phylogenetics / evolution

High evolutionary and taxonomic diversity of gerbils (Gerbillus) in the Horn of Africa

This study provides genetic data on Microdillus peeli and a new lineage from the Horn of Africa, revealing it as the center of evolutionary diversity for the genus Gerbillus.

An integrative taxonomic approach reveals unexplored diversity in Croatian planarians

Degenerate COI primers combined with histology, karyology and transcriptomics raise the known Croatian freshwater planarian species from eight to sixteen and describe Dendrocoelum pigmentatum sp. nov.

A Phylogenetic Model of Established and Enabled Biome Shifts

The paper introduces a phylogenetic model, RFBS, to distinguish between established and enabled biome affinities in species evolution and applies it to flowering plants.

Bayesian inference of gene flow between sister lineages using genomic data

The paper develops a Bayesian method to detect gene flow between sister lineages, showing it has low false-positive rates and high power, and applies it to Sceloporus lizards data.

Unraveling the Genomic and Phylogenetic Complexity of the understudied microfungus Basidiobolus: Insights from 19 Newly Sequenced Genomes

This study sequenced 19 Basidiobolus genomes, revealing two major clades and cryptic species, along with diverse biosynthetic gene clusters.

A deep-time landscape of plant cis-regulatory sequence evolution

Conservatory, an orthogroup-centric conserved noncoding sequence finder, catalogs 2.3 million unique CNSs across 314 plant genomes and reveals regulatory elements older than angiosperms and seed plants.

Reconstructing the demographic history of blacklegged ticks (Ixodes scapularis) in the northern United States

This study reconstructs the demographic history of blacklegged ticks in the northern U.S. using genomic data, finding multiple independent populations that expanded after the Last Glacial Maximum.

Discovery of the closest free-living relative of the domesticated "magic mushroom" Psilocybe cubensis in Africa

The paper identifies the closest wild relative of Psilocybe cubensis in sub-Saharan Africa, P. ochraceocentrata nom. prov., and shows its divergence from P. cubensis occurred 1.5 million years ago, predating cattle domestication.

Improving the Robustness of Phylogenetic Independent Contrasts: Addressing Abrupt Evolutionary Shifts with Outlier- and Distribution-Guided Correlation

This paper introduces O(D)GC, a method to improve phylogenetic correlation analysis by detecting and handling abrupt evolutionary shifts, showing lower error rates than existing methods.

Reliable inference of phylogenomic relationship via assembly-based strategy accommodating raw reads and proteins

VEHoP infers phylogenetic trees from raw reads and proteins, outperforming assembly-free methods and enabling robust phylogenomic analysis of difficult-to-sample species.

Integrating Secondary Structure Information Enhances Phylogenetic Signal in Mitochondrial Protein Coding Genes

The paper improves phylogenetic analysis of mitochondrial protein coding genes by integrating secondary structure information using a new pipeline called TRAMPO.

HP2NET: Empowering Efficient Phylogenetic Network Analysis through High-Performance Computing

HP2NET is a framework for efficient and scalable phylogenetic network analysis using HPC, reducing runtime by up to 90.96% through parallel processing and data reuse.

CactEcoDB: Trait, spatial, environmental, phylogenetic and diversification data for the cactus family

CactEcoDB provides integrated ecological, trait, and phylogenetic data for over 1,000 cactus species to support comparative research on trait evolution and macroevolutionary dynamics.

Side-necked turtle genomes reveal chromosomal dynamics, skeletal innovation and cancer resistance

This study presents seven reference genomes of side-necked turtles, revealing chromosomal dynamics, sex chromosome evolution, and molecular mechanisms underlying skeletal innovation and cancer resistance.

Evolutionary emergence and preservation of microproteins encoded by upstream ORFs

The paper identifies conserved microproteins from upstream ORFs in yeast using Ribo-Seq and Nanopore data, showing they are subject to purifying selection.

Insight into the evolution of symbiosis in the Cupriavidus genus: high conserved symbiotic island and a patchy phylogenetic distribution.

The paper analyzes the evolution of symbiosis in Cupriavidus genus, identifying five distinct lineages and a high conserved symbiotic island with low conservation among plasmids.

Emergence of mpox in Guinea: sporadic clade IIa cases and a clade IIb upsurge

The paper reports the emergence of mpox in Guinea, identifying both clade IIa and IIb strains, with clade IIb associated with sustained human-to-human transmission.

Nested birth-death processes are competitive with parameter-heavy neural networks as time-dependent models of protein evolution

The paper compares nested birth-death processes with neural networks for modeling protein evolution, finding the former more parameter-efficient and competitive.

Phylogenomic analysis of the collagen-like BclA proteins in Clostridioides difficile

This study analyzes the conservation and variability of BclA proteins across C. difficile clades using genomic data from over 25,000 genomes, revealing clade-specific differences in bclA gene presence and structure.

SplitAligner: A Gene-Species Tree Reconciliation Framework Using Split-Based Branch Mapping

SplitAligner evaluates branch-specific concordance across genes in a species tree, identifying missingness and discordance in phylogenomic data.

The Phylogeny and the Evolution of Parasitic Strategies in Trematoda

This study reconstructs the evolutionary history of trematode parasitic strategies using mitogenomic and nuclear genomic data, finding that ancestral trematodes had direct life cycles with no intermediate hosts.

STEQ: A statistically consistent quartet distance based species tree estimation method

STEQ is a fast and accurate distance-based method for estimating species trees from gene trees, maintaining competitive accuracy while being asymptotically faster than existing methods.

Scalable mass-spectrometry-based molecular phylogeny with TreeMS2

TreeMS2 constructs molecular phylogenies from raw MS/MS data, revealing relationships based on molecular phenotype and identifying deviations from genetic-based trees.

Displacement-Optimized Tanglegrams for Trees and Networks

The paper introduces a new method for visualizing phylogenetic trees and networks by minimizing taxon and reticulate displacement, showing improved performance over existing approaches.

Detecting cryptic ghost lineage introgression in four-taxon genomic datasets

This paper introduces ghostbuster, a statistical test to detect ghost lineage introgression in genomic data, showing it accurately identifies such events in simulations and corrects a previously misinterpreted introgression in Brassicaceae.

High-throughput phenomics of global ant biodiversity

Antscan provides 2,193 standardized whole-body 3D synchrotron micro-CT datasets across 792 ant species (212 genera), pairing morphological volumes with automated deep-learning segmentation and genome sequencing projects.

Arborist: Prioritizing Bulk DNA Inferred Tumor Phylogenies via Low-pass Single-cell DNA Sequencing Data

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

Complete chloroplast genome of African Baobab (Adansonia digitata L.): structural characterization, comparative genomics, and phylogenetic placement within Malvaceae

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

Caenorhabditis diversity on Pohnpei, Micronesia, provides evidence that the Elegans Supergroup has its roots in the Americas and diversified in the Pacific en route to Asia

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.

Multi-gene phylogeny and morphology of Pleurotus in Aotearoa New Zealand reveal a new variety of Pleurotus pulmonarius

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