phylogenetics / evolution

The paper introduces larch, a tool that explores the space of optimal phylogenetic trees to find more parsimonious trees and increase diversity in the set of optimal solutions.

The paper analyzes over 30,000 bacterial genomes to show that CPR bacteria have fewer ribosome biogenesis factors, suggesting evolutionary flexibility in ribosome assembly.

The paper describes a new Early Miocene rhinocerotid species from the Canadian High Arctic and presents phylogenetic hypotheses, suggesting the North Atlantic Land Bridge was crossable for mammals longer than previously thought.

This paper explores the use of tree size in phylodynamic inference, showing it provides additional insights for diversification questions not captured by shape or branch lengths alone.

This study investigates the evolutionary origins of host association and polycistronic transcription in trypanosomatids using comparative genomics across 47 genomes.

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

This paper introduces NeuralNJ, a deep learning method for phylogenetic inference that improves accuracy and efficiency by using an end-to-end framework and reinforcement learning.

The paper identifies highly recurrent multi-nucleotide mutations in SARS-CoV-2 and shows they are linked to transcription regulatory sequences, affecting computational evolutionary biology analyses.

The paper describes two new Telonemia species, highlights morphological and phylogenetic differences, and provides insights into their biology and evolutionary significance.

This paper introduces CASTLES-Pro, a method for estimating species tree branch lengths that accounts for gene duplication, loss, and incomplete lineage sorting, showing improved accuracy over existing methods.

The paper examines the phylogeography of lizards in Baja California, identifying divergence events and range expansions, particularly in Callisaurus draconoides.

This study evaluates a deep learning model for detecting mass extinctions in fossilized phylogenies, finding it slightly better than Bayesian methods but limited by simulation stochasticity and definition specificity.

This paper presents a second high-quality Denisovan genome from a 200,000-year-old molar, revealing genetic contributions from multiple Denisovan groups and refining the Denisovan genetic lineage.

The paper develops a Bayesian method with composite likelihood adjustment to improve credible interval coverage in species tree estimation under the multispecies coalescent model.

The paper examines the evolutionary history of seipin across eukaryotes, finding it conserved in the Last Eukaryotic Common Ancestor and highlighting functional divergence between yeast and human seipin.

The paper analyzes population genomics of lichens, finding that rarity and reproductive biology drive core metrics, while expression regulation genes respond to environmental factors.

The paper describes a new species of blind mole rat, Spalax lyapunovae, based on genetic, morphological, and chromosomal analyses of S. microphthalmus across its range.

This study models latency in Ebola virus using a novel phylogenetic approach, finding evidence of extended quiescence in the reservoir, which changes understanding of its evolutionary history and geographic spread.

The paper describes a new salamander species, Pachytriton, from Anhui, China, based on morphological and molecular analyses.

This study investigates the genomic and genetic factors underlying speciation and pigment pattern diversification in Danio fishes, revealing introgression, functional divergence of specific genes, and evolutionary changes in protein and regulatory sequences.

The paper uses genomic data from 186 dipteran species to show bicoid exists in non-cyclorrhaphan flies and originated in the common ancestor of Bombyliidae, Asiloidea, and Eremoneura.

The paper analyzes 27 radiations using a new fossilized birth-death model to show that clade diversity follows rise and decline dynamics driven by species-level processes rather than clade-level mechanisms.

This study investigates RIP-like mutation signatures across fungi, finding a 30-fold genome size increase in leotiomycetes linked to loss of RIP-related genes and identifying a zinc-finger protein as a novel genome defense mechanism.

Integrating 1,794 records from museum collections, literature, GBIF, and iNaturalist with COI DNA barcoding establishes a checklist of 15 Bombus species and their floral interaction networks across continental Ecuador.

This study uses simulations to show that plant longevity and overlapping generations explain phylogenetic patterns, with somatic mutations potentially exacerbating these effects.

The paper investigates the evolutionary origins of ALG1 and ALG2 mannosyltransferases, finding that ALG2 likely originated from bacterial ancestors and ALG1 homologs are exclusive to bacterial lineages.

The paper introduces a SLiM 5 model for simulating whole-genome human evolution, including sex chromosomes and mitochondrial DNA, and demonstrates its utility through simple analyses.

The paper evaluates character recoding schemes for phylogenetic analysis using a likelihood framework to assess their impact on evolutionary information.

This study presents new genome assemblies from Asymmetron and Epigonichthys, revealing phylogenetic discordance and gene innovation in cephalochordates.

This study identifies ancient S. enterica Paratyphi C DNA in 19th-century Mexico, linking it to European strains and showing its persistence in urban settings.