phylogenetics / evolution

QRAFT: Scaling coalescent-based species tree inference to one million taxa

QRAFT efficiently infers species trees for up to a million taxa using coalescent-based methods, outperforming existing tools in speed and memory usage.

Rates of molecular and morphological evolution are uncoupled across the eukaryote Tree of Life

The paper investigates correlations between molecular and morphological evolutionary rates across eukaryotes and finds little evidence of a link, suggesting differing evolutionary dynamics at genomic and phenotypic levels.

Adaptation and conservation of turtle visual opsins over a deep phylogenetic divergence

This study investigates visual opsin evolution in turtles using transcriptomic and genomic data from 59 species, revealing conserved sequences and habitat-driven selective pressures.

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.

Convergent genome- and gene-level constraints shape repeated environmental adaptation in grasses

This study identifies convergent genomic and gene-level constraints in grasses adapting to extreme environments using phylogenomic data and large language models.

Evolutionary Coupling of Flagellar Motility and Type VI Secretion Systems Across Bacteria

The paper investigates the evolutionary relationship between flagellar motility and bacterial secretion systems, finding strong coupling with T6SS but not bacteriocins.

In silico codon optimization and phylogenetic analysis of various strains of Sapovirus

The paper optimizes codon usage for Sapovirus VP1 and VP2 genes in Escherichia coli and performs phylogenetic analysis of twelve human strains.

Genomic expansion in the dark: A repeat-rich genome of a cave-dwelling remipede sheds light on the evolution of the hexapod sister group.

This paper presents the first high-quality genome assembly of a cave-dwelling remipede, revealing a repeat-rich genome with extensive gene family turnover and phylogenetic signals.

H5N5 virus transmission is driven by repeated cross-Atlantic introductions and transmission among high latitude seabirds

This study shows H5N5 viruses have been repeatedly introduced across the Atlantic by high latitude seabirds, with more frequent introductions in fall and spring, and a distinct ecology from H5N1.

DGM Is Dead; Long Live DGM-Star! A Quantization-Theoretic Approach to Gamma Rate Discretization

The paper introduces a new method to discretize Gamma rate distributions in phylogenetics, reducing branch length bias compared to the standard DGM.

Speciation, sexual selection, and the macroevolution of cricket mating signals

This study shows that mating signal traits involved in species recognition diverge rapidly during speciation, while traits involved in sexual selection do not, challenging the idea that sexual selection drives interspecific divergence.

The globally dispersed sun-coral species is _Tubastraea coccinea_ (Cnidaria: Anthozoa)

The paper resolves taxonomic confusion in sun corals by combining molecular phylogenetics and genome assemblies, revealing T. coccinea as the cosmopolitan species and T. tagusensis as endemic to the Galapagos.

A 4,000-year genomic history of Bantu speakers from the Congo rainforest

This study uses genomic data from ancient and present-day individuals to trace the 4,000-year demographic history of Bantu speakers in the Congo rainforest, revealing early dispersals and a population crisis.

Mobile genetic elements accompany the emergence of clonal crop lineages from weed-associated populations of Xanthomonas campestris

The paper analyzes Xanthomonas campestris strains from weed and crop hosts to show that mobile genetic elements accompany the emergence of clonal crop lineages and are present in diverse weed-associated strains.

Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration

Region-stratified scRNA-seq of 607,370 cells plus 500-gene MERFISH maps adult Danionella cerebrum cell types body-wide, revealing fibroblast Hox and limb-identity programs and telencephalon regeneration dynamics.

A single freshwater invasion gave rise to the world's dominant freshwater fish group

The paper challenges the hypothesis of multiple freshwater invasions in otophysan fish by showing that a single invasion is more likely, based on phylogenetic and biogeographic analyses.

Gene tree conflict between genomic and functional partitions impacts phylogenetic inference in Zygophylloideae

This study investigates gene tree conflicts in Zygophylloideae by analyzing chloroplast and nuclear ribosomal data to understand challenges in phylogenetic inference.

Phylogenetic position and expanded host range of the photosymbiont Brandtodinium nutricula (Peridiniales, Dinophyceae)

This study identifies the phylogenetic position of Brandtodinium nutricula and shows its free-living abundance in the ocean, challenging previous assumptions about its symbiotic exclusivity.

Cave-dwelling Planariidae in Croatia exhibit differing levels of cave trait evolution

This study examines cave-dwelling planariids in Croatia, revealing multiple genera, increased diversity, and independent cave colonization events, highlighting convergent evolution of cave traits.

Durophagous adaptations in a new crocodyliform from the Santonian of Hungary and a systematic reassessment of European Cretaceous atoposaurids

The paper describes a new crocodyliform species from the Santonian of Hungary and reassesses the taxonomy of European Cretaceous atoposaurids, finding potential polyphyly in Theriosuchus.

Genomic detection of domoic acid biosynthesis uncovers expanded toxigenic diversity across Pseudo-nitzschia diatoms

The paper identifies genomic features of domoic acid biosynthesis in Pseudo-nitzschia diatoms, revealing expanded toxigenic diversity and environmental expression patterns.

Traits and hidden states: is self-fertilization associated with rates of diversification across mating and sexual systems?

The paper examines how mating and sexual systems affect diversification rates across 18 plant families, finding that sexual systems better explain diversification than mating systems.

Horizontal transfer of an antimicrobial peptide across insects

The paper identifies horizontal gene transfer of the Drosomycin antimicrobial peptide gene across insect species, suggesting HGT contributes to immune system novelty and defense capabilities.

Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations

This study presents the first comprehensive phylogenomic analysis of Cypriniformes, establishing a robust backbone topology and identifying unresolved conflicts in evolutionary relationships.

A New Information Theoretic Approach Shows that Mixture Models Outperform Partition Models for Phylogenetic Analyses of Amino Acid Data

The paper compares mixture and partition models for phylogenetic analyses using the mAIC and finds mixture models consistently outperform partition models.

Phylogenomic screening reveals idsA2 loss conferring nitroimidazole cross-resistance in Mycobacterium tuberculosis

A length- and mutation-load-corrected homoplasy screen of 1,813 MDR-TB genomes flags idsA2; its loss raises pretomanid MIC fourfold, delamanid and ethambutol twofold, via isoprenoid flux redirection.

Pygopods are an exceptional radiation of snake-like geckos

This study shows that pygopods, limbless geckos, have undergone similar evolutionary adaptations to snakes, with exceptional morphological and dietary evolution despite limited species diversity.

Once in a blue moon: an unexpected evolutionary route to blue floral pigmentation in orchids

The paper investigates the genetic basis of blue floral pigmentation in orchids, finding an unexpected pathway involving duplicated genes and regulatory changes rather than the expected CYP75A pathway.

Global biogeography of geckos (Squamata: Gekkota) reveals Old-World origins and region-specific heterogeneity in diversification

This study investigates gecko biogeography and diversification, finding Old-World origins and region-specific diversification patterns without evidence of mass extinctions.