phylogenetics / evolution

The paper evaluates methods for detecting trait lability in grasses, finding inconsistent results across approaches and suggesting life history is stable in some clades.

Across 269 functional responses from 45 freshwater fish species, invasive species exceed non-invasive species only when sampled in their native range; introduced populations match non-invasive species.

This study uses phylogenomic data to resolve the evolutionary history of Rhinogobius gobies, revealing a north-south divergence and key morphological traits in Chinese species.

This study uses genome data from 48 chondrichthyan species to test shark monophyly, finding conflicting results across genomic markers.

The paper examines mtDNA diversity in sockeye salmon populations to trace biogeographical history, finding evidence of multi-origin postglacial expansions and refugia in Asia.

This study evaluates how ancient protein sequences can inform hominid evolution, showing they provide limited resolution compared to DNA data but can still offer insights when combined with better modeling.

This study identifies an aromatic patch in Mtb Wbl proteins that mediates interaction with the primary sigma 70 factor, revealing a conserved binding mechanism and evolutionary relationship with actinobacterial phages.

Splicer performs phylogenetic placement in sub-linear time, enabling efficient classification of large-scale genetic sequences with high accuracy.

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

The paper improves pandemic-scale phylogenetic analysis by addressing mutation rate variation and sequence errors, reconstructing a reliable phylogenetic tree of over 2 million SARS-CoV-2 genomes.

This study reconstructs a time-calibrated hummingbird phylogeny, finding stepwise diversification in the Andes rather than a monophyletic Andean clade.

The paper identifies a concurrent chickenpox outbreak during an Mpox outbreak in Uganda by analyzing metagenomic data from Mpox-negative samples.

The paper presents SHE, a phylogeny of eukaryotic proteomes based on structural comparisons, revealing a bipartite model of evolution and a framework for model organism selection.

The paper quantifies the energetic cost of sporulation in bacteria, showing it requires nearly 10^10 ATP and becomes optimal under prolonged harsh conditions.

The paper develops a model to analyze pangenome dynamics and finds that differences in bacterial pangenomes are mainly due to variation in the number of rapidly exchanged genes.

PhyloSOLID improves phylogenetic reconstruction from single-cell data by addressing error and sparsity, achieving better accuracy than existing methods.

This study evaluates how reference genome choice affects RAD-seq analyses in Petunia and Calibrachoa, finding that closely related genomes yield consistent results while distantly related ones reduce SNP recovery but not evolutionary inference.

This study analyzes the genetic diversity and historical range dynamics of silver fir to identify conservation priorities under climate change.

This paper introduces a multi-type fossilized birth-death model to jointly infer phylogenies and diversification rates with fossils and extant species, showing improved accuracy when morphological data are available.

The paper introduces CORAL, a scalable framework to infer mutation rates and spectra across species, revealing variation linked to life-history traits and identifying evolutionary mutational signatures.

This study clarifies Cryptolestes species status by re-evaluating mitochondrial DNA sequences and phylogenetic relationships, identifying genetic gaps and taxonomic challenges.

The paper compares R packages for phylogenetic generalised linear mixed models and shows glmmTMB is faster and more flexible for fitting PGLMMs with likelihood-based models.

This paper introduces BELLA, a Bayesian neural network framework for modeling complex phylodynamic processes, showing improved accuracy over linear models in capturing nonlinear relationships between predictors and evolutionary rates.

Molecular screening of bladder urine from 567 asymptomatic dogs and cats across seven Thai provinces detected pathogenic Leptospira in 9.8% of animals, including the first animal detection of Leptospira yasudae.

D-BPP detects ghost introgression in Panthera and Thuja by combining heuristic D-statistic with Bayesian phylogenomic inference.

Whole-genome sequencing and geolocation tracking indicate that high pathogenicity avian influenza H5N1 reached Tristan skuas on remote Gough Island via sub-Antarctic marine networks linked to South Georgia rather than Africa.

This study quantifies introgression's role in phylogenetic discordance among diploid Oryza species, finding it explains most gene tree-species tree conflict.

This study reconstructs the phylogeny of Neotropical leaf beetles and reveals a complex history of host plant switches among restricted plant families.

Morphometric and micro-CT analysis of 110 fossil and 354 extant Solanaceae seeds identifies 10 specimen-backed fossil species, including four new genera and a fossilized elaiosome, spanning Eocene to Holocene deposits.

This study investigates interploidy admixture in Thymus sect. Mastichina using genomic data, revealing distinct diploid and tetraploid groups with complex genetic structuring and potential for cryptic diversity.