Bayesian inference

Bayesian phylogenetic inference accounting for recombination in whole bacterial genomes

This paper introduces ClonalFrame2, a Bayesian method for phylogenetic inference in bacteria that accounts for recombination, showing improved accuracy in simulated and real datasets.

Described eukaryotic species in published species-level phylogenies: placement by molecular data, dates and date uncertainty

The paper analyzes published eukaryotic phylogenies to assess molecular placement, dating, and uncertainty across species groups.

Bayesian Variable Selection Approaches to Identifying Selection in Evolutionary Datasets

This paper introduces a Bayesian variable selection method for identifying selection in phylogenetic datasets, showing it outperforms Dirichlet-process models and avoids phantom selection artifacts.

Bayesian phylogenetics with incomplete lineage tracing data

This paper introduces a Bayesian framework to improve phylogenetic inference from sparse lineage tracing data by modeling barcode loss, showing it enhances accuracy and recovers higher growth rates than standard filtering methods.

The limits of Bayesian estimates of divergence times in measurably evolving populations

This paper examines the limits of Bayesian divergence time estimates in microbial evolution, finding that uncertainty scales with distance to calibration points rather than absolute age.

Bayesian inference of global land plant diversification dynamics across the Phanerozoic

This study uses Bayesian methods to analyze land plant diversification dynamics across the Phanerozoic, identifying key patterns and drivers of diversification and extinction.

Full-Support Conditional Clade Distribution for Bayesian Tree Topology Testing

This paper introduces KRegCCD, a new Bayesian phylogenetic model that improves posterior tree estimation and enables topology testing by providing full support over tree space.

Fast pace of life is associated with host status in small mammals, despite pervasive surveillance bias

Arenavirus and hantavirus surveillance in small mammals tracks night-lights and accessibility; after adjusting for effort, fast-lived and synanthropic species are somewhat more often detected as hosts.

Synchronizing speciation, extinction, and dispersal to island paleodynamics through Bayesian phylogenetics in a Hawaiian plant radiation

The paper introduces a Bayesian phylogenetic framework to infer divergence times, ancestral ranges, and diversification rates in Hawaiian plants without fossil calibration.

Ultra-deep duplex sequencing reveals unique features of somatic evolution in the normal tissues of a family with Li-Fraumeni syndrome

Duplex sequencing of a Li-Fraumeni family links germline TP53 p.R181H to higher neutral-region mutagenesis and weaker blood TP53 selection, plus recurrent p.R248Q/W hits across proband tissues.

Minimally invasive monitoring of clonal evolution through integrated single cell and ctDNA analysis

cfClone, a Bayesian model, deconvolves cfDNA whole-genome sequencing using scWGS-derived haplotype-specific clone copy-number profiles to estimate tumour fraction, clonal prevalence, and flag missed clones.

Evolution of multicellularity and reproductive strategies in yellow-green algae (Xanthophyceae, Heterokontophyta)

This study reconstructs the evolution of multicellularity and reproductive strategies in Xanthophyceae using phylogenomic data, showing multiple transitions to multicellularity linked to changes in propagule types.

A hierarchical clock-mixture model for Bayesian phylogenetic dating

This paper introduces a hierarchical clock-mixture model for Bayesian phylogenetic dating to better handle uncertainty in clock choice and improve timescale estimation.

Ancient Rapid Radiation Underlies Persistent Phylogenomic Conflict in Early Collembola Diversification

This study resolves phylogenetic conflicts in Collembola by showing ancient rapid radiation and incomplete lineage sorting, supporting Poduromorpha as the earliest-diverging lineage.

Indirect genomic effects shape cancer risk across species

This study identifies genes linked to cancer risk variation across species, showing indirect effects on body size dominate cancer suppression, while direct effects increase tumour prevalence.

A global map for introgressed structural variation and selection in humans

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

Replaying germinal center evolution on a quantified affinity landscape

Across 119 monoclonal germinal centers, B cell affinity rises reliably despite divergent phylogenies. Selection is noisy but persistent; mutability limits exploration. A DMS-based landscape shows saturating fitness and survivorship biases.

PHYFUM: Phylogenetic Reconstruction of Normal and Pre-malignant Tissue Evolution Using Fluctuating Methylation

PHYFUM reconstructs the evolutionary history of normal and pre-malignant tissues using methylation data, revealing early gland divergence in the gut and later divergence in the endometrium.

Parallel algorithms for phylogenetic inference under a structured coalescent approximation

The paper introduces parallel algorithms to improve the computational efficiency of structured coalescent models for phylogeographic analysis, enabling faster and larger-scale studies of pathogen spread.

The conquest and diversification of leafy spurges across the Holarctic and beyond: biogeography and evolution of life-history of Euphorbia subgenus Esula

This study investigates the biogeography and evolution of life-history traits in Euphorbia subgenus Esula, showing that perenniality and range expansion are linked to diversification.

Efficient Bayesian Phylogenetics under the Infinite Sites Model

The paper introduces inPhynite, an efficient Bayesian phylogenetics algorithm under the infinite sites model, achieving 225x speedup without accuracy loss on large datasets.

Cross-species transmission of human hepatitis B virus to wild Neotropical primates

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.

Mixture Models Unveil the Origin of the Enigmatic Satyrine Butterfly Genera Calisto and Llorenteana (Lepidoptera, Nymphalidae, Satyrinae).

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.

Estimating Bayesian phylogenetic information content using geodesic distances

The paper introduces a Bayesian measure of phylogenetic information content using geodesic distances and demonstrates its application with simulated and empirical examples.

Bayesian inference of gene flow between sister lineages using genomic data

The paper develops a Bayesian method to detect gene flow between sister lineages, showing it has low false-positive rates and high power, and applies it to Sceloporus lizards data.

The Phylogeny and the Evolution of Parasitic Strategies in Trematoda

This study reconstructs the evolutionary history of trematode parasitic strategies using mitogenomic and nuclear genomic data, finding that ancestral trematodes had direct life cycles with no intermediate hosts.

Functional response predicts invasiveness but not trophic impact

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.

PhyloSOLID: Robust phylogeny reconstruction from single-cell data despite inherent error and sparsity

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

Integrating fossils samples with heterogeneous diversification rates: a combined Multi-Type Fossilized Birth-Death model

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.

Bayesian neural networks enable inference of complex phylodynamic processes

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.