phylogenetics / evolution

Phlag: Scalable detection of genomics regions with unexplained phylogenetic heterogeneity

Phlag detects genomic regions with inconsistent evolutionary processes by modeling gene trees as a stochastic process along the genome.

Principal Components Analysis fails to recover phylogenetic structure in hominins

This paper shows that PCA fails to recover phylogenetic structure in hominin datasets, highlighting flaws in using PCA for phylogenetic inference.

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.

High-resolution insights into the geographic differentiation and hybridisation of Odontobutis gobies through integrated eDNA and SNP analyses

This study uses integrated eDNA and SNP analyses to reveal geographic differentiation and hybridization in Odontobutis gobies, showing hybrid origin of O. hikimius.

Latitude, not geography, globally structures Oscheius tipulae into three deeply divergent lineages

The paper analyzes genome-wide variation in Oscheius tipulae and finds three deeply divergent lineages structured by latitude rather than geography.

Interspecies variation of 45S ribosomal DNA in vertebrates

This study analyzes interspecies variation in the 45S rDNA locus across vertebrates, revealing lineage-specific differences in organization, copy number, and sequence evolution.

Genomic Distortion of Jawed Vertebrate Phylogeny

This study investigates how genomic evolution affects phylogenetic relationships and divergence times in jawed vertebrates, showing that rapid radiations and varying mutation rates obscure evolutionary timelines.

Revisiting the genome assembly of Lupinus species reveals differential diploidization after a shared whole-genome duplication

The paper corrects genome assemblies of two Lupinus species, revealing differential diploidization after a shared whole-genome duplication across six Lupinus species.

Puzzling parasitic plants: phylogenetics and classification of Santalales revisited

The paper revisits the phylogenetics and classification of Santalales, finding better-supported relationships and proposing a new taxonomic framework.

Towards a Unified Exact Solution of Rearrangement Small Parsimony for Natural Genomes

This paper solves the exact Small Parsimony Problem by introducing a cost to indel operations, enabling tractable solutions for small and recently related genomes.

CHLOROPLAST GENOME AND PHYLOGENETIC ANALYSIS OF KATMON (Dillenia philippinensis Rolfe), A PHILIPPINE ENDEMIC FRUIT

This study sequences and analyzes the chloroplast genome of Dillenia philippinensis, revealing its structure, gene content, and phylogenetic relationships with related species.

Global population structures and demographic history of Suillus luteus, a pine co-introduced ectomycorrhizal fungus associated with exotic forestry and invasion.

This study analyzes the population genetics of Suillus luteus, showing all introductions originated from Europe and showing genetic differentiation in introduced regions linked to forestry practices.

Incremental AMR acquisition driving successive genotype replacements and the rise of extensively drug resistant (XDR) Shigella sonnei in Australia over 20 years.

This study tracks the rise of extensively drug-resistant Shigella sonnei in Australia over 20 years, linking genotype changes to antimicrobial resistance and public health threats.

biomeStat: Using Agentic AI for Scalable Genomic Epidemiology Demonstrated Through End-to-End Analysis of 1,000 Asian Dengue Virus Genomes

biomeStat automates genomic epidemiology analysis of 1,000 Dengue virus genomes, revealing immune escape sites and conserved drug targets in under 24 hours.

No silver bullet: Patterns of macrosynteny recapitulate systemic conflicts in the higher-level relationships of the arachnids

The paper uses genomic data to investigate arachnid phylogeny, finding that ancient whole genome duplications and fusion-with-mixing events do not resolve conflicts in higher-level relationships.

First outbreak of Lumpy Skin disease in Catalonia, Spain, 2025-2026

The paper reports two LSDV genomes from the first LSD outbreak in Catalonia, Spain, placing them in clade 1.2 and linking them to recent European and African strains.

Ecological axes of skull diversification in a massive 1 vertebrate radiation

The paper analyzes skull diversification in eupercarian fishes, showing habitat and trophic ecology independently shape skull shape, with rapid evolution in certain clades and convergence in freshwater lineages.

Multiple evidence supporting a novel species amid complex phylogenomic discordance: a case of Indian Ledebouria based on Angiosperms353 target capture sequencing

The paper uses Angiosperms353 target capture sequencing to clarify phylogenetic relationships among Indian Ledebouria species, identifying L. hyderabadensis as a distinct species and other accessions as incipient species.

The Shifting Tempo of Evolution: Mapping Site-Specific Rate Shifts Across the Tree of Life

This study maps lineage-specific rate shifts in protein sequences across the tree of life, finding they are widespread and influenced by evolutionary ancestry and phylogenetic depth.

The first reference genome assembly of the Chilean sea fig (Carpobrotus chilensis)

The paper presents a draft genome assembly of Carpobrotus chilensis, revealing low heterozygosity, high transposable element content, and low sequence divergence from its invasive relative C. edulis.

From Nuisance to Signal: Leveraging Close Relatives in Biobank-Scale Demographic Inference

This paper evaluates the impact of retaining close relatives on demographic inference using IBD-based methods and finds that retaining relatives reduces bias in Ne estimates.

GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics

GTRspmix improves protein phylogenetics by incorporating multiple exchangeability matrices into mixture models, enhancing fit and reducing long-branch attraction artifacts.

Genetic structures of the Japanese stone loach Barbatula oreas (Cypriniformes: Nemacheilidae) in Sakhalin and Hokkaido: back dispersal from Hokkaido to Sakhalin

The paper investigates the genetic structure and phylogeographic history of Barbatula oreas in Hokkaido and Sakhalin, finding back dispersal from islands to the mainland and challenging the conventional dispersal paradigm.

A Practical and Cost-Effective Approach to Long-Fragment eDNA Sequencing for High-Resolution Genetic Diversity Assessment

This paper develops a low-cost method for long-fragment eDNA sequencing to assess genetic diversity, finding it effective for high-resolution phylogeographic analysis.

Summarizing Evolutionary Trajectories from Phylogenetic Character Maps of Discrete Traits

This paper introduces a framework to summarize evolutionary trajectories of discrete traits using trajectory trees, applied to lizard biogeography and ecomorph evolution, revealing more unique paths than expected under standard models.

A review of Sisyphini Dung Beetles (Coleoptera: Scarabaeinae) endemic to Mauritius: insights from subfossil evidence and phylogenetic analysis

This study reviews Nesosisyphus dung beetles in Mauritius, identifies a new extinct species, and uses phylogenetic analysis and niche modeling to assess their extinction and historical distribution.

Co-Circulation of Multiple Kolmiovirus Lineages Through Vertebrate Evolution

This paper identifies novel kolmioviruses in vertebrates, showing multiple lineages co-circulated through vertebrate evolution, with HDV-HBV association emerging recently.

Phylogenetic tree inference using generative models

This paper introduces BetaInfer, a generative model for phylogenetic tree inference that maps unaligned sequences to trees, achieving competitive performance compared to traditional methods.

The phylogenetic signal of extinction through the rise and fall of early vertebrates: field of bullets or clustered strike?

This study examines how extinction patterns varied over time in early vertebrates, showing shifts from clustered to overdispersed extinction during key evolutionary periods.

Better data, better trees: GenBank-GISAID deduplication and source-specific artifact masking in viral genomics

The paper presents tools to harmonize viral genomic data across repositories and mask lab-specific artifacts, improving phylogenetic analysis accuracy.