phylogenetics / evolution

Guide-tree bias of whole genome alignment can mislead phylogenomic analyses

The paper shows guide-tree bias in whole-genome alignment can mislead phylogenomic analyses and proposes a consensus alignment strategy to reduce this bias.

Sea slugs unplugged: Review of subpopulation sampling in phylogeographic studies of nudibranchs and their allies

The paper reviews subpopulation sampling in phylogeographic studies of sea slugs, finding varied sampling designs and two significant associations between sampling and genetic differentiation.

Pareto fronts reveal constraints on the evolution of ecological niches

The paper uses Pareto fronts to detect evolutionary constraints on niche-determining traits in phytoplankton, showing that trade-offs persist across scales despite differing evolutionary outcomes.

simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants

simSOMA links plant branching topology to meristem cell-lineage dynamics; in simulations, niche size and turnover drive fixation, while terminal organ growth produces most private low-frequency variants.

Mapping the Trade-Offs That Shape Mammalian Brain Network Architecture

Across 25,000 generative-model networks scored on 29 properties, 635 human and 224 mammalian connectomes cluster in one narrow niche, trading wiring economy for computational capability and robustness.

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.

Benchmarking Universal Single-Copy Orthologs for Phylogenomics: The Impact of Paralogy

This study benchmarks USCOs for phylogenomics, finding that paralogs are common in BUSCO gene sets and can affect phylogenetic accuracy.

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.

DensiTree 3: Making Sense of Pairs of Sets of Trees

DensiTree 3 is an interactive tool for comparing pairs of tree sets, providing visualizations and CCDs to assess differences in tree distributions and clade support.

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.

Misleading inference of schistosome epidemiology from ribosomal internal transcribed spacer (ITS) and mitochondrial DNA

Whole-genome SNVs from Nigerian schistosomes show cox1/ITS genotyping wrongly flags human-derived parasites as recent hybrids or zoonotic infections; they are S. haematobium with low livestock introgression.

Rapid whole genome- and annotation-based multilocus sequence typing of the fungal pathogen Histoplasma capsulatum

This paper develops and validates genome-based MLST typing for Histoplasma capsulatum using 406 genome assemblies, achieving lineage separation with >8,000 markers.

A meta-analysis of Neotropical butterflies reveals long-term signature of the Pebas wetland on Neotropical biogeography

This study uses a meta-analysis of 1,361 Neotropical butterfly species to show that the Pebas wetland selectively constrained dispersal between the Andes and Amazonia, contributing to the modern diversity imbalance.

Selfing-aware demographic inference highlights local population structure and bottlenecks in Hawaiian Caenorhabditis elegans

The paper applies a selfing-aware demographic inference method to Hawaiian C. elegans populations, revealing population structure, bottlenecks, and the impact of self-fertilization on demographic estimates.

Is level-1 blob reconstruction under the network multispecies coalescent easy?

The paper investigates whether reconstructing level-1 blobs in phylogenetic networks is easy once the tree of blobs is known, presenting a fast algorithm that achieves comparable accuracy to existing methods.

Horizontal gene transfer rivals gene duplication as a source of anti-parasitoid immune innovation in the Drosophilidae

The paper investigates anti-parasitoid immune mechanisms in Drosophilidae, finding that horizontal gene transfer of CdtB is more prevalent than melanotic encapsulation in some clades.

Sequence Generation and Phylogenetic Inference with Generative Flow Networks

This paper introduces AncestorGFN, a method using Generative Flow Networks for alignment-free sequence generation and phylogenetic inference, showing it can recover ancestral relationships and generate novel sequences.

Improved ancestral genome reconstruction using a learned gene-content grammar

This paper improves ancestral genome reconstruction by incorporating gene-content grammar, leading to more accurate and consistent reconstructions across different methods.

PartitionFinder-mAIC: Phylogenetic Partitioning using Marginal Akaike Information Criterion

PartitionFinder-mAIC improves phylogenetic partitioning by using marginal AIC, resulting in fewer partitions and better inference of green plant evolution.

Assessing the robustness of SNaQ to violations induced by high-level phylogenetic networks

This study evaluates SNaQ's performance on non-level-1 phylogenetic networks and introduces new metrics to assess structural recovery.

A large-scale evaluation of tree shape indices reveals potential pitfalls

The paper evaluates 54 tree shape indices on 45 million empirical trees, revealing rooting and size dependencies, and recommends selecting uncorrelated indices for reliable tree shape analysis.

Metric-dependent genomic diversity reveals phylogenetic and ecological structure in saproxylic beetles

The paper shows that genomic diversity metrics vary in their ability to detect phylogenetic and ecological patterns in saproxylic beetles, emphasizing the importance of denominator choice.

ntSynt-viz: Visualizing synteny patterns across multiple genomes

ntSynt-viz sorts genomes and chromosomes by synteny, normalizes strands, and draws chromosome-painting ribbon plots easier to interpret than NGenomeSyn output for human and hoverfly genomes.

Quartet-based species tree methods enable fast and consistent tree of blobs reconstruction under network multispecies coalescent

The paper introduces TOB-QMC, a method for scalable and accurate tree of blobs reconstruction under network multispecies coalescent, improving upon TINNiK in both speed and accuracy.

FigTreeKit: A Python toolkit for programmatic FigTree styling, taxonomy-aware clade auditing, and phylogenetic tree rendering

FigTreeKit provides a Python toolkit for programmatically styling and auditing phylogenetic trees, with scalability testing on large bacterial and archaeal datasets.

Computing coalescence rates for complex demographies and sampling configurations

The paper introduces demestats, a software library to compute coalescence rates for demographic models, showing improved accuracy in inferring recent population history from genetic data.

Differential Effects of Incomplete Lineage Sorting and Gene Tree Estimation Error on Gene Tree Distributions and Species Tree Inference

This study compares the effects of incomplete lineage sorting and gene tree estimation error on species tree inference using simulated and real datasets.

Partitioning amino acid substitution models by structure improves fit and meaningfully differentiates exchangeability values, but does not improve gene tree inference

The paper partitions amino acid substitution models by protein structure, improving model fit but not gene tree inference in mammals.

Local ancestry inference identifies robust evidence of selection in Neolithic Europe

Local ancestry methods on 176 imputed Neolithic genomes disagree on tract lengths; replicated meta-analysis supports selection at SLC24A5 and FADS1/2, while HLA signals look artefactual.

Sparse sampling and rare-variant depletion distort PCA visualizations of population structure: recovery with objective-guided manifold learning

Sparse or clustered sampling plus rare-variant filtering collapse PCA plots into triangles and three-ray patterns; objective-guided manifold learning on high-dimensional classic PC scores recovers obscured structure.