phylogenetics / evolution

Vicariance and dispersal shape the colonization history of the Galapagos carpenter bee, Xylocopa darwini

This study examines the colonization and diversification of Xylocopa darwini across Galapagos islands, finding long-term isolation, divergence between eastern and western islands, and recent founder events.

neissflow: Streamlining Genomic Epidemiology of Neisseria gonorrhoeae with Nextflow

neissflow is a Nextflow pipeline for analyzing Neisseria gonorrhoeae genomes, achieving high accuracy in species identification, AMR profiling, and phylogenetic analysis.

Evolutionary dynamics of the Timopheevii wheat lineage

The paper presents genomic resources for the Timopheevii wheat lineage, revealing evolutionary dynamics including homoeologous exchange, genome instability, and geographic range expansion.

Statistical Inconsistency of Error-correction Objectives for Perfect Phylogenies

The paper shows that error-correction objectives for perfect phylogenies are statistically inconsistent, often favoring incorrect trees over the true one in simulated data.

An active-matrix digital microfluidic platform for simultaneous short- and long-read viral genomic surveillance

This paper develops a digital microfluidic platform that enables simultaneous short- and long-read viral genomic surveillance with improved efficiency and accuracy.

Genomic diversity of elm trees for future treescapes

The paper analyzes genomic diversity in elm trees to assess the genetic potential of resistant cultivars for restoration.

Persistent, Multi-Species Outbreaks and Long-Range Transmissions of a Measles-Like Virus

The paper shows CDV persists in Arctic foxes for over a decade and spreads across species and regions, connecting North America to Eurasia.

338 coleopteran genomes reveal exceptional rearrangement variation compared to other insect orders

From 338 beetle genomes, eight ancestral linkage groups were inferred; rearrangement rates vary widely, peaking in major radiations, and the X chromosome dates to Holometabola's ancestor.

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.

Evolutionary dynamics of the arthropod moulting machinery

This study presents a comparative genomic analysis of arthropod moulting machinery across four subphyla to understand evolutionary dynamics of key gene families.

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

This study introduces CLOAK, an MSA cleaning algorithm that improves gene tree inference by removing alignment errors while preserving informative residues.

Towards an evolutionary baseline model of Plasmodium falciparum for population-genomic inference

The paper identifies key components for building a baseline evolutionary model of Plasmodium falciparum to better understand genomic variation and drug resistance.

Evolutionary dynamics of sex chromosomes and candidate sex-determining genes across the beetle phylogeny

This study examines sex chromosome evolution in beetles using genome assemblies, finding conserved X regions, variable Y chromosomes, and independent neo-X and neo-Y formation.

Optimization of High Molecular Weight DNA Extractions from Dried, Museum-Grade Insects Enables Long-Read Sequencing, Phylogenetics, and Methylation Profiling

This paper develops a DNA extraction protocol for museum-grade insects, enabling long-read sequencing, phylogenetics, and methylation profiling from degraded samples.

HapNet: a new Python package for automated population-aware haplotype network analysis and visualization

HapNet automates haplotype network construction and visualization from FASTA files, incorporating population metadata for population-aware analysis.

Monotremes provide novel insights into evolution of the DMRT gene family in vertebrates

The paper analyzes DMRT gene family evolution in monotremes and other vertebrates, identifying conserved genes and unique features in monotremes.

Geographic structuring of genetic variation differs across two contact zones in the Diglossa carbonaria superspecies

The paper examines genetic differentiation and hybridization in three closely related bird taxa at contact zones using RADSeq data, finding weak genetic differentiation and evidence of introgressive hybridization in one zone.

Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens

Standardized Snakemake pipelines on GitHub Actions fetch open sequence data, curate it, and publish daily or weekly updated phylogenies for 21 viruses and Mycobacterium tuberculosis.

Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid Proterozoic

The paper uses molecular clocks and diversification models to show steady eukaryote diversification starting in the mid-Proterozoic, challenging the view of limited innovation during this era.

Integrating lineage-specific and universal genomic probes illuminates phylogenetic relationships and molecular evolution in Sauvagesieae (Ochnaceae)

The paper uses dual-hybridisation probes to reconstruct phylogenetic relationships in Sauvagesieae, finding evidence of polyploidisation and hybridisation affecting tree resolution.

Three phylogenetic metrics are compatible with natural evolution of the earliest SARS-CoV-2 sequence

The paper develops a method to detect recombination breakpoints and signs of human-made manipulation in viral sequences, finding no evidence of such manipulation in SARS-CoV-1, MERS-CoV, or SARS-CoV-2.

An Empirical Bayes approach for the study of phenotypic evolution from high-dimensional data

The paper introduces an Empirical Bayes framework for analyzing high-dimensional trait evolution, showing it is faster and more efficient than existing methods.

Invasion history of Aedes (Stegomyia) albopictus into Mesoamerica based on mitogenomes and Wolbachia symbionts: Multiple introductions with temperate origins.

This study traces the invasion history of Aedes albopictus in Panama using mitogenomes and Wolbachia, finding multiple introductions from Asia via the Panama Canal rather than overland routes.

Plastome phylogenomics of the tribe Spermacoceae (Rubiaceae): taxonomic implications and a key to the genera

This study presents the first plastome-scale phylogenomic analysis of the tribe Spermacoceae, clarifying generic boundaries and supporting taxonomic revisions.

Shifts in Genetic Diversity of Porcine Reproductive and Respiratory Syndrome Virus 2 in Vietnam Before and After African Swine Fever: Increased Diversity and Novel Sub-lineages

This study analyzes shifts in PRRSV-2 genetic diversity in Vietnam before and after ASF, finding increased diversity and novel sub-lineages.

One Health genomic surveillance reveals structured urban rabies transmission and major surveillance gaps

The paper uses genomic surveillance to analyze rabies transmission in Arequipa, revealing structured urban spread and significant surveillance gaps.

Evolutionary dynamics of Aegilops revealed through comparative genome assembly of all 25 species

The paper presents high-quality genome assemblies for all 25 Aegilops species, revealing evolutionary dynamics and gene content variation through comparative genomics.

GenCore: Genomic distance estimation using Locally Consistent Parsing

GenCore uses Locally Consistent Parsing to sketch and estimate genomic distances between closely related large genomes, successfully reconstructing simulated progression trees and recapitulating primate phylogeny.

Making the most out of it: shallow genome-skimming possibilities for the systematics of prickly lineages of Solanum (Solanaceae)

This study evaluates shallow genome-skimming for phylogenetic inference in Solanum, finding it effective for SNP datasets but limited in recovering complete mitochondrial genomes and low-copy nuclear genes.

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.