phylogenetics / evolution

Horizontal transfer of an antimicrobial peptide across insects

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.

Phylogenomic screening reveals idsA2 loss conferring nitroimidazole cross-resistance in Mycobacterium tuberculosis

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.

Population structure of human-infecting and environmental isolates of Coccidioides immitis, the fungus causing Valley fever

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

Rye stem rust is a reservoir of diversity and virulence for wheat stem rust

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.

Distinct mechanisms of CNV formation at the human 15q13.3 locus

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.

Origin and evolution of acrocentric chromosomes in human and great apes

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.

The limits of Bayesian estimates of divergence times in measurably evolving populations

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.

kamino: fast proteome-wide variant calling for amino acid phylogenomics

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 chromosome level genome of the Blueberry Stem Gall Wasp, Hemadas nubilipennis (Hymenoptera: Ormyridae) on lowbush blueberry (Vaccinium angustifolium) reveals repeat-driven expansion

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.

One species, two lives: cryptic population structure and life-history divergence in a vineyard spittlebug (Aphrophora sp.), a candidate vector for Pierce's disease

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: Nonparametric Demographic Inference from the Site Frequency Spectrum at Biobank Scale

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

Gene conversion is a key driver of diversity hotspots in M. tuberculosis antigens and virulence-associated loci

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.

Emergence of short-lived meningococci causing focal epidemics can be associated with gene transfer from carriage-associated Neisseria

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.

Ancient DNA perspectives on North American cervids identify fluctuations in genetic diversity

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.

Joint dog and wolf genealogies reveal the evolution of the canine genome

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.

Parallel evolution under constraint shapes echinocandin resistance in Candida auris

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.

A Curated Pharmacogenomic Allele Catalog for Sub-Saharan African Populations

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

The Genomic Landscape of Post-Black Death Epidemics in Northern Europe and the Caucasus

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.

A Method to Analyze Low-Quality Archaic Human Genomes and its Application to the Teshik-Tash 1 Neandertal

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: A plasmid reconstruction tool from short-read assemblies

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

TBpop: an open-access genomic portal integrating genomic variation, population genetic statistics, phylogeny, pangenome composition, and strain metadata of epidemic Mycobacterium tuberculosis strains from China

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

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.

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.

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.

neissflow: Streamlining Genomic Epidemiology of Neisseria gonorrhoeae with Nextflow

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

An active-matrix digital microfluidic platform for simultaneous short- and long-read viral genomic surveillance

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

Genomic diversity of elm trees for future treescapes

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

Towards an evolutionary baseline model of Plasmodium falciparum for population-genomic inference

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

Geographic structuring of genetic variation differs across two contact zones in the Diglossa carbonaria superspecies

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: 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.