Molecular Biology and Evolution

Modeling the Evolution of Ultraconserved Elements by Indels Abstract. Ultraconserved elements are segments of DNA that are identical or nearly identical in distantly related species. Finding 100% identity over long

Priscila Biller develops a mutation-length–based model of DNA sequence evolution to explain the size distribution of ultraconserved elements. The framework predicts key genome-evolution features, including indel rates and functional conservation.

🔗 doi.org/10.1093/molbev/msaf299

#evobio #molbio

Abstract submission & Award applications for SMBE 2026 are now open!

Abstract submission & Award applications for SMBE 2026 are now open!

Submit your research and apply for SMBE awards via the submission portal.
📝 Read more & submit here: smbe2026.org/abstracts

And symposium selection is now finalized!
👉 See all accepted symposia: smbe2026.org/programme

#SMBE2026

MBE | Genomic Signatures of Selection Across Climate Gradients and a Geographic Mosaic of Coevolution in an Ant Social Parasite–Host System Face to face: the social parasite Temnothorax americanus (left) and an enslaved host worker, Temnothorax longispinosus (right).

Macit, @socialinsectlab.bsky.social investigated selection in response to climate and a geographic mosaic of coevolution between two ant species, a social parasite and its host.

🔗 doi.org/10.1093/molbev/msaf293

#evobio #molbio #coevolution

SAI: A Python Package for Statistics for Adaptive Introgression Abstract. Adaptive introgression is an important evolutionary process, which can be identified with widely used summary statistics, such as the number of u

Huang, @kuhlwilm.bsky.social et al. present SAI, a Python package for computing introgression statistics, and demonstrate its application in two datasets.

🔗 doi.org/10.1093/molbev/msaf295

#evobio #molbio #compbio

Robust and Efficient Confidence Limits for Phylogenomic Inference of Organismal Relationships Abstract. Phylogenomic data are indispensable for establishing reliable relationships needed to build a robust Tree of Life. The superalignment approach co

Sharma & Kumar present the Net Bootstrap Support (NBS) approach that accounts for phylogenetic variation in the estimates of bootstrap confidence.

🔗 doi.org/10.1093/molbev/msaf296

#evobio #molbio #phylogenetics

Molecular Biology and Evolution | December 2025 cover

The December cover of Molecular Biology and Evolution features the work of Chiu et al., who showed that later-evolving strains of SARS-CoV-2 acquired infectivity towards cultivated cells expressing New World monkey ACE2.

🔗 doi.org/10.1093/molbev/msaf281

#evobio #molbio #sarscov2

MBE | Mitonuclear Discordance of Beetles Shaped by Incomplete Lineage Sorting and Introgression Under Loose Interaction Mechanism

Zhao et al. analysed phylogenetic signal in OXPHOS genes, mtDNA genes and nuclear genes in 53 beetle species, detecting two major cases of mitonuclear discordance caused by introgressive hybridization and incomplete lineage sorting.

🔗 doi.org/10.1093/molbev/msaf291

#evobio #molbio

Pan-Angiosperm Analysis of the CLE Signaling Peptide Gene Family Unveils Paths, Patterns, and Predictions of Paralog Diversification Abstract. The compositions of conserved gene families often vary widely between species, complicating predictions and experimental tests of shared versus d

Gentile et al. investigate the evolution of the conserved plant CLV3/EMBRYO-SURROUNDING REGION (CLE) peptide family, showing how both peptide and cis-regulatory erosion shape CLE redundancy.

🔗 doi.org/10.1093/molbev/msaf294

#evobio #molbio #PlantSky

Fast and Memory-Efficient Dynamic Programming Approach for Large-Scale EHH-Based Selection Scans Abstract. Haplotype-based statistics are widely used for finding genomic regions under positive selection. At the heart of many such statistics is the comp

Rahman, Smith & Szpiech present selscan v2.1, a dynamic programming algorithm to improve runtime and memory usage in the calculation of extended haplotype homozygosity.

🔗 doi.org/10.1093/molbev/msaf275

#evobio #molbio #compbio

#Connectivity in the #deepsea! EXCELLENT study on the key sponge ground species ‘Geodia hentscheli’, shows strong genetic and microbiome structures segregated by depth. 👇
academic.oup.com/mbe/article/...

Identifying Single-Origin Rare Variants in Population Genomic Data Abstract. Genomic analyses have shown that some mutations in large population genomic datasets may be the result of repeated, independent events at the sam

Reynolds, Koufopanou & Burt developed methods focused on doubletons, the rarest of rare variants that can be informative about relatedness between individuals, and used them to analyze published data of mosquitoes.

🔗 doi.org/10.1093/molbev/msaf283

#evobio #molbio

Tandem Duplication of Serpin Genes Yields Functional Variation and Snake Venom Inhibitors Abstract. Tandem duplication of genes can play a critical role in the evolution of functional novelty, yet our understanding is limited concerning the role

Ward et al. characterized duplications in the SERPINA gene subfamily, finding evidence of diversifying selection on rodent genes, with experimental evidence suggesting an adaptive role in snake venom inhibition.

🔗 doi.org/10.1093/molbev/msaf290

#evobio #molbio #venome #adaptation

Spread of a Single Superclone Drives Insecticide Resistance in Acyrthosiphon kondoi Across an Invasive Range Abstract. Populations under similar selection pressures may adapt via parallel evolution or dispersal of advantageous alleles. Here, we investigated insect

Thia et al. investigated insecticide resistance in the invasive blue-green aphid in Australia, combining genomics and transcriptomics to demonstrate the spread of a resistant “superclone” lineage that is distinct from susceptible strains.

🔗 doi.org/10.1093/molbev/msaf246

#evobio #molbio #pest

SARS-CoV-2 Evolution in Humans Enables Its Transmission to Nonhuman Primates Abstract. Zoonotic viruses frequently cross-species barriers, but the molecular processes enabling reverse zoonosis remain poorly defined. The COVID-19 pan

Chiu et al. used assayed cells expressing New World monkey ACE2 to show that later-evolving strains of SARS-CoV-2 acquired infectivity. Human-driven evolution of viral cells enhanced the potential for human-to-non-human transmission.

🔗 doi.org/10.1093/molbev/msaf281

#evobio #molbio #sarscov2

Highly Recurrent Multinucleotide Mutations in SARS-CoV-2 Abstract. Multinucleotide mutations simultaneously replace multiple nucleotides. They are a significant contributor to evolution and disease, as well as to

De Maio et al. processed >2 million genomes to show that certain multinucleotide mutations are highly recurrent in SARS-CoV-2, including some that have independently occurred hundreds of times across all SARS-CoV-2 lineages.

🔗 doi.org/10.1093/molbev/msaf272

#evobio #molbio #sarscov2

Convergent Evolution and Host-Limiting Impacts of SARS-CoV-2 Revealed by Cellular Experiments Abstract. The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the virus's remarkable ability to evo

Zhang et al. passaged SARS-CoV-2 virus in seven cell lines derived from four tissues across five mammalian species, uncovering host-specific selective forces in shaping SARS-CoV-2 evolution.

🔗 doi.org/10.1093/molbev/msaf274

#evobio #molbio #sarscov2

Genomic Features Underlying the Origin of Sociality and the Diversification of Caste Systems in Termites Abstract. Termite colonies consist of distinct castes whose developmental pathways fall into 2 types and vary among lineages. Understanding caste evolution

Findings support the hypothesis that gene duplications, particularly in reproduction and development, contributed to termite eusociality academic.oup.com/mbe/article/...

Evolutionary Flexibility of Ribosome Biogenesis in Bacteria Abstract. Ribosomes are essential for protein synthesis and require ribosome biogenesis factors for assembly. To uncover the evolutionary diversity of ribo

@amikura.bsky.social et al. analyzed >30,000 bacterial genomes, suggesting that ribosomal biogenesis is more flexible than recognized, and small cell and genome sizes of Candidate Phyla Radiation bacteria influence ribosome biogenesis factors.

🔗 doi.org/10.1093/molbev/msaf288

#evobio #molbio

Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom

Kwun et al. test whether transformation is an efficient mechanism for deleting prophage despite sensitivity to the ssDNA imported by competence machinery, identifying key interfaces in the evolutionary arms race between prophage and their hosts.

🔗 doi.org/10.1093/molbev/msaf259

#evobio #molbio

MBE | Genomic Features Underlying the Origin of Sociality and the Diversification of Caste Systems in Termites

Fujiwara et al. performed WGS and RNAseq of the termite Zootermopsis nevadensis, finding that gene duplications contributed to eusociality, and that lineage-specific Doublesex-related expression underlies caste diversification pathways.

🔗 doi.org/10.1093/molbev/msaf284

#evobio #molbio #eusociality

Unraveling Epistatic Interactions Between Sites Under Drug-Dependent Selection in the Mycobacterium tuberculosis Genome Abstract. Many Mycobacterium tuberculosis genome sites experience different selective forces depending on whether a patient is treated with antibiotics. He

Popova et al. studied the evolution of M. tuberculosum under drug pressure using a unified phylogeny-based approach to reveal both drug-dependent evolution and epistatic interactions between sites.

🔗 doi.org/10.1093/molbev/msaf264

#evobio #molbio #epistasis

The Core MICOS Complex Subunit mic60 has Been Substituted by Two Cryptic Mitofilin-containing Proteins in Euglenozoa Abstract. Cristae enclose respiratory chain complexes, making them the bioenergetic subcompartments of mitochondria. The Mitochondrial contact site and Cri

Sheikh et al. show that Mic60 - responsible for forming the cristae that enclose mitochondrial respiratory chain complexes - has been replaced in euglenozoans by two cryptic mitofilin domain-containing MICOS subunits.

🔗 doi.org/10.1093/molbev/msaf289

#evobio #molbio

MBE | Environment-by-Environment Interactions Differ Across Genetic Backgrounds

Schmidlin, @kgslab.bsky.social et al. analyzed ~1,000 mutant antifungal-resistant yeast strains to investigate environment-by-environment-by-genotype interactions.

🔗 doi.org/10.1093/molbev/msaf287

#evobio #molbio #yeast

Stable Hypermutators Revealed by the Genomic Landscape of Genes Involved in Genome Stability Among Yeast Species Abstract. Mutator phenotypes are short-lived due to the rapid accumulation of deleterious mutations. Yet, recent observations reveal that certain fungi can

Gonçalves, @rokaslab.bsky.social @hittingerlab.bsky.social et al. surveyed 1,154 yeast genomes to examine gene repertoires linked to genome stability and elevated evolutionary rates, showing hypermutators persist across macroevolutionary timescales.

🔗 doi.org/10.1093/molbev/msaf285

#evobio #molbio

Evolution of Large Polymorphic Inversions in a Panmictic Songbird Abstract. Chromosomal inversions have long been appreciated as an important source of genetic diversity, local adaptation, and speciation. However, selecti

Pei et al. used SNP and linked read data from 20 wild and 7 captive zebra finches to characterize large segregating inversions. These findings highlight how inversions are maintained by weak heterosis with small fitness effects.

🔗 doi.org/10.1093/molbev/msaf262

#evobio #molbio #inversions

Seeing in the Deep: Evolution of the Opsin Gene Expression in Bermin Crater Lake Cichlids Abstract. Cichlid visual systems can evolve rapidly during adaptive radiations. The Bermin crater lake species flock in Cameroon, comprising 13 (nine valid

Kłodawska, @fishevo.bsky.social et al. examine visual opsin genes sequences and expression in Bermin crater lake cichlids, recovering little coding sequence divergence but high variation in expression profile.

🔗 doi.org/10.1093/molbev/msaf286

#evobio #molbio #cichlids #opsins

This article has made the cover of the November 2025 edition of Molecular Biology and Evolution.

MBE | Imprinting and DNA Methylation in Water Lily Endosperm: Implications for Seed Evolution

Povilus et al. examined DNA methylation and genetic imprinting in water lily species, finding that maternal gene expression and parent-specific DNA methylation in the endosperm likely represent the ancestral condition of seed development.

🔗 doi.org/10.1093/molbev/msaf271

#evobio #molbio #PlantSky

Genomic Signatures of Selection Across Climate Gradients and a Geographic Mosaic of Coevolution in an Ant Social Parasite-Host System Abstract. Coevolutionary dynamics in host-parasite systems are shaped by reciprocal selection and environmental context. When hosts and parasites share anc

Investigating #genome-wide signatures of selection in response to a broad climatic gradient and a geographic mosaic of coevolution between a social parasite and its host academic.oup.com/mbe/advance-...

New (to me) pop gen tool: GONE (genetic optimization for Ne estimation)—finds very recent population size changes using linkage disequilibrium
academic.oup.com/mbe/article/...

4 ways to install: compiled/to-compile on Mac/Linux. I tried all 4 and all failed. But worked on a different Linux server.