phylogenetics / evolution

Phylogenomic and comparative genome analysis of the Juglandaceae family reveals black walnut (Juglans nigra) as an ancient lineage of the Rhysocaryon section.

The paper uses genomic data to analyze the Juglans genus, finding black walnut as an ancient lineage with implications for conservation and climate adaptation.

A General Framework for Branch Length Estimation in Ancestral Recombination Graphs

This paper introduces POLEGON, a method for estimating branch lengths in Ancestral Recombination Graphs using uninformative priors, showing improved coalescence time estimates and population size inferences.

Rodent Origins and Human-Mediated Evolutionary Dynamics of PRRSV

This study traces the evolutionary origins of PRRSV, revealing rodent ancestry and human-driven factors shaping its diversification and spread.

Four Decades of Genomic Stability and Adaptive Divergence in Xanthomonas arboricola pv. pruni-Infecting Phages: Defining Duraznoxanthovirus arenicola and Its Evolutionary Framework

The paper characterizes 15 phages infecting Xanthomonas arboricola pv. pruni, identifying a new genus and species and proposing taxonomic changes within the Anamaviridae family.

MTBseq-nf: Enabling Scalable Tuberculosis Genomics "Big Data" Analysis through a User-Friendly Nextflow Wrapper for MTBseq pipeline

The paper introduces MTBseq-nf, a Nextflow wrapper for the MTBseq pipeline, improving scalability and efficiency for tuberculosis genomics analysis.

Emergent Salmonella enterica serovar Infantis forms a monophyletic lineage shaped by geographic structuring

The paper analyzes global Salmonella Infantis genomes to show a monophyletic lineage shaped by geographic structuring and links its spread to antibiotic resistance gene dissemination.

The five divergent amino acids rule and evolution analysis of cytochrome c oxidase as new methods for Scolopendra Linnaeus, 1758 species differentiation (Chilopoda. Scolopendromorpha).

The paper identifies five divergent amino acids in COI sequences to differentiate Scolopendra species and proposes a rule for molecular species delimitation, with exceptions resolved using amino acid frequency and substitution probability analysis.

Scaling coalescent-based species tree inference to 100,000 taxa with STELAR-X

STELAR-X is a scalable triplet-based method for species tree inference that outperforms existing methods in speed and memory usage on large datasets.

PhyloCNN: Improving tree representation and neural network architecture for deep learning from trees in phylodynamics and diversification studies

PhyloCNN improves tree representation and neural network architecture for deep learning in phylodynamics and diversification studies, achieving high accuracy with smaller training sets.

Genomic evidence for phylogenetic congruence with sporadic host shifts in leishmaniaviruses and their parasite hosts

This study investigates the co-phylogenetic history of Leishmania parasites and Leishmaniavirus, finding strong phylogenetic congruence at the subgenus and species level, with weaker signals in some cases due to intraspecific host switching.

Limb proportions predict aquatic habits and soft-tissue flippers in extinct amniotes

Gordon et al. use a phylogenetic machine-learning approach to predict soft-tissue flippers and aquatic habits in extinct amniotes with >90% accuracy using limb proportions.

Bayesian model-averaging of parametric coalescent models for phylodynamic inference

This paper introduces a Bayesian Model Averaging framework for phylodynamic inference that integrates multiple coalescent models to better capture demographic histories without pre-specifying a single model.

A curated dataset of great ape genome diversity

The paper curates a dataset of 332 high-coverage great ape genomes to address evolutionary and diversity questions.

Hidden in Plain Sight. How Ks histogram dynamics can reveal and obscure ancient whole genome duplications.

The paper shows that Ks histograms can reveal or obscure ancient whole genome duplications depending on evolutionary and demographic factors.

The distribution of the time to the most recent pairwise genetic common ancestor of a set of sampled genomes

The paper derives the distribution of the time to the most recent pairwise genetic common ancestor in a recombining population, finding a characteristic scaling with population size.

Whole Genome Assembly of the Atlantic Bluefin Tuna Thunnus thynnus, with Phased Haplotypes

The paper presents a phased whole genome assembly for Atlantic bluefin tuna using PacBio HiFi and Omni-C scaffolding, enabling improved phylogenomic and evolutionary studies.

SNaQ.jl: Improved Scalability for Phylogenetic Network Inference

SNaQ.jl improves scalability for phylogenetic network inference by enhancing computational efficiency without altering method accuracy.

Divergent evolution of insecticidal protein families across bacteria and ferns

The paper investigates the evolutionary origins of insecticidal protein families, finding evidence of divergent evolution and horizontal gene transfer across bacteria, ferns, and other organisms.

Whole-genome polymorphisms and relatedness of rice varieties circulating in the Mediterranean market

The paper analyzes whole-genome polymorphisms of high-value rice cultivars in the Mediterranean market to assess genetic relationships and identify variants linked to quality and drought traits.

Learning the Language of Phylogeny with MSA Transformer

This study evaluates how MSA Transformer captures evolutionary distance and epistasis in protein sequences, showing it can reconstruct phylogenetic trees consistent with maximum likelihood methods.

The mitochondrial genome of Palythoa tuberculosa (Esper, 1805) contains a novel ORF with unknown function.

The paper reports a novel ORF insertion in the mitochondrial genome of Palythoa tuberculosa, distinct from previously reported ORF extensions in zoantharians.

Sparse learning for scalable phylogenetic network inference

This paper introduces Qsin, a sparse learning method that reduces the size of concordance factors tables for phylogenetic network inference while maintaining accuracy and reducing computational time.

The first complete mitogenome of the endangered spotted eagle ray, Aetobatus ocellatus, reinforces its classification within the family Aetobatidae

The paper determines the first complete mitogenome of Aetobatus ocellatus, confirms its classification in Aetobatidae, and highlights taxonomic implications for conservation.

No innocent bystanders: pertussis vaccination epitomizes evolutionary parallelisms between Bordetella parapertussis and B. pertussis

This paper shows that Bordetella parapertussis evolved similarly to Bordetella pertussis after pertussis vaccination, including loss of pertactin and changes in regulatory regions.

Time-resolved phylogenomics analysis reveals patterns in biosphere nutrient limitation through Earth history

This study uses phylogenomic analysis to trace the timing of nutrient limitation genes across Earth's history, showing phosphorus genes emerged early, nitrogen later, and iron-related siderophores possibly as early as the Archean.

Covary: A translation-aware framework for alignment-free phylogenetics using machine learning

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.

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy.

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.

Augmenting microbial phylogenomic signal with tailored marker gene sets

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

Incorporating continuous characters in joint estimation of dicynodont phylogeny

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.

Deciphering the global genomic landscape of C. neoformans: Population dynamics, molecular epidemiology and genomic signatures of pathogenicity

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