phylogenetics / evolution

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.

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.

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.

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.

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.

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.

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.

CTCF gradually acquires novel function modalities during bilaterian evolution

This study investigates how CTCF's functional properties evolved across bilaterian species, revealing gradual changes in its ability to regulate chromatin structure and transcription.

Statistical analysis provides new insights into patterns and mechanisms of the WANCY hotspot on vertebrate mitochondrial genomes

The paper uses statistical analysis of mitochondrial genome data to identify convergent rearrangements in the WANCY region, suggesting it is a TDRL hotspot with higher convergence frequency than previously thought.

Phenotypic and genomic changes associated with the evolutionary loss of heterostyly in primroses

The paper investigates the genetic and phenotypic changes associated with the loss of heterostyly in Primula boveana, revealing a disrupted CYP gene and developmental shifts leading to autonomous selfing.

Molecular Data From Herbarium Specimens Reveal A Potential Extirpation of Azolla microphylla From California

The paper analyzes molecular data from historical herbarium specimens and modern samples to assess the status of Azolla species in California, finding potential extirpation of Azolla microphylla.

Phylogenomic Characterization of Two Alternaria Lineages Associated with Cotton Leaf Spot in Tennessee

The paper identifies two phylogenetically distinct Alternaria lineages associated with cotton leaf spot in Tennessee, confirming one as a causal agent.

Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals

EZHIP, a PRC2 inhibitor, arose on the placental mammal X chromosome, evolves under positive selection in primates, and duplicated, including a testis-expressed primate paralog, EZHIP2, whose gorilla copy inhibits H3K27me3.

Testing Thirty Years of Hypotheses: Ancient Trout-Salmon Introgression and Limited Pre-Colonial Gene Flow Between Rainbow and Cutthroat Trout Shaped Pacific Salmonid Evolution

This study tests hypotheses about ancient introgression and gene flow in Pacific salmonids, finding introgression between trout and salmon ancestors but not between trout lineages.

A Sense of Direction: Detecting Natural Selection Across Non-Stationary Genomes

dFEL extends FEL to model lineage-specific GC/AT drift as per-branch mixtures of three shared regime matrices, correcting selection calls at 1%–4% of boundary codons.

Evolution of histone mRNA 3' end processing machinery in eukaryotes

This study reconstructs the evolution of histone mRNA 3' end processing machinery across eukaryotes, revealing broader conservation of SLBP and related factors than previously thought.

Global delimitation of Cyanoboletus, Cacaoporus and Cupreoboletus (Basidiomycota: Boletaceae)

This paper redefines the genera Cyanoboletus, Cacaoporus, and Cupreoboletus based on phylogenetic analysis of ITS sequences, identifying new species and clarifying taxonomic boundaries.

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.

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.

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.

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.

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.

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.

Paleogenomic time series reveal past population dynamics and their relevance for the conservation of the Alpine ibex

This study uses ancient genomes of Alpine ibex to show that past population dynamics and genetic diversity loss are critical for understanding current conservation challenges.

Panic at the Discordance: the Asparagaceae Phylogenetic Backbone

This study investigates phylogenetic discordance in the Asparagaceae family using nuclear gene data, identifying sources like incomplete lineage sorting and ancient hybridization.

Benchmarking Universal Single-Copy Orthologs for Phylogenomics: The Impact of Paralogy

This study benchmarks USCOs for phylogenomics, finding that paralogs are common in BUSCO gene sets and can affect phylogenetic accuracy.

Placing very long branch taxa in the plant tree of life: a case study with Dioscoreales mycoheterotrophs

This study examines how very long branch taxa affect phylogenetic inference in Dioscoreales, finding that they reduce branch support and challenge current classifications.

Misleading inference of schistosome epidemiology from ribosomal internal transcribed spacer (ITS) and mitochondrial DNA

Whole-genome SNVs from Nigerian schistosomes show cox1/ITS genotyping wrongly flags human-derived parasites as recent hybrids or zoonotic infections; they are S. haematobium with low livestock introgression.

A feedback between dispersal and hybridization may facilitate the repeated emergence of flight in field crickets

The paper investigates how dispersal and hybridization feedback loops may explain the repeated evolution of flight in Gryllus field crickets using genomic data.