timeline for evolution of metabolism in early microbes

The paper uses machine learning and phylogenomics to date 14 metabolic forms and 6 traits in early microbes, finding three waves of metabolic evolution starting >3.4 Ga.

Bayesian phylogenetic inference accounting for recombination in whole bacterial genomes

This paper introduces ClonalFrame2, a Bayesian method for phylogenetic inference in bacteria that accounts for recombination, showing improved accuracy in simulated and real datasets.

Structural and evolutionary insights into FcαμR recognition of polymeric immunoglobulins

This study determines cryo-EM structures of FcR bound to IgM and IgA, revealing its binding mechanism and evolutionary insights into pIg receptor recognition.

Adaptation and conservation of turtle visual opsins over a deep phylogenetic divergence

This study investigates visual opsin evolution in turtles using transcriptomic and genomic data from 59 species, revealing conserved sequences and habitat-driven selective pressures.

Guide-tree bias of whole genome alignment can mislead phylogenomic analyses

The paper shows guide-tree bias in whole-genome alignment can mislead phylogenomic analyses and proposes a consensus alignment strategy to reduce this bias.

Sea slugs unplugged: Review of subpopulation sampling in phylogeographic studies of nudibranchs and their allies

The paper reviews subpopulation sampling in phylogeographic studies of sea slugs, finding varied sampling designs and two significant associations between sampling and genetic differentiation.

Convergent genome- and gene-level constraints shape repeated environmental adaptation in grasses

This study identifies convergent genomic and gene-level constraints in grasses adapting to extreme environments using phylogenomic data and large language models.

Evolutionary Coupling of Flagellar Motility and Type VI Secretion Systems Across Bacteria

The paper investigates the evolutionary relationship between flagellar motility and bacterial secretion systems, finding strong coupling with T6SS but not bacteriocins.

In silico codon optimization and phylogenetic analysis of various strains of Sapovirus

The paper optimizes codon usage for Sapovirus VP1 and VP2 genes in Escherichia coli and performs phylogenetic analysis of twelve human strains.

Genomic expansion in the dark: A repeat-rich genome of a cave-dwelling remipede sheds light on the evolution of the hexapod sister group.

This paper presents the first high-quality genome assembly of a cave-dwelling remipede, revealing a repeat-rich genome with extensive gene family turnover and phylogenetic signals.

H5N5 virus transmission is driven by repeated cross-Atlantic introductions and transmission among high latitude seabirds

This study shows H5N5 viruses have been repeatedly introduced across the Atlantic by high latitude seabirds, with more frequent introductions in fall and spring, and a distinct ecology from H5N1.

DGM Is Dead; Long Live DGM-Star! A Quantization-Theoretic Approach to Gamma Rate Discretization

The paper introduces a new method to discretize Gamma rate distributions in phylogenetics, reducing branch length bias compared to the standard DGM.

Speciation, sexual selection, and the macroevolution of cricket mating signals

This study shows that mating signal traits involved in species recognition diverge rapidly during speciation, while traits involved in sexual selection do not, challenging the idea that sexual selection drives interspecific divergence.

A 4,000-year genomic history of Bantu speakers from the Congo rainforest

This study uses genomic data from ancient and present-day individuals to trace the 4,000-year demographic history of Bantu speakers in the Congo rainforest, revealing early dispersals and a population crisis.

Mobile genetic elements accompany the emergence of clonal crop lineages from weed-associated populations of Xanthomonas campestris

The paper analyzes Xanthomonas campestris strains from weed and crop hosts to show that mobile genetic elements accompany the emergence of clonal crop lineages and are present in diverse weed-associated strains.

A single freshwater invasion gave rise to the world's dominant freshwater fish group

The paper challenges the hypothesis of multiple freshwater invasions in otophysan fish by showing that a single invasion is more likely, based on phylogenetic and biogeographic analyses.

Phylogenetic position and expanded host range of the photosymbiont Brandtodinium nutricula (Peridiniales, Dinophyceae)

This study identifies the phylogenetic position of Brandtodinium nutricula and shows its free-living abundance in the ocean, challenging previous assumptions about its symbiotic exclusivity.

Durophagous adaptations in a new crocodyliform from the Santonian of Hungary and a systematic reassessment of European Cretaceous atoposaurids

The paper describes a new crocodyliform species from the Santonian of Hungary and reassesses the taxonomy of European Cretaceous atoposaurids, finding potential polyphyly in Theriosuchus.

Characterization of the Preclinical in Vitro and in Vivo Pharmacokinetic Properties of the Cyclic Oligomeric Depsipeptide Ryanodine Receptor 2 Inhibitor ent-Verticilide

This study characterizes the pharmacokinetic properties of ent-verticilide, identifying limited intestinal availability and CYP-mediated metabolism as key factors affecting its oral exposure.

Genomic detection of domoic acid biosynthesis uncovers expanded toxigenic diversity across Pseudo-nitzschia diatoms

The paper identifies genomic features of domoic acid biosynthesis in Pseudo-nitzschia diatoms, revealing expanded toxigenic diversity and environmental expression patterns.

Traits and hidden states: is self-fertilization associated with rates of diversification across mating and sexual systems?

The paper examines how mating and sexual systems affect diversification rates across 18 plant families, finding that sexual systems better explain diversification than mating systems.