phylogenetics / evolution

The Mitochondrial Palindrome Scaffold and Architectural Domains

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

Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum

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.

Anopheles barbirostris in Indonesia: A more complex metapopulation than expected.

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.

Staphylococcus haemolyticus Population Genomics Provides Insights into Pathogenicity and Commensalism

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

Phylogenomics and Fossilized Birth-Death Dating Reveals Extensive Post-Cretaceous Worldwide Diversification of Cicadidae (Hemiptera, Auchenorrhyncha)

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

Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life

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

Comparative genomics and pathogenicity of Pantoea stewartii subsp. stewartii reveal multiple introductions and limited distribution in Europe

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

A rapidly closing window for coral persistence under global warming

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.

Heterozygosity at a conserved candidate sex determination locus is associated with female development in the clonal raider ant (Ooceraea biroi)

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

The Duality of Insect Macroevolution: Pulsed Genomes and Gradual Morphology Shape Lineage Diversification

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.

Spatially heterogeneous gene flow may hinder linking phylogeographic data to macroevolutionary patterns

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 evolution lifecycle of ribosome hibernation factors

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.

The shared genomic history of Middle to Late Holocene Southern Cone populations

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.

Phylogenomics of the sigmodontine rodents: Cloud forests and Pliocene extinction explain timing and spread of the radiation of South American mice and rats

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.

Shedding light on Amazonian phylogeographic patterns and evolutionary history of night monkeys (Genus: Aotus) using reconstructed fecal metagenomic shotgun sequencing

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.

Century-old ethanol-preserved Vega Collection reveal the unexpected phylogeography of Slender bitterling Tanakia lanceolata in Japan

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

Whole-genomes illuminate the drivers of gene tree discordance and the tempo of tinamou diversification (Aves: Tinamidae)

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.

Cryptic diversity arises from glacial cycles in Pacific herring, a critical forage fish

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

The auxin gatekeepers: Evolution and diversification of the YUCCA family

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.

Synchronous Miocene radiations and geographic-dependent diversification of pantropical Xylopia (Annonaceae)

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

Charting the landscape of cytoskeletal diversity in microbial eukaryotes

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.

Phylogenomics and species delimitation in the brown snake Storeria dekayi (Natricidae)

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.

When discrete characters are wanting: Continuous character integration under the phylospecies concept informs the revision of the Australian land snail Thersites (Eupulmonata, Camaenidae)

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.

Telomeric assemblies of Paracoccidioides genomes

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

Landscape genomics and demography of California Azolla

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.

larch: mapping the parsimony-optimal landscape of trees for directed exploration

The paper introduces larch, a tool that explores the space of optimal phylogenetic trees to find more parsimonious trees and increase diversity in the set of optimal solutions.

Evolutionary flexibility of ribosome biogenesis in bacteria

The paper analyzes over 30,000 bacterial genomes to show that CPR bacteria have fewer ribosome biogenesis factors, suggesting evolutionary flexibility in ribosome assembly.

Mid-Cenozoic Rhinocerotid Dispersal via the North Atlantic

The paper describes a new Early Miocene rhinocerotid species from the Canadian High Arctic and presents phylogenetic hypotheses, suggesting the North Atlantic Land Bridge was crossable for mammals longer than previously thought.

The Untapped Potential of Tree Size in Reconstructing Evolutionary and Epidemiological Dynamics

This paper explores the use of tree size in phylodynamic inference, showing it provides additional insights for diversification questions not captured by shape or branch lengths alone.

The evolutionary origin of host association and polycistronic transcription in trypanosomatids

This study investigates the evolutionary origins of host association and polycistronic transcription in trypanosomatids using comparative genomics across 47 genomes.