phylogenetics / evolution

Beyond Level-1: Fast Inference of Generic Semi-directed Phylogenetic Networks

This paper extends the SNaQ method to infer complex semi-directed phylogenetic networks, showing improved accuracy and scalability for reconstructing reticulate evolutionary histories.

Stochastic Phylogenetic Models of Shape

This study introduces a stochastic framework for phylogenetic shape analysis using diffusion processes and applies it to butterfly wing data.

NTM-DB: A Comprehensive Non-Tuberculosis Mycobacteria Genomic Database

NTM-DB provides a comprehensive genomic database for non-tuberculosis mycobacteria, offering genome assemblies, strain data, and analysis tools to support research and clinical applications.

Effect of cellular nutrient economy on the evolution of genome size in phytoplankton

This study develops a theoretical framework linking cellular nutrient economy to genome size evolution in phytoplankton, showing that 1-bp indels can be counterselected under minimal nutrient conditions.

Beyond infinite sites: Generalized ABBA-BABA statistic for deeper phylogenies

The paper introduces D+ and D* statistics to improve detection of gene flow by addressing saturation bias in deeper phylogenies using multiallelic site patterns.

Ultrafast and Ultralarge Distance-Based Phylogenetics Using DIPPER

DIPPER is a GPU-accelerated distance-based phylogenetic tool that achieves ultrafast and ultralarge phylogenetic reconstruction with improved speed, accuracy, and memory efficiency.

Evolutionary dynamics of temporal transcription factor series in the insect visual brain

This study reconstructs the evolutionary history of temporal transcription factor series in insect visual brains, showing conserved patterns and species-specific variations that influence neuronal diversity.

A novel phylogenomics pipeline reveals extensive topological conflict in the evolution of the angiosperm order Cucurbitales

The paper introduces CAPTUS, a phylogenomics pipeline that efficiently handles mixed sequencing data, revealing topological conflicts in the evolution of Cucurbitales.

UVfinder: a tool to extract bryophyte sex-linked gene copies from the GoFlag408 probe set

UVfinder identifies sex-linked gene copies in moss genomes, revealing neo-sex chromosome formation and phylogenetic insights from sex-linked loci.

Insights into the phylogeny and enigmatic mitochondrial biology of eustigmatophyte algae from over 50 newly sequenced organellar genomes

This study presents over 50 newly sequenced organellar genomes from eustigmatophyte algae, revealing insights into their phylogeny and unique mitochondrial gene evolution.

Diverse megamammals exploited by humans, chronology and palaeoecology at Taima-Taima, Late Pleistocene, South America

Bone modification analyses, tooth enamel radiocarbon dates, and dental calculus microfossils indicate that Late Pleistocene humans exploited at least five megaherbivore species at a savannah watering hole in Venezuela.

African origin and Late Cretaceous divergence of the Middle American catfish Lacantunia enigmatica corroborated by a global mitogenome phylogeny

The paper sequenced the mitochondrial genome of Lacantunia enigmatica and used it to construct a global catfish phylogeny, supporting its African origin and Late Cretaceous divergence.

Contrasting Mitochondrial Diversity of Endemic Corbicula Clams in Sulawesis Ancient Lakes: Phylogeography and Implications for Conservation

This study examines mitochondrial diversity in two endemic Corbicula clams from Sulawesi lakes, revealing deep divergence and distinct phylogeographic patterns with conservation implications.

Modeling Site-Specific Mutation Patterns in Pandemic-Scale Phylogenetics

This paper introduces a site-specific mutation model (SSM) for pandemic-scale phylogenetics, showing it better captures mutation patterns in SARS-CoV-2 genomes than classical models.

Quantifying Asymmetric Coevolutionary Dynamics using Normalized Phylogenetic Costs

The paper introduces normalized asymmetric phylogenetic costs to quantify coevolutionary dynamics, showing they capture complex relationships in virus-host systems and detect novel gene pairings in viral genomes.

Dici: a novel DNA transposon reshaping the genome of the opportunistic yeast Diutina catenulata

This study presents genomic analyses of Diutina catenulata, revealing genetic structuring, drug resistance homologs, and a novel DNA transposon family associated with chromosomal instability.

Phylogenomic assessment of microhylid frogs reveals widespread taxonomic confusion in the Asterophryinae and establishes the timing of diversification in Australia

This study uses phylogenomic data to clarify the evolutionary history of microhylid frogs, revealing taxonomic issues in the Asterophryinae subfamily and timing of diversification in Australia.

A Chromosome-Scale Genome of Nanomia septata Reveals Extensive Rearrangement But No Clear Driver of the Unique Colony-Level Organization of Siphonophores

The paper sequenced the chromosome-scale genome of Nanomia septata, revealing genome rearrangements and expansion but no clear genomic drivers for siphonophore colony-level organization.

Models trained with noisy genomes extend bacterial phenotype prediction into deep time

This paper shows that adding noise to gene content data improves machine learning predictions of bacterial phenotypes across evolutionary time, concluding the last bacterial common ancestor was anaerobic, double-membraned, and moderately thermophilic.

Quaternary ice ages shaped protists phylogeography: the case of Arcellinida in the Iberian Peninsula

The study examines how Quaternary ice ages influenced the phylogeography of Arcellinida protists in the Iberian Peninsula, finding genetic diversity hotspots aligned with glacial refugia and supporting the GLQ paradigm for microbial eukaryotes.

CAMUS: Scalable Phylogenetic Network Estimation

CAMUS estimates phylogenetic networks using a constraint tree and quartet trees, achieving high accuracy and speed for large datasets.

Southern Iberia as a hotspot of wild grapevine genetic diversity

This study identifies three ancestral populations and four genetic refugia in southern Iberia, showing gene flow from North Africa to Iberian wild grapevines during the late Pleistocene and early Holocene.

Nuclear phylogenomics clarifies the family-level backbone and gene-tree conflict in Zingiberales

This study uses nuclear phylogenomics to resolve the family-level backbone of Zingiberales, finding that deep node instability is due to rapid divergence and incomplete lineage sorting, not hybridization.

Global distribution of isoprenoid quinones across Bacteria

This study maps the distribution of isoprenoid quinones in Bacteria using genomic data and phylogenetic analysis, revealing new insights into their evolutionary history and metabolic adaptations.

The effects of post-divergence gene flow on simultaneous divergence time (SDT) testing

This study evaluates how post-divergence gene flow affects the accuracy of simultaneous divergence time estimates using simulations and Bayesian methods.

Genvectors: exploring patterns and unveiling processes driving the geographic distribution of genetic lineages

This paper introduces genvector analysis to infer biogeographic drivers of genetic turnover by decomposing genetic dissimilarities into eigenvectors and testing null models.

Structural Organization of the Nvj3-Mdm1 Complex Reveals a Conserved Lipid-Compatible Contact Site Module

The paper identifies a conserved lipid-compatible tunnel in the Nvj3-Mdm1 complex, suggesting a conduit-based model for lipid transfer at the nuclear-vacuolar junction.

Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages

The paper designs a custom probe set to improve phylogenetic resolution in the challenging Clusioid clade, showing better performance than a universal probe set.

Phlag: Scalable detection of genomics regions with unexplained phylogenetic heterogeneity

Phlag detects genomic regions with inconsistent evolutionary processes by modeling gene trees as a stochastic process along the genome.

Principal Components Analysis fails to recover phylogenetic structure in hominins

This paper shows that PCA fails to recover phylogenetic structure in hominin datasets, highlighting flaws in using PCA for phylogenetic inference.