phylogenetics / evolution

Living representatives of the spiralian ancestral karyotype revealed by two Lima genomes

The paper reports two Lima species with a 20-chromosome karyotype matching a proposed ancestral spiralian karyotype, revealing conserved synteny and lineage-specific fusions.

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.

Phylogenetic evidence for the emergence of bacterial σ-factors by domain fusion

The paper uses phylogenetic analysis to show that bacterial σ-factors evolved from single-domain DNA-binding transcription factors through domain fusion.

Porcine epidemic diarrhea virus Whole-Genome Diversity Reveals Divergence of Contemporary Populations in the United States

This study analyzes complete PEDV genomes to reveal temporal genetic differentiation and recombination in US PEDV populations, expanding the known geographic distribution of S1 clades.

Multidimensional divergence supports parapatric speciation along an elevational gradient in ground-dwelling frogs on an oceanic island

This study shows that ecological divergence along an elevational gradient in frogs can drive parapatric speciation despite geographic continuity.

Genome-wide parallelism in divergence and diversity across three Hydrophis sea snake species

This study examines genomic divergence and diversity in three Hydrophis sea snake species, finding shared demographic patterns and linked selection, with chemosensory genes showing elevated diversity.

Sperm length ornamentation associates with survival and sterility after heatwaves among Drosophila species

This study finds that longer sperm in Drosophila species correlates with higher heat survival but greater heat-induced sterility, linking sexual selection to climate resilience and infertility risks.

Anvaya: phylogenomic analysis of chromosome fusion-and-mixing characters and detection of shared whole-genome duplication

Anvaya analyzes chromosome fusion and mixing events to infer phylogenetic trees and detect whole-genome duplications using synteny data.

Unexpected excess heterozygosity in a threatened, mycoheterotrophic, self-pollinating orchid

The paper investigates excess heterozygosity in the self-pollinating orchid Corallorhiza bentleyi, finding overdominance likely explains the phenomenon despite selfing and small population size.

Morphological evolution and phylogeny are unlinked in Hawaiian Doryopteris (Cheilanthoideae: Pteridaceae)

The paper uses genome-wide sequencing to study the evolutionary relationships and biogeography of Hawaiian Doryopteris, finding that phylogeny is more linked to geography and climate than morphology.

Taking a BREATH (Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories) to simultaneously infer phylogenetic and transmission trees for partially sampled outbreaks

BREATH simultaneously infers phylogenetic and transmission trees for outbreaks using sequence data, improving resolution and origin timing estimates in a tuberculosis outbreak.

Protein response to deleterious episodes of GC-biased gene conversion in mammals of different Ne

The paper investigates post-GC-biased gene conversion (gBGC) compensatory evolution in mammals, finding evidence in non-primate taxa but not in primates.

A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

Genomic Diversity, Host Associations, and Tissue Tropism of Hydrangea Ringspot Virus: A Global and Regional Perspective

This study characterizes the genomic diversity, host associations, and tissue tropism of Hydrangea ringspot virus (HdRSV) using transcriptomic data from multiple Hydrangea species and cultivars.

Posterior simulation-based calibration tests of phylogenetic dating methods

This study uses posterior simulation-based calibration to assess phylogenetic dating methods in BEAST 2, finding good calibration but limited precision in node age estimates.

Cross-species convergence of surface polysaccharides shapes the virulence of an atypical carbapenem resistant uropathogenic Escherichia coli clone

The paper identifies a new carbapenem-resistant E. coli clone, ST361, associated with UTI and shows its virulence is linked to surface polysaccharides and mobile genetic elements.

Distinct mechanisms of CNV formation at the human 15q13.3 locus

The paper identifies distinct mechanisms of CNV formation at the human 15q13.3 locus, showing that non-allelic homologous recombination is the primary mechanism, influenced by inversion polymorphisms and population-specific susceptibility.

D-plus: Beyond the D-statistic -- Accurate Detection and Characterization of Introgression Despite Among-Lineage Rate Variation

D-plus improves introgression detection by addressing rate heterogeneity and ghost lineages, re-analyzing Jaltomata data to challenge prior interpretations.

Origin and evolution of acrocentric chromosomes in human and great apes

The paper identifies evolutionary processes in acrocentric chromosomes of great apes, including repeat enrichment, inversion, and gene family amplification, with implications for human genomic instability.

Evolution of membrane rotary ATP synthases: A trade-off between the net productivity and mechanistic stability?

This study investigates the evolution of rotary ATP synthases, finding that efficiency gains in F-ATPases came at the cost of mechanistic stability, while lateral gene transfers contributed to the diversification of A-ATPases.

Insights into the molecular systematics of montane voles of the Western Himalayan Mountains

The paper analyzes mitochondrial and nuclear DNA sequences of Kashmir voles to revise their taxonomy and phylogenetic placement within the arvicoline family.

A unified framework reveals how evolutionary scale and abundance weighting shape phylogenetic community structure

The paper introduces qiMPD, a framework for analyzing phylogenetic community structure with tunable scale and abundance weighting, showing its impact on local and broad-scale patterns in wastewater microbiomes.

Ancient mitogenomes reveal unexpected diversity in Madagascar's extinct hippopotamuses

This study uses ancient mitochondrial genomes from Malagasy hippos to reveal unexpected diversity and a complex diversification history, challenging traditional taxonomy and showing a recent radiation of large-bodied island mammals.

The olfactory ventricle: an overlooked and evolutionarily conserved feature of the mammalian brain

The paper identifies the olfactory ventricle as an ancestral and conserved feature in mammals, showing its persistence into adulthood and conserved cellular organization across species.

Towards an understanding of the taxonomy of the Eurasian montane riparian genus Myricaria (Tamaricaceae) through Angiosperms353 herbariomics

This study uses phylogenomic analysis to clarify the taxonomy of the genus Myricaria, identifying two infrageneric sections and synonymizing several species.

Within- and between-host dynamics of highly pathogenic avian influenza in domestic birds from Pennsylvania farms and live bird markets

The paper analyzes within- and between-host dynamics of H5 avian influenza in domestic birds and live bird markets, revealing viral evolution, transmission patterns, and risk factors for human spillover.

Convergent and divergent patterns of holobiont evolution in co-distributed chemosynthetic symbioses

The paper examines convergent and divergent patterns of holobiont evolution in co-distributed chemosynthetic symbioses, finding eco-geographical barriers and convergent adaptations in symbiont traits.

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.

Statistical inference of virus evolution using ancestral recombination graphs

This paper develops ARG-based methods to analyze virus evolution, showing EBV coalesces predominantly inter-host and revealing gene-level selective structure.

Hiding in plain sight: rare Bacillus cereus group species are present among unassembled metagenomic samples in public databases

The paper identifies rare Bacillus cereus group species in unassembled metagenomic samples, revealing their potential geographic distribution and genomic diversity.