phylogenetics / evolution

Genetic diversity and phylogeography of swine influenza A virus in 2013-2022 in Europe using a harmonized genotyping nomenclature

This study analyzes genetic diversity and evolution of European swine influenza A viruses from 2013 to 2022, identifying 150 genotypes and highlighting pig trade as a driver of viral spread.

Shifts in high-light acclimation strategies associated with molecular evolutionary rates in duckweeds

The paper investigates how molecular evolutionary rates in duckweeds correlate with acclimation strategies to high light, finding differences in mutation rates and metabolic adaptations between lineages.

Evolution of form I-related RuBisCOs updated: Uncertainties and diversity encompassing Bacteria and Archaea.

This study updates the understanding of form I-related RuBisCOs by analyzing their phylogenetic relationships and identifying a form I RuBisCO gene in an archaeal MAG, highlighting uncertainties in their evolutionary history.

Trait evolution with incomplete lineage sorting and gene flow: the Gaussian Coalescent model

The paper introduces the Gaussian Coalescent model to account for incomplete lineage sorting and gene flow in trait evolution, showing improved accuracy over standard models.

Sociality in weevils is shaped by sheltering and convergent gene losses

This study investigates the molecular evolution of sociality in weevils, finding relaxed selection and gene loss rather than adaptive innovation in socially complex species.

The diversity, evolution, and conservation of African plants

The paper evaluates diversification rates and phylogenetic diversity across African plant genera, revealing mismatches between diversification hotspots and conservation priorities.

A meta-analysis of Neotropical butterflies reveals long-term signature of the Pebas wetland on Neotropical biogeography

This study uses a meta-analysis of 1,361 Neotropical butterfly species to show that the Pebas wetland selectively constrained dispersal between the Andes and Amazonia, contributing to the modern diversity imbalance.

Phylogenetic parallelograms: visual comparison of discordant phylogenetic trees

The paper introduces phylogenetic parallelograms to visually compare multiple discordant phylogenetic trees and applies them to study introgression and organellar discordance.

Continued genomic surveillance of Vibrio cholerae O1 isolates from cholera cases in Europe, 2023-2024

The paper uses whole genome sequencing to analyze Vibrio cholerae O1 isolates from 2023-2024 European cholera cases, confirming their lineage and identifying drug-resistant clones.

Selfing-aware demographic inference highlights local population structure and bottlenecks in Hawaiian Caenorhabditis elegans

The paper applies a selfing-aware demographic inference method to Hawaiian C. elegans populations, revealing population structure, bottlenecks, and the impact of self-fertilization on demographic estimates.

Deep ancestral structure, admixture and peripheral persistence shape diversity in the Papilio bianor species complex

This study analyzes whole-genome variation in butterflies to show how ancestral polymorphism, admixture, and incomplete lineage sorting shape lineage diversity in the Papilio bianor complex.

Phylogenomics reveals distinct evolutionary lineages of Japanese Cinnamomum species in the Nansei Islands

The paper uses genomic data to identify distinct evolutionary lineages of Japanese Cinnamomum species in the Nansei Islands, revealing genomic differentiation shaped by deep-sea barriers and isolation.

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

Mapping the evolutionary path towards multi-drug resistance in the pandemic Escherichia coli ST131 lineage

This study traces the evolutionary path from ST131-B to ST131-C clades in E. coli by analyzing genomic data from ST131-B0 isolates, revealing genetic changes associated with antibiotic resistance and host adaptation.

Assessing the Evolutionary Trajectory of Arbuscular Mycorrhizal Conserved Genes in Seagrasses and Aquatic Close Relatives

The paper examines the evolutionary patterns of AMF-related genes in aquatic and terrestrial plants, finding gene losses or divergence in aquatic lineages but retention in some seagrass species.

One species, two lives: cryptic population structure and life-history divergence in a vineyard spittlebug (Aphrophora sp.), a candidate vector for Pierce's disease

The paper analyzes genome data from spittlebugs in vineyards and quasi-natural populations, revealing cryptic population structure, life-history divergence, and insecticide resistance.

Multiple introductions shaped genomic diversity and demographic history of invasive box tree moth (Cydalima perspectalis) populations in North America

The paper investigates the invasion history of box tree moth in North America using genomic and morphological data, finding multiple introductions and genetic structuring.

Developmental variation in pterygoid segmentation clarifies patterns of avian bony palate evolution

Micro-computed tomography of 69 immature and mature bird specimens finds complete post-hatching pterygoid segmentation (hemipterygoid detaches from pterygoid, fuses to palatine) only in Neoaves, not Galloanserae or palaeognaths.

Stairway Plot v3: Nonparametric Demographic Inference from the Site Frequency Spectrum at Biobank Scale

Stairway Plot v3 infers nonparametric effective population size trajectories from the site frequency spectrum at biobank scale, achieving high resolution with large samples.

Gene conversion is a key driver of diversity hotspots in M. tuberculosis antigens and virulence-associated loci

Complete genomes from 151 clinical M. tuberculosis isolates show gene conversion between paralogs creating diversity hotspots in PE/PPE/ESX genes and T cell antigens, including PPE18.

Phylogenetic Mosaic of an Arms Race with Asymmetrical Sexual Conflict and Its Macroevolutionary Consequences in a Lineage of Small Water Striders

The paper examines the macroevolutionary consequences of asymmetrical sexual conflict in water striders, finding that male-driven trait evolution drives diversification while female resistance traits show greater flexibility.

Emergence of short-lived meningococci causing focal epidemics can be associated with gene transfer from carriage-associated Neisseria

A 21-case nightclub-linked meningococcal outbreak variant differed from its closest relatives by horizontal gene transfer from carriage-associated Neisseria, affecting iron acquisition and type IV pili genes.

Molecular epidemiology of the globally spreading genetic lineage IV of peste des petits ruminants virus

This study analyzes the evolutionary history of peste des petits ruminants virus lineage IV using genome sequences from historical and recent isolates, identifying genetic changes potentially linked to its recent spread in West Africa.

Comparison of the Distribution of Fitness Effects Across Primates

Across 38 catarrhine subspecies, the population-scaled distribution of fitness effects (DFE) tracks effective population size while the unscaled deleterious DFE appears conserved, with no detectable epistasis.

Is level-1 blob reconstruction under the network multispecies coalescent easy?

The paper investigates whether reconstructing level-1 blobs in phylogenetic networks is easy once the tree of blobs is known, presenting a fast algorithm that achieves comparable accuracy to existing methods.

Ancient DNA perspectives on North American cervids identify fluctuations in genetic diversity

This study uses ancient DNA from North American cervids to trace genetic diversity changes over time, revealing historical population dynamics and impacts of external pressures.

Universal single-copy genes and 16S rDNA present incongruent evolutionary histories in Vibrio

The paper compares the evolutionary histories of universal single-copy genes (USCGs) and 16S rDNA in Vibrio, finding that USCGs produce more resolved and congruent phylogenies than rDNA.

ASTRAL-X: Scaling Coalescent-Based Species Tree Inference to 300,000 Taxa

ASTRAL-X enables statistically consistent species tree inference for up to 300,000 taxa by improving scalability and reducing computational requirements.

Comparative Mitogenomics and Molecular Phylogeny of Agriculturally Significant Tephritid Fruit Fly Pests in Bangladesh

The paper presents a comparative mitogenomic and molecular phylogenetic analysis of five agriculturally significant Tephritid fruit fly species in Bangladesh using existing GenBank sequences.

Ancestral genomic stasis and coordinated genome erosion underlies asymmetric acarine diversification

This study investigates the genomic mechanisms underlying diversification in mites and ticks, revealing contrasting patterns of genome evolution and gene-family expansion across lineages.