phylogenetics / evolution

The locomotor behavior of subfossil Malagasy sloth-lemurs (Strepsirrhini: Palaeopropithecidae) and koala-lemurs (Strepsirrhini: Megaladapidae): new insights from limb trabecular bone

Low femoral trabecular anisotropy and bone volume fraction mark suspensory/bridging mammals, and a phylogenetic discriminant model classifies extinct Palaeopropithecus ingens and Megaladapis edwarsi as suspensory.

Are theoretical advances in distance-based tree learning practical for phylogenetic inference?

This study evaluates a theoretical algorithm for phylogenetic inference in realistic biological datasets, finding it robust but requiring adjustments for real-world applications.

Dynamics of complex genomic regions in giant genomes: MHC evolution in newts

This study investigates MHC evolution in seven newt species, finding a compact core MHC region and lineage-specific duplications, challenging previous assumptions about MHC expansion in giant genomes.

Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection

This study shows that phylodynamic migration rate estimates for HIV-1 within hosts are overestimated under selection using common models like BEAST2.

Unraveling the Phylogenetic Complexities of Ischyropsalis C.L. Koch, 1839 (Opiliones: Dyspnoi: Ischyropsalididae) in the North Iberian Peninsula, with the description of three new species.

The paper describes three new species of Ischyropsalis from the North Iberian Peninsula and investigates their phylogenetic relationships using molecular markers.

Whole-Genome Characterization of Proteus mirabilis Isolated from Fermented Soybean, hawaijar: Insights into Foodborne Virulence and Antimicrobial Resistance Determinants

This study characterizes the genome of a Proteus mirabilis strain isolated from fermented soybean, identifying virulence factors, antimicrobial resistance genes, and genomic adaptations to the fermentation environment.

A dual genomic-epigenomic map of clonal evolution in grapevine

This paper maps clonal genetic and epigenetic variation in grapevine using a phased diploid genome and Oxford Nanopore sequencing, showing that CG methylation patterns accurately reconstruct clonal phylogeny.

Spatial inference of ancestor locations suggests northern refugia for canopy-forming kelps in the Northeast Pacific

The paper uses genetic data and ecological models to infer that canopy-forming kelps in the Northeast Pacific survived in northern refugia during the Last Glacial Maximum.

Independent origins of spicules reconcile palaeontological and molecular evidence of the evolutionary history of sponges

The paper reconciles molecular and fossil evidence by showing sponges emerged in the early Ediacaran without spicules, which evolved independently multiple times later.

Disagreement among Genomic Markers Profoundly Influences Phylogenetic Inference in Squamates

The paper investigates phylogenetic conflicts in squamates by analyzing genomic markers and finds that data quality, model fit, and sampling bias contribute to discordance.

Draft mitochondrial genome assembly of Neltuma alba (Caesalpinioideae, tribe Mimoseae), a vulnerable tree from the Atacama Desert, Chile

This study assembles and analyzes the mitochondrial genome of Neltuma alba, confirming its placement within the Mimoseae tribe and providing a resource for evolutionary studies.

Molecular phylogeny of Catenulida (Platyhelminthes) with special focus on their diversity in Poland

The paper surveys catenulid diversity in Central and Western Europe, focusing on Poland, using molecular markers to infer phylogeny and identify taxonomic challenges.

A large phylogenetic tree for euphyllophytes

The paper constructs the largest dated phylogenetic tree for euphyllophytes by integrating backbone phylogenies and species-level trees, revealing increased topological and age estimation uncertainty in recent times.

Guide scaffolding improves phylogenetic accuracy and enables integration across 16S amplicon regions

This paper introduces a guide scaffolding method to improve phylogenetic accuracy and enable integration of 16S amplicon datasets across variable regions.

A Palearctic divide, niche conservatism and host-fungal endophyte interactions shaped the phylogeography of the grass Brachypodium sylvaticum

This study investigates the phylogeography of Brachypodium sylvaticum and its fungal symbiont Epichloe sylvatica, revealing co-divergence, niche conservatism, and geographic isolation as key factors in lineage splitting.

Extensive nuclear datasets resolve the phylogeny of siphonous green algae and identify genome duplications as a contributing factor to evolutionary adaptations

The paper presents extensive nuclear genome data for 44 Bryopsidales taxa, resolves their phylogeny, and identifies ancient gene duplications, including potential whole genome duplications, as factors in evolutionary adaptations.

Lizards on a sky archipelago: Genomic approaches to the evolution of the mountain genus Iberolacerta

This study presents a chromosome-level genome assembly for Iberolacerta aurelioi and uses whole-genome sequencing to investigate phylogenomic relationships and adaptive traits in the genus Iberolacerta.

Comparative genomic analyses shed light on the introduction routes of rice-pathogenic Burkholderia gladioli strains into Bangladesh

The paper uses genomic analysis to trace the introduction routes of pathogenic B. gladioli strains into Bangladesh and identifies virulence gene changes associated with host transitions.

Demographic history inferred from an inversion-rich spruce bark beetle genome

This study uses genome-wide data from spruce bark beetles to infer demographic history and assess the impact of chromosomal inversions on evolutionary inferences.

Impact of Data Error on Phylogenetic Network Inference from Gene Trees Under the Multispecies Network Coalescent

This study examines how data errors affect phylogenetic network inference and shows that many methods are vulnerable to these errors, leading to unreliable results.

The Macroevolution of Filamentation Morphology Across the Saccharomycotina Yeast Subphylum

The paper examines filamentation morphology evolution in Saccharomycotina yeasts using integrated genomic, metabolic, and environmental data from 1,154 strains, finding that filamentation is common and linked to phylogeny and environmental factors.

Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases

Structome-TM assembles datasets for structural phylogenetics by prioritizing local structural similarity to address size-based biases in homologous structure identification.

Genomic and Transcriptomic Insights into the Evolution and Parasitic Strategy of the Woody-Plant Nematode Pratylenchus vulnus

This study presents the genome and transcriptome of Pratylenchus vulnus, revealing evolutionary relationships, genomic features, and parasitism-related genes in a woody-plant nematode.

Rapid evolution of gene expression patterns in flowering plants

This study shows that gene expression patterns in flowering plants evolve rapidly, with divergence rates exceeding those in mammals, and highlights differences in conservation across organs.

Phylogenetic analysis of enteroviruses from non-human primates reveals two new species within the genus Enterovirus and inter-species recombination

The whole genome analysis of four Orf virus strains from Europe and South America.

The paper analyzes the whole genome sequences of four Orf virus strains to study genetic variation and divergence, finding a median divergence time of 1661.

Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees

This paper introduces Spinney, a method that estimates quantitative trait evolution rates by considering gene tree discordance, improving accuracy over species-tree-only approaches.

Morphogenomic description of Cranifera cranifera (Chitwood, 1932) Kloss, 1960 from captive Blaptica dubia Serville, 1838 cockroach

Third nuclear genome for arthropod pinworms (Thelastomatoidea): a PacBio long-read Cranifera cranifera assembly (242 Mb, N50 43 kb, 90.5-94% BUSCO) plus a 24644-base mitogenome and male redescription.

On rRNA gene cluster variation, phylogeny and local ecological differentiation in the Jaera albifrons complex (Crustacea: Isopoda)

This study examines rRNA gene variation in the Jaera albifrons complex to assess their utility for species identification and phylogenetic analysis, finding low variability and evidence of hybridization.

A large replicase of nidovirus-like complexity in a putative RNA virus order "Quisvirales" expands the known diversity of helicase superfamilies

The paper identifies a new order of RNA viruses, Quisvirales, with a novel helicase superfamily replacing the nidovirus SF1 helicase, suggesting convergent evolution of large replicases.