phylogenetics / evolution

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.

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.

The paper analyzes genetic structure and diversity of Coccidioides immitis in environmental and human isolates to understand disease transmission and environmental distribution.

The paper analyzes 385 Pg genomes to show Kazakhstan hosts a diverse sexual clade with many HD haplotypes, and Pgs contributes virulent alleles to wheat rust pathogens.

The paper identifies distinct mechanisms of CNV formation at the human 15q13.3 locus, showing that non-allelic homologous recombination is the primary mechanism, influenced by inversion polymorphisms and population-specific susceptibility.

The paper identifies evolutionary processes in acrocentric chromosomes of great apes, including repeat enrichment, inversion, and gene family amplification, with implications for human genomic instability.

This paper examines the limits of Bayesian divergence time estimates in microbial evolution, finding that uncertainty scales with distance to calibration points rather than absolute age.

Proteome-wide variant calling builds amino acid phylogenomic alignments orders of magnitude faster than a BUSCO marker pipeline, with similar tree signal in three of four test taxa.

The paper presents the first chromosome-level genome of the blueberry stem gall wasp, revealing repeat-driven genome expansion and insights into symbiont interactions and host adaptation.

The paper analyzes genome data from spittlebugs in vineyards and quasi-natural populations, revealing cryptic population structure, life-history divergence, and insecticide resistance.

Stairway Plot v3 infers nonparametric effective population size trajectories from the site frequency spectrum at biobank scale, achieving high resolution with large samples.

Complete genomes from 151 clinical M. tuberculosis isolates show gene conversion between paralogs creating diversity hotspots in PE/PPE/ESX genes and T cell antigens, including PPE18.

A 21-case nightclub-linked meningococcal outbreak variant differed from its closest relatives by horizontal gene transfer from carriage-associated Neisseria, affecting iron acquisition and type IV pili genes.

This study uses ancient DNA from North American cervids to trace genetic diversity changes over time, revealing historical population dynamics and impacts of external pressures.

This study uses joint genealogies of dogs, wolves, and coyotes to uncover evolutionary forces shaping the dog genome, identifying mutation-rate pulses, selection signatures, and introgression events.

Across 681 matched isolates and 22,388 genomes, high-level micafungin resistance in Candida auris arises through recurrent FKS1 hotspot mutations amid strong purifying selection, and FKS2 appears dispensable.

The paper curates a pharmacogenomic allele catalog for Sub-Saharan African populations, highlighting population-specific frequencies and functional annotations for six pharmacogenes.

Twenty-three new Yersinia pestis genomes from Scandinavia, the Netherlands, Iceland and Armenia extend the Second Plague Pandemic phylogeny, with the first Icelandic plague genome and eastward-spreading pestis secunda strains.

The paper develops a computational method to analyze low-quality archaic human genomes and applies it to the Teshik-Tash 1 Neandertal, showing genetic similarity to later Western Eurasian Neandertals.

plsMD improves plasmid reconstruction from short-read assemblies, outperforming existing tools in recall, precision, and F1 scores on benchmark and novel datasets.

TBpop integrates genomic variation, population genetics, and metadata for Mycobacterium tuberculosis strains from China to enable comprehensive analysis of genetic diversity and evolution.

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

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

neissflow is a Nextflow pipeline for analyzing Neisseria gonorrhoeae genomes, achieving high accuracy in species identification, AMR profiling, and phylogenetic analysis.

This paper develops a digital microfluidic platform that enables simultaneous short- and long-read viral genomic surveillance with improved efficiency and accuracy.

The paper analyzes genomic diversity in elm trees to assess the genetic potential of resistant cultivars for restoration.

The paper identifies key components for building a baseline evolutionary model of Plasmodium falciparum to better understand genomic variation and drug resistance.

The paper examines genetic differentiation and hybridization in three closely related bird taxa at contact zones using RADSeq data, finding weak genetic differentiation and evidence of introgressive hybridization in one zone.

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.