comparative / phylogenetic analysis

The paper investigates genetic and developmental divergence in the neural crest programme between cichlid fish species, identifying sox10 paralogs as key drivers of morphological differences.

This paper describes the mitogenome of Mantamonas sphyraenae, which has the most gene-rich mitochondrial genome outside of jakobids, encoding a complete mitochondrial Sec translocation system.

This study identifies homology in lysosome-related organelle sorting machinery across eukaryotes, showing its origin predates the last eukaryotic common ancestor.

The paper compares morphological and gene expression convergence and divergence between two cichlid radiations, finding similar pharyngeal jaw morphotypes but distinct body shape patterns and genetic differences.

This study compares aquatic and terrestrial vertebrates to identify shifts in demographic and evolutionary constraints affecting life-history evolution, finding reduced diversification potential on land and differences in viviparity transitions.

This study reveals that soft-shelled turtles have a single origin of their ZW-type sex chromosomes, coinciding with the Paleocene-Eocene thermal maximum.

This study examines how sociality correlates with demographic traits across 152 species, finding that more social species live longer, mature later, and have longer reproductive windows.

This study shows that the common symbiotic pathway genes are essential for arbuscular mycorrhizal symbiosis in bryophytes, indicating conservation of this pathway for 450 million years.

This study analyzes the SARS-CoV2-human protein interaction network, finding that associated human proteins are hubs, part of more complexes, and have slower evolution, potentially contributing to SARS-CoV2's higher infectivity.

This study shows how sexual parasitism and immune gene degeneration in anglerfishes enabled their evolutionary radiation into deep-sea pelagic habitats during a global warming event.

The paper reconstructs the evolution and sub-functionalization of the momilactone biosynthetic gene cluster in Oryza species using comparative genomics.

The paper reveals hidden strain dynamics in skin microbiome species, showing that while strains are transient, some are more stable and may be targets for therapeutic interventions.

This study identifies phylogenetically distinct Planctomycetota groups with diverse CAZyme capabilities for complex polysaccharide degradation, highlighting potential biotechnological applications.

The paper maps tRNA modifications and their synthesis genes in two Bartonella species, identifying gene reductions linked to reductive evolution.

The paper constructs a single-cell chromatin accessibility atlas in rice and compares it across grass species to study the evolution of cell-type-specific cis-regulatory elements.

The paper introduces SRCompiler, a tool that translates Stella dynamic models into R scripts, enabling the use of R's advanced mathematical tools while maintaining scalability and error handling.

This study reconstructs the evolution of SMC complexes across eukaryotes, showing LECA had all four types and condensin II was repeatedly lost.

This paper introduces DETOPT, a method for accurately placing SNVs affected by CNAs in tumor progression trees, showing improved accuracy on simulated data and biologically plausible results on breast cancer metastases.

The paper proposes a northern migration route for modern humans into Eurasia and Australasia using phylogenetic analysis of genetic markers.

This study examines how protein reduction in microsporidia affects function, showing that most proteins cannot complement yeast orthologs and are more reduced in length.

This study examines eye size allometry and ecological factors in spiders, finding variable growth dynamics and significant allometric shifts linked to ecological adaptations.

This study compares alternative splicing across 1,494 species to show lineage-specific variation, with mammals and birds having the highest levels and plants showing moderate but variable splicing.

This study identifies the timing of gene evolution related to multicellularity in cyanobacteria leading up to the Great Oxidation Event.

The paper identifies five new Streptococcus species and one subspecies from human distal lung microbiota, revealing genetic diversity and metabolic functions.

This study examines the evolution of nodule symbiosis in Chamaecrista species, finding that the shift from fixation threads to symbiosomes correlates with changes in growth form and habitat.

The paper compares SARS-CoV-2 variants from China and other countries, finding that Chinese variants have more dispersed RBD mutations with higher ACE2 binding and less immune evasion potential due to a distinct immune background.

The paper examines the faster-Z effect in Leptidea sinapis, showing that neo-Z chromosomes evolve at different rates due to varying selective pressures and W gametolog presence.

The paper compares metagenomics/metatranscriptomics of cloudy and clear atmospheric conditions, showing clouds activate microbial metabolic functions similar to soil rewetting.

The paper examines the evolutionary loss and degradation of plaat1 in vertebrates adapted to low-light environments, showing its role in visual acuity and its loss through relaxed selection.

This study determines the Paleocene origin of a symbiotic relationship between Cassidinae leaf beetles and their bacterial symbiont, showing how the symbiont enhances digestive capabilities and promotes host diversification.