phylogenetics / evolution

The paper tests bryophyte monophyly using a large genome dataset and shows it is supported despite phylogenetic disputes and outgroup effects.

The paper challenges the statistical validity of syntenies used to support phylogenetic groupings, arguing that current methods overestimate significance and may miss real linkage groups.

This study uses long-read sequencing and genome graphs to analyze structural variation in Mycobacterium tuberculosis, identifying SVs linked to drug resistance and virulence.

This study uses mutational spectra to infer influenza virus transmission routes and adaptive mutations enabling sustained respiratory transmission.

The paper quantifies introgression in tinamou species, showing asymmetric patterns linked to chromosomal features and resolving their species tree through genome-architecture-aware phylogenomics.

The paper uses genomic data to analyze the Juglans genus, finding black walnut as an ancient lineage with implications for conservation and climate adaptation.

This paper introduces POLEGON, a method for estimating branch lengths in Ancestral Recombination Graphs using uninformative priors, showing improved coalescence time estimates and population size inferences.

This study traces the evolutionary origins of PRRSV, revealing rodent ancestry and human-driven factors shaping its diversification and spread.

The paper characterizes 15 phages infecting Xanthomonas arboricola pv. pruni, identifying a new genus and species and proposing taxonomic changes within the Anamaviridae family.

The paper introduces MTBseq-nf, a Nextflow wrapper for the MTBseq pipeline, improving scalability and efficiency for tuberculosis genomics analysis.

The paper analyzes global Salmonella Infantis genomes to show a monophyletic lineage shaped by geographic structuring and links its spread to antibiotic resistance gene dissemination.

The paper identifies five divergent amino acids in COI sequences to differentiate Scolopendra species and proposes a rule for molecular species delimitation, with exceptions resolved using amino acid frequency and substitution probability analysis.

STELAR-X is a scalable triplet-based method for species tree inference that outperforms existing methods in speed and memory usage on large datasets.

PhyloCNN improves tree representation and neural network architecture for deep learning in phylodynamics and diversification studies, achieving high accuracy with smaller training sets.

This study investigates the co-phylogenetic history of Leishmania parasites and Leishmaniavirus, finding strong phylogenetic congruence at the subgenus and species level, with weaker signals in some cases due to intraspecific host switching.

Gordon et al. use a phylogenetic machine-learning approach to predict soft-tissue flippers and aquatic habits in extinct amniotes with >90% accuracy using limb proportions.

This paper introduces a Bayesian Model Averaging framework for phylodynamic inference that integrates multiple coalescent models to better capture demographic histories without pre-specifying a single model.

The paper curates a dataset of 332 high-coverage great ape genomes to address evolutionary and diversity questions.

The paper shows that Ks histograms can reveal or obscure ancient whole genome duplications depending on evolutionary and demographic factors.

The paper derives the distribution of the time to the most recent pairwise genetic common ancestor in a recombining population, finding a characteristic scaling with population size.

The paper presents a phased whole genome assembly for Atlantic bluefin tuna using PacBio HiFi and Omni-C scaffolding, enabling improved phylogenomic and evolutionary studies.

SNaQ.jl improves scalability for phylogenetic network inference by enhancing computational efficiency without altering method accuracy.

The paper investigates the evolutionary origins of insecticidal protein families, finding evidence of divergent evolution and horizontal gene transfer across bacteria, ferns, and other organisms.

The paper analyzes whole-genome polymorphisms of high-value rice cultivars in the Mediterranean market to assess genetic relationships and identify variants linked to quality and drought traits.

This study evaluates how MSA Transformer captures evolutionary distance and epistasis in protein sequences, showing it can reconstruct phylogenetic trees consistent with maximum likelihood methods.

The paper reports a novel ORF insertion in the mitochondrial genome of Palythoa tuberculosa, distinct from previously reported ORF extensions in zoantharians.

This paper introduces Qsin, a sparse learning method that reduces the size of concordance factors tables for phylogenetic network inference while maintaining accuracy and reducing computational time.

The paper determines the first complete mitogenome of Aetobatus ocellatus, confirms its classification in Aetobatidae, and highlights taxonomic implications for conservation.

This paper shows that Bordetella parapertussis evolved similarly to Bordetella pertussis after pertussis vaccination, including loss of pertactin and changes in regulatory regions.

This study uses phylogenomic analysis to trace the timing of nutrient limitation genes across Earth's history, showing phosphorus genes emerged early, nitrogen later, and iron-related siderophores possibly as early as the Archean.