phylogenetics / evolution

Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes

The paper analyzes over 2,000 Caenorhabditis briggsae wild strains to uncover genetic diversity, population structure, and evolutionary mechanisms shaping phenotypic variation.

New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales

The paper describes 81 new SAR11 isolate genomes and identifies 29 monophyletic ecotypes within the Pelagibacterales, providing a classification system correlated with ecology and evolution.

A new deep-branching environmental lineage of algae

The paper identifies a new deep-branching algal lineage, leptophytes, through metagenomic analysis of Tara Oceans data, revealing hidden plastid genome diversity and evolutionary insights.

A SABATH family enzyme regulates development via the gibberellin-related pathway in the liverwort Marchantia polymorpha

This study identifies MpSABATH2 in liverwort Marchantia polymorpha as essential for development, linking it to gibberellin metabolism and showing convergent evolution of SABATH functions in land plants.

Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism

The paper identifies convergent genomic adaptations in brood parasitic birds, including genes related to spermatogenesis and nervous system development, across independent origins of parasitism.

Chromosomal evolution and polyploidy dynamics in tribe Andropogoneae (Poaceae: Panicoideae): insights from phylogenomic reconstruction

The paper analyzes chromosomal evolution and polyploidy in 230 Andropogoneae species using phylogenomic methods, finding high chromosomal diversity and multiple evolutionary events.

Species delimitation using genome-wide estimates of Dxy and Fst

The paper uses genome-wide Dxy and Fst metrics to identify species boundaries in mammals, finding high accuracy thresholds and suggesting taxonomic revisions.

Transcriptomic plasticity is a hallmark of metastatic pancreatic cancer

The paper analyzes transcriptomic changes in metastatic pancreatic cancer using a patient's autopsy data to identify site-specific gene programs and clonal phylogeny.

Lineage-wide evolution of 3D genome organisation and centromeres in brown algae

The paper presents a lineage-wide evolutionary analysis of 3D genome architecture and organization across brown algae, revealing conserved chromosomal features, lineage-specific rearrangements, and long-term co-evolution of centromeres and retrotransposons.

Human outbreak detection and best practice MPXV analysis and interpretation with squirrel

This paper introduces squirrel, a tool for analyzing MPXV genomes to detect outbreaks and classify APOBEC3 mutations, aiding public health responses.

Diversity of the dwarf palmetto: A phylogeographic analysis of the North American coastal plain and investigation of stem polymorphism in Sabal minor (Jacq.) Pers.

This study uses population genomics to analyze genetic diversity in Sabal minor, finding that caulescent and acaulescent forms are phenotypic variants of a single species, not separate species.

Finite-State Likelihood: an Approximation for Genome Phylogeny Inference based on Generalized Gene Contents

This paper introduces a finite-state maximum likelihood approximation to improve genome phylogeny inference by reducing computational burden while accounting for gene duplication, loss, and horizontal transfer.

Candidatus Rickettsia mendelii has the smallest and most ancestral-like genome in the genus Rickettsia

The paper isolates and analyzes six Candidatus Rickettsia mendelii strains, finding they have the smallest genome in the genus Rickettsia and retain features of the ancestral Rickettsia genome.

Molecular evolution of octopamine receptors in Drosophila

The paper examines the molecular evolution of octopamine receptors in Drosophila, identifying positive selection in specific regions of two receptors linked to ligand binding and signal transduction.

Genome Report: De novo genome assembly of the greater Bermuda land snail, Poecilozonites bermudensis (Mollusca:Gastropoda), confirms ancestral genome duplication

This paper presents the first de novo genome assembly of Poecilozonites bermudensis, confirming an ancestral genome duplication in land snails and supporting evolutionary hypotheses.

Evolution of Insulin, Insulin-like Growth Factor, and Their Cognate Receptors in Vertebrates, Invertebrates, and Viruses

This study analyzes the evolutionary origins and molecular diversification of insulin, IGFs, and their receptors across vertebrates, invertebrates, and viruses, revealing lineage-specific adaptations and conserved features.

Whole-genome resequencing reveals exceptions to panmixia in the exploited top fish predator Antarctic toothfish (Dissostichus mawsoni)

The paper uses whole-genome resequencing to analyze population structure and diversity in Antarctic toothfish, finding exceptions to panmixia and reduced diversity in the Ross Sea post-2000.

Detection and Characterization of West Nile Virus with evidence of Transovarial Transmission in the Coastal region, Kenya

The paper detects and genetically characterizes West Nile virus in Kenyan mosquitoes, identifies transovarial transmission in Aedes aegypti, and finds lineage-specific evolution and mutations.

Elucidating continental-wide phylogeographic and adaptive processes shaping the genome-wide diversity of North America's most widely distributed tree

This study uses genomic data from quaking aspen to investigate historical population dynamics and adaptive divergence across its range, identifying genomic regions associated with local adaptation.

Species-specific responses to paleoclimatic changes and landscape barriers drive contrasting phylogeography of co-distributed lemur species in northeastern Madagascar

Evolution of the Metazoan Protein Domain Toolkit Revealed by a Birth-Death-Gain Model

The paper uses a Birth-Death-Gain model to analyze the evolution of protein domains in metazoa, finding that domains involved in metazoan innovations evolve faster and that domain repertoires undergo ongoing remodeling.

Distinct intraspecific diversification dynamics in Neotropical montane versus lowland birds revealed by whole-genome comparative phylogeography

This study compares phylogeographic dynamics between Neotropical montane and lowland birds, finding greater population structuring and genetic diversity differences in the Andes.

Expanding Ventilago to incorporate Smythea: new combinations in Ventilagineae (Rhamnaceae) based on novel sequence data and phylogenetic analysis

This paper proposes merging Smythea into Ventilago based on phylogenetic analysis showing Ventilago is paraphyletic.

Five-year (2017-2022) evolutionary dynamics of human coronavirus OC43 in southern France based on whole genome next-generation sequencing

This study analyzed HCoV-OC43 genomes from southern France between 2017-2022, revealing evolutionary dynamics and amino acid substitutions across three genotypes.

Biogeographic affinities, phylogenetic relationships, and diversity of ant species of the genus Camponotus (Hymenoptera: Formicidae) present in Chile

This study examines the biogeographic affinities and phylogenetic relationships of Chilean Camponotus ants using molecular data, revealing greater Neotropical and Afrotropical affinities and cryptic diversity.

Rooting the deep divergence of land plants

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

Sponges, ctenophores and the statistical significance of syntenies

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.

Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance

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

Mutational spectra reveal influenza virus transmission routes and adaptation

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

The genomic landscape of asymmetric introgression tracks chromosomal characteristics in tinamous (Aves: Tinamidae)

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