Molecular Biology and Evolution
@molbioevol.bsky.social
MBE publishes fresh insights into the patterns and processes that impact the evolution of life at molecular levels.
🔗 academic.oup.com/mbe
🏠 @official-smbe.bsky.social
🤝 @genomebiolevol.bsky.social
#evobio #molbio #science #biology #societyjournal
🔗 academic.oup.com/mbe
🏠 @official-smbe.bsky.social
🤝 @genomebiolevol.bsky.social
#evobio #molbio #science #biology #societyjournal
Pinned
The November cover of Molecular Biology and Evolution features the work of Povilus et al., who examined DNA methylation and genetic imprinting in water lily endosperm.
🔗 doi.org/10.1093/molbev/msaf271
#evobio #molbio #PlantSky #epigenetics
🔗 doi.org/10.1093/molbev/msaf271
#evobio #molbio #PlantSky #epigenetics
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
🔗 doi.org/10.1093/molbev/msaf284
#evobio #molbio #eusociality
November 25, 2025 at 1:46 PM
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
🔗 doi.org/10.1093/molbev/msaf284
#evobio #molbio #eusociality
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
🔗 doi.org/10.1093/molbev/msaf264
#evobio #molbio #epistasis
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
doi.org
November 25, 2025 at 1:28 PM
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
🔗 doi.org/10.1093/molbev/msaf264
#evobio #molbio #epistasis
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
🔗 doi.org/10.1093/molbev/msaf289
#evobio #molbio
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
doi.org
November 25, 2025 at 1:21 PM
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
🔗 doi.org/10.1093/molbev/msaf289
#evobio #molbio
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
🔗 doi.org/10.1093/molbev/msaf287
#evobio #molbio #yeast
November 25, 2025 at 1:15 PM
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
🔗 doi.org/10.1093/molbev/msaf287
#evobio #molbio #yeast
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
🔗 doi.org/10.1093/molbev/msaf285
#evobio #molbio
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
doi.org
November 25, 2025 at 1:08 PM
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
🔗 doi.org/10.1093/molbev/msaf285
#evobio #molbio
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
🔗 doi.org/10.1093/molbev/msaf262
#evobio #molbio #inversions
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
doi.org
November 24, 2025 at 10:33 AM
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
🔗 doi.org/10.1093/molbev/msaf262
#evobio #molbio #inversions
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
🔗 doi.org/10.1093/molbev/msaf286
#evobio #molbio #cichlids #opsins
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
doi.org
November 24, 2025 at 10:21 AM
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
🔗 doi.org/10.1093/molbev/msaf286
#evobio #molbio #cichlids #opsins
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
🔗 doi.org/10.1093/molbev/msaf271
#evobio #molbio #PlantSky
November 24, 2025 at 9:56 AM
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
🔗 doi.org/10.1093/molbev/msaf271
#evobio #molbio #PlantSky
Reposted by Molecular Biology and Evolution
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-...
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
academic.oup.com
November 21, 2025 at 10:11 AM
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-...
Reposted by Molecular Biology and Evolution
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.
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.
Validate User
academic.oup.com
November 14, 2025 at 6:12 PM
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.
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.
Reposted by Molecular Biology and Evolution
#microsky #phagesky #phage
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
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
academic.oup.com
November 23, 2025 at 4:39 PM
#microsky #phagesky #phage
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Howell et al. used WGS of wild-caught deer mice from two islands and one mainland location in British Columbia to investigate chromosomal inversions and non-equilibrium demographic history of this species.
🔗 doi.org/10.1093/molbev/msaf254
#evobio #molbio #peromyscus
🔗 doi.org/10.1093/molbev/msaf254
#evobio #molbio #peromyscus
The Genomic Imprint of Chromosomal Inversions and Demographic History in Island Populations of Deer Mice
Abstract. Populations that colonize islands experience novel selective pressures, fluctuations in size, and changes to their connectivity. Owing to their u
doi.org
November 21, 2025 at 12:19 PM
Howell et al. used WGS of wild-caught deer mice from two islands and one mainland location in British Columbia to investigate chromosomal inversions and non-equilibrium demographic history of this species.
🔗 doi.org/10.1093/molbev/msaf254
#evobio #molbio #peromyscus
🔗 doi.org/10.1093/molbev/msaf254
#evobio #molbio #peromyscus
Maclary & Shapiro used comparative genomics to examine coding variation in EDNRB2, a candidate gene for loss of plumage melanin across birds, finding widespread coding variation in EDNRB2 and other pigmentation genes with limited pleiotropy.
🔗 doi.org/10.1093/molbev/msaf267
#evobio #molbio #color
🔗 doi.org/10.1093/molbev/msaf267
#evobio #molbio #color
Widespread Variation in EDNRB2 Is Associated With Diverse Melanin Loss Phenotypes Across Avian Species
Abstract. Plumage pigmentation plays critical roles in survival and reproductive success in birds, from providing camouflage and thermoregulation to mediat
doi.org
November 21, 2025 at 12:15 PM
Maclary & Shapiro used comparative genomics to examine coding variation in EDNRB2, a candidate gene for loss of plumage melanin across birds, finding widespread coding variation in EDNRB2 and other pigmentation genes with limited pleiotropy.
🔗 doi.org/10.1093/molbev/msaf267
#evobio #molbio #color
🔗 doi.org/10.1093/molbev/msaf267
#evobio #molbio #color
Price et al. characterized germline and somatic intercellular bridges in the cnidarian Hydra vulgaris, revealing that the molecular and structural features of intercellular bridges in Hydra are conserved across lineages.
🔗 doi.org/10.1093/molbev/msaf248
#evobio #molbio #hydra
🔗 doi.org/10.1093/molbev/msaf248
#evobio #molbio #hydra
November 21, 2025 at 12:10 PM
Price et al. characterized germline and somatic intercellular bridges in the cnidarian Hydra vulgaris, revealing that the molecular and structural features of intercellular bridges in Hydra are conserved across lineages.
🔗 doi.org/10.1093/molbev/msaf248
#evobio #molbio #hydra
🔗 doi.org/10.1093/molbev/msaf248
#evobio #molbio #hydra
Reposted by Molecular Biology and Evolution
Very pleased to see this one out. Unexpected and fascinating finding. I look forward to follow-up on this story 😁
Roussel, Suh, @fjruizruano.bsky.social & @amdioncote.bsky.social characterized TE content in naturally occurring killifish hybrids, finding higher TE load and accumulation of Neptune subfamilies in hybrids.
🔗 doi.org/10.1093/molbev/msaf266
#evobio #molbio #TEsky
🔗 doi.org/10.1093/molbev/msaf266
#evobio #molbio #TEsky
Accumulation of a Biparentally Inherited Neptune Transposable Element in Natural Killifish Hybrids (Fundulus diaphanus × F. heteroclitus)
Abstract. Transposable elements (TEs) are abundant selfish genetic elements that can mobilize in their host genome, causing DNA damage, mutations, and chro
doi.org
November 20, 2025 at 4:44 PM
Very pleased to see this one out. Unexpected and fascinating finding. I look forward to follow-up on this story 😁
In a new MBE Perspective, @jomcinerney.bsky.social introduces the concepts of epaktovars and xenotypes, providing a framework for describing phenotypic convergence and shared genetic material resulting from gene transfer across diverse lineages.
🔗 doi.org/10.1093/molbev/msaf279
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf279
#evobio #molbio
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes
Abstract. The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomi
doi.org
November 20, 2025 at 3:48 PM
In a new MBE Perspective, @jomcinerney.bsky.social introduces the concepts of epaktovars and xenotypes, providing a framework for describing phenotypic convergence and shared genetic material resulting from gene transfer across diverse lineages.
🔗 doi.org/10.1093/molbev/msaf279
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf279
#evobio #molbio
Aharonoff et al. show that dosage compensation mechanisms continue to evolve in species with shared X chromosome ancestry, and that the process of evolving chromosome-wide gene regulatory mechanisms is constrained.
🔗 doi.org/10.1093/molbev/msaf270
#evobio #molbio #celegans
🔗 doi.org/10.1093/molbev/msaf270
#evobio #molbio #celegans
Parallel Evolution of X Chromosome-Specific Structural Maintenance of Chromosomes Complexes in Two Nematode Lineages
Abstract. Mechanisms of X chromosome dosage compensation have been studied in model organisms with distinct sex chromosome ancestry. However, the diversity
doi.org
November 20, 2025 at 2:57 PM
Aharonoff et al. show that dosage compensation mechanisms continue to evolve in species with shared X chromosome ancestry, and that the process of evolving chromosome-wide gene regulatory mechanisms is constrained.
🔗 doi.org/10.1093/molbev/msaf270
#evobio #molbio #celegans
🔗 doi.org/10.1093/molbev/msaf270
#evobio #molbio #celegans
Meneguzzi et al. combined targeted enrichment with long-read sequencing to create the TELSVirus workflow for rapid detection and genomic characterization of multiple low-abundance viruses from single samples using long-read sequencing.
🔗 doi.org/10.1093/molbev/msaf261
#evobio #molbio #virus
🔗 doi.org/10.1093/molbev/msaf261
#evobio #molbio #virus
Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples
Abstract. At present, no single workflow is available for quick and accurate identification and analysis of genomes of various viruses present together in
doi.org
November 20, 2025 at 2:53 PM
Meneguzzi et al. combined targeted enrichment with long-read sequencing to create the TELSVirus workflow for rapid detection and genomic characterization of multiple low-abundance viruses from single samples using long-read sequencing.
🔗 doi.org/10.1093/molbev/msaf261
#evobio #molbio #virus
🔗 doi.org/10.1093/molbev/msaf261
#evobio #molbio #virus
Roussel, Suh, @fjruizruano.bsky.social & @amdioncote.bsky.social characterized TE content in naturally occurring killifish hybrids, finding higher TE load and accumulation of Neptune subfamilies in hybrids.
🔗 doi.org/10.1093/molbev/msaf266
#evobio #molbio #TEsky
🔗 doi.org/10.1093/molbev/msaf266
#evobio #molbio #TEsky
Accumulation of a Biparentally Inherited Neptune Transposable Element in Natural Killifish Hybrids (Fundulus diaphanus × F. heteroclitus)
Abstract. Transposable elements (TEs) are abundant selfish genetic elements that can mobilize in their host genome, causing DNA damage, mutations, and chro
doi.org
November 20, 2025 at 2:45 PM
Roussel, Suh, @fjruizruano.bsky.social & @amdioncote.bsky.social characterized TE content in naturally occurring killifish hybrids, finding higher TE load and accumulation of Neptune subfamilies in hybrids.
🔗 doi.org/10.1093/molbev/msaf266
#evobio #molbio #TEsky
🔗 doi.org/10.1093/molbev/msaf266
#evobio #molbio #TEsky
Chen et al. present the v4 upgrade of the DIVERGE software for identifying amino acid residues critical to functional shifts between protein subfamilies, including DIVERGE-Chat, a conversational AI agent for code-free exploration.
🔗 doi.org/10.1093/molbev/msaf277
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msaf277
#evobio #molbio #compbio
November 19, 2025 at 1:20 PM
Chen et al. present the v4 upgrade of the DIVERGE software for identifying amino acid residues critical to functional shifts between protein subfamilies, including DIVERGE-Chat, a conversational AI agent for code-free exploration.
🔗 doi.org/10.1093/molbev/msaf277
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msaf277
#evobio #molbio #compbio
He et al. sequenced whole genomes from 21 Tibeto-Burman-speaking groups and genotyped individuals from 60 Sino-Tibetan-speaking groups to reconstruct the origins of Tibeto-Burman populations on the eastern Tibetan Plateau.
🔗 doi.org/10.1093/molbev/msaf258
#evobio #molbio #humanevolution
🔗 doi.org/10.1093/molbev/msaf258
#evobio #molbio #humanevolution
November 18, 2025 at 11:21 AM
He et al. sequenced whole genomes from 21 Tibeto-Burman-speaking groups and genotyped individuals from 60 Sino-Tibetan-speaking groups to reconstruct the origins of Tibeto-Burman populations on the eastern Tibetan Plateau.
🔗 doi.org/10.1093/molbev/msaf258
#evobio #molbio #humanevolution
🔗 doi.org/10.1093/molbev/msaf258
#evobio #molbio #humanevolution
Zhang et al. present NeuralNJ, an accurate and efficient approach to phylogenetic inference whose innovation lies in a learnable neighbor joining mechanism, which iteratively joins neighbors guided by learned priority scores for tree reconstruction
🔗 doi.org/10.1093/molbev/msaf260
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf260
#evobio #molbio
Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning
Abstract. Accurate phylogenetic inference is crucial for understanding evolutionary relationships among species. Deep learning technique has been introduce
doi.org
November 18, 2025 at 11:17 AM
Zhang et al. present NeuralNJ, an accurate and efficient approach to phylogenetic inference whose innovation lies in a learnable neighbor joining mechanism, which iteratively joins neighbors guided by learned priority scores for tree reconstruction
🔗 doi.org/10.1093/molbev/msaf260
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf260
#evobio #molbio
Reposted by Molecular Biology and Evolution
New work led by members of the @rokaslab.bsky.social! ☺️ 1,154 yeast genomes in the Saccharomycotina subphylum were surveyed for their relationship between reduced gene repertoires broadly associated with genome stability functions and elevated evolutionary rates.🧬
academic.oup.com/mbe/advance-...
academic.oup.com/mbe/advance-...
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
academic.oup.com
November 11, 2025 at 4:51 PM
New work led by members of the @rokaslab.bsky.social! ☺️ 1,154 yeast genomes in the Saccharomycotina subphylum were surveyed for their relationship between reduced gene repertoires broadly associated with genome stability functions and elevated evolutionary rates.🧬
academic.oup.com/mbe/advance-...
academic.oup.com/mbe/advance-...
Reposted by Molecular Biology and Evolution
OMG MY ACYANIC SNAPDRAGON MUTANT IS SELF COMPATIBLE!!!
All my other ones need to be crossed since they have an s-locus self incompatibility.
THIS ONE DOESN'T????
Reference:
academic.oup.com/mbe/article/...
All my other ones need to be crossed since they have an s-locus self incompatibility.
THIS ONE DOESN'T????
Reference:
academic.oup.com/mbe/article/...
November 12, 2025 at 8:09 PM
OMG MY ACYANIC SNAPDRAGON MUTANT IS SELF COMPATIBLE!!!
All my other ones need to be crossed since they have an s-locus self incompatibility.
THIS ONE DOESN'T????
Reference:
academic.oup.com/mbe/article/...
All my other ones need to be crossed since they have an s-locus self incompatibility.
THIS ONE DOESN'T????
Reference:
academic.oup.com/mbe/article/...
Reposted by Molecular Biology and Evolution
New guidelines for discrete #phylogeography introduce an adjusted Bayes factor (BFₐ𝑑𝑗) that integrates sampling-state abundance, reducing false positives in lineage transition inference under bias. #Phylodynamics #Bioinformatics 🧬📊
📄 https://doi.org/10.1093/molbev/msaf253
👤 EVBC: Simon Dellicour
📄 https://doi.org/10.1093/molbev/msaf253
👤 EVBC: Simon Dellicour
doi.org
November 15, 2025 at 10:56 AM
New guidelines for discrete #phylogeography introduce an adjusted Bayes factor (BFₐ𝑑𝑗) that integrates sampling-state abundance, reducing false positives in lineage transition inference under bias. #Phylodynamics #Bioinformatics 🧬📊
📄 https://doi.org/10.1093/molbev/msaf253
👤 EVBC: Simon Dellicour
📄 https://doi.org/10.1093/molbev/msaf253
👤 EVBC: Simon Dellicour