Subject: New issue: Molecular Biology and Evolution, Volume 42, Issue 4, April 2025

Volume 42, Issue 4, April 2025

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Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost

Clinton A Elg,Erin Mack and others

Reconstruction of Ancestral Protein Sequences Using Autoregressive Generative Models

Matteo De Leonardis,Andrea Pagnani and others

Comprehensive Genomic Analysis Reveals Novel Transposable Element-Derived MicroRNA Regulating Caste Differentiation in Honeybees

Yan Jiang,Jingsong Hu and others

Evolutionary History of Bilaterian FoxP Genes: Complex Ancestral Functions and Evolutionary Changes Spanning 2R-WGD in the Vertebrate Lineage

Fu-Yu Tsai,Che-Yi Lin and others

Temporal Patterns of Haplotypic and Allelic Diversity Reflect the Changing Selection Landscape of the Malaria Parasite Plasmodium falciparum

Angela M Early,StÃ©phane Pelleau and others

Discoveries

Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases

Andrey O Demkiv,Saacnicteh Toledo-PatiÃ±o and others

A Segregating Structural Variant Defines Novel Venom Phenotypes in the Eastern Diamondback Rattlesnake

Pedro G Nachtigall,Gunnar S Nystrom and others

Localized Tissue-Specific Gene Expression and Gene Duplications are Important Sources of Social Morph Differences in a Social Bumblebee

Hongfei Xu,Thomas J Colgan and others

Estimates of the Mutation Rate per Year Can Explain Why the Molecular Clock Depends on Generation Time

Loveday Lewin,Adam Eyre-Walker and others

On the Probability of Reaching High Peaks in Fitness Landscapes by Adaptive Walks

Yang Li,Jianzhi Zhang and others

A Million Years of Mammoth Mitogenome Evolution

J Camilo ChacÃ³n-Duque,Jessica A Thomas Thorpe and others

The Expansion and Diversification of Epigenetic Regulatory Networks Underpins Major Transitions in the Evolution of Land Plants

Romy Petroll,Ranjith K Papareddy and others

Genomic Divergence Shaped the Genetic Regulation of Meiotic Homologous Recombination in Brassica Allopolyploids

Alexandre PelÃ©,Matthieu Falque and others

Functional Decline of a Bitter Receptor Gene in New World Vultures

Ling Xiang,Yanhong Chen and others

Evolutionary Process Underlying Receptor Gene Expansion and Cellular Divergence of Olfactory Sensory Neurons in Honeybees

Weixing Zhang,Yage Nie and others

An Alternative Self-Splicing Intron Lifecycle Revealed by Dynamic Intron Turnover in Epichloë Endophyte Mitochondrial Genomes

Jennie Chan,Mauro Truglio and others

Purging of Highly Deleterious Mutations Through an Extreme Bottleneck

Oliver P Stuart,Rohan Cleave and others

Road to Extinction? Past and Present Population Structure and Genomic Diversity in the Koala

Binia De Cahsan,Marcela Sandoval Velasco and others

Gene-by-environment Interactions and Adaptive Body Size Variation in Mice From the Americas

Katya L Mack,Nico P Landino and others

Stronger Evidence for Relaxed Selection Than Adaptive Evolution in High-elevation Animal mtDNA

Erik N K Iverson,Abby Criswell and others

Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of Gastrodia (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera

Hanchen Wang,Deyi Wang and others

Sex-Biased Admixture Followed by Isolation and Adaptive Evolution Shaped the Genomic and Blood Pressure Diversity of the LopNur People

Jia Wen,Hao Chen and others

Robustness of Ancestral Sequence Reconstruction to Among-site and Among-lineage Evolutionary Heterogeneity

Ricardo MuÃ±iz-Trejo,Yeonwoo Park and others

Methods

Phyloformer: Fast, Accurate, and Versatile Phylogenetic Reconstruction with Deep Neural Networks

Luca Nesterenko,Luc Blassel and others

Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments

Niels Holtgrefe,Katharina T Huber and others

A New Comparative Framework for Estimating Selection on Synonymous Substitutions

Hannah Verdonk,Alyssa Pivirotto and others

Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA)

Romain Derelle,Kieran Madon and others

Incorporating Epidemiological Data into the Genomic Analysis of Partially Sampled Infectious Disease Outbreaks

Jake Carson,Matt Keeling and others

Brief Communications

A Phylogenetic Method Identifies Candidate Drivers of the Evolution of the SARS-CoV-2 Mutation Spectrum

Russ Corbett-Detig,Kelley Harris

Correction

Correction to: Red Deer Resequencing Reveals the Importance of Sex Chromosomes for Reconstructing Late Quaternary Events

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