phylogenetics / evolution

Durophagous adaptations in a new crocodyliform from the Santonian of Hungary and a systematic reassessment of European Cretaceous atoposaurids

The paper describes a new crocodyliform species from the Santonian of Hungary and reassesses the taxonomy of European Cretaceous atoposaurids, finding potential polyphyly in Theriosuchus.

Characterization of the Preclinical in Vitro and in Vivo Pharmacokinetic Properties of the Cyclic Oligomeric Depsipeptide Ryanodine Receptor 2 Inhibitor ent-Verticilide

This study characterizes the pharmacokinetic properties of ent-verticilide, identifying limited intestinal availability and CYP-mediated metabolism as key factors affecting its oral exposure.

Genomic detection of domoic acid biosynthesis uncovers expanded toxigenic diversity across Pseudo-nitzschia diatoms

The paper identifies genomic features of domoic acid biosynthesis in Pseudo-nitzschia diatoms, revealing expanded toxigenic diversity and environmental expression patterns.

Traits and hidden states: is self-fertilization associated with rates of diversification across mating and sexual systems?

The paper examines how mating and sexual systems affect diversification rates across 18 plant families, finding that sexual systems better explain diversification than mating systems.

Horizontal transfer of an antimicrobial peptide across insects

The paper identifies horizontal gene transfer of the Drosomycin antimicrobial peptide gene across insect species, suggesting HGT contributes to immune system novelty and defense capabilities.

Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations

This study presents the first comprehensive phylogenomic analysis of Cypriniformes, establishing a robust backbone topology and identifying unresolved conflicts in evolutionary relationships.

A New Information Theoretic Approach Shows that Mixture Models Outperform Partition Models for Phylogenetic Analyses of Amino Acid Data

The paper compares mixture and partition models for phylogenetic analyses using the mAIC and finds mixture models consistently outperform partition models.

Phylogenomic screening reveals idsA2 loss conferring nitroimidazole cross-resistance in Mycobacterium tuberculosis

A length- and mutation-load-corrected homoplasy screen of 1,813 MDR-TB genomes flags idsA2; its loss raises pretomanid MIC fourfold, delamanid and ethambutol twofold, via isoprenoid flux redirection.

Pygopods are an exceptional radiation of snake-like geckos

This study shows that pygopods, limbless geckos, have undergone similar evolutionary adaptations to snakes, with exceptional morphological and dietary evolution despite limited species diversity.

Once in a blue moon: an unexpected evolutionary route to blue floral pigmentation in orchids

The paper investigates the genetic basis of blue floral pigmentation in orchids, finding an unexpected pathway involving duplicated genes and regulatory changes rather than the expected CYP75A pathway.

Global biogeography of geckos (Squamata: Gekkota) reveals Old-World origins and region-specific heterogeneity in diversification

This study investigates gecko biogeography and diversification, finding Old-World origins and region-specific diversification patterns without evidence of mass extinctions.

Data mining of global sequence datasets markedly expands known diversity within the Tobamovirus genus

Serratus-guided Snakemake mining, expert curation, clustering and phylogenetic placement identify at least 32 putative novel tobamoviruses in public short-read data, mostly Amazon River metatranscriptomes; a random-forest classifier partly automates curation.

CTCF gradually acquires novel function modalities during bilaterian evolution

This study investigates how CTCF's functional properties evolved across bilaterian species, revealing gradual changes in its ability to regulate chromatin structure and transcription.

Described eukaryotic species in published species-level phylogenies: placement by molecular data, dates and date uncertainty

The paper analyzes published eukaryotic phylogenies to assess molecular placement, dating, and uncertainty across species groups.

Panagram reveals pangenome architectures underlying trait variation in plants and animals

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

Statistical analysis provides new insights into patterns and mechanisms of the WANCY hotspot on vertebrate mitochondrial genomes

The paper uses statistical analysis of mitochondrial genome data to identify convergent rearrangements in the WANCY region, suggesting it is a TDRL hotspot with higher convergence frequency than previously thought.

Phenotypic and genomic changes associated with the evolutionary loss of heterostyly in primroses

The paper investigates the genetic and phenotypic changes associated with the loss of heterostyly in Primula boveana, revealing a disrupted CYP gene and developmental shifts leading to autonomous selfing.

Bayesian Variable Selection Approaches to Identifying Selection in Evolutionary Datasets

This paper introduces a Bayesian variable selection method for identifying selection in phylogenetic datasets, showing it outperforms Dirichlet-process models and avoids phantom selection artifacts.

Reference mapping and whole-genome alignment yield comparable phylogenomic inferences

The paper compares phylogenomic inferences from reference mapping and whole-genome alignment across Ursidae species, finding comparable results despite sequence loss.

Inverse covariation between the neocortex and the limbic system is concentrated at deep evolutionary divergences

The paper shows that the tradeoff between neocortex and limbic system volume is concentrated at deep evolutionary divergences in mammals.

Molecular Data From Herbarium Specimens Reveal A Potential Extirpation of Azolla microphylla From California

The paper analyzes molecular data from historical herbarium specimens and modern samples to assess the status of Azolla species in California, finding potential extirpation of Azolla microphylla.

Phylogenomic Characterization of Two Alternaria Lineages Associated with Cotton Leaf Spot in Tennessee

The paper identifies two phylogenetically distinct Alternaria lineages associated with cotton leaf spot in Tennessee, confirming one as a causal agent.

An unconstrained Euclidean parametrisation of phylogenetic tree space

This paper introduces a parametrisation of phylogenetic tree space using unconstrained Euclidean coordinates, enabling new methods for Bayesian phylogenetic inference.

Development and pharmacological characterization of a stable HEK293 cell model for the study of human FLT3 signaling and its pharmacological modulation

The paper develops a stable HEK293 cell line expressing FLT3 for pharmacological studies and shows it effectively models FLT3 signaling and response to inhibitors.

Pareto fronts reveal constraints on the evolution of ecological niches

The paper uses Pareto fronts to detect evolutionary constraints on niche-determining traits in phytoplankton, showing that trade-offs persist across scales despite differing evolutionary outcomes.

DIMPLE: A Tree-Guided Divide-and-Conquer Framework for ILS-Aware Phylogenetic Network Inference on Large-Scale Data

DIMPLE infers phylogenetic networks from large-scale data using a divide-and-conquer approach, achieving accurate merging and improved reticulation recovery over existing methods.

Solving Paleobotany's 200-year problem with fluorescence and artificial intelligence

This paper uses fluorescence and AI to solve paleobotany's 200-year problem by revealing detailed leaf venation in fossils.

Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals

EZHIP, a PRC2 inhibitor, arose on the placental mammal X chromosome, evolves under positive selection in primates, and duplicated, including a testis-expressed primate paralog, EZHIP2, whose gorilla copy inhibits H3K27me3.

Insights into goatpox virus and sheeppox virus genomes from pangenome graphs

This study compares the genomic diversity and evolution of goatpox and sheeppox viruses using pangenome graphs, revealing structural variation at inverted terminal repeats as a key driver of diversity.

Testing Thirty Years of Hypotheses: Ancient Trout-Salmon Introgression and Limited Pre-Colonial Gene Flow Between Rainbow and Cutthroat Trout Shaped Pacific Salmonid Evolution

This study tests hypotheses about ancient introgression and gene flow in Pacific salmonids, finding introgression between trout and salmon ancestors but not between trout lineages.