phylogenetics / evolution

The paper introduces a Bayesian measure of phylogenetic information content using geodesic distances and demonstrates its application with simulated and empirical examples.

The paper constructs a pangenome of threatened mink subspecies to identify adaptive signatures and evolutionary history using genome assemblies and functional analysis.

A 1,474-species 10-marker phylogeny and a 110-taxon Angiosperms353 phylogenomic dataset support a rank-free PhyloCode classification defining 38 clades across Solanaceae, including 16 infrageneric clades in Solanum.

The paper reconstructs 3,500 years of sheeppox virus evolution using ancient genomes from archaeological and medieval parchment sources, showing divergence events and gene inactivation.

The paper identifies a rapidly expanding multidrug-resistant M. tuberculosis clade originating from Russia and circulating in Moldova, posing a threat to MDR-TB control.

This study evaluates how mass extinctions affect phylogenetic dating by simulating their impact and testing detectability using total-evidence dating methods.

Panmap efficiently aligns, genotypes, and places reads on large pangenomes using phylogenetic compression, enabling rapid analysis of up to 8 million genomes.

The paper introduces a method for stochastic character mapping of continuous traits on phylogenies, showing higher trait evolution rates in smaller eucalypt trees.

This study investigates the evolutionary history of the TLR2 cavity in vertebrates and invertebrates using AI protein structure predictions, showing its ancestral origin and convergent evolution in different species.

This study reconstructs the genome and karyotype evolution of Sesamum and related species, revealing hybridization events and genetic changes linked to metabolic specialization.

The paper identifies SIRC ensembles in plant genomes, showing their ancient origin and phylogenetic signal, suggesting their utility in tracing evolutionary history and aiding genomic analysis.

This study challenges the late origin of crown eukaryotes by showing that evolutionary dynamics require an earlier last eukaryotic common ancestor (LECA) to explain observed diversity and fossil records.

Phyling is a tool for phylogenetic inference from protein sequences, offering faster performance than OrthoFinder with comparable accuracy.

This study uses discrete diffusion models to generate tumor phylogenies, finding that mid-scale models outperform deeper ones and that diverse training improves cross-regime generalization.

The paper analyzes genetic and morphological data of Korean wild mice to determine their phylogenetic relationships and taxonomic status within the Mus musculus subspecies.

The paper introduces the Duplicate Monophyly Criterion to calibrate distance-matrix perturbations for phylogenetic support estimation using synthetic duplicates.

This study identifies and classifies over 400 metallothioneins (MTs) in chelicerates, revealing three types with distinct structural and evolutionary features.

This paper evaluates how gene tree dependence affects species tree inference accuracy using ASTRAL, finding that dependence reduces effective sample size but does not require full independence for accurate results.

The paper analyzes whole genome sequences of Neisseria gonorrhoeae isolates from the G-ToG trial to characterize gonococcal diversity and AMR patterns in England, showing sexual network-driven phylogenetic structure and AMR differences between transmission groups.

This paper derives a geometric state equation for the tree of life, showing evolution embeds into 2D hyperbolic space with curvature determined by entropy, and confirms this across multiple biological systems.

The paper presents CattleGTEx, a resource characterizing regulatory effects in cattle, resolving GWAS signals and providing insights into adaptive evolution and selection.

The paper analyzes 1,001 wolf genomes to reveal distinct evolutionary lineages and genetic health issues across Europe, highlighting the need for region-specific conservation strategies.

This study uses deep learning to perform ancestral state reconstruction for phylogenetic models with intractable likelihoods, comparing performance to Bayesian inference on empirical datasets.

This paper develops efficient date interpolation algorithms to fully date a large phylogenetic tree, enabling robust estimates of phylogenetic diversity across 2.3 million species.

This study presents a chromosome-anchored genome assembly of Asymmetron lucayanum, revealing genome architecture and gene evolution in cephalochordates.

This study analyzes gene functional repertoires across Amoebozoa, Fungi, and Metazoa to reveal distinct evolutionary trajectories, showing Amoebozoa retained ancestral gene functions while Fungi and Metazoa specialized in metabolism and multicellularity.

WASTER infers shallow phylogenies from low-coverage short reads without assembly or alignment, achieving accuracy comparable to traditional methods at lower costs.

OxBreaker is a species-agnostic pipeline for analyzing bacterial and plasmid outbreaks using nanopore sequencing, offering high accuracy and accessibility for real-time genomic surveillance.

This paper optimizes phylogenetic eigenvector regression by improving eigenvector selection, robustness to evolutionary shifts, and flexibility in model complexity.

The paper predicts RfaH homolog structures using AlphaFold2, identifies active-state homologs, and supports a stepwise evolutionary model of RfaH specialization.