phylogenetics / evolution

Diversity and evolution of the ribovirian class Stelpaviricetes

This study identifies 103 putative families within the Stelpaviricetes class of ribovirians, revealing their evolutionary relationships and suggesting a protist origin for the class and fungal origin for Potyviridae.

Transcriptomes resolve phylogenetic relationships and reveal undescribed diversity in taildropper slugs (Genus Prophysaon)

The paper uses transcriptomes to resolve phylogenetic relationships and uncover undescribed diversity in Prophysaon slugs, questioning existing classifications and suggesting introgression.

LACHESIS: real-time inference of evolutionary trajectories of malignant transformation from whole-genome sequencing data

LACHESIS infers evolutionary trajectories of malignant transformation from whole-genome sequencing data and provides risk stratification for childhood and adult cancers.

Long-distance dispersal drives global tropical distributions in a widespread moth lineage (Lepidoptera: Limacodidae)

This study uses phylogenetic analysis to show that long-distance dispersal, not vicariance, primarily shaped the pantropical distribution of the moth genus Parasa.

Phylogenomics supports monophyly of marsupial crustaceans: a journey to direct development

This paper presents a comprehensive phylogenomic analysis of Peracarida, confirming their monophyly and identifying a new taxon, Panmancoida, with insights into their evolutionary developmental transitions.

Quantifying the predictability of evolution by analysis of coalescent rate variation

The paper develops coalescent models to quantify evolutionary predictability by analyzing lineage coalescence rates and applies them to microbial and viral datasets to detect selective effects.

MitoDate: a Nextflow pipeline for molecular clock dating and phylogenetic inference using ancient mitogenomes

Scalable and robust phylogenetic tree reconstruction from copy-number data with Sparse Rooted Neighbor Joining

This paper introduces SRNJ, a scalable rooted Neighbor Joining method for phylogenetic tree reconstruction from copy-number data, showing improved accuracy and efficiency over standard NJ.

The role of reticulate evolution in biodiversity formation: the case of neotropical Adiantum ferns

This study investigates reticulate evolution in neotropical Adiantum ferns using phylogenomic data and bioinformatic methods, revealing widespread hybridization and its impact on biodiversity and taxonomy.

Evolutionary and biological insights into the paternally expressed Snord116-Ipw-Snord115 gene array at the imprinted Prader-Willi syndrome domain

The paper investigates the role of Snord116 and Snord115 genes in Prader-Willi syndrome using knockout mice and comparative genomics, finding their impact on growth, metabolism, and gene regulation.

A tribal-scale phylogenomic perspective on ancestry and major lineages of the allotetraploid Hawaiian silversword alliance (Madieae, Compositae)

The paper uses phylogenomic analysis to resolve the ancestry and subgenome origins of the allotetraploid Hawaiian silversword alliance, identifying its allopolyploid origin and relationships to diploid relatives.

Parallel and scalable balanced minimum evolution algorithm for large-scale phylogenetic inference

This paper introduces a parallel and scalable implementation of the balanced minimum evolution algorithm for large-scale phylogenetic inference, achieving significant speedup and memory efficiency.

Unexpected diversity of Isidoides (Anthozoa: Octocorallia: Isidoidae) revealed by morphology and phylogenomic analysis with descriptions of three new species

The paper uses morphology and phylogenomic analysis to reveal unexpected diversity in Isidoides, identifying three new species and showing UCEs have higher resolution than other markers for species discrimination.

Global genomic diversity of the selfing nematode Caenorhabditis tropicalis correlates with geography

The paper analyzes the genomic diversity of C. tropicalis, finding geographic correlation and hyper-divergent regions linked to environmental adaptation.

Pangenome Analysis Reveals Gene Content Variation and Evolutionary Dynamics Across the Culex pipiens Species Complex

VINE: Variational inference for scalable Bayesian reconstruction of species and cell-lineage phylogenies

This paper introduces a variational inference method for Bayesian phylogenetic reconstruction, showing faster speeds than traditional Bayesian methods on real-world datasets.

The free-living wellspring of symbiotic nitrogen fixation in Bradyrhizobium

This paper identifies free-living Bradyrhizobium as the ancestral state of nitrogen fixation, showing that symbiotic nitrogen fixation evolved multiple times independently from free-living ancestors.

On the ancestry and evolution of the extinct dire wolf

This study uses paleogenomes of dire wolves to resolve their evolutionary relationships and identify genes under diversifying selection.

PhyloRBT: A Phylogenetic Approach to Detect Reference Bias in Phylogenomic Datasets

PhyloRBT detects reference bias in phylogenomic datasets by comparing locus reconstructions across multiple reference genomes, identifying biased loci that affect species tree inference.

Population Genetic Structure of Ariolimax columbianus around Corvallis, Oregon, USA

This study examines the population genetic structure of Ariolimax columbianus around Corvallis, Oregon, using CO1 and ITS-2 sequencing, revealing genetic breaks potentially caused by anthropogenic and natural factors.

The evolutionary processes of bacterial aromatic polyketide ketosynthases

The paper uses a protein language model to analyze the evolutionary history of bacterial aromatic polyketide ketosynthases and chain length factors, identifying a shared ancestral cluster and distinct evolutionary paths.

A parasitic flagellate among the Nucleariae: a new perspective on the phylogeny of Holomycota (Opisthokonta)

The paper describes a new parasitic nucleariid with a flagellated life cycle, placing it as a basal lineage within Holomycota and revising evolutionary hypotheses.

Multidimensional variation and population stratification across 8000 complete human centromeres

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

Rapid floral syndrome convergence in Penstemon through independent genetic variation

This study identifies four independent origins of hummingbird syndrome in Penstemon and finds rapid floral trait convergence without stepwise modification or adaptive introgression.

Whole-Genome Sequencing and Phylogenetic Analysis of Anolis adenovirus 2 Reveals Conserved Genome Organization and Gene-Specific Evolutionary Patterns

This study presents whole-genome sequences of two Anolis adenovirus 2 isolates, revealing conserved gene order and evolutionary patterns in Barthadenovirus.

Population structure, genetic diversity and global migration of the banana Fusarium wilt pathogen, Fusarium oxysporum f. sp. cubense tropical race 4

The paper analyzes the population structure and genetic diversity of Foc TR4 using whole genome sequences to trace its origin and migration patterns.

Cumulative cgMLST provides increased discrimination of nested phylogenetic groups

This paper introduces a cumulative cgMLST approach to improve discrimination of nested phylogenetic groups by adding conserved loci, showing increased allelic distances and utility for epidemiological analysis.

Phylogenomics resolves a 200-year-old puzzle: a revised tribal classification of Afro-Eurasian dung beetles (Coleoptera: Scarabaeinae)

This paper resolves a long-standing taxonomic issue in dung beetles by using phylogenomic data to propose a revised tribal classification for Afro-Eurasian species.

Home is where the host is: Evolutionary history of geographic spread, host switching, and adaptive genomic signatures in two generalist Group B Streptococcus clonal groups

This study analyzes the evolutionary history and host adaptation of two GBS clonal groups, revealing host switching, regional AMR gene distribution differences, and biased sampling in multi-host pathogens.

Phylogeny informed international clone assignment with PhyloMLST

PhyloMLST, a Python command-line tool, groups MLST sequence types into clonal complexes and international clones, optionally using a phylogeny to remove spuriously chained 'straggly' assignments.