phylogenetics / evolution

Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree

Omni2Tree directly analyzes raw sequencing reads to reconstruct viral phylogenies and identify diversification, outperforming assembly and reference-based methods in low-coverage scenarios.

Phylogenetic and population genetic analyses reveal patterns of divergence among isolates in the Ceratocystis manginecans complex

This study uses phylogenetic and population genetic analyses to identify two genetically distinct groups within the Ceratocystis manginecans complex, showing ecological divergence and evidence of hybridization.

UCE phylogenomics inform the systematics and geographic range evolution of the harvester ant genus Pogonomyrmex

This study uses UCE phylogenomics to reconstruct the evolutionary history and geographic spread of Pogonomyrmex harvester ants, finding an early Eocene origin and climate-driven diversification.

Phylogenomic Taxonomic Analysis of Ralstonia solanacearum Strains causing Bacterial Wilt Disease in Northeastern Argentina.

This paper analyzes genomic data from Ralstonia solanacearum strains in Argentina, revealing two closely related phylotype IIA lineages and highlighting issues with current sequevar classification.

The morphology and small subunit rDNA gene phylogeny of the novel goniomonad genus Ebisugoniomonas and two novel Poseidogoniomonas species

This study describes a new goniomonad genus and two species, updates the SSU rDNA phylogeny, and reports cellular features of goniomonads.

Atlantic and Indo-Pacific separation in Palythoa sibling species: phylogenomic analyses using ultraconserved elements

This study uses ultraconserved elements to analyze the phylogenetic relationships between Palythoa sibling species, finding intermixed lineages and gene tree discordance, suggesting a species complex rather than distinct species.

Predator-prey scaling laws support a suspension-feeding lifestyle in Cambrian luolishaniid lobopodians

Cambrian luolishaniid lobopodian appendage mesh spacing scales sublinearly with body length, and their predator-prey size ratios match modern suspension feeders rather than raptorial chaetognaths.

Phylogenomics reveals reticulate evolution in the Chenopodium album complex

This study uses phylogenomic data to show reticulate evolution in the Chenopodium album complex through hybridization and polyploidy.

Target capture sequencing provides insights into hybridogenetic water frogs

This study uses target capture sequencing to analyze hybridogenetic water frogs, revealing mtDNA introgression and polyploidy in P. esculentus.

Parallel algorithms for phylogenetic inference under a structured coalescent approximation

The paper introduces parallel algorithms to improve the computational efficiency of structured coalescent models for phylogeographic analysis, enabling faster and larger-scale studies of pathogen spread.

PhytClust: Efficient and Optimal Monophyletic Partitioning of Rooted Phylogenetic Trees

PhytClust partitions rooted phylogenetic trees into monophyletic clusters without user-defined thresholds, achieving optimal and reproducible results across diverse biological datasets.

An Extended Clade Framework for Annotated Trees in the Context of Phylogeography and Transmission Tree Inference

The paper introduces an extended clade framework to better summarize annotated phylogenetic trees in phylogeography and transmission tree inference.

EMPIRE: The Ellipse Model for Phylogenetic Inference of Range Evolution

The paper introduces EMPIRE, a model for inferring range evolution in phylogenetics, and applies it to skinks in Australia, finding speciation linked to aridification but not ecological partitioning in daughter lineages.

The evolution of plant actins

This study investigates the evolutionary diversification of plant actins, finding that actin copy number increases correlate with plant complexity and that functional distinctions are maintained through specific sequence changes.

Origin and evolution of grapevine genomes

This study investigates the origin and evolution of grapevines through phylogenomic analysis of 29 genome assemblies, revealing evolutionary relationships and genomic features contributing to their adaptation.

Understanding cryptic diversity within the honeypot ant species complex of Myrmecocystus mendax

This study identifies cryptic species within the honeypot ant M. mendax complex using phylogenomic and population genomic analyses of UCE data.

Ancient regulatory evolution shapes individual language abilities in present-day humans

Polygenic score variants in HAQERs (Human Ancestor Quickly Evolved Regions, <0.1% of the genome) predict spoken language but not nonverbal IQ; language associations replicate in SPARK, ABCD and UK Biobank.

A deep genetic structure phylogenomically frames the closest algal relatives of land plants

The paper sequences 43 new transcriptomes of Zygnematophyceae algae and builds a phylogenomic tree, revealing deep genetic structure and ancient radiations within this algal class.

Disparity analyses are robust to ancestral state estimation uncertainty

This study evaluates how ancestral state estimation affects disparity analyses, finding that fossil sampling density is more critical than estimation method choice.

Convergent genome streamlining accompanies independent miniaturization in the world's smallest fishes

This study investigates the genomic correlates of miniaturization in Cypriniformes, finding convergent genome streamlining in progenetic miniatures but not proportioned dwarfs.

Statistical Model Comparison Supports a Pitcher Origin of Utricularia Suction Traps

The paper tests the pitcher hypothesis for the evolution of Utricularia bladder traps using statistical model comparison of phylogenetic data.

Revisiting the Monascus genus (Eurotiales, Aspergillaceae): A Multilocus Phylogenetic Approach to Species Delimitation

This study uses multilocus phylogenetic analysis to clarify species boundaries within the Monascus genus, identifying 11 species and resolving synonymies.

A Seychelles warbler genomic toolkit

The paper develops a genomic toolkit for Seychelles warblers, enabling genetic pedigree assignment and correcting sample identity errors using high-quality genomic data.

The conquest and diversification of leafy spurges across the Holarctic and beyond: biogeography and evolution of life-history of Euphorbia subgenus Esula

This study investigates the biogeography and evolution of life-history traits in Euphorbia subgenus Esula, showing that perenniality and range expansion are linked to diversification.

Detection of positive selection driving antimicrobial resistance in the core genome of Staphylococcus epidermidis

The paper identifies genes under positive selection in the core genome of Staphylococcus epidermidis, including those linked to antimicrobial resistance and metabolism.

Genic and phylogenomic discordances reveal conflicting hybridization episodes in temperate Loliinae grasses

This study reveals hybridization episodes in Loliinae grasses using phylogenomic data, showing lineage-specific hybridization rates and discordances between nuclear and plastome trees.

Frequent seasonal reassortment between high and low path viruses drives the diversification of influenza A/H5N1

The paper shows that seasonal reassortment between high and low pathogenic influenza A/H5N1 viruses drives genotype diversification, with ducks, geese, and the Central flyway as key sources.

Efficient Bayesian Phylogenetics under the Infinite Sites Model

The paper introduces inPhynite, an efficient Bayesian phylogenetics algorithm under the infinite sites model, achieving 225x speedup without accuracy loss on large datasets.

Statistical and structural bias in birth-death models

The paper examines statistical and structural biases in birth-death models for estimating speciation and extinction rates from phylogenetic trees and provides corrections to improve accuracy.

Ancestral Genome Reconstruction.

This paper introduces AGR, a pipeline to infer paleogenomes from modern species by using inter-species chromosomal synteny and hierarchical clustering.