phylogenetics / evolution

Reliable delineation of Clostridioides difficile and related members of the family Peptostreptococcaceae using phylogenomics and spore coat protein-specific molecular markers

This study improves classification of Clostridioides difficile and related bacteria using phylogenomics and spore coat protein markers, leading to taxonomic revisions.

Bioclimatic variables influence the strength of purifying selection on mitochondrial DNA in an avian clade (Aves: Piciformes)

The paper examines how bioclimatic variables affect purifying selection on mitochondrial DNA in Piciformes birds, finding a negative correlation between temperature range and substitution rates.

Phylogenomic description of three novel species of the Microbulbifer genus, phylum Pseudomonadota, isolated from marine sponges and corals

The paper describes three new species of the Microbulbifer genus using phylogenomic analysis of isolates from marine sponges and corals.

Whole genome sequencing reveals the phylogenetic relationship and reticulate evolution of Phrynocephalus lizards in Eurasia

This study uses whole-genome sequencing to reveal the phylogenetic relationships and reticulate evolution of Phrynocephalus lizards, identifying hybridization and historical dispersal as key drivers of diversification.

Tumour evolution as ground truth for cancer whole-genome sequencing

This paper introduces SCOUT, a synthetic whole-genome sequencing resource for benchmarking cancer genomic analysis, revealing performance issues in complex tumours and highlighting the importance of evolutionary ground truth.

A global map for introgressed structural variation and selection in humans

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

Drift drives phenotypic evolution in a rapid island radiation

The paper shows that genetic drift, not selection, drives rapid phenotypic evolution in island bird populations by linking color trait evolution to genomic diversity decline.

The Iberian white-oak syngameon as a legacy of introgression in southern Europe

The paper uses RAD-seq to study Iberian white oaks, revealing hybrid swarms and redefining species boundaries through introgression and phylogeography.

Phylogenetic Investigation of the 100 kDa Hexokinase Enzyme Family with the Topiary Ancestral Sequence Reconstruction Pipeline

This study uses Topiary to reconstruct and characterize ancestral HK enzymes, revealing evolutionary changes in allosteric regulation within the HK family.

Genetic diversity of pangolin coronaviruses reveals a key immuno-evasive substitution at spike residue 519

The paper analyzes pangolin coronaviruses to identify a key immuno-evasive mutation at spike residue 519, similar to SARS-CoV-2, suggesting independent spillover events from bat reservoirs.

Recovery of an 18th Century Rhinovirus Genome through Ancient RNA Isolation of Human Lungs

This study recovers an 18th-century rhinovirus genome from ancient RNA isolated from human lung specimens, revealing insights into viral evolution.

Low-Coverage Genome Sequencing Outperforms Target Enrichment Phylogenomics

This study compares low-coverage whole genome sequencing (lcWGS) and target enrichment methods for phylogenomics, finding lcWGS outperforms target enrichment in locus recovery and phylogenetic performance, especially with degraded DNA.

DipSkmer: Reference-free population genomics with diploid genome skims

DipSkmer improves population genomics by accurately estimating genetic diversity in diploid organisms using low-coverage genome skims, outperforming existing methods.

Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma

This study uses single-cell whole-genome sequencing to show that Burkitt lymphoma develops through convergent evolution, with early genetic diversity and accelerated mutation accumulation.

Reconciling fast Hepatitis B evolutionary rates with ancient co-divergence

This study uses a Bayesian mixed-effects molecular clock model to analyze HBV genomic data, revealing declining evolutionary rates and linking viral spread to human migration patterns.

PhyloNOW: Using Variable Window Sizes for Phylogenomic Analyses of Whole Genome Alignments

PhyloNOW improves phylogenomic analyses by allowing variable window sizes across chromosomes, outperforming fixed-size methods on simulated data and showing size variation in empirical datasets.

The phylogenetic affinities of Chaetognathifera, with considerations of systematic error and the robusticity of macrosyntenic results

This study investigates the phylogenetic relationships within Chaetognathifera using genomic data and evaluates the robustness of macrosyntenic results, finding that macrosynteny cannot reliably resolve these relationships.

Enformer-Based Phylogenetic Tree Reconstruction

The paper uses Enformer to reconstruct phylogenetic trees across multiple species by analyzing regulatory signals from orthologous genes, showing strong correlation with known evolutionary relationships.

Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae)

This study evaluates paralog processing methods in polyploid-rich Packera genus to improve phylogenomic accuracy and understanding of evolutionary history.

Peculiar Pigment Pattern and Population Profile of a Poisonous Pufferfish

This study investigates the phylogenetic origin and pigment patterns of mushifugu, finding it to be a distinct species with evidence of past hybridization with komonfugu.

Salmonberry Transcriptome Reveals Phylogeny and Novel Badnavirus Species

The paper characterizes the salmonberry leaf transcriptome, identifies conserved lncRNAs, and detects a novel badnavirus species.

Global diversity and dispersal routes of the Ostreid herpesvirus type 1 infecting Magallana gigas

This study analyzes 275 OsHV-1 genomes to investigate global diversity and dispersal routes of the virus infecting Pacific oysters.

Replaying germinal center evolution on a quantified affinity landscape

Across 119 monoclonal germinal centers, B cell affinity rises reliably despite divergent phylogenies. Selection is noisy but persistent; mutability limits exploration. A DMS-based landscape shows saturating fitness and survivorship biases.

Diversifying the Northern Neotropics: Phylogenomics and Evolutionary History of the Early-Diverging Herichthyine Cichlids Thorichthys and Trichromis

This study uses phylogenomic data to explore the evolutionary history and diversification of two cichlid genera, revealing unrecognized diversity, species boundary uncertainty, and ghost introgression in northern Neotropical fish.

Phylodynamic Analysis of the Global Dispersal and Spatiotemporal Dynamics of HIV-1 Subtype C

This study benchmarks phylodynamic methods to analyze HIV-1 subtype C dispersal, finding robust spatial transmission patterns despite methodological variability in temporal estimates.

340 dipteran genomes reveal the origin of Muller elements and sex chromosomes in Diptera

The paper reconstructs ancestral linkage groups in 340 dipteran genomes to study chromosome evolution, finding conserved groups in Nematoceran lineages and chromosomal fissions in Brachycera.

A simple method of estimating rabies outbreak sizes from phylogenies

This paper introduces a method to estimate rabies outbreak sizes using phylogenies and validates it with simulated data and a real outbreak in the Philippines.

Epidemiology and phylodynamic analysis of canine distemper virus circulating in Michigan, USA

This study analyzes CDV circulation in Michigan from 2008 to 2023, identifying three circulating lineages and demonstrating the utility of genomic surveillance for tracking viral evolution.

Independent evolutionary trajectories of genomic repeats and non-repeat genome features in Actinomycetota

The paper compares the evolutionary patterns of genomic repeats and non-repeat features in Actinomycetota, finding repeats are more labile and non-repeats show punctuated evolution.

Breeding pig transport drives the dispersal of swine influenza A virus across Europe

This study identifies breeding pig trade as a key driver of swine influenza A virus dispersal across Europe using phylogeographic analysis of genomic sequences.