Jesse Bloom argues that the earliest available sequences of SARS-CoV-2 are not fully representative of actual early cases.

doi.org/10.1093/molbev/msaf118

Florence Débarre and Zach Hensel‬ offer a new perspective on available SARS-CoV-2 sequencing data, in particular regarding the earliest reported sequences.

doi.org/10.1093/molbev/msaf109

Yaddehige et al. present GBRAP, a parser and database for analyzing RefSeq genomes. This publicly available tool offers over 200 metrics per genome element with flexible retrieval, visualization, and export options.

doi.org/10.1093/molbev/msaf114

John Allard‬ & Sudhir Kumar introduce MEGA-GPT, an AI assistant that aims to improve the usability of the feature-heavy MEGA software by guiding users through MEGA's options via natural language queries.

https://doi.org/10.1093/molbev/msaf101

Jones et al. investigate gene regulation in the social supergene of the fire ant, finding widespread impacts on chromatin accessibility, enhancer activity, and transcription.

doi.org/10.1093/molbev/msaf112

The June cover of Molecular Biology and Evolution features the work of de Bakker et al., who studied the developmental genetics of amniote limb phenotypes.

doi.org/10.1093/molbev/msaf113

Gerda Lamers

Thompson et al. model gene expression as a binary trait to examine transcriptome turnover across Drosophila species, inferring gains and losses of organ-specific expression.

doi.org/10.1093/molbev/msaf106

Policarpo et al. use phylogenetic and synteny data to identify 19 teleost-to-teleost horizontal gene transfers in 11 orders, involving genes linked to immunity or pore formation; this suggests eukaryote-to-eukaryote HGT has shaped teleost evolution.

doi.org/10.1093/molbev/msaf107

Okuno et al. assemble male genomes for three spiny rat species, tracing Y chromosome loss and gene translocation. Authors show that segmental duplications and rearrangements enabled preservation of Y-linked genes on the X.

doi.org/10.1093/molbev/msaf102

She et al. studied cardiac adaptation to high-elevation in birds, showing that regulatory variation in cardiac phenotypes involves the differential expression of genes in a conserved cardiomyocyte hypertrophy pathway.

doi.org/10.1093/molbev/msaf103

Szasz-Green et al examined recombination in birds and teleosts, showing that avian genes show strong signatures of selection, mirroring those seen in mammals but not teleosts, and revealing clade-specific drivers of recombination rate evolution.

doi.org/10.1093/molbev/msaf100

Asgari & Tate uncover the evolutionary forces shaping the multilayered regulation of signaling pathways by negative feedback loops.

doi.org/10.1093/molbev/msaf104

Kumar et al. show how caspase-8 adapted to interact with the adaptor ASC, enabling PANoptosome formation and PANoptosis, key processes in inflammation and host defense.

doi.org/10.1093/molbev/msaf096

ERCnet by Forsythe et al. improves the prediction of protein interactions using evolutionary rate covariation, overcoming challenges like gene duplication and other sources of phylogenetic noise.

doi.org/10.1093/molbev/msaf089

In Artemia franciscana, sex-biased gene expression and dosage compensation on the Z chromosome are linked to chromatin state. H4K16ac histone mark enrichment in female-limited Z chr. suggests a role in dosage compensation. New paper by Bett el al in MBE:

https://doi.org/10.1093/molbev/msaf085

Lau et al. show that bioluminescent luciferases in brittle stars and octocorals evolved in parallel from haloalkane dehalogenases, highlighting how gene function and genomic availability shape convergent evolution.

https://doi.org/10.1093/molbev/msaf081

Akopyan et al. analysed 168 genomes of Atlantic silverside, showing that high gene flow leads to clustered divergence in large inversions, while low recombination at centromeres mimics differentiation.

https://doi.org/10.1093/molbev/msaf092

Liang et al. assembled 22 Quercus variabilis genomes, identifying variants associated with local adaptation. A region of Chr9 had evidence of introgression from Q. acutissima, supporting a role for structural variants in oak adaptation.

https://doi.org/10.1093/molbev/msaf088

#molbio #evobio #oak #evolution

New paper in MBE by Pfalz et al - genetic variation at a near-cryptic QTL for defense metabolites in Arabidopsis is shaped by balancing selection and ectopic gene conversion among duplicated O-methyltransferase genes.

https://doi.org/10.1093/molbev/msaf086

The May cover of Molecular Biology and Evolution features the work of Zhang et al., who used single-cell multi-omics to study odorant receptor expression patterns in honeybees.

https://doi.org/10.1093/molbev/msaf080

Zhang et al.