phylogenetics / evolution

Evolutionary Dynamics of Paramecium Mitochondrial Genomes

This study analyzes mitochondrial genomes of Paramecium to explore evolutionary dynamics, revealing cryptic diversity, conserved genes, and patterns of molecular evolution.

Species phylogenetics using intraprotein residue dependence inferred with protein foundation models

This study compares RAM-NJ and SAM-NJ phylogenies using protein foundation models to reconstruct species relationships without conventional substitution models or multiple sequence alignments.

Resolving the Taxonomic Status of the Marbled Toad (Bufonidae: Incilius marmoreus): 2RAD-based Phylogeography Including an Isolated Population in Veracruz, Mexico

This paper reevaluates the phylogeography and taxonomy of the Marbled Toad using genomic and morphological data, finding support for the current classification and a historical north-south split followed by an east-west split.

Evolutionary divergence in sympatric populations of the fungal pathogen Alternaria alternata across wild tomato hosts

The paper analyzes genomic divergence in Alternaria alternata populations across wild tomato hosts, finding two divergent clades not linked to host, geography, or habitat.

Haplotype-phased genomes of the barley leaf rust pathogen reveal evidence of repeat element expansion and somatic hybridization

The paper presents haplotype-phased, chromosome-scale genomes of Puccinia hordei isolates, revealing repeat expansion, somatic hybridization, and genome plasticity.

Progress in the molecular Phylogeny of Cotesia acuminata and C. melitaearum cryptic species complexes

This study reconstructs the phylogeny of Cotesia wasps parasitizing Melitaeini butterflies, revealing polyphyletic origins and clarifying cryptic species relationships using multi-locus data.

Modeling site-and-branch-heterogeneity with GFmix

The paper improves the GFmix model to better handle site-and-branch compositional heterogeneity in phylogenetic inference, showing improved accuracy in tree estimation.

Whole-genome phylogenomics and synteny resolve a single origin of body-plan asymmetry in flatfishes

The paper uses whole-genome phylogenomic and synteny data to resolve the evolutionary origin of flatfish body asymmetry, finding strong support for a single origin.

LINGUINE: a phylogeny-aware, orthogroup-based framework for robust ancestral linkage group inference

LINGUINE improves ancestral linkage group inference by using orthogroups and a Hidden Markov Model to handle gene loss and paralogy, outperforming existing methods in nematodes and clitellate annelids.

Range-wide phylogeography, population genomics, and demography of three widespread Ara macaws (Psittacidae)

This study uses genomic data to analyze the evolutionary history and demographic processes of three Ara macaw species, identifying genetic structure and adaptation signals across different biomes.

Lift&Add - rapid and robust addition of new species to alignments of conserved non-coding sequences

The paper introduces a method to add new marsupial genomes to existing vertebrate whole-genome alignments, improving phylogenetic coverage for comparative genomic analysis.

Variability and scale-dependence in molecular evolution rate impacts interpretation of eukaryotic evolutionary histories

The paper shows that molecular evolution rates vary with timescale, affecting evolutionary history inferences, and is analogous to the Sadler effect in geology.

Evolutionary analysis of vertebrate KCNH voltage-gated potassium channels and their expression in zebrafish embryos

The paper analyzes the evolutionary history and embryonic expression of KCNH voltage-gated potassium channels in zebrafish, revealing their origins in invertebrates and expanded gene numbers in vertebrates.

Evolutionary analysis of Trehalose breakdown pathways

This study analyzes the evolutionary distribution of trehalose breakdown pathways across 4000 genomes, revealing ancestral origins and lineage-specific losses.

Competition among freshwater clades explains cave colonization in blind cavefishes

The paper uses genomic data to determine whether flatfish asymmetry evolved once or multiple times, finding strong support for a single origin.

Min-frame transformation enables more sensitive viral genome alignment

The paper introduces Min-Frame Transformation (MFT) to improve viral genome alignment by enhancing MUM-based seeding, resulting in longer and more contiguous matches with better alignment coverage and SNP recall.

Genomic Evidence for a Novel Introduction and Intra-host Diversity of DENV-2 in Dar es Salaam, Tanzania

The paper uses Nanopore sequencing to analyze DENV-2 in Tanzanian mosquitoes, finding a distinct clade related to Asian strains and identifying intra-host variants, suggesting a silent introduction of genotype II.

Whole genome sequencing reveals a novel Renibacterium salmoninarum lineage and suggests geographic endemism combined with anthropogenic spread in the North-East Atlantic area

Genomic footprints of selfing, introduction history, and long-distance dispersal in an invasive alien plant

This study uses genome-wide data to investigate the colonization history and genetic structure of the invasive plant Cotula coronopifolia, revealing multiple lineages, high selfing rates, and the role of dispersal in its spread.

Coalescent-based branch length estimation improves dating of species trees

This paper introduces a scalable pipeline for dating species trees that improves accuracy and scalability by addressing gene tree discordance in multi-locus datasets.

Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity

The paper identifies a bias in phylogenetic branch lengths when using the discrete Gamma model and recommends replacing it with the FreeRate model.

Variant emergence, not vaccine deployment, drives episodic positive selection on the SARS-CoV-2 spike at provincial scale in Canada

The paper analyzes SARS-CoV-2 spike evolution in Canada, finding that variant emergence, not vaccine deployment, drove episodic positive selection at the provincial level.

Macroevolutionary dynamics of beetles reveal long-term coupling with vascular plant diversification

This study uses Bayesian models on fossil data to show beetles have low extinction rates and their diversification is driven by vascular plant evolution, particularly angiosperms.

Computational predictions and evolutionary analysis of LrK10 kinase-related putative PSTOL1 gene homeologs in wheat and orthologs of its wild relatives.

The paper identifies and analyzes putative PSTOL1 homeologs in wheat and their evolutionary relationship with LrK10 orthologs, finding recent divergence and structural differences.

Phylogenomics and Systematics of African Sesuvium (Aizoaceae)

The paper uses genome skimming to resolve the phylogeny of African Sesuvium species, finding a C3 species sister to a C4 clade with discordant gene trees.

Substitution rate variation, not hidden paralogy, drives false hybridization signal in phylogenetic network inference

The paper evaluates how substitution rate variation and hidden paralogy affect phylogenetic network inference methods, finding that rate variation causes false hybridization signals.

A complete-genome view of phylum Nanobdellota and recurrent Form III RuBisCO transfer between archaea and Patescibacteriota

The paper presents 208 complete Nanobdellota genomes and identifies recurrent Form III RuBisCO transfer between archaea and Patescibacteriota.

Optimal Control and the Dynamics of Ancestral Lineages

This paper introduces a framework to infer selection coefficients from phylogenetic trees by integrating optimal control theory with evolutionary dynamics.

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.