phylogenetics / evolution

Explaining the rapid evolution of mammalian meiotic recombination proteins

The paper analyzes evolutionary rates of 100 meiotic recombination proteins across 400 placental mammals, finding that rapid evolution is driven by reduced purifying selection and linked to chromosome pairing proteins in long-lived species.

Divergent evolution of the PRPS enzymes across the tree of life

This study analyzes PRPS enzyme evolution across domains of life, identifying new classes and regulatory mechanisms through phylogenetic and biochemical approaches.

Sea-level and climate changes drive lineage diversification in the imperiled Venus flytrap (Dionaea muscipula J. Ellis, Droseraceae)

This study uses genomic data to show that climate and sea-level changes drove lineage diversification in Venus flytraps, with population declines linked to historical climate optima and human impacts.

Genomic insights into Candidatus Argioplasma dusa, a bacterial symbiont of the wasp spider Argiope bruennichi

The paper reports the genome of Candidatus Argioplasma dusa, a spider symbiont, and finds it has a small genome with limited biosynthetic capabilities, suggesting an endosymbiotic lifestyle.

The hypercubic Mk model in reduced state space for the coupled, reversible coevolution of multiple binary characters

The paper introduces HyperMk2, a method to efficiently model the coevolution of multiple binary characters by reducing state space, enabling analysis of larger systems than previous methods.

Tracing Sticky Trails: The Historical Biogeography of Australia's Glandular Goose-foots (Dysphania, Chenopodioideae, Amaranthaceae)

This study reconstructs the evolutionary history of Australian Dysphania, finding that diversification was driven by ecological factors rather than polyploidy or geographic isolation.

The mitochondrial genome of the hammerhead flatworm Bipalium nobile and its phylogenetic implications

This study sequences the mitochondrial genome of Bipalium nobile and uses it to support the monophyly of a clade within the Geoplanidae family.

Molecular characterization of spiny lobsters from the Saint Martins Island, Bangladesh: a new record of Panulirus longipes (A. Milne-Edwards, 1868)

The paper identifies a new spiny lobster species, Panulirus longipes, in Bangladesh using morphological and mitochondrial DNA analysis.

Early evolution of the prokaryotic transcription factor repertoire

The paper traces the evolutionary history of transcription factor repertoires in prokaryotes, finding early diversification and steady innovation contrasting with eukaryotic bursts.

Whole genome analyses of the endangered Northern abalone (Haliotis kamtschatkana) reveal population differentiation and a genomic signature of a dramatic population decline

The paper uses whole genome resequencing data to analyze population differentiation and decline in Northern abalone, finding genetic structure and a signature of population decline despite previous claims of panmixia.

Distinct evolutionary trajectories of two integration centres, the central complex and mushroom bodies, across Heliconiini butterflies

The paper compares the evolutionary changes in the central complex and mushroom bodies across Heliconiini butterflies, finding conservation in the central complex and expansion in the mushroom bodies linked to foraging behavior.

Ancient and recent riverine gene flow contributed to the adaptive radiation of sailfin silversides in Wallace's Dreampond

This study investigates gene flow and hybridization in sailfin silversides, finding evidence of both ancient and recent introgression between riverine and lacustrine species in Lake Matano.

The tree labeling polytope: a unified approach to ancestral reconstruction problems

This paper introduces a polyhedral framework for ancestral reconstruction in phylogenetic trees, enabling efficient algorithms with additional constraints and improved performance on real datasets.

Ancient species diversity and niche adaptation in Tannerella and Porphyromonas revealed through pangenomics

This study uses pangenomics and phylogenetics to analyze ancient and modern bacterial genomes of Tannerella and Porphyromonas, revealing new species, niche adaptations, and geographic patterns in oral microbiota.

SILAC-Site: A streamlined workflow for determining phosphopeptide stoichiometries

SILAC-Site directly measures phosphosite stoichiometries without enrichment, showing low stoichiometry for most phosphopeptides and correlating with direct detection.

Initial identification of genomic islands in Taylorella equigenitalis and Taylorella asinigenitalis and their distribution in isolates from around the world

This study identifies genomic islands in Taylorella species and examines their distribution and stability across isolates, highlighting their potential role in virulence.

Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes

This study uses genome sequences from Cercis canadensis and Chamaecrista fasciculata to infer legume genome structures and histories, including the timing of whole genome duplications and the ancestral karyotype.

New approaches to detecting and characterizing introgression in large species trees

The paper introduces a new method to detect and characterize introgression in large species trees by analyzing discordant attachment frequencies of gene trees, demonstrating its application in cichlids and Drosophila.

Phylogeography of the electric rays of the family Narcinidae (Gill, 1862): systematic review and evidence of the dispersal routes to America.

This study investigates the phylogeography of electric rays in the family Narcinidae, identifying dispersal routes and molecular systematics, revealing non-monophyly and new species distributions.

ERGA-BGE reference genomes of Hyalomma lusitanicum and its obligate Francisella endosymbiont as a genomic resource for One Health research

The paper presents genomic resources for Hyalomma lusitanicum and its Francisella endosymbiont, providing insights into host-symbiont evolution and disease transmission.

Statistical inference of the Tree of Blobs of a phylogenetic network from quartet concordance factors

This paper introduces ECToBlob, an algorithm to estimate the tree of blobs from quartet concordance factors, providing a statistically consistent method for inferring phylogenetic networks.

Cohort-HMM marker recruitment with per-OG orthology QC for phylogenomic supermatrices

The paper introduces a cohort-HMM marker recruitment pipeline to improve phylogenomic supermatrix construction by addressing biases in orthogroup recovery and paralog filtering across different taxonomic scales.

A probabilistic and phylogenetic principal component analysis for modelling high-dimensional trait evolution

This paper introduces P3CA, a probabilistic and phylogenetic PCA method for high-dimensional trait evolution, showing improved accuracy in parameter estimation and missing data reconstruction.

GRAFT: phylogenetic signal in patent applications across the tree of life

The paper tests for phylogenetic signal in patent applications across species using a knowledge graph linking taxonomy to patents, finding significant correlation between phylogenetic distance and patent profile similarity.

Genome evolution in parthenogenetic nematodes shaped by chromosome rearrangements and rare sex

This study examines genome evolution in parthenogenetic nematodes, revealing chromosome fusions, rearrangements, and evidence of rare sexual reproduction events.

Graph-based pangenome provides insights into the adaptive evolution of Cucurbita pepo

The paper constructs a graph-based pangenome of Cucurbita pepo to study adaptive evolution, identifying structural variants and showing parallel domestication and environmental adaptation.

Mitotree: The Universal Human Mitochondrial Reference Phylogeny at 10x the Resolution

Mitotree constructs the largest human mitochondrial phylogeny with higher resolution, identifying new branches and improving accuracy over previous references.

Rapid speciation in Harlequin Toads (Anura: Bufonidae) endemic to the Sierra Nevada de Santa Marta

This study uses genomic data to investigate rapid speciation in four endemic Atelopus species in the Sierra Nevada de Santa Marta, finding recent divergence without gene flow and suggesting topography and ecological factors drove speciation.

Shifts in the population-genetic landscape of the ciliate genus Paramecium

This study sequenced genomes of hundreds of Paramecium isolates worldwide to investigate population-genetic patterns, finding geographic differentiation and speciation driven by genetic isolation.

Alignment-free phylogenetic inference via hyperbolic protein language models

LucaPhylo infers phylogenetic trees from unaligned protein sequences using hyperbolic geometry and protein language models, achieving accuracy comparable to alignment-based methods for divergent RNA viruses.