Molecular Biology and Evolution

William S. Henriques

Henriques et al: The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals

🔗 doi.org/10.1093/molbev/msae061

Julien Joseph

Joseph et al: Increased Positive Selection in Highly Recombining Genes Does not Necessarily Reflect an Evolutionary Advantage of Recombination

🔗 doi.org/10.1093/molbev/msae107

MBE Best Student Paper of 2024 award | Julien Joseph (Winner), William S. Henriques (Honorable mention)

The MBE Best Student Paper award of 2024 goes to Julien Joseph (winner) and William S. Henriques (runner-up).

👏 Congratulations Julien and William for this recognition of your amazing work!

Check below for details on their research ⬇️

MBE | Large-scale Genome Analyses Provide Insights into Hymenoptera Evolution

He et al. performed large-scale comparative genomics on 131 species of Hymenoptera, providing insights finto genome evolution and the genomic basis of diversification in these insects

🔗 doi.org/10.1093/molbev/msaf221

#evobio #molbio #hymenoptera

Arthropod Pax Gene Evolution: A Role for Vanessa Cardui Twin of Eyeless in Eye Development Abstract. Pax genes encode transcription factors involved in diverse processes. First identified in Drosophila, they have been found throughout the animal

Ramos & Pick analyzed the distribution and classification of Pax genes and established the painted lady butterfly (Vanessa cardui) as a model to study Pax gene expression and function.

🔗 doi.org/10.1093/molbev/msaf220

#evobio #molbio #pax

Congratulations, Zheng and colleagues, thank you for publishing your research with MBE!

eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA Abstract. Extrachromosomal circular DNA (eccDNA) refers to small, circular DNA molecules that originate from chromosomal sequences and are prevalent across

1/5: ☺️☺️ Recently, we have published a database paper in the MBE journal @molbioevol.bsky.social titled "eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA". #eccDNA #disease #multi_species

academic.oup.com/mbe/article/...

Fantastic paper Claudèle, thank you for publishing with MBE!

How does catalysis emerge from non-catalytic domains?

In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.

A striking case of catalysis evolving from binding.

MBE | Chromosome-Level Genome Assembly of Eden's Whale Clarifies the Taxonomy and Speciation of Bryde's Whale Complex

Lin et al. present a chromosome-level genome of Eden's whale to elucidate the speciation and taxonomy of balaenopterids; findings show Eden's whale is the sister species of Bryde's whale, sharing a common ancestor approximately 7.84 Mya.

🔗 doi.org/10.1093/molbev/msaf234

#evobio #molbio #whale

Seasonal Influenza Viruses Show Distinct Adaptive Dynamics During Growth in Chicken Eggs Abstract. Human influenza viruses are grown in chicken eggs for vaccine production. Sequences of these egg-passaged viruses give us the opportunity to exam

Kistler & Bedford analysed the evolution of human influenza virus from strains grown in chicken eggs for several generations for vaccine production.

🔗 doi.org/10.1093/molbev/msaf227

#evobio #molbio #virus #influenza

Distinct Evolutionary Signatures of Human Parainfluenza Viruses 2 and 4 Reveal Host Antagonism Divergence and Phylogenetic Discordance Abstract. Human parainfluenza virus 2 (HPIV-2) and human parainfluenza virus 4 (HPIV-4) are significant but underappreciated respiratory pathogens, particu

Goya & Greninger sequenced human parainfluenza virus genomes, with their findings highlighting distinct evolutionary histories of HPIV-2 and HPIV-4, raising hypotheses around complex Paramyxoviridae zoonotic events.

🔗 doi.org/10.1093/molbev/msaf217

#evobio #molbio #virus

Phylogenetic Comparative Approach Reveals Evolutionary Conservatism, Ancestral Composition, and Integration of Vertebrate Gut Microbiota Abstract. How host-associated microbial communities evolve as their hosts diversify remains equivocal: how conserved is their composition? What was the com

The extent to which closely related hosts share similar gut microbiota fascinates me. Work that truely stands out to me comes from @bperezlamarque.bsky.social and colleagues using process-based modelling over correlative approaches - a 'must' read #mevosky academic.oup.com/mbe/article/...

Congratulations on this excellent article, Anastasia and team!

The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies Abstract. Recent breakthroughs have enabled the accurate inference of large-scale genealogies. Through modelling the impact of recombination on the correla

Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)

From Binding to Catalysis: Emergence of a Rudimentary Enzyme Conferring Intrinsic Antibiotic Resistance Abstract. How does enzymatic activity emerge? To shed light on this fundamental question, we study type B dihydrofolate reductases (DfrB), which were disco

@claudele.bsky.social et al. studied the fundamental question of how enzymatic activity emerges by focusing on type B dihydrofolate reductases, suggesting DfrB domains evolved rudimentary catalysis from a binding capacity.

🔗 doi.org/10.1093/molbev/msaf215

#evobio #molbio

Introducing the Y-chromosomal Ancestral-like Reference Sequence—Improving the Capture of Human Evolutionary Information. #Ychromosome #EvolutionaryInformation #GeneticVariants #HumanGenome @molbioevol.bsky.social 🧬 🖥️
academic.oup.com/mbe/article/...

eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA Abstract. Extrachromosomal circular DNA (eccDNA) refers to small, circular DNA molecules that originate from chromosomal sequences and are prevalent across

Zhang et al. eccDNABase, a comprehensive and curated resource for browsing, searching, and analyzing Extrachromosomal circular DNAs across multiple species.

🔗 doi.org/10.1093/molbev/msaf223

#evobio #molbio #compbio

Introducing the Y-chromosomal Ancestral-like Reference Sequence—Improving the Capture of Human Evolutionary Information Abstract. Reference sequences are essential for reproducible genetic analyses but are often chosen without regard to evolutionary relevance within the anal

Köksal et al. introduce the Y-chromosomal ancestral-like reference sequence to improve the detection of evolutionarily informative variants on the Y chromosome, and introduce the tool polaryzer to annotate variants in Y chromosome data

🔗 doi.org/10.1093/molbev/msaf222

#evobio #molbio

Flexibility in Gene Coexpression at Developmental and Evolutionary Timescales Abstract. The explosion of next-generation sequencing technologies has allowed researchers to move from studying single genes to studying thousands of gene

Fischer et al. characterize differences in gene network connectivity and density, suggesting that flexibility in gene coexpression relationships could promote evolvability.

🔗 doi.org/10.1093/molbev/msaf194

#evobio #molbio

Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors Abstract. Recent theoretical and algorithmic advances in introgression detection, coupled with the growing availability of genome-scale data, have highligh

Pang, Liu & Zhang combined theoretical analyses and simulations to evaluate the robustness of methods to detect gene flow in the face of rate variation across phylogenetic timescales.

🔗 doi.org/10.1093/molbev/msaf216

#evobio #molbio

Great work, Sven and colleagues. Thank you for publishing your research with MBE!

Resolving the stasis-dynamism paradox: Genome evolution in tree ferns Abstract. The paradox of evolutionary stasis and dynamism—how morphologically static lineages persist through deep geological periods despite environmental

...and three more fern genomes @molbioevol.bsky.social !

Not-so-static static lineages!

academic.oup.com/mbe/advance-...

Evolutionary refinement of mitochondrial and plastid targeting sequences coincides with the late diversification of land plants Abstract. Plastids and mitochondria are key to plant survival and adaptation. The evolutionary progress of land plants (embryophytes) witnessed gene and ge

The evolution of land plants involved a charge-based adaption in the targeting sequences for #mitochondria and #chloroplasts and the origin of their de/phosphorylation.

#science 🧪

academic.oup.com/mbe/advance-...

We connected molecular signatures of selection with their mechanistic and functional relevance opening new ways of guiding experimental assays without requiring exhaustive testing of tens or hundreds of candidates.
Read in Molecular Biology and Evolution: academic.oup.com/mbe/advance-...

Molecular Biology and Evolution | October 2025 cover

The October cover of Molecular Biology and Evolution features the work of Han et al., who investigated the origins of East Asian domestic pigs.

🔗 doi.org/10.1093/molbev/msaf214

#evobio #molbio #domestication

General Principle of Neuronal Evolution Reveals a Human-Accelerated Neuron Type Potentially Underlying the High Prevalence of Autism in Humans | Molecular Biology and Evolution | Oxford Academic Abstract. The remarkable ability of a single genome sequence to encode a diverse collection of distinct cell types, including the thousands of cell types f

Fascinating paper on ASD in humans compared to other mammals.

tl;dr - very roughly: we have evolved some fancy neurons and selected for reduced expression of asd-related genes (which do not seem to cause autism in other mammals)

academic.oup.com/mbe/article/...

We have just hit our first 1,000 followers since joining Bluesky in April!

Thank you to all our followers, readers, and the authors of our articles for helping us promote the fantastic research published in Molecular Biology and Evolution!

Resolving the stasis-dynamism paradox: Genome evolution in tree ferns Abstract. The paradox of evolutionary stasis and dynamism—how morphologically static lineages persist through deep geological periods despite environmental

Resolving the stasis-dynamism paradox: Genome evolution in tree ferns url: academic.oup.com/mbe/article/..., nice work from @52ying.bsky.social!

Spectral Tuning in Mammalian Melanopsins Abstract. Melanopsin is a light-sensitive G-protein coupled receptor responsible for essential visual and non-visual light-mediated behaviors in mammals. H

McDowell et al. find that melanopsin spectral sensitivity is constrained across mammalian species via molecular mechanisms that are substantially distinct from those of other opsins.

🔗 doi.org/10.1093/molbev/msaf158

#evobio #molbio #opsins