phylogenetics / evolution

Covary is a machine learning framework that uses alignment-free, translation-aware embeddings to cluster and compare genetic sequences, achieving accurate phylogenetic analysis across diverse datasets.

The paper quantifies introgression across bacterial lineages, finding varying levels of gene flow and its association with ecological proximity, but not substantial blurring of species borders.

The paper improves microbial phylogenetic analysis by selecting tailored marker genes from functional databases, enhancing tree accuracy across genomes and metagenomes.

This study estimates dicynodont phylogeny using continuous traits under Brownian motion models and finds they contribute different signal compared to discrete traits, leading to different tree topologies.

The paper analyzes the global genomic diversity of C. neoformans over three decades, identifying key genetic features, lineage divergence, and resistance mechanisms.

The paper identifies mitochondrial palindromic motifs that form architectural domains, revealing a system balancing stability and flexibility across human and non-human genomes.

The paper analyzes plasmid transmission dynamics in Rhizobium leguminosarum, finding variation in plasmid types and their association with partner quality decline due to nitrogen fertilization.

The paper identifies nine distinct populations within the Anopheles barbirostris complex in Indonesia, including new reports of An. wejchoochotei and a unique population in Magelang.

This study analyzes the population genomics of Staphylococcus haemolyticus to understand its transition from commensal to pathogenic states.

The paper uses phylogenomic and fossilized birth-death dating to show Cicadidae diversified extensively after the K-Pg extinction event.

This study evaluates methods for inferring large-scale avian phylogenies, finding that fast tree search approaches balance computational efficiency and accuracy.

This study uses whole-genome sequencing to analyze Pantoea stewartii subsp. stewartii diversity and introduction routes in Europe, revealing multiple introductions and limited distribution.

Eco-evolutionary simulations of 3,806 Great Barrier Reef reefs project coral cover falling to ∼14% by 2040 under every emission scenario; recovery afterwards needs warming below 2°C.

The paper identifies a conserved CSD locus in Ooceraea biroi where heterozygosity triggers female development, showing evolutionary conservation across ant species.

The paper examines the macroevolutionary patterns of insect morphology and genome evolution, finding that genomic changes are pulsed while morphology is gradual, with distinct patterns in species-rich and species-poor clades.

The paper shows that spatially heterogeneous gene flow can lead to incorrect macroevolutionary inferences by causing monophyly of adjacent populations and longer branches for peripheral taxa in simulations.

The paper analyzes 46,015 bacterial genomes to show hibernation factors evolved from large proteins, reduced in size, and were lost in over 10% of species, with some bacteria borrowing factors from others.

This study analyzes genomic data from 52 individuals across the central Southern Cone to trace genetic ancestry and movements during the Middle to Late Holocene.

This study uses genomic data to analyze the timing and spread of Sigmodontinae rodent radiation, linking it to climatic and geological events in South America.

This study uses fecal metagenomic sequencing to refine the phylogenetic classification and evolutionary history of Aotus night monkeys, revealing three main clades and clarifying species boundaries.

The study analyzes degraded DNA from century-old ethanol-preserved fish specimens to reveal unexpected dispersal patterns in Tanakia lanceolata in Japan.

The paper uses whole-genome data from tinamous to reconstruct their phylogeny, estimate divergence times, and assess the impact of incomplete lineage sorting and introgression on genome evolution.

The paper identifies cryptic genetic diversity in Pacific herring, showing a biogeographic break linked to glacial cycles.

The paper presents a comprehensive phylogenetic analysis of the YUCCA gene family, identifying six classes and 41 subclasses, and explores factors driving its evolutionary diversification.

This study investigates the diversification patterns of Xylopia across tropical regions, finding synchronous Miocene radiations with region-specific environmental drivers.

Ultrastructure expansion microscopy applied to 221 cultured planktonic eukaryotes maps diverse microtubule and centrin-based cytoskeletons, including dinoflagellate apical centrin rings and cryptophyte cortical centrin meshes.

This study uses genomic data to analyze the phylogenetic relationships and species delimitation within the brown snake Storeria dekayi, identifying potential new species in Mexico and Central America.

The paper addresses species delimitation in the Australian snail genus Thersites by integrating molecular and morphological data, finding that two species should be synonymized and proposing two new species.

The paper presents the first telomere-to-telomere assemblies for two Paracoccidioides species, revealing chromosomal rearrangements and mitochondrial introgression.

The paper analyzes genetic diversity and demographic history of Azolla populations in California, identifying three groups and finding evidence of recent invasions for two newly reported taxa.