Molecular Biology and Evolution

Molecular phylogeny of the SELMA translocation machinery recounts the evolution of complex photosynthetic eukaryotes Abstract. Photosynthetic eukaryotes and their relatives are the result of an intricate evolutionary history involving a series of plastid acquisitions thro

🚨 Fresh off the press! We have just published our paper on the evolution of the SELMA translocon of red secondary plastids‬. We analyze the phylogeny of each individual protein and the implications for the evolutionary history of the entire complex.

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

Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes Abstract. Horizontal gene transfer (HGT) is less frequent in eukaryotes than in prokaryotes, yet can have strong functional implications and was proposed a

New paper in Molecular Biology and Evolution using @gbif.org mediated data:

Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes

#CiteTheDOI: ❌

https://doi.org/10.1093/molbev/msaf107

@haoranxue.bsky.social
@stepheniwright.bsky.social

The August cover of Molecular Biology and Evolution features the work of Xue et al., who describe the genetic architecture and supergene control of tristyly, in Eichhornia paniculata.

🔗 doi.org/10.1093/molbev/msaf170

🖌️ Diane K. Johnson and Elizabeth Campolin

#evobio #molbio #plantsky

Horizontal Gene Transfer Inference: Gene Presence–Absence Outperforms Gene Trees Abstract. Horizontal gene transfer is a fundamental driver of prokaryotic evolution, facilitating the acquisition of novel traits and adaptation to new env

@swstkm.bsky.social & @martinlercher.bsky.social evaluate HGT inference methods, showing that those analyzing gene family presence/absence patterns across species trees outperform approaches based on gene tree-species tree reconciliation.

🔗 doi.org/10.1093/molbev/msaf166

#evobio #molbio #HGT

Host-Associated Genetic Differentiation in the Face of Ongoing Gene Flow: Ecological Speciation in a Pathogenic Parasite of Freshwater Fish Abstract. Adaptive evolution in response to varying environments, leading to population divergence, is among the most intriguing processes of speciation. H

Nazarizadeh, @jstefka.bsky.social et al. investigate whether distinct fish host species impose different selective pressures on populations of the tapeworm parasite Ligula intestinalis; results support selection underlying ecological speciation.

🔗 doi.org/10.1093/molbev/msaf163

#evobio #molbio

Host-associated Genetic Differentiation in the Face of Ongoing Gene Flow: Ecological Speciation in a Pathogenic Parasite of Freshwater Fish Abstract. Adaptive evolution in response to varying environments, leading to population divergence, is among the most intriguing processes of speciation. H

Last chapter of my student Masoud Nazarizadeh's thesis, showcasing the emergence of host-selected parasite lineages in the presence of gene flow, was just published in MBE. Great job, Masoud! doi.org/10.1093/molb...

Thank you for publishing your work with MBE Nicolas!

Here I told the story about this project, which originated 15 years ago at an SMBE meeting.

bsky.app/profile/nico...

Integrative Genomic, Transcriptomic and Epigenomic Analysis Reveals cis-regulatory Contributions to High-altitude Adaptation in Tibetan Pigs Abstract. The Qinghai-Tibet Plateau, characterized by its extreme environmental conditions, presents significant challenges to life, making it an ideal reg

Using 484 genomes from Chinese and Western pig breeds across various altitudes, Lai et al. identify genomic targets of selection in Tibetan pigs, pinpointing the regulatory basis of high-altitude adaptation in these breeds.

🔗 doi.org/10.1093/molbev/msaf169

#evobio #molbio #altitude

Compensatory Evolution Following Deleterious Episodes of GC-biased Gene Conversion in Rodents Abstract. GC-biased gene conversion (gBGC) is a widespread evolutionary force associated with meiotic recombination that favors the accumulation of deleter

Riffis, Saclier & @nicolasgaltier.bsky.social analyzed coding sequences in murine rodents, finding that GC-biased gene conversion episodes caused deleterious AT→GC substitutions, followed by rapid compensatory evolution.

🔗 doi.org/10.1093/molbev/msaf168

#evobio #molbio

Check out our paper to explore how the evolutionary history of SELMA supports or challenges various hypotheses on the origin of red complex plastids.

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

Connectivity and Adaptation Patterns of the Deep-Sea Ground-Forming Sponge Geodia hentscheli Across Its Entire Distribution Abstract. Geodia hentscheli, a species forming sponge grounds in the North Atlantic and Arctic Oceans, is a common deep-sea organism, that plays a fundamen

New research led by Museo Nacional de Ciencias Naturales and involving School of Ocean Sciences @bangoruniversity.bsky.social found genetic connectivity in a deep sea species over 1000s of km, but genetic isolation over depth. Read all about it here:
academic.oup.com/mbe/article/...

Convolutional neural networks can improve accuracy and robustness in detecting positive selection in coding sequences, particularly in the presence of alignment errors, compared to traditional statistical methods. Trained on simulated data, the model performs well across varying levels of sequence divergence and offers faster inference.

West et al. apply convolutional neural network models to detect selection across a specific range of phylogenetic scenarios and evolutionary modes, showing it is an accurate and scalable method for large-scale, multigene analyses.

🔗 doi.org/10.1093/molbev/msaf154

#evobio #molbio #selection

Pospelova et al. present a comparative analysis of adaptive immune loci across diverse mammalian species, uncovering relationships between locus architecture, characteristics of immune genes, and population dynamics. The artwork illustrates how the structure of immunoglobulin heavy chain loci influences gene variability in three representative species from the study – the mountain lion, the ring-tailed lemur, and European hedgehog.

Pospelova et al. present a comparative analysis of full-length sequences of IG/TR loci across 46 mammalian species, demonstrating these as rapidly evolving genomic regions, with implications for immunogenomics.

🔗 doi.org/10.1093/molbev/msaf152

#evobio #molbio

The evolution of bird viruses remains obscure - He et al. perform phylogenomic mining of endogenous retroviruses in 758 bird genomes, revealing a highly diverse and complex retrovirus repertoire in birds.

🔗 doi.org/10.1093/molbev/msaf171

#evobio #molbio #virus #birds

Divergence of Leptin Receptor and Interleukin-6 Receptor Subunit b in Early Vertebrate Evolution and Physiological Insights from the Sea Lamprey Abstract. Current knowledge of class-I cytokine receptors comes primarily from studies in jawed vertebrates (gnathostomes), and their origin and evolution

Gong et al. employ structural, phylogenetic, and synteny analyses in sea lamprey to study the early evolution of class-I cytokine receptors and reveal diverse functions of the leptin signaling system in jawless vertebrates.

🔗 doi.org/10.1093/molbev/msaf157

#evobio #molbio

Nested Admixture During and After the Trans-Atlantic Slave Trade on the Island of São Tomé Abstract. Human genetic admixture, involving the contact between two or more previously isolated populations, can be a complex process influenced by social

To investigate the human genetic history of São Tomé island, Ciccarella et al. genotyped genome-wide SNP in 96 individuals, identifying five genetic clusters, retracing slave trade and labor-driven migrations, and identifying nested admixture.

🔗 doi.org/10.1093/molbev/msaf156

#evobio #molbio

Genome-wide Parallelism Underlies Rapid Freshwater Adaptation Fueled by Standing Genetic Variation in a Wild Fish Abstract. A fundamental focus of ecological and evolutionary biology is determining how natural populations adapt to environmental changes. Rapid parallel

Yang et al. compare four freshwater-resident populations of fish Neosalanx brevirostris with their common ancestral anadromous population, showing that rapid parallel adaptation to freshwater followed a complex but parallel polygenic architecture.

🔗 doi.org/10.1093/molbev/msaf160

#evobio #molbio

Thank you Alex for choosing to publish your fantastic work with MBE!

Repressive cytosine methylation is a marker of viral gene transfer across divergent eukaryotes Abstract. Cytosine DNA methylation patterns vary widely across eukaryotes, with its ancestral roles being understood to have included both transposable ele

Happy to see our latest work out in @molbioevol.bsky.social. We revisit the evolution of 5-methylcytosine across neglected eukaryotic supergroups, establishing an ancestral repressive role silencing genome invaders, both transposons and viral elements👾: academic.oup.com/mbe/advance-... 🧵 1/7

We are excited to announce the SMBE Fellows Program! ✍️

Designed to provide networking and mentorship opportunities to early-career researchers through scientific writing in evolutionary biology for @molbioevol.bsky.social and @genomebiolevol.bsky.social

📆 Aug. 31

🔗 smbe.org/smbe-fellows-program

A Trade-Off between Body Mass and Cancer Resistance in Cetaceans Is Mediated by Cell Cycle-Related Gene Evolution Abstract. Cetaceans, well-known for their exceptionally long lifespans and substantial body masses, demonstrate a lower risk of cancer mortality compared t

Sun et al. analyzed 50 cell cycle genes to study trade-offs between body size and cancer resistance in cetaceans, providing molecular support for Peto's paradox (no correlation between body size, lifespan, and cancer risk across species).

🔗 doi.org/10.1093/molbev/msaf159

#evobio #molbio #cancer

Dynamics of Deleterious Mutations and Purifying Selection in Small Population Isolates Abstract. The genomic consequences of prolonged population decline and isolation are increasingly recognized, but quantitative assessments of mutation load

Chen et al investigate deleterious mutations and purifying selection in 17 stickleback populations, finding that inbreeding predicts realized loads of deleterious mutations, and genomic consequences of isolation in small populations are predictable.

🔗 doi.org/10.1093/molbev/msaf110

#evobio #molbio

The MBE/GBE Associate editor's symposium is starting now.

@molbioevol.bsky.social • @genomebiolevol.bsky.social

#SMBE2025

Don't forget to stop by the Q&A session hosted by @molbioevol.bsky.social and @genomebiolevol.bsky.social, starting at 13h in building 8.

#SMBE2025

Long et al. integrate population genomics, experimental evolution, and environmental modeling to elucidate the evolutionary responses to climate change in Populus lasiocarpa.

This study has made the July cover of MBE.

🔗 doi.org/10.1093/molbev/msaf116

#evobio #molbio

📅 The day is today!

#SMBE2025 in Beijing starts now, as the registration desk opens to all participants.

Join us for five days full of the latest discoveries in molecular biology and evolution 🧬 We hope all attendees enjoy the many opportunities for discussion and networking among our community.

Extensive Recombination Suppression and Genetic Degeneration of a Young ZW Sex Chromosome System in Halfbeak Fish Abstract. Sex chromosome systems have evolved independently across the tree of life, at different times in the past, and the evolutionary consequences of l

Xing et al. study sex chromosome evolution in two species of halfbeak fish, identifying a large sex-linked ZW region in Hyporhamphus sajori and a small sex-linked region on a different chromosome, with male heterogamety, in H. intermedius.

🔗 doi.org/10.1093/molbev/msaf151

#evobio #molbio

The recent article by Walunjkar et al. on the evolution of protein thermostability is the focus of this month's Highlight feature.

Highlight: Cellular Environment and Protein Structure Help Organisms Cope with Temperature Stress

🔗 doi.org/10.1093/molbev/msaf155

#evobio #molbio