phylogenetics / evolution

A Refined Phylochronology of the Second Plague Pandemic in Western Eurasia

This paper uses genomic and historical data to refine the timeline and origin of the Second Plague Pandemic in Western Eurasia.

Reticulate History of Southern South American Wild Potatoes: Recurrent Hybridization, Cytonuclear Discordance, and Phylogenetic Placement of Solanum malmeanum

This study investigates the evolutionary history of wild potatoes in the Petota clade, revealing recurrent hybridization, cytonuclear discordance, and chloroplast capture affecting species boundaries.

Deep shifts in Evolutionary Rate Trajectories of Ancient Bacterial Genes

The paper reconstructs evolutionary rate trajectories of 528 genes from the Last Bacterial Common Ancestor across 2.1 billion years, identifying four clusters with distinct patterns linked to gene function and environmental changes.

PartitionFinder-mAIC: Phylogenetic Partitioning using Marginal Akaike Information Criterion

PartitionFinder-mAIC improves phylogenetic partitioning by using marginal AIC, resulting in fewer partitions and better inference of green plant evolution.

BROOQS: Quartet-based Resolution of Level-1 Hybridization Cycles without Tests of Symmetry

BROOQS resolves level-1 phylogenetic networks by efficiently aggregating quartet information without quartet symmetry tests, improving accuracy and scalability.

Why woodiness repeatedly evolves--and disappears

The paper investigates the evolution and reversal of woodiness in flowering plants, finding that drought supports persistence while reduced frost drives gains and increased frost leads to loss.

Molecular clock dating under mixture substitution models indicates contemporaneous emergence of Bradyrhizobium nodulation and legumes anchored by non-symbiotic relatives

The paper uses molecular clock dating with non-symbiotic Bradyrhizobium relatives to show nodulation and legumes emerged around 90-80 million years ago.

Joint dog and wolf genealogies reveal the evolution of the canine genome

This study uses joint genealogies of dogs, wolves, and coyotes to uncover evolutionary forces shaping the dog genome, identifying mutation-rate pulses, selection signatures, and introgression events.

Molecular characterization of chikungunya viruses associated with outbreaks in Kenya from 2017 to 2020

This study characterizes CHIKV outbreaks in Kenya from 2017 to 2020, identifying molecular features and clinical symptoms associated with the virus.

A divergent betacoronavirus with a functional furin cleavage site in South American bats

The paper reports a new bat betacoronavirus from Brazil with a functional furin cleavage site in its spike protein, highlighting its phylogenetic distinctiveness and potential zoonotic risk.

Was the extinct Spectacled Cormorant part of the North Pacific kelp-associated fauna?

This paper uses ancient DNA to reconstruct the evolutionary history of the extinct Spectacled Cormorant, finding it diverged from relatives around 6.98 Mya and may have been a kelp-forest predator.

Assessing the robustness of SNaQ to violations induced by high-level phylogenetic networks

This study evaluates SNaQ's performance on non-level-1 phylogenetic networks and introduces new metrics to assess structural recovery.

A large-scale evaluation of tree shape indices reveals potential pitfalls

The paper evaluates 54 tree shape indices on 45 million empirical trees, revealing rooting and size dependencies, and recommends selecting uncorrelated indices for reliable tree shape analysis.

Partitioning convergent modules separates phylogenetic signal from ecological information in mosaic fossils

The paper introduces a character-partitioning framework to separate phylogenetic signal from ecological information in mosaic fossils, using mid-Cretaceous crickets as a case study.

Poxvirus gene repertoires are shaped by expansion-biased birth-and-death dynamics and genome architectural constraints

This study analyzes poxvirus gene repertoires and finds that they evolve through expansion-biased birth-and-death dynamics and genome architectural constraints.

Metric-dependent genomic diversity reveals phylogenetic and ecological structure in saproxylic beetles

The paper shows that genomic diversity metrics vary in their ability to detect phylogenetic and ecological patterns in saproxylic beetles, emphasizing the importance of denominator choice.

Genomic Epidemiology of Canine Distemper Virus (CDV) in Neotropical Primates in Brazil Reveals Multiple Spillover Events and Convergent Evolution at Hemagglutinin Residue 519

The paper identifies multiple CDV spillover events into Neotropical primates in Brazil and identifies residue 519 of the hemagglutinin protein as a candidate marker of adaptation to primates.

Madagascar as an evolutionary source for the Paleotropical flora: New insights from the biogeography of Grewia (Malvaceae)

This study reconstructs the evolutionary history of Grewia, showing a Malagasy origin and dispersal to Africa, Arabia, and Asia via fleshy fruits.

ntSynt-viz: Visualizing synteny patterns across multiple genomes

ntSynt-viz sorts genomes and chromosomes by synteny, normalizes strands, and draws chromosome-painting ribbon plots easier to interpret than NGenomeSyn output for human and hoverfly genomes.

Sea stickleback genome reveals repeated chromosomal rearrangements in sticklebacks

The paper presents a high-quality genome assembly of the sea stickleback and reveals chromosomal fusions and fissions that reshape understanding of karyotype evolution in sticklebacks.

Emended description of the genus Henriciella: morphological and phylogenetic analysis identifies two subgenera with different reproductive strategies

The paper reclassifies Henriciella into two subgenera based on reproductive strategies and phylogenetic analysis, correcting previous classifications.

Parallel evolution under constraint shapes echinocandin resistance in Candida auris

Across 681 matched isolates and 22,388 genomes, high-level micafungin resistance in Candida auris arises through recurrent FKS1 hotspot mutations amid strong purifying selection, and FKS2 appears dispensable.

Microsynteny Analysis Clarifies the Early Diversification of Cypriniform Fishes

This paper uses microsynteny analysis to resolve deep phylogenetic relationships in Cypriniform fishes, showing it outperforms sequence-based methods in resolving contentious nodes.

Whole brain mapping of spinal-projecting neurons in larval zebrafish

Two-photon optical backfills of pan-neuronal photoactivatable GFP in larval zebrafish yield an estimated 1,300 spinal-projecting neurons per larva across hindbrain, midbrain and diencephalon, with tentative homologies to mammalian nuclei.

Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys)

This study uses phylotranscriptomics to distinguish between gene flow and incomplete lineage sorting in Ophrys orchids, revealing ancient adaptive gene flow events.

Convergence and conflict among telomere specialized transposons across 60 million years of Drosophilid evolution

The paper analyzes telomere-specialized transposons across Drosophila species, revealing rapid evolution, convergent loss, horizontal transfer, and gene capture mechanisms.

A phylogenomic framework for avian feather lice (Phthiraptera: Ischnocera)

This study constructs a comprehensive phylogenomic tree of avian feather lice using 260 samples and 2,395 genes, resolving higher-level relationships and providing a framework for future comparative studies.

A Curated Pharmacogenomic Allele Catalog for Sub-Saharan African Populations

The paper curates a pharmacogenomic allele catalog for Sub-Saharan African populations, highlighting population-specific frequencies and functional annotations for six pharmacogenes.

Discovering 25 novel phyla that fill gaps in the eukaryotic tree of life

The paper identifies 25 novel phyla in the eukaryotic tree of life through global environmental DNA surveys and proposes formal names for 150 species.

Synchronizing speciation, extinction, and dispersal to island paleodynamics through Bayesian phylogenetics in a Hawaiian plant radiation

The paper introduces a Bayesian phylogenetic framework to infer divergence times, ancestral ranges, and diversification rates in Hawaiian plants without fossil calibration.