phylogenetics / evolution

Resolving the oak tree of life: comparing RADseq and whole genome resequencing methods for oak phylogenetics

The paper compares RADseq and whole genome resequencing methods to resolve oak phylogeny and address uncertainties in divergence times and gene tree discordance.

Phylogenomic framework and virulence gene boundaries of emerging Shiga toxin producing Escherichia coli O118 informed by the comprehensive profiling of 359 O118 genomes

This study analyzes 359 O118 STEC genomes to characterize their phylogenetic relationships, virulence factors, and resistance traits, identifying novel pathogenicity islands and genetic diversity.

A long-read human pangenome initiative for comprehensive interpretation of nuclear-embedded mitochondrial DNA

The paper develops a method to detect and analyze NUMTs in human and non-human primate genomes, revealing their genomic features, population dynamics, and evolutionary implications.

Phylogenomic coupling of F1 chemosensory and archaellum systems across archaea and monoderm bacteria

This study examines the co-distribution of archaellum loci with chemosensory systems in archaea and monoderm bacteria, revealing horizontal gene transfer and shared evolutionary trajectories.

A new method based on genome alignments provides a highly resolutive target enrichment set for weevils (Coleoptera, Curculionoidea)

This paper introduces GABBI, a new method for designing target capture probes using genome alignments, which identifies more phylogenetically informative loci than existing methods for weevils.

Detection and phylogenetic characterization of Jingmen tick virus in Amblyomma mixtum ticks from Costa Rica

The paper detects and phylogenetically characterizes Jingmen tick virus in Amblyomma mixtum ticks from Costa Rica, identifying two distinct clades and suggesting potential human relevance.

First Lithic Age Caribbean genomes document pre-Ceramic genetic continuity and affinities to Central America and northern South America

This paper generates genome-wide data from pre-Ceramic Caribbean individuals, showing genetic continuity with Central America and northern South America and small, locally structured communities.

Genetic diversity of tomato brown rugose fruit virus in Morocco

The paper investigates the genetic diversity of Tomato brown rugose fruit virus in Morocco using viral gene analysis and haplotype networks, finding low diversity and geographic structure.

Complete Genome Sequencing and Molecular Characterization of Indigenous Enterovirus A71 Genogroups D and G of India

The paper characterizes two indigenous EV-A71 genogroups (D and G) from India through genome sequencing and phylogenetic analysis, revealing their distinct evolutionary paths and geographic restriction.

Know Your Alphabet: Conformational Noise, Latent-Space Encodings, and the Future of Structural Phylogenetics

The paper introduces a metric to quantify conformational noise in structural alphabets and shows its impact on phylogenetic inference using NMR ensembles and molecular dynamics simulations.

An expansive animal gut microbiome dataset elucidates major compositional shifts across bilaterian evolution

The paper presents a large-scale gut microbiome dataset across 1,553 host species and identifies major compositional shifts in gut microbiomes during animal evolution.

Eleven deep-sea coral genome assemblies unveil insights into evolution, adaptation, and coral biodiversity

The paper presents 11 deep-sea coral genome assemblies, revealing evolutionary dynamics, environmental adaptation, and genetic differences between deep-sea and shallow-sea corals.

PHYFUM: Phylogenetic Reconstruction of Normal and Pre-malignant Tissue Evolution Using Fluctuating Methylation

PHYFUM reconstructs the evolutionary history of normal and pre-malignant tissues using methylation data, revealing early gland divergence in the gut and later divergence in the endometrium.

EssentCell: Discovering Essential Evolutionary Relations in Noisy Single-Cell Data

EssentCell identifies essential evolutionary relations in noisy single-cell data by solving a minimum-flip problem with false positive constraints.

Phylogenomics, Biogeography, and a New Family-level Classification of Silversides, Rainbowfishes, and Allies (Teleostei: Atheriniformes)

This study generates a phylogenomic dataset to resolve relationships and biogeographic history of Atheriniformes, revealing polyphyly in Atherinidae and proposing a new family classification.

Genomic rearrangement of the capsule operon in a phylogenetically distinct cluster of the multi-drug resistant Escherichia coli lineage ST131

This study analyzes the capsule operon genetics of E. coli ST131 using 3,033 genomes, identifying a monophyletic group with divergent kpsM and kpsT genes linked to host-pathogen interactions.

Repeated evolutionary turnover of vertebrate skeletal muscle myosins

This study models the evolutionary history of over 1100 myosin heavy-chain proteins across vertebrates, revealing repeated gene duplication-loss turnover and independent evolution of core myosin subfamilies in each major vertebrate group.

Geographic Divergence in Population Genomics and Shell Morphology Reveal History of Glacial Refugia in a Coastal Dogwhelk

The paper uses genomic and morphological data from coastal dogwhelks to identify glacial refugia and their impact on population structure and shell morphology.

The Culicinae are Monophyletic and Ancient: A response to Pierce et al. 2025

This paper challenges recent claims that mosquito subfamilies are not monophyletic by presenting evidence supporting two monophyletic subfamilies and an ancient divergence.

The Genetic Legacy of Introgression from Two Deeply Divergent Lineages in the Genus Homo

This paper uses genetic data to show that two distinct superarchaic populations contributed to modern human ancestry, with one contributing ~20% to African populations and the other to Eurasian archaics.

Near telomere-to-telomere Linum genomes reveal a lineage-specific DNA transposon associated with chromosome architecture remodeling

The paper generates near telomere-to-telomere genomes for Linum species to study chromosome evolution, finding lineage-specific DNA transposon expansion linked to pericentromeric restructuring.

Short repeats drive mitochondrial genome expansion and record hybridization in Camellia

The paper analyzes mitochondrial genomes of Camellia species to show short repeats drive genome expansion and reveals hybridization signatures through phylogenomic conflicts.

Are interphylum spiralian relationships resolvable?

The paper analyzes phylogenomic datasets to resolve relationships among Spiralian phyla, finding that interphylum branches are short and relationships are poorly supported, suggesting an explosive radiation.

South Asian Maternal Lineage haplogroup R30 Provides Phylogenetic Evidence of human dispersal across South Asia

The paper analyzes haplogroup R30 in South Asia to trace human dispersal, finding it originated in the Indian subcontinent ~50 kya and shows evidence of multiple migrations.

Genomes of two arid-zone marsupials uncover contrasting responses to climatic change

The paper generates genome assemblies for two arid-zone marsupials and finds contrasting demographic responses to historical climate changes.

Inferring the demographic history of coppery titi monkeys (Plecturocebus cupreus) from high-quality, whole-genome, population-level data

This study uses whole-genome sequencing of coppery titi monkeys to infer their demographic history, finding population size changes align with speciation times and climatic events.

Evolutionary origin of prolonged delayed fertilization in the Fagaceae

This study investigates the evolutionary origins of 2-year fruiting in Fagaceae by analyzing phylogenetic data and ancestral state reconstructions across 88 species.

Whole-Genome sequencing of Indigenous Withania somnifera accession and comparative cytochrome P450 phylogenomics

The paper presents the first high-quality genome assembly of Withania somnifera and identifies CYP450 gene families involved in triterpenoid biosynthesis, revealing lineage-specific innovations and conserved subfamilies.

Inferring patterns of purifying, positive and balancing selection in the coppery titi monkey (Plecturocebus cupreus) utilizing a well-fit evolutionary baseline model

This study identifies patterns of purifying, positive, and balancing selection in the coppery titi monkey using a demographic model and genome-wide scans.

Tangled evolutionary history: genetically divergent taxa and hybrids characterise lantana invasions in Australia

This study investigates the population genomics and phylogeography of invasive lantana in Australia, revealing genetically divergent taxa and hybrids, and highlights the need for taxonomic revision to improve management.