phylogenetics / evolution

The paper challenges the claim that gene tree correction methods cause overfitting and shows they can still provide benefits despite incomplete lineage sorting.

Cattle B3.13 H5N1 polymerase gained PB2 M631L and PA K497R, boosting replication in bovine and human cells via better bovine ANP32A use; later PB2 E627K and D740N add activity.

This study estimates the origin of nightshade lineages using a total evidence timetree analysis, finding the family originated around 98 Mya, with major splits three times older than previous estimates.

This study uses Bayesian analysis of TSWV genome sequences to estimate its evolutionary origin, divergence date, and demographic history, finding it originated in South Korea around 1768 CE and expanded with agricultural development.

Constrained-tree hypothesis testing on 4,290 core eukaryotic protein clusters attributes 50% of likelihood weight to Asgard archaea; Alphaproteobacterial ancestry is largely confined to oxidative phosphorylation and iron-sulfur cluster biogenesis.

Low femoral trabecular anisotropy and bone volume fraction mark suspensory/bridging mammals, and a phylogenetic discriminant model classifies extinct Palaeopropithecus ingens and Megaladapis edwarsi as suspensory.

This study evaluates a theoretical algorithm for phylogenetic inference in realistic biological datasets, finding it robust but requiring adjustments for real-world applications.

This study investigates MHC evolution in seven newt species, finding a compact core MHC region and lineage-specific duplications, challenging previous assumptions about MHC expansion in giant genomes.

This study shows that phylodynamic migration rate estimates for HIV-1 within hosts are overestimated under selection using common models like BEAST2.

The paper describes three new species of Ischyropsalis from the North Iberian Peninsula and investigates their phylogenetic relationships using molecular markers.

This study characterizes the genome of a Proteus mirabilis strain isolated from fermented soybean, identifying virulence factors, antimicrobial resistance genes, and genomic adaptations to the fermentation environment.

This paper maps clonal genetic and epigenetic variation in grapevine using a phased diploid genome and Oxford Nanopore sequencing, showing that CG methylation patterns accurately reconstruct clonal phylogeny.

The paper uses genetic data and ecological models to infer that canopy-forming kelps in the Northeast Pacific survived in northern refugia during the Last Glacial Maximum.

The paper reconciles molecular and fossil evidence by showing sponges emerged in the early Ediacaran without spicules, which evolved independently multiple times later.

The paper investigates phylogenetic conflicts in squamates by analyzing genomic markers and finds that data quality, model fit, and sampling bias contribute to discordance.

This study assembles and analyzes the mitochondrial genome of Neltuma alba, confirming its placement within the Mimoseae tribe and providing a resource for evolutionary studies.

The paper surveys catenulid diversity in Central and Western Europe, focusing on Poland, using molecular markers to infer phylogeny and identify taxonomic challenges.

The paper constructs the largest dated phylogenetic tree for euphyllophytes by integrating backbone phylogenies and species-level trees, revealing increased topological and age estimation uncertainty in recent times.

This paper introduces a guide scaffolding method to improve phylogenetic accuracy and enable integration of 16S amplicon datasets across variable regions.

This study investigates the phylogeography of Brachypodium sylvaticum and its fungal symbiont Epichloe sylvatica, revealing co-divergence, niche conservatism, and geographic isolation as key factors in lineage splitting.

The paper presents extensive nuclear genome data for 44 Bryopsidales taxa, resolves their phylogeny, and identifies ancient gene duplications, including potential whole genome duplications, as factors in evolutionary adaptations.

This study presents a chromosome-level genome assembly for Iberolacerta aurelioi and uses whole-genome sequencing to investigate phylogenomic relationships and adaptive traits in the genus Iberolacerta.

The paper uses genomic analysis to trace the introduction routes of pathogenic B. gladioli strains into Bangladesh and identifies virulence gene changes associated with host transitions.

This study uses genome-wide data from spruce bark beetles to infer demographic history and assess the impact of chromosomal inversions on evolutionary inferences.

This study examines how data errors affect phylogenetic network inference and shows that many methods are vulnerable to these errors, leading to unreliable results.

The paper examines filamentation morphology evolution in Saccharomycotina yeasts using integrated genomic, metabolic, and environmental data from 1,154 strains, finding that filamentation is common and linked to phylogeny and environmental factors.

Structome-TM assembles datasets for structural phylogenetics by prioritizing local structural similarity to address size-based biases in homologous structure identification.

This study presents the genome and transcriptome of Pratylenchus vulnus, revealing evolutionary relationships, genomic features, and parasitism-related genes in a woody-plant nematode.

This study shows that gene expression patterns in flowering plants evolve rapidly, with divergence rates exceeding those in mammals, and highlights differences in conservation across organs.