M. Robinson-Rechavi

Sudden shifts in expression after small-scale duplication in vertebrates and strong support for the ortholog conjecture

The paper tests the ortholog conjecture by analyzing gene expression shifts after duplication in vertebrates, finding strong support for the conjecture and showing trait jumps affect small-scale paralogs more than genome-wide duplicates.

Beyond venomous fangs: Uloboridae spiders have lost their venom but not their toxicity

This study investigates Uloboridae spiders' venom loss and toxicity, finding they lack venom glands but retain toxin-like genes in digestive fluids with different toxic mechanisms.

Matreex: compact and interactive visualisation for scalable studies of large gene families

Matreex provides a scalable visualization tool for large gene families by using phylogenetic profiles to minimize information loss during subtree collapsing.

Genome structures resolve the early diversification of teleost fishes

The paper uses genome assemblies to resolve the evolutionary relationships among early diverging teleost lineages, placing Elopomorpha and Osteoglossomorpha as sister groups.

Parallel evolution of amphioxus and vertebrate small-scale gene duplications

This study compares small-scale gene duplication patterns between amphioxus and vertebrates, finding similar duplication histories and functional constraints despite amphioxus' slower evolution.

X chromosomes show relaxed selection and complete somatic dosage compensation across Timema stick insect species

The paper analyzes X chromosome evolution in five Timema stick insect species, finding relaxed selection, slower evolution, and partial dosage compensation across species.

Convergent evolution of venom gland transcriptomes across Metazoa

This study compares venom gland transcriptomes across 20 venomous species to determine if similar molecular mechanisms underlie venom evolution, finding strong convergence in gene expression profiles.

Two levels of selection of rhythmicity in gene expression: energy saving for rhythmic proteins and noise optimization for rhythmic transcripts

The paper investigates evolutionary origins of gene expression rhythms, finding that protein rhythmicity reduces energy cost while mRNA rhythmicity optimizes noise and allows adaptive flexibility.

Dynamics of sex-biased gene expression over development in the stick insect Timema californicum

This study examines sex-biased gene expression dynamics during development in the hemimetabolous stick insect Timema californicum and compares it to the holometabolous fly Drosophila melanogaster.

Haplotype divergence supports ancient asexuality in the oribatid mite Oppiella nova

The paper uses genomic and transcriptomic data to show haplotype divergence patterns in asexual and sexual mite species, supporting ancient asexuality in Oppiella nova.

First annotated draft genomes of non-marine ostracods (Ostracoda, Crustacea) with different reproductive modes

The paper presents the first annotated draft genomes of three non-marine ostracod species, providing genomic resources for evolutionary and ecological studies.

Convergent consequences of parthenogenesis on stick insect genomes

This study compares parthenogenetic and sexual stick insect species to show reduced heterozygosity, less effective selection, and no TE accumulation in parthenogens.

The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection

The paper identifies a higher proportion of conserved enhancers during the phylotypic period of Drosophila embryogenesis and detects positive selection on enhancers at early and late stages.

Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication

This study compares two methods for detecting functional evolution differences between orthologs and paralogs under various evolutionary scenarios, finding that both have limitations but improved pairwise comparisons are more robust.

Special care is needed in applying phylogenetic comparative methods to gene trees with speciation and duplication nodes

The paper reanalyzes gene trees to assess phylogenetic comparative methods for studying gene function evolution, finding biases in tree calibration and supporting the ortholog conjecture with corrected methods.

Robust inference of positive selection on regulatory sequences in human brain

The paper introduces a new method to detect positive selection on regulatory sequences, finding that human brain-related cell types show the highest proportion of positive selection.

Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases

This paper explores data quality issues in biological databases, focusing on duplication and other problems, and highlights the role of biocuration in addressing them.

Sex-biased gene expression is repeatedly masculinized in asexual females

The paper examines gene expression in asexual stick insect females and finds masculinized expression patterns, suggesting shifts in optimal gene expression after the suppression of sex.

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5

This study identifies genomic changes in Lactobacillus Firm5 strains from honey bees and bumble bees that underlie host specialization, showing honey bee strains have greater metabolic flexibility.

Repeated evolution of asexuality involves convergent gene expression changes

The paper identifies convergent gene expression changes across multiple independent transitions to asexuality in stick insects, suggesting constrained molecular pathways for asexual reproduction.

Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles

This study identifies adaptive gene family expansions in polyphagan beetles associated with their shift to plant-feeding, supporting the role of plant chemical defenses in beetle diversification.

Adaptive evolution of animal proteins over development: support for the Darwin selection opportunity hypothesis of Evo-Devo

The paper tests the Darwin selection opportunity hypothesis by analyzing positive selection in genes expressed during late development in three species, finding stronger positive selection in late-developing genes.

Developmental constraints on genome evolution in four bilaterian model species

The paper analyzes developmental constraints on genome evolution in four species, finding sequence evolution follows an hourglass model while phyletic age and duplicability follow an early conservation model.

Low Rate of Somatic Mutations in a Long-Lived Oak Tree

The paper sequenced two branches of a 234-year-old oak tree and found few somatic mutations, suggesting shoot meristems are mutation-resistant.

Detection of pathways affected by positive selection in primate lineages ancestral to humans

The paper detects pathways affected by positive selection in primate lineages ancestral to humans, identifying significant signals in immune response, sensory perception, metabolism, and energy production.

No evidence for the radiation time lag model after whole genome duplications in Teleostei

This study tests the radiation time lag model after whole genome duplications in teleost fishes using fossil data and molecular phylogenies, finding no evidence of delayed evolutionary success.

Selective constraints on coding sequences of nervous system genes are a major determinant of duplicate gene retention in vertebrates

The paper shows that nervous system gene duplicates are more likely to be retained after whole-genome duplication due to selective constraints on their coding sequences.