#evobio — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #evobio, aggregated by home.social.
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IAP proteins play central roles in regulating apoptosis - Lopes et al. show that IAP expansion in animals has repeatedly emerged through lineage-specific duplication events
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Goff et al. measure collateral fitness landscapes of TEM-1 β-lactamase in conditions expected to alter protein aggregation or stability, proposing that mutational destabilization is associated with deleterious collateral fitness effects.
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Li et al. present a genomic reassessment of the endangered black-and-white snub-nosed monkey, suggesting the species is divided into five genetically distinct clusters.
🔗 doi.org/10.1093/molbev/msag104
📷 Xinming He
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The May issue of MBE is here, featuring the work of Topaloudis et al., who evaluated genotype imputation accuracy in a large barn owl low-coverage WGS dataset.
🔗 https://academic.oup.com/mbe/issue/43/5
📷 Alex Labhardt
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Berruga-Fernández et al. show that bacterial hybrid chromosome formation driven by conjugative mobile genetic elements may be an important and widespread mechanism in the emergence and evolution of high-risk bacterial pathogens.
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Ceriotti et al. investigate the rewiring of organellar translation in the holoparasitic Balanophoraceae, revealing extreme changes in the anciently conserved machinery of plant organellar translation.
🔗 https://doi.org/10.1093/molbev/msag077
📷 Tuber and two inflorescences of the holoparasitic plant Lophophytum pyramidale collected from Parque Nacional Calilegua, Argentina
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Pinto et al. present SCINKD as a framework to identify unannotated sex chromosomes and curate diploid genome assemblies from a single individual.
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Cui et al. investigate the evolutionary trajectory leading to dim-light vision in vertebrates, concluding that it evolved via three main stages of molecular adaptation, at the origins of ancestral rhodopsin pigments.
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Cochetel & Cantu publish a new MBE Review on plant pangenomes, outlining major paradigms from gene-based catalogs to haplotype-resolved graphs, core and variable compartments, and how graph-based frameworks enable analyses that are difficult with single linear references.
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MBE's April issue Highlight features the article by Ewan Harney and Josefa González on transgenerational inheritance of heat shock responses in fruit flies, written by SMBE Fellow Shady Kuster.
"A gift from a great-grand-fly—transgenerational epigenetic inheritance of heat shock response"
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Didelot et al. present the R package DiagnoDating for diagnosing issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking and residual analysis.
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Bazzicalupo et al analyzed introgression in Iberian and Eurasian lynx with the application of a deep convolutional neural network, detecting specific regions of the genome with signals of gene flow in three populations of these species.
🖌️Paula Martin Art
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Böhm et al. resolve the structural basis of the NADP-malic enzyme divergence in C4 isoforms and propose that tetramerization mitigates aggregation at the high expression levels demanded by the C4 cycle.
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Ewan Harney & Josefa González show evidence of transgenerational developmental plasticity as a result of heat shock in fruit flies, documenting gene expression and phenotype changes 3+ generations following heat shock.
🔗 https://doi.org/10.1093/molbev/msag069
This study is featured in our newest Highlight article, by SMBE Fellow Shady Kuster:
Highlight: A gift from a great-grand-fly—transgenerational epigenetic inheritance of heat shock response
🔗 https://doi.org/10.1093/molbev/msag083 -
Wang et al. analyzed the genomes of three Mauritius bird species that experienced extreme population bottlenecks, showing that evolutionary context is essential for interpreting genomic risk.
📷 Gregory Guida
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Tan et al. present panCG, an integrative pipeline for family-level super-pangenome analysis across coding and noncoding sequences, enabling the reference-free construction of pangene and pan-conserved noncoding sequences.
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MBE is excited to launch our newest Call for Papers on the Major Transitions of Life, covering all aspects of phylogenomic research.
🔗 academic.oup.com/mbe/pages/call-for-papers-on-the-major-transitions-of-life
Guest Editors:
Davide Pisani
Anja SpangAccepted manuscripts will receive a 20% discount on the APCs, on top of the SMBE membership discount.
Toward a genomic understanding of the tree of life
🔗 https://doi.org/10.1093/molbev/msag043 -
Glass et al. review recent progress in understanding NF-κB transcription factors in unicellular holozoans, Porifera, Placozoa, and Cnidaria, which are involved in multiple biological functions.
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The April issue of Molecular Biology and Evolution features the work of Gu et al., who performed large-scale phylogenomic analyses of the white-bellied pangolin.
🔗 https://academic.oup.com/mbe/issue/43/4
🖌️ Ting Bai
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Yang et al. sequenced ancient individuals from the Bronze Age to historical periods in Xinjiang, revealing divergent genetic profiles of the western and eastern Tianshan, underscoring a complex population-culture interplay.
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Li et al. studied the genomic basis of mimicry in Epicopeiidae moths, finding that TE-driven regulatory innovation rewired developmental gene networks, facilitating the emergence of multiple mimetic forms.
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Daniel Huson introduces displacement-optimized tanglegrams (DO-tanglegrams), a new approach that applies equally to trees and rooted phylogenetic networks, performing better than cophylo on trees and then NN-tanglegram on networks.
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McArthur et al. present piqtree, an easy to use, open-source Python package that provides Python script-based control of IQ-TREE’s phylogenetic inference engine.
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Xuhua Xia shows that codon usage in bacteria is more optimized in long ribosomal protein genes; results demonstrate that translation optimization reflects functional stoichiometry and protein length constraints.
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@sishuowang & Meade introduce phyloHessian to enable the use of complex mixture substitution models in molecular dating. Empirical analysis of ancient symbiont lineages leads to a revised understanding of their host association origins.
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Robbins, Liu & Kelly present RECUR, a method for identifying recurrent amino acid substitutions from multiple sequence alignments that is fast, easy to use, and scalable to thousands of sequences.
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Deng et al. present TreeProfiler, a tool for automated annotation and interactive exploration of hundreds of features along large gene and species trees, with seamless summarization of mapped traits at internal nodes.
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Martí-Gómez et al. developed gpmap-tools, integrating models for inference, phenotypic imputation, and error estimation from multiplex assays of variant effect data or natural sequences in the presence of genetic interactions.
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Ramos-González et al. present PharaohFUN, a web application designed for the evolutionary and functional analysis of protein sequences in photosynthetic eukaryotes, leveraging orthology relationships.
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Shankar et al. present the updated MicrobeTrace 2.0 as a next-generation, interoperable tool for genomic epidemiology and data-driven public health response.
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Song et al. discover and characterize three co-opted/captured ERV envelope gene clades, revealing that each plays a distinct and critical role in neural regulation, reproductive maturation, and viviparity in vertebrates.
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Song et al. discover and characterize three co-opted/captured ERV envelope gene clades, revealing that each plays a distinct and critical role in neural regulation, reproductive maturation, and viviparity in vertebrates.
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Song et al. discover and characterize three co-opted/captured ERV envelope gene clades, revealing that each plays a distinct and critical role in neural regulation, reproductive maturation, and viviparity in vertebrates.
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Song et al. discover and characterize three co-opted/captured ERV envelope gene clades, revealing that each plays a distinct and critical role in neural regulation, reproductive maturation, and viviparity in vertebrates.
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Song et al. discover and characterize three co-opted/captured ERV envelope gene clades, revealing that each plays a distinct and critical role in neural regulation, reproductive maturation, and viviparity in vertebrates.
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Thawornwattana, Rannala & Yang use simulation to study the false positive rate of a Bayesian test of gene flow under the MSC with multiple influencing factors.
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Haller, Ralph & Messer present SLiM 5, a major extension of the SLiM simulation framework for simulating multiple chromosomes, enabling a heightened level of realism for full-genome simulations.
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To address uncertainty in model choice for reconstructing population history, Xu et al. introduce a new Bayesian model averaging (BMA) framework.
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Mirchandani et al. introduce Callable Loci And More (clam), a tool that leverages callable loci to accurately estimate population genetic statistics (π, dxy, and FST).
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Szymanski et al. developed quicksand, an open-source Nextflow pipeline designed for rapid and accurate taxonomic classification of mammalian mitochondrial DNA in sedimentary ancient DNA samples.
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Macit et aL investigated selection in response to climate and a geographic mosaic of coevolution between two ant species, a social parasite and its host.
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Huang et al. present SAI, a Python package for computing introgression statistics, and demonstrate its application in two datasets.
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Sharma & Kumar present the Net Bootstrap Support (NBS) approach that accounts for phylogenetic variation in the estimates of bootstrap confidence.
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Rahman, Smith & Szpiech present selscan v2.1, a dynamic programming algorithm to improve runtime and memory usage in the calculation of extended haplotype homozygosity.
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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.
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Kłodawska 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, suggesting plasticity at the onset of sensory evolution.
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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.
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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.
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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.
