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GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences J. Mol. Evol. (IF 3.9) Pub Date : 2024-03-15 Riccardo G. Kyriacou, Peter O. Mulhair, Peter W. H. Holland
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Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution J. Mol. Evol. (IF 3.9) Pub Date : 2024-03-15
Abstract Cyanobacteria are recognised for their pivotal roles in aquatic ecosystems, serving as primary producers and major agents in diazotrophic processes. Currently, the primary focus of cyanobacterial research lies in gaining a more detailed understanding of these well-established ecosystem functions. However, their involvement and impact on other crucial biogeochemical cycles remain understudied
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Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions J. Mol. Evol. (IF 3.9) Pub Date : 2024-03-14 Zachery W. Dickson, G. Brian Golding
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Frustration can Limit the Adaptation of Promiscuous Enzymes Through Gene Duplication and Specialisation J. Mol. Evol. (IF 3.9) Pub Date : 2024-03-12 Michael Schmutzer, Pouria Dasmeh, Andreas Wagner
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Assembly Theory: What It Does and What It Does Not Do J. Mol. Evol. (IF 3.9) Pub Date : 2024-03-07 Johannes Jaeger
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Multiple Ecological Axes Drive Molecular Evolution of Cone Opsins in Beloniform Fishes J. Mol. Evol. (IF 3.9) Pub Date : 2024-02-28 Katherine D. Chau, Frances E. Hauser, Alexander Van Nynatten, Jacob M. Daane, Matthew P. Harris, Belinda S. W. Chang, Nathan R. Lovejoy
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Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin J. Mol. Evol. (IF 3.9) Pub Date : 2024-02-07 Benjamin M. Scott, Steven K. Chen, Alexander Van Nynatten, Jing Liu, Ryan K. Schott, Elise Heon, Sergio G. Peisajovich, Belinda S. W. Chang
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FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus J. Mol. Evol. (IF 3.9) Pub Date : 2024-01-29
Abstract Autoimmune Regulator 1 (AIRE1) and Forebrain Embryonic Zinc Finger-Like Protein 2 (FEZF2) play pivotal roles in orchestrating the expression of tissue-restricted antigens (TRA) to facilitate the elimination of autoreactive T cells. AIRE1’s presence in the gonads of various vertebrates has raised questions about its potential involvement in gene expression control for germline cell selection
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Evolution of the Major Components of Innate Immunity in Animals J. Mol. Evol. (IF 3.9) Pub Date : 2024-01-28 Rafael Cardoso Maciel Costa Silva, Fábio Mendonça Gomes
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Odorant-Binding and Chemosensory Proteins in Fig Wasps: Evolutionary Insights From Comparative Studies J. Mol. Evol. (IF 3.9) Pub Date : 2024-01-27 Hui Yu, Xiaojue Nong, Weicheng Huang, Chantarasuwan Bhanumas, Xiaoxia Deng, Yamei Ding, Wanzhen Liu
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Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1 J. Mol. Evol. (IF 3.9) Pub Date : 2024-01-08 Forrest Weghorst, Martí Torres Marcén, Garrison Faridi, Yuh Chwen G. Lee, Karina S. Cramer
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Functional Divergence and Origin of the Vertebrate Praja Family J. Mol. Evol. (IF 3.9) Pub Date : 2023-12-29 Wataru Onodera, Kotaro Kawasaki, Mizuho Oishi, Shiho Aoki, Toru Asahi
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APGW/AKH Precursor from Rotifer Brachionus plicatilis and the DNA Loss Model Explain Evolutionary Trends of the Neuropeptide LWamide, APGWamide, RPCH, AKH, ACP, CRZ, and GnRH Families J. Mol. Evol. (IF 3.9) Pub Date : 2023-12-16 Cristian E. Cadena-Caballero, Nestor Munive-Argüelles, Lina M. Vera-Cala, Carlos Barrios-Hernandez, Ruben O. Duarte-Bernal, Viviana L. Ayus-Ortiz, Luis A. Pardo-Díaz, Mayra Agudelo-Rodríguez, Lola X. Bautista-Rozo, Laura R. Jimenez-Gutierrez, Francisco Martinez-Perez
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Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus) J. Mol. Evol. (IF 3.9) Pub Date : 2023-12-13 Gunnar S. Nystrom, Schyler A. Ellsworth, Micaiah J. Ward, Darin R. Rokyta
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Origins and Functional Significance of Eukaryotic Protein Folds J. Mol. Evol. (IF 3.9) Pub Date : 2023-12-07 Martin Romei, Mathilde Carpentier, Jacques Chomilier, Guillaume Lecointre
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The Hypervariable Tpr Multigene Family of Theileria Parasites, Defined by a Conserved, Membrane-Associated, C-Terminal Domain, Includes Several Copies with Defined Orthology Between Species J. Mol. Evol. (IF 3.9) Pub Date : 2023-11-28 Nicholas C. Palmateer, James B. Munro, Sushma Nagaraj, Jonathan Crabtree, Roger Pelle, Luke Tallon, Vish Nene, Richard Bishop, Joana C. Silva
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Ancestral Information Analysis of Chinese Korean Ethnic Group via a Novel Multiplex DIP System J. Mol. Evol. (IF 3.9) Pub Date : 2023-11-25 Meiming Cai, Shuanglin Li, Xingru Zhang, Weibing Xie, Jianfeng Shi, Xi Yuan, Jun Yao, Bofeng Zhu
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Unusual Evolution of Cephalopod Tryptophan Indole-Lyases J. Mol. Evol. (IF 3.9) Pub Date : 2023-11-26 Hajime Julie Yuasa
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Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn Genus Macrobrachium: Convergent Evolution Following Multiple Independent Colonization Events J. Mol. Evol. (IF 3.9) Pub Date : 2023-11-27 Md Lifat Rahi, Peter B. Mather, Marcelo de Bello Cioffi, Tariq Ezaz, David A. Hurwood
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Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians J. Mol. Evol. (IF 3.9) Pub Date : 2023-11-27 Elisa Ramos, Giovanna Selleghin-Veiga, Letícia Magpali, Beatriz Daros, Felipe Silva, Agnello Picorelli, Lucas Freitas, Mariana F. Nery
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Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair J. Mol. Evol. (IF 3.9) Pub Date : 2023-11-25 Lasha Bukhnikashvili
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Functional Diversification and the Plant Secondary Cell Wall J. Mol. Evol. (IF 3.9) Pub Date : 2023-11-18 Joseph B. Colbert, Heather D. Coleman
Much evidence exists suggesting the presence of genetic functional diversification in plants, though literature associated with the role of functional diversification in the evolution of the plant secondary cell wall (SCW) has sparsely been compiled and reviewed in a recent context. This review aims to elucidate, through the examination of gene phylogenies associated with its biosynthesis and maintenance
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Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production J. Mol. Evol. (IF 3.9) Pub Date : 2023-11-14 Alexander Fedosov, Carmen Federica Tucci, Yuri Kantor, Sarah Farhat, Nicolas Puillandre
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Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors J. Mol. Evol. (IF 3.9) Pub Date : 2023-11-13 Abigail García-Morales, Daniel Balleza
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Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins J. Mol. Evol. (IF 3.9) Pub Date : 2023-11-09 Sitara Palecanda, Elizabeth Madrid, Megan L. Porter
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Post-Subfunctionalization Functions of HIF-1αA and HIF-1αB in Cyprinid Fish: Fine-Tuning Mitophagy and Apoptosis Regulation Under Hypoxic Stress J. Mol. Evol. (IF 3.9) Pub Date : 2023-11-04 Wei Chi, Juanjuan Fu, Chris J. Martyniuk, Jiangyong Wang, Libin Zhou
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Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species J. Mol. Evol. (IF 3.9) Pub Date : 2023-10-31 Johnny Sousa Ferreira, Daniel Pacheco Bruschi
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The MultiFurcating Neighbor-Joining Algorithm for Reconstructing Polytomic Phylogenetic Trees J. Mol. Evol. (IF 3.9) Pub Date : 2023-10-21 Alberto Fernández, Natàlia Segura-Alabart, Francesc Serratosa
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Kinetic Modeling and Parameter Estimation of a Prebiotic Peptide Reaction Network J. Mol. Evol. (IF 3.9) Pub Date : 2023-10-05 Hayley Boigenzahn, Leonardo D. González, Jaron C. Thompson, Victor M. Zavala, John Yin
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Pseudogenization of the Hair-Related Genes PADI3 and S100A3 in Cetaceans and Hippopotamus amphibius J. Mol. Evol. (IF 3.9) Pub Date : 2023-10-03 Kyomi Nagasawa, Takashi Kitano
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Left–Right Reversal Recurrently Evolved Regardless of Diaphanous-Related Formin Gene Duplication or Loss in Snails J. Mol. Evol. (IF 3.9) Pub Date : 2023-09-25 Takeshi Noda, Noriyuki Satoh, Edmund Gittenberger, Takahiro Asami
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A Law of Redundancy Compounds the Problem of Cancer and Precision Medicine J. Mol. Evol. (IF 3.9) Pub Date : 2023-09-04 Rama S. Singh
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Domain Architecture Based Methods for Comparative Functional Genomics Toward Therapeutic Drug Target Discovery J. Mol. Evol. (IF 3.9) Pub Date : 2023-08-25 Pavan Gollapalli, Sushmitha Rudrappa, Vadlapudi Kumar, Hulikal Shivashankara Santosh Kumar
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Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection J. Mol. Evol. (IF 3.9) Pub Date : 2023-08-25 Michael A. Savageau
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Systematic Analysis of Diverse Polynucleotide Kinase Clp1 Family Proteins in Eukaryotes: Three Unique Clp1 Proteins of Trypanosoma brucei J. Mol. Evol. (IF 3.9) Pub Date : 2023-08-22 Motofumi Saito, Rerina Inose, Asako Sato, Masaru Tomita, Haruo Suzuki, Akio Kanai
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Pangenomic Analysis of Nucleo-Cytoplasmic Large DNA Viruses. I: The Phylogenetic Distribution of Conserved Oxygen-Dependent Enzymes Reveals a Capture-Gene Process J. Mol. Evol. (IF 3.9) Pub Date : 2023-08-01 J. A. Campillo-Balderas, A. Lazcano, W. Cottom-Salas, R. Jácome, A. Becerra
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Informatic Capabilities of Translation and Its Implications for the Origins of Life J. Mol. Evol. (IF 3.9) Pub Date : 2023-08-01 Bruno Cuevas-Zuviría, Zachary R. Adam, Aaron D. Goldman, Betül Kaçar
The ability to encode and convert heritable information into molecular function is a defining feature of life as we know it. The conversion of information into molecular function is performed by the translation process, in which triplets of nucleotides in a nucleic acid polymer (mRNA) encode specific amino acids in a protein polymer that folds into a three-dimensional structure. The folded protein
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Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes J. Mol. Evol. (IF 3.9) Pub Date : 2023-07-01 Diksha Bhalla, Vera van Noort
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Evolutionary Consequences of Functional and Regulatory Divergence of HD-Zip I Transcription Factors as a Source of Diversity in Protein Interaction Networks in Plants J. Mol. Evol. (IF 3.9) Pub Date : 2023-06-23 Natalia Żyła, Danuta Babula-Skowrońska
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A Micro-evolutionary Change in Target Binding Sites as a Key Determinant of Ultrabithorax Function in Drosophila J. Mol. Evol. (IF 3.9) Pub Date : 2023-06-21 Soumen Khan, Saurabh J. Pradhan, Guillaume Giraud, Françoise Bleicher, Rachel Paul, Samir Merabet, L. S. Shashidhara
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Alternative Reading Frames are an Underappreciated Source of Protein Sequence Novelty J. Mol. Evol. (IF 3.9) Pub Date : 2023-06-16 Zachary Ardern
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Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation–Drift Equilibrium J. Mol. Evol. (IF 3.9) Pub Date : 2023-06-03 Ramses Alejandro Rosales-García, Rhett M. Rautsaw, Erich P. Hofmann, Christoph I. Grünwald, Hector Franz-Chavez, Ivan T. Ahumada-Carrillo, Ricardo Ramirez-Chaparro, Miguel Angel de la Torre-Loranca, Jason L. Strickland, Andrew J. Mason, Matthew L. Holding, Miguel Borja, Gamaliel Castañeda-Gaytan, Edward A. Myers, Mahmood Sasa, Darin R. Rokyta, Christopher L. Parkinson
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Main Factors Shaping Amino Acid Usage Across Evolution J. Mol. Evol. (IF 3.9) Pub Date : 2023-06-01 Guillermo Lamolle, Diego Simón, Andrés Iriarte, Héctor Musto
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Decay of Skin-Specific Gene Modules in Pangolins J. Mol. Evol. (IF 3.9) Pub Date : 2023-05-30 Bernardo Pinto, Raul Valente, Filipe Caramelo, Raquel Ruivo, L. Filipe C. Castro
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Unraveling the Drivers of Tumorigenesis in the Context of Evolution: Theoretical Models and Bioinformatics Tools J. Mol. Evol. (IF 3.9) Pub Date : 2023-05-29 Xunuo Zhu, Wenyi Zhao, Zhan Zhou, Xun Gu
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Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch J. Mol. Evol. (IF 3.9) Pub Date : 2023-05-27 Grant Kinsler, Kara Schmidlin, Daphne Newell, Rachel Eder, Sam Apodaca, Grace Lam, Dmitri Petrov, Kerry Geiler-Samerotte
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On the Unknown Proteins of Eukaryotic Proteomes J. Mol. Evol. (IF 3.9) Pub Date : 2023-05-23 Yves-Henri Sanejouand
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Best Practices in Microbial Experimental Evolution J. Mol. Evol. (IF 3.9) Pub Date : 2023-05-20 Kerry Geiler-Samerotte, Gregory I. Lang
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Phylogenetic and Evolutionary Analysis of Plant Small RNA 2′-O-Methyltransferase (HEN1) Protein Family J. Mol. Evol. (IF 3.9) Pub Date : 2023-05-16 Behzad Hajieghrari, Ali Niazi
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Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designs J. Mol. Evol. (IF 3.9) Pub Date : 2023-05-09 Anurag Limdi, Michael Baym
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Next Generation Sequencing Revolutionizes Organismal Biology Research in Bats J. Mol. Evol. (IF 3.9) Pub Date : 2023-05-08 Kritika M. Garg, Vinita Lamba, Avirup Sanyal, Pilot Dovih, Balaji Chattopadhyay
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Discovery of Teleost Plasma Kallikrein/Coagulation Factor XI-Like Gene from Channel Catfish (Ictalurus punctatus) and the Evidence that the Protein Encoded by it Acts as a Lectin J. Mol. Evol. (IF 3.9) Pub Date : 2023-05-08 Shigeyuki Tsutsui, Asuka Yoshimura, Yoshiharu Iwakuma, Osamu Nakamura
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Adaptive Selection in the Evolution of Aquaglyceroporins in Mammals J. Mol. Evol. (IF 3.9) Pub Date : 2023-05-07 Shiveeli Rajput, Devika Gautam, Ashutosh Vats, Chanchal Rana, Manisha Behera, Mayank Roshan, Ashutosh Ludri, Sachinandan De
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Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers J. Mol. Evol. (IF 3.9) Pub Date : 2023-05-05 Phoebe Mudaki, Lydia N. Wamalwa, Catherine W. Muui, Felister Nzuve, Reuben M. Muasya, Simon Nguluu, Wilson Kimani
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Barcoding Populations of Pseudomonas fluorescens SBW25 J. Mol. Evol. (IF 3.9) Pub Date : 2023-04-25 Loukas Theodosiou, Andrew D. Farr, Paul B. Rainey
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A Genomic Conceptualization of Species J. Mol. Evol. (IF 3.9) Pub Date : 2023-04-20 David A. Liberles
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PAReTT: A Python Package for the Automated Retrieval and Management of Divergence Time Data from the TimeTree Resource for Downstream Analyses J. Mol. Evol. (IF 3.9) Pub Date : 2023-04-20 Louis-Stéphane Le Clercq, Antoinette Kotzé, J. Paul Grobler, Desiré Lee Dalton
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Evolutionary Aspects of Selenium Binding Protein (SBP) J. Mol. Evol. (IF 3.9) Pub Date : 2023-04-11 Irene Dervisi, Chrysanthi Valassakis, Aikaterini Koletti, Vassilis N. Kouvelis, Emmanouil Flemetakis, Christos A. Ouzounis, Andreas Roussis
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Analysis of Programmed Cell Death-1 (PD-1) Gene Variations (re11568821 and rs41386349) in HTLV-1 Infection Using One Primer Pair and Proviral Load J. Mol. Evol. (IF 3.9) Pub Date : 2023-04-05 Yalda Amiri Hezave, Zohreh Sharifi, Fahime Ranjbar Kermani
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A Possible Aquatic Origin of the Thiaminase TenA of the Human Gut Symbiont Bacteroides thetaiotaomicron J. Mol. Evol. (IF 3.9) Pub Date : 2023-04-06 Régis Stentz, Jitender Cheema, Mark Philo, Simon R. Carding