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
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
This blog post by @jaisonjseq.bsky.social reminds us of how attending scientific meetings can be a great opportunity to expand your academic network - in his case, leading to collaboration in our new GHIST paper.
Read more on GHIST in this month's issue of MBE: doi.org/10.1093/molbev/msaf257
Read more on GHIST in this month's issue of MBE: doi.org/10.1093/molbev/msaf257
Check out my blog summarising my experience at the SMBE2024 conference. You can also learn about my recent work on the Proto-Dravidian ancestry component. @official-smbe.bsky.social @mitopr.bsky.social @mashaals.bsky.social @ryangutenkunst.bsky.social popgenworld.blogspot.com/2025/11/from...
From Conference Attendee to Co-Author: The Journey I Never Expected
F or years, I dreamed of it: standing in a room full of international scientists, sharing my research, and being a part of the global conv...
popgenworld.blogspot.com
November 14, 2025 at 3:53 PM
This blog post by @jaisonjseq.bsky.social reminds us of how attending scientific meetings can be a great opportunity to expand your academic network - in his case, leading to collaboration in our new GHIST paper.
Read more on GHIST in this month's issue of MBE: doi.org/10.1093/molbev/msaf257
Read more on GHIST in this month's issue of MBE: doi.org/10.1093/molbev/msaf257
Dias et al. used genetic data from 27 Drosophilidae species and 6 outgroups to reconstruct the evolutionary relationships of fruit flies, recovering Drosophilidae as nonmonophyletic, underscoring the need for taxonomic revision.
🔗 doi.org/10.1093/molbev/msaf269
#evobio #molbio #drosophila
🔗 doi.org/10.1093/molbev/msaf269
#evobio #molbio #drosophila
November 14, 2025 at 10:46 AM
Dias et al. used genetic data from 27 Drosophilidae species and 6 outgroups to reconstruct the evolutionary relationships of fruit flies, recovering Drosophilidae as nonmonophyletic, underscoring the need for taxonomic revision.
🔗 doi.org/10.1093/molbev/msaf269
#evobio #molbio #drosophila
🔗 doi.org/10.1093/molbev/msaf269
#evobio #molbio #drosophila
Our recent article on GHIST, the community competition to benchmark methods in genomic history inference, is the focus of this month's Highlight.
Highlight: Community Tournament GHIST Fuels Advances in Computational Genetics
🔗 doi.org/10.1093/molbev/msaf278
#evobio #molbio #compbio
Highlight: Community Tournament GHIST Fuels Advances in Computational Genetics
🔗 doi.org/10.1093/molbev/msaf278
#evobio #molbio #compbio
November 14, 2025 at 9:32 AM
Our recent article on GHIST, the community competition to benchmark methods in genomic history inference, is the focus of this month's Highlight.
Highlight: Community Tournament GHIST Fuels Advances in Computational Genetics
🔗 doi.org/10.1093/molbev/msaf278
#evobio #molbio #compbio
Highlight: Community Tournament GHIST Fuels Advances in Computational Genetics
🔗 doi.org/10.1093/molbev/msaf278
#evobio #molbio #compbio
Hart et al. integrated cell biology, phylogenetics, transcriptomics, and genomics to investigate Trichomonas–bacteria interactions, identifying a conserved molecular toolkit that targets bacterial peptidoglycan and its precursor.
🔗 doi.org/10.1093/molbev/msaf276
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf276
#evobio #molbio
November 14, 2025 at 8:51 AM
Hart et al. integrated cell biology, phylogenetics, transcriptomics, and genomics to investigate Trichomonas–bacteria interactions, identifying a conserved molecular toolkit that targets bacterial peptidoglycan and its precursor.
🔗 doi.org/10.1093/molbev/msaf276
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf276
#evobio #molbio
The origin of plasmid core genes remains poorly understood - Picazo et al. show that acquisition of LLP-1/LPP-2 plasmids by the bacteria Pantoea introduced genetic redundancy with chromosomal genes, followed by waves of differential gene loss.
🔗 doi.org/10.1093/molbev/msaf273
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf273
#evobio #molbio
November 14, 2025 at 8:36 AM
The origin of plasmid core genes remains poorly understood - Picazo et al. show that acquisition of LLP-1/LPP-2 plasmids by the bacteria Pantoea introduced genetic redundancy with chromosomal genes, followed by waves of differential gene loss.
🔗 doi.org/10.1093/molbev/msaf273
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf273
#evobio #molbio
Reposted by Molecular Biology and Evolution
I am happy to share our manuscript summarising the outcome of GHIST2024 (ghist.bio). With so many statistical tools and software, population genetics research seems easy. But every case is different. The approaches used vary! doi.org/10.1093/molbev/msaf257 @ryangutenkunst.bsky.social
GHIST 2024: The First Genomic History Inference Strategies Tournament
Abstract. Evaluating population genetic inference methods is challenging due to the complexity of evolutionary histories, potential model misspecification,
doi.org
November 14, 2025 at 2:05 AM
I am happy to share our manuscript summarising the outcome of GHIST2024 (ghist.bio). With so many statistical tools and software, population genetics research seems easy. But every case is different. The approaches used vary! doi.org/10.1093/molbev/msaf257 @ryangutenkunst.bsky.social
Zhou et al. present SMTdb, a spatial meta-transcriptome database that provides insights into the abundance, distribution, and enriched tumor microenvironment regions of 1,218 microbiota in spatial tissue slices.
🔗 doi.org/10.1093/molbev/msaf263
#evobio #molbio #cancer
🔗 doi.org/10.1093/molbev/msaf263
#evobio #molbio #cancer
November 7, 2025 at 9:35 AM
Zhou et al. present SMTdb, a spatial meta-transcriptome database that provides insights into the abundance, distribution, and enriched tumor microenvironment regions of 1,218 microbiota in spatial tissue slices.
🔗 doi.org/10.1093/molbev/msaf263
#evobio #molbio #cancer
🔗 doi.org/10.1093/molbev/msaf263
#evobio #molbio #cancer
Reposted by Molecular Biology and Evolution
This year's competition features demographic history inference and sweep detection. It closes in 1 week, so there's still time to enter! ghist.bio
November 6, 2025 at 4:22 PM
This year's competition features demographic history inference and sweep detection. It closes in 1 week, so there's still time to enter! ghist.bio
Community competitions help benchmark approaches in computational biology. Struck et al. now present GHIST 2024 - The First Genomic History Inference Strategies Tournament, for the inference of evolutionary history from genome data.
🔗 doi.org/10.1093/molbev/msaf257
#evobio #molbio #compbio #popgen
🔗 doi.org/10.1093/molbev/msaf257
#evobio #molbio #compbio #popgen
November 6, 2025 at 3:20 PM
Community competitions help benchmark approaches in computational biology. Struck et al. now present GHIST 2024 - The First Genomic History Inference Strategies Tournament, for the inference of evolutionary history from genome data.
🔗 doi.org/10.1093/molbev/msaf257
#evobio #molbio #compbio #popgen
🔗 doi.org/10.1093/molbev/msaf257
#evobio #molbio #compbio #popgen
Independently evolved supergenes control colony social organization and queen reproductive strategies in several ant lineages. Sigeman et al. uncover a novel 9 Mb supergene controlling queen size and social organization in Myrmica ruginodis.
🔗 doi.org/10.1093/molbev/msaf255
#evobio #molbio #ants
🔗 doi.org/10.1093/molbev/msaf255
#evobio #molbio #ants
November 5, 2025 at 11:24 AM
Independently evolved supergenes control colony social organization and queen reproductive strategies in several ant lineages. Sigeman et al. uncover a novel 9 Mb supergene controlling queen size and social organization in Myrmica ruginodis.
🔗 doi.org/10.1093/molbev/msaf255
#evobio #molbio #ants
🔗 doi.org/10.1093/molbev/msaf255
#evobio #molbio #ants
Calvelo et al. present a comprehensive analysis of spliced leader (SL) trans-splicing of mRNA using genomic/ transcriptomic data of 24 cestode and trematode species, identifying a main pattern of concerted evolution of SL-RNA loci in most flatworms.
🔗 doi.org/10.1093/molbev/msaf228
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf228
#evobio #molbio
Evolution of SL-RNA Genes and Their Splicing Targets in Parasitic Flatworms
Abstract. Spliced leader (SL) trans-splicing is a key step in the processing of many mRNAs in different eukaryotic lineages, including in parasitic flatwor
doi.org
November 4, 2025 at 11:27 AM
Calvelo et al. present a comprehensive analysis of spliced leader (SL) trans-splicing of mRNA using genomic/ transcriptomic data of 24 cestode and trematode species, identifying a main pattern of concerted evolution of SL-RNA loci in most flatworms.
🔗 doi.org/10.1093/molbev/msaf228
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf228
#evobio #molbio