phylogenetics / evolution

The paper examines local adaptation in five song sparrow subspecies in Alaska, finding evidence of positive selection in two genes and a novel phylogeny suggesting M. m. maxima colonized earliest.

The paper develops and validates a clinical whole genome sequencing assay for heritable disease and pharmacogenomics testing, showing high sensitivity, specificity, and accuracy in a large cohort.

This study uses molecular phylogenies and biogeographical models to show that bird-dispersed fruits with narrow shapes and specific colors in Meiogyne are linked to increased macroevolutionary dispersal.

This study adds Bhutanese red panda mitochondrial sequences to a global dataset, showing they form a single species with a genetic cline across their range, not distinct subspecies.

DupLoss-2 improves species tree inference under gene duplication and loss by enhancing gene loss computation, outperforming existing methods on benchmark datasets.

This paper develops SMART-PTA for single-cell whole-genome and transcriptome sequencing, revealing clonal evolution in aged human esophageal tissue over 70 years.

The paper introduces a structure-informed phylogenetic framework to study the evolutionary diversification of RRNPPA quorum sensing receptors in gram-positive bacteria and their viruses.

The paper presents the first complete chloroplast genome of Paeonia suffruticosa 'Cun Song Ying', compares it with related species, and identifies potential DNA barcode regions.

This study examines mitochondrial and plastid genome evolution in parasitic plants, revealing an inverse relationship between genome compaction and inflation across the parasitic continuum.

This paper improves ancestral state reconstruction by introducing joint reconstructions and uncertainty quantification, showing higher accuracy and biological insights in antibiotic resistance evolution.

The paper investigates mitonuclear discordance in Tropidurus lizards, finding that ancient mitochondrial introgression and demographic processes explain the observed genetic mismatches.

The paper introduces a new molecular marker using histone H3 and H4 genes and their spacer for phylogenetic studies in dragonflies, showing effectiveness in resolving species relationships.

The paper investigates the spatio-temporal evolution of annual species in the Arabideae tribe using plastid genome data and ecological modeling to test migration versus adaptation hypotheses.

The paper applies state space models to analyze trait evolution in fossil lineages, finding that spine number in diatoms correlates with solar insolation changes.

The paper develops ultraconserved elements (UCEs) and machine learning classifiers to improve phylogenetic analysis and taxonomy in nematodes, achieving accurate genus-level classification with minimal loci.

mrpast infers complex demographic histories from whole-genome genealogies, accurately recovering parameters like migration rates and population sizes in various models.

The paper uses mitochondrial sequencing and venom-gland transcriptomics to study phylogenetic relationships and venom gene diversity in Palauan cone snails.

This paper investigates overfitting in ML phylogenetic inference using cross-validation and finds no significant overfitting in most tools.

This paper develops a scalable long-read sequencing method for HPV16 genome analysis, showing high accuracy and capturing full genetic diversity across multiple lineages.

The paper characterizes a laboratory contaminant, Noodlococcus, as a new species within the Kocuria genus, revealing two phylogenetically distinct clades with significant ANI differences.

The paper evaluates how well phylogenetic tip rate methods predict future diversification using fossil and extant tetrapod data, finding moderate success with some methods.

This study uses palaeoproteomics to resolve the evolutionary placement of cave bears, finding Ursus dolinensis basal within the speloid lineage.

Plant LRR-Malectin receptor kinase IGP1 binds cellooligomers via its leucine-rich repeat domain while a conserved cysteine pair in its malectin domain senses hydrogen peroxide to attenuate immune signaling.

This paper evaluates an adjusted Bayes factor method to reduce sampling bias in discrete phylogeographic analysis using CTMC models.

The paper presents transcriptomic data for 11 free-living neobodonid kinetoplastids and reveals they are paraphyletic, with other metakinetoplastids descending from them.

The paper traces the evolution of mating-type loci in Cryptococcus and related species, revealing genomic dynamics like locus expansions, GC-content changes, and linkage transitions.

The paper identifies a conserved motif linked to β-sheet oligomerization in EAA1 isoforms through evolutionary analysis of helix-to-sheet transitions across species.

This study uses machine learning to select informative genetic loci for improved phylogenetic analysis of Neisseria gonorrhoeae, achieving higher accuracy and efficiency than traditional methods.

The paper rediscoveres Paroxygraphis in China, reclassifies it within Oxygraphis using phylogenetic analysis, and highlights its critically endangered status.

The paper investigates the evolutionary history of Wolbachia symbiosis in filarial nematodes by analyzing nuclear Wolbachia transfers and genome sequences, revealing complex patterns of cospeciation, loss, and replacement.