phylogenetics / evolution

Arborist improves tumor phylogeny reconstruction by integrating bulk DNA-seq and low-pass scDNA-seq data, outperforming existing methods on simulated and biological datasets.

This paper characterizes the complete chloroplast genome of Adansonia digitata, compares it with other Adansonia species, and places it phylogenetically within Malvaceae.

The paper surveys Caenorhabditis nematodes on Pohnpei, finds new species, and uses phylogenetics to infer that the Elegans Supergroup originated in the Americas and diversified in the Pacific before reaching Asia.

The paper identifies a new variety of Pleurotus pulmonarius in New Zealand through phylogenetic and morphological analysis, with implications for biosecurity and cultivation.

The paper identifies a hybrid lineage in the Austral podocarps using phylogenomic analyses, revealing that Podocarpus nivalis is a hybrid between P. laetus and P. lawrencei.

The paper presents telomere-to-telomere genome assemblies of a Thoroughbred horse and donkey derived from a mule, revealing insights into equid centromere evolution and plasticity.

This study reconstructs the evolutionary history of palms using 1,033 nuclear genes and fossil evidence, finding the family originated in the Early Cretaceous and diversified rapidly.

The paper identifies coding DNA sequence density as a universal predictor of chromatin compartmentalization across species, revealing its conservation over evolutionary time.

This study compares the EF-1α intergenic region across Babesia divergens isolates, identifying TA repeat variation and its potential regulatory impact on gene expression.

This study evaluates six methods for calling single-nucleotide variants from scRNA-seq data and finds that some methods provide phylogenetically informative genotype calls, with implications for understanding cancer progression.

This paper introduces a method for automatically selecting optimal discrete character models using regularization and simulated annealing, showing improved statistical performance and biological realism.

This paper introduces DICAROS, a method for ancestral shape reconstruction that outperforms existing methods by combining LDDMM and Felsensteins Independent Contrasts, and applies it to swallowtail butterflies.

This study presents a densely sampled phylogenetic analysis of Macromiidae dragonflies, revealing three major lineages and biogeographic origins across multiple regions.

The paper analyzes plasmid distribution in Mycobacterium abscessus using whole genome sequencing to show how plasmid transfer increases genomic diversity and aids in estimating bacterial contact history.

The paper examines two new loricate choanoflagellate strains that show morphological discrepancies with their genetic relatives, challenging current taxonomic classifications based on morphology.

The paper uses genomic, cytometric, and morphometric data to clarify taxonomic relationships in the Juncus bufonius complex, finding that polyploids and diploids are distinct taxa, and morphometric characters are not reliable for species delimitation.

The paper shows that mutations increasing ORF9b expression are common in SARS-CoV-2 variants and PCI sequences, suggesting ORF9b's role in viral evolution and immune evasion.

This study investigates how transposable elements and gene family dynamics contribute to diatom diversification across different scales and evolutionary timescales.

The paper introduces krepp, a k-mer-based method for phylogenetic placement of reads on large reference phylogenies, showing improved scalability and accuracy compared to alignment-based methods.

The paper introduces a sparse learning method to identify phylogenetically informative sites in alignments, showing it matches full alignment results and provides an objective metric for evaluating alignment filtering tools.

This paper introduces the covariomorph model, an extension of the covarion model for morphological phylogenetics, showing it improves accuracy by accounting for lineage- and character-specific rate variation in 50% of empirical datasets.

PEINT simulates realistic protein evolution by modeling sequence changes over time, generating functional proteins that retain enzymatic activity.

The paper identifies a new 7SL RNA-derived SINE in shrew moles, Urop, which is structurally similar to primate Alu and shows evolutionary parallels.

The paper analyzes the genomes of Golden Horde elites to confirm Genghis Khan's Y-chromosome haplogroup and trace their genetic ancestry.

This study traces the evolutionary history and dispersal of the rice bacterial blight pathogen Xoo, linking its emergence to rice domestication and trade routes.

The paper analyzes 449 SARS-CoV-2 genomic sequences from Algeria to trace viral evolution, identifying mutations, recombination events, and superspreading dynamics.

Sapling infers and summarizes tumor phylogenies from bulk data using backbone trees, demonstrating high-quality results on simulated and real data.

TriMouNet infers level-1 phylogenetic networks from multi-locus gene tree distributions, identifying reticulations with low false positive rates when gene trees are accurate.

The paper presents and analyzes the complete mitochondrial genome of the Madras hedgehog, providing insights into its evolutionary history and divergence within Erinaceidae.

This paper introduces phyloHessian, a tool using complex mixture substitution models to improve molecular clock dating accuracy for deep-time and fast-evolving lineages.