phylogenetics / evolution

AmpliPhy improves gene trees by adding homologous sequences without affecting alignments

Genetic basis of R-phase H:z27 antigen expression and phylogenetic relationships of Salmonella enterica serovar Senftenberg

This study identifies the genetic basis of H:z27 antigen expression in Salmonella Senftenberg and reveals two distinct genomic lineages within the serovar.

Parallel genomic remodeling associated with independent terrestrialization events in arthropods

This study identifies parallel genomic changes across arthropod lineages that independently transitioned to land, revealing shared molecular strategies for terrestrial adaptation.

Multi-genome synteny detection using minimizer graph mappings

The paper introduces ntSynt, a tool for detecting multi-genome synteny blocks using minimizer graphs, showing high coverage and efficiency across diverse genomes.

Genome evolution and convergent innovation in the carnivorous plant Sarracenia purpurea

This study presents a chromosome-scale genome assembly for Sarracenia purpurea and identifies genomic mechanisms underlying convergent evolution in carnivorous plants.

Mandibular morphology clarifies phylogenetic relationships near the origin of crown birds

Mandibular µCT reconstructions favour galliform-like, not palaeognath, affinities for Asteriornis; Vegavis and pelagornithid jaws lack key galloanseran synapomorphies and instead share features with stem bird Ichthyornis.

Complex genomic ancestry in southern regions and drivers of continental-level genetic diversity in the wolves of Asia

The paper uses whole genomes of wolves across Eurasia to study their genetic diversity and evolutionary history, finding major lineage barriers and admixture events shaping their genetic structure.

Reconstructing substitution histories on phylogenies, with accuracy, precision, and coverage

This paper introduces a new package for reconstructing substitution histories on phylogenies, showing improved accuracy and precision using relaxed clocks and codon-partition models.

Genetic Diversity and Phylogenetic Relationships of Cultivated and Wild Urochloa Species Conserved in the ILRI Forage Genebank

This study analyzes genetic diversity and phylogenetic relationships of 545 Urochloa species accessions using SNP and SilicoDArT markers, revealing distinct clades and admixture patterns in cultivated and wild species.

Leveraging Comparative Phylogenetics for Evolutionary Medicine: Applications to Comparative Oncology

This paper argues for integrating phylogenetic comparative methods into evolutionary medicine, using comparative oncology to show how these methods can reveal evolutionary patterns in disease traits.

The complex evolutionary history of Capparis L. (Capparaceae Juss.) in Australia, and the description of five new species and two new subspecies

This paper analyzes the phylogenetic relationships of Australian Capparis species, identifies a whole-genome duplication event, and describes five new species and two new subspecies.

The phylogenetic context for the origin of a unique purple-green photosymbiosis

This study investigates the evolutionary history of Pseudoblepharisma tenue to understand the factors limiting the frequency of purple photosymbioses.

A phylogenetic contribution to understanding the panzootic spread of African swine fever: from the global to the local scale

This study uses genomic data to analyze the spread of African Swine Fever virus, identifying long-distance transmissions and multiple introduction events in Europe.

Does more data solve the problem of deep support? A phylogenomic approach to clarifying evolutionary relationships in the Lecanoraceae

This study uses genome-scale data to resolve the phylogeny of Lecanoraceae, finding that while more data improve resolution, increasing gene count alone cannot fully clarify deep relationships.

Out of Antarctica: new insights into Antarctic Subcluster 5.2 picocyanobacteria based on high-quality genomes

This study reconstructs high-quality genomes of Antarctic and Arctic cyanobacteria, revealing an Out-of-Antarctica dispersal scenario within subcluster 5.2.

Chromosomal Fusions and Evolutionary Forces: Exploring theNeo-Sex Chromosome System of Anolis distichus

This study presents a high-quality genome assembly of Anolis distichus, revealing insights into neo-sex chromosome evolution and differential evolutionary pressures.

Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids

The paper presents chromosome-level genome assemblies of four Diamesa species, revealing gene family contractions and expansions linked to cold tolerance and high-altitude adaptations.

Using gene trees with lineage-specific duplicates for phylogenetic inference mitigates the effects of long-branch attraction

This paper shows that using larger gene families with multiple copies can reduce long-branch attraction errors in phylogenetic analysis, improving accuracy compared to single-copy genes.

Bypassing the Batch Effects to Improve the Reusability of RAD-seq Data: A Case Study of Recurrent Hybridization in the Japanese Torreya Species Complex

The paper improves RAD-seq data reusability by addressing allele dropout using lc-WGS, revealing hybridization events in Japanese Torreya species.

MFAID-Net: A Multi-modal Feature Fusion Deep Learning Network for Robust Adaptive Introgression Detection Across Diverse Evolutionary Scenarios

MFAID-Net detects adaptive introgression using a dual-encoder deep learning model with attention fusion, outperforming existing methods in diverse evolutionary scenarios.

IS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium

This study identifies IS1216 as a key driver in the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium through comparative genomic analysis of 152 plasmid sequences.

Conserved accessory genes link a phylogenetically distinct Bacillus subtilis strain from Indian bekang to the Japanese natto clade

The paper identifies a single Indian bekang strain with a conserved accessory gene profile similar to the Japanese natto clade, suggesting a shared adaptive strategy despite phylogenetic divergence.

Unpouching Peracarida relationships with ultraconserved elements

This study uses ultraconserved elements to resolve the phylogenetic relationships within Peracarida, finding strong support for monophyly and specific clades.

Diversification dynamics of the Palaeozoic actinopterygian radiation

Birth-death-sampling models of Palaeozoic ray-finned fish occurrences detect no origination increase after the Hangenberg event; cryptic Late Devonian diversification and survival likely explain Carboniferous diversity gains.

The complete mitochondrial genomes of Litophyton sp. and Stereonephthya sp., members of family Nephtheidae (Cnidaria: Anthozoa: Octocorallia).

This study sequences the complete mitochondrial genomes of two Nephtheidae species, confirming their gene arrangement and phylogenetic placement within the family.

Phylogenomic analyses of the diverse desert-alpine plant lineage Cistantheae

This study presents a phylogenomic analysis of the Cistantheae plant lineage, revealing patterns of life history evolution and gene flow across desert and alpine habitats.

Drift, selection and convergence in the evolution of a nonribosomal peptide

The paper studies the evolution of nonribosomal peptides in entomopathogenic bacteria, finding evidence of both neutral drift and natural selection driving structural convergence and toxicity diversification.

Evaluating 18S Phylogenetic Placement Accuracy to Uncover Hidden Diversity in Early Branching Animals

The paper evaluates 18S rRNA barcode performance for phylogenetic placement in non-bilaterian metazoans, finding full-length 18S most accurate for uncovering hidden diversity.

Whole-Genome Population Genomics Reveals Lineage Structure and Adaptive Potential of Philaenus spumarius, the Principal Vector of Xylella fastidiosa in Europe

Universal genomic constraints in the evolvability of thermal physiology

The paper uses simulations to show that body temperature evolution is constrained by protein thermal performance, leading to predictable patterns of rapid initial change followed by slow adaptation.