phylogenetics / evolution

The paper examines statistical and structural biases in birth-death models for estimating speciation and extinction rates from phylogenetic trees and provides corrections to improve accuracy.

This paper introduces AGR, a pipeline to infer paleogenomes from modern species by using inter-species chromosomal synteny and hierarchical clustering.

Spatial transcriptomics of live healthy donor livers shows most hepatocyte genes are zonated, with key functions pericentrally shifted versus mouse, pig, boar and cow.

This study uses molecular and morphological data to clarify the phylogenetic relationships of three Crenotia species, showing their monophyly and distinct interspecific relationships.

The paper introduces bifrost, an R package for detecting shifts in multivariate trait evolution across phylogenetic trees, using a greedy search and information-criterion weights.

The paper introduces a method for accurate mitochondrial haplotyping using split k-mers and applies it to mitogenome datasets of mammalian and insect species.

The paper examines the relationship between neuronal and glial cell densities in the visual cortex and their associations with visual acuity and lifespan across mammals.

This paper uses genomic and epidemiological data to analyze the dynamics of a Mycoplasma bovis outbreak in New Zealand from 2017 to 2023, showing the impact of control measures and the persistence of infection.

The paper re-evaluates the eukaryotic Tree of Life using an independent phylogenomic dataset, finding different placements for some lineages and supporting a small number of high-rank supergroup lineages.

This study analyzes 10,839 Bacillus genomes to explore taxonomy, functional potential, and biotechnological applications, identifying gene variability and key traits across species.

The paper identifies an introgressed galectin-like protein in Cryptosporidium parvum anthroponosum as a potential driver of its human tropism through interaction with the human insulin-degrading enzyme.

This study constructs a comprehensive phylogenomic framework for Vanilla, revealing evolutionary relationships, historical biogeography, and hybridization patterns.

This study analyzes 63 Megalocytivirus genomes, revealing widespread recombination and identifying genes from outside the Iridoviridae family, leading to the designation of two new species.

The paper analyzes whole genome sequences of Black Soldier Fly populations to reveal cryptic genetic diversity and the impacts of domestication on genetic variation.

The paper improves phylogenetic inference by incorporating lineage abundance into maximum likelihood methods, showing significant accuracy gains in SARS-CoV-2 data.

This study sequenced ancient and modern genomes from the Ryukyu Archipelago to show genetic differentiation between Ryukyu Jomon and Hondo populations, with admixture occurring around 1,000 YBP.

This paper presents 84 complete genomes of Actinomarina, a marine bacterial order, revealing novel species, a hypervariable region, selenocysteine usage, and extensive auxotrophies.

The paper assembles complete mitochondrial genomes for three searobin species and performs a phylogenetic analysis to clarify their relationships within the Prionotinae subfamily.

The paper analyzes whole-genome sequencing data from 548 Nakaseomyces glabratus isolates to assess the concordance between MLST and WGS-based phylogenies, finding strong agreement and proposing a hybrid naming system.

This paper introduces k-NCL, an algorithm for completing rooted phylogenetic trees with overlapping taxa, preserving topology and branch lengths, and shows it improves clustering performance when combined with RF.

The paper compares selection pressures on orthologous genes between aquatic and terrestrial plants to understand adaptations to their respective environments.

Sequenced HBV from wild Amazonian primates in a deforested, densely settled region matched human genotypes A and D, while pristine-forest monkeys were all negative, consistent with human-to-primate spillover.

The paper uses nucleomorph genes to reconstruct the phylogeny of cryptophyte plastids, finding they are sister to Cyanidiophytina, suggesting an ancient origin of red complex plastids outside known Rhodophyta subgroups.

This study evaluates how subsampling affects species tree inference by analyzing simulated and empirical datasets using a new measure of phylogenetic information content.

The paper identifies exonic enhancers as dual-function regulatory elements that influence gene expression and are associated with disease and evolution.

This study reports the pharmacokinetics and tissue distribution of 6βCHV in rats after oral administration, showing delayed absorption and wide tissue distribution.

This study provides the first comprehensive phylogeny of Chloropidae using genomic data, redefines classification, and reveals evolutionary insights.

The paper analyzes how phylogenetic signal, noise, and bias affect tree resolution in phylogenomics and shows their divergent scaling properties with character sampling.

The paper identifies chalk river salmon in southern England and northern France as genetically distinct and proposes they be classified as a subspecies due to local adaptation and unique genetic diversity.

The paper uses genomic data and phylogenetic methods to resolve the origins of two Satyrinae butterfly genera, finding Calisto originated from Old World ancestors and Llorenteana split early in Euptychiina.