phylogenetics / evolution

An Alternative Approach to Compute the Likelihood for the DAISIE (Dynamic Assembly of Island biota through Speciation, Immigration, and Extinction) Model

This paper proposes an alternative method to compute the likelihood for the DAISIE model, improving computational efficiency and enabling state-dependent dynamics in island biodiversity studies.

Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages

The paper uses phylogenetic methods to determine the root of the Archaea, finding support for a methanogenic ancestor and a derived origin for host-associated lineages.

plsMD: A plasmid reconstruction tool from short-read assemblies

plsMD improves plasmid reconstruction from short-read assemblies, outperforming existing tools in recall, precision, and F1 scores on benchmark and novel datasets.

High prevalence of KPC-3 in carbapenem-resistant Pseudomonas aeruginosa across multiple clonal lineages in China

This study identifies a high prevalence of KPC-3 in carbapenem-resistant Pseudomonas aeruginosa isolates in China, showing clonal expansion and horizontal transmission across multiple lineages.

TBpop: an open-access genomic portal integrating genomic variation, population genetic statistics, phylogeny, pangenome composition, and strain metadata of epidemic Mycobacterium tuberculosis strains from China

TBpop integrates genomic variation, population genetics, and metadata for Mycobacterium tuberculosis strains from China to enable comprehensive analysis of genetic diversity and evolution.

APOBEC3G Splicing Defects in Nonhuman Primate Models Result in Disparate Viral Mutational Profiles Relative to Humans

This study identifies APOBEC3G splicing defects in nonhuman primates that lead to different viral mutation profiles compared to humans.

No signal of a super-archaic origin of the Denisovan AMBN gene, a comment on the protein affinity of Homo erectus and Denisovan enamel proteins.

The paper challenges a model proposing Denisovan AMBN introgression from Homo erectus by showing no signal of super-archaic origin in late Denisovans.

Genomic plasticity and homologous recombination drive the evolution of Pectobacterium jejuense across hosts and geographic regions

This study analyzes the genomic diversity and evolutionary dynamics of Pectobacterium jejuense across hosts and geographic regions, revealing homologous recombination and genome plasticity as key drivers of adaptation and pathogenic evolution.

Evolution of multicellularity and reproductive strategies in yellow-green algae (Xanthophyceae, Heterokontophyta)

This study reconstructs the evolution of multicellularity and reproductive strategies in Xanthophyceae using phylogenomic data, showing multiple transitions to multicellularity linked to changes in propagule types.

Phylogenomics and comparative genomics of the genus Erwinia reveal taxonomic inconsistencies and evolutionary diversification

This study uses phylogenomic and comparative genomic analyses of 104 Erwinia genomes to resolve evolutionary relationships, identify taxonomic inconsistencies, and uncover lineage-specific genomic features associated with virulence and ecological adaptation.

ChlORIS: Chloroplast Orthologs Resource & Identification Suite

Open plastid orthogroup resource for algae: 496 named orthogroups from 893 genomes, 224 core profile hidden Markov models with calibrated cutoffs, alignments, predicted structures, 859-genome phylogeny, CheckM-compatible marker sets.

orthoSynAssign: refine orthogroups using synteny information

orthoSynAssign refines orthogroups using synteny information, improving precision and scalability for phylogenomic analyses.

Phylogenetic inference from an incomplete fossil record

This study investigates how stratigraphic gaps affect phylogenetic inference using a simulation framework and finds that total-evidence analysis is robust to gap distribution but dominated by morphological character data.

Found in translation: CCA-adding enzymes reveal bacterialization of Asgard archaea prior to eukaryogenesis

The paper identifies CCA2 enzymes in Asgard archaea and Heimdallarchaeia, challenging the evolutionary separation between archaeal and eukaryotic CCA-adding enzymes and supporting bacterial gene integration prior to eukaryogenesis.

Stratigraphic Paleobiology of Carbonate Systems

Simulated tropical carbonate platforms and temperate ramps under identical sea-level forcing yield different fossil records: platform tops push apparent extinctions into transgressive tracts, while ramp unconformity bias fades gradually offshore.

Consequences of intra-locus recombination for branch-length-based inference of gene flow

This paper evaluates how intra-locus recombination affects gene-flow inference using the Aphid method on African cichlid data, showing reduced temporal resolution but accurate prevalence estimation.

The fate of a dynasty: Population genomics uncovers the demographic history of Ardea insignis, one of the rarest bird species in the world

This study uses population genomics to reveal the long-term demographic history of the critically endangered White-bellied Heron, showing persistent small population size rather than recent collapse.

ABC1K7: A 350-Myr chloroplast rheostat fine-tuned during coconut domestication

The paper identifies a chloroplast kinase, ABC1K7, under strong purifying selection in seed plants, with a single amino acid change in coconut linked to domestication traits.

Physical interactions between pollen and pistil tissues mediate cryptic female choice in Brassica rapa

Brassica rapa pollen tube length after growing through recipient pistil tissue is donor-by-recipient specific, predicts siring success under competition, and matters more in longer-styled recipients.

The Tangled History and Taxonomy of an Iconic Chorus Frog Complex Clarified using Genomic Analyses

This study clarifies the taxonomy of the Pacific Treefrog complex using genomic analyses and proposes a two-species classification.

Exotic catenulid flatworms (Platyhelminthes, Catenulida) and where to find them in a temperate climate - a field study in a botanic garden

The paper reports the discovery of exotic catenulid flatworm species in a temperate botanic garden greenhouse and provides molecular evidence for their phylogenetic placement.

Chloroplast Genome Evolution, Heteroplasmy, and Inverted Repeat Dynamics in the Elymus Complex (Triticeae, Poaceae): Insights from Single-Molecule Sequencing of Elymus ciliaris and Comparative Analysis of St-Genome Lineages

The paper uses single-molecule sequencing to analyze chloroplast genome heteroplasmy and structural dynamics in Elymus species, revealing inversion polymorphisms and lineage-specific IR boundary shifts.

The topography of gene tree topology space in a plant genus with a legacy of recent polyploidy and introgression

The paper analyzes gene tree topology space in the plant genus Glycine, finding a flat distribution of topologies with no clear peak at the species tree, suggesting complex historical signals from introgression and polyploidy.

A hybrid approach combining a phylogenetic method and Approximate Bayesian Computation Random Forest for phylogenetic network inference: application to the rice domestication process in Asia

This paper introduces a hybrid method combining phylogenetic networks and machine learning to infer rice domestication history, finding a single Japonica domestication followed by introgression events.

Genetic and epigenetic divergence among Arabidopsis thaliana Col-0 laboratory lineages since the 1950s

This study analyzes genetic and epigenetic divergence in Arabidopsis thaliana Col-0 laboratory lineages over decades, revealing substantial divergence and functional consequences.

BirdCODE: Detecting bird communication at scale

BirdCODE detects and classifies bird vocalizations from large audio datasets, enabling large-scale studies of bird communication with improved temporal resolution and species coverage.

The Monophyly of Nycteria and Polychromophilus Parasites A Missing Piece in the Evolution of Malaria and Other Haemosporida

This study resolves the evolutionary relationships of bat-restricted haemosporidian parasites Nycteria and Polychromophilus using near-complete mitochondrial genomes, showing they form a monophyletic clade not supported by smaller datasets.

Finding the relatives of a critically endangered island endemic reveals the heterogeneous evolution of land snail mitogenomes (Gastropoda: Helicidae)

The paper analyzes the mitogenomes of a critically endangered snail to resolve phylogenetic relationships and identifies challenges in mitogenome-based phylogenetics due to compositional variation and annotation issues.

Phylogenomics of the mega genus Bulbophyllum (Orchidaceae) with implications for infrageneric classification in the Asian clade

This study reconstructs the phylogenetic relationships of Bulbophyllum using plastid genes, revealing five major lineages and clarifying infrageneric classification in the Asian clade.

The sponge Hymeniacidon perlevis is introduced and widespread in the Western Atlantic

The paper clarifies the taxonomy and biogeography of the marine sponge Hymeniacidon perlevis by comparing morphology and genetics across regions, revealing H. heliophila as a junior synonym and suggesting a European origin with introductions elsewhere.