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Molecular Biology and Evolution  
Volume 41 Issue 11
 
November 2024
 
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Perspective
 
 
 
 
Sex Chromosome Evolution: Hallmarks and Question Marks border= 
 
Paul A Saunders, Aline Muyle
 
 
 
Review
 
 
 
 
The Meaning and Measure of Concordance Factors in Phylogenomics border= 
 
Robert Lanfear, Matthew W Hahn
 
 
 
Discoveries
 
 
 
 
Ancient Secretory Pathways Contributed to the Evolutionary Origin of an Ecologically Impactful Bioluminescence System border= 
 
Lisa Y Mesrop, Geetanjali Minsky, Michael S Drummond, Jessica A Goodheart, Stephen R Proulx ...
 
 
 
Deep Ancestral Introgressions between Ovine Species Shape Sheep Genomes via Argali-Mediated Gene Flow border= 
 
Feng-Hua Lv, Dong-Feng Wang, Si-Yi Zhao, Xiao-Yang Lv, Wei Sun ...
 
 
 
Recent and Recurrent Autopolyploidization Fueled Diversification of Snow Carp on the Tibetan Plateau border= 
 
Xinxin Li, Min Wang, Ming Zou, Xiaotong Guan, Shaohua Xu ...
 
 
 
 
Genetic and Developmental Divergence in the Neural Crest Program between Cichlid Fish Species border= 
 
Aleksandra Marconi, Grégoire Vernaz, Achira Karunaratna, Maxon J Ngochera, Richard Durbin ...
 
 
 
Transposable Element Diversity and Activity Patterns in Neotropical Salamanders border= 
 
Louis Paul Decena-Segarra, Sean M Rovito
 
 
 
χ-Conotoxins are an Evolutionary Innovation of Mollusk-Hunting Cone Snails as a Counter-Adaptation to Prey Defense border= 
 
Samuel Espino, Maren Watkins, Rodolfo Probst, Thomas Lund Koch, Kevin Chase ...
 
 
 
Repeated Shifts in Sociality Are Associated With Fine-tuning of Highly Conserved and Lineage-Specific Enhancers in a Socially Flexible Bee border= 
 
Beryl M Jones, Andrew E Webb, Scott M Geib, Sheina Sim, Rena M Schweizer ...
 
 
 
Specialization Restricts the Evolutionary Paths Available to Yeast Sugar Transporters border= 
 
Johnathan G Crandall, Xiaofan Zhou, Antonis Rokas, Chris Todd Hittinger
 
 
 
 
Conjugation Mediates Large-Scale Chromosomal Transfer in Streptomyces Driving Diversification of Antibiotic Biosynthetic Gene Clusters border= 
 
Caroline Choufa, Pauline Gascht, Hugo Leblond, Anthony Gauthier, Michiel Vos ...
 
 
 
Rewiring of Uric Acid Metabolism in the Intestine Promotes High-Altitude Hypoxia Adaptation in Humans border= 
 
Qian Su, Yu-Chun Li, Dao-Hua Zhuang, Xin-Yuan Liu, Han Gao ...
 
 
 
Evolution of Sex-linked Genes and the Role of Pericentromeric Regions in Sex Chromosomes: Insights from Diploid Willows border= 
 
Yi Wang, Ren-Gang Zhang, Elvira Hörandl, Zhi-Xiang Zhang, Deborah Charlesworth ...
 
 
 
Diversity of Transcriptional Regulatory Adaptation in E. coli border=  
 
Christopher Dalldorf, Ying Hefner, Richard Szubin, Josefin Johnsen, Elsayed Mohamed ...
 
 
 
Genomic and Acoustic Biogeography of the Iconic Sulphur-crested Cockatoo Clarifies Species Limits and Patterns of Intraspecific Diversity border= 
 
Arthur F Sands, Astrid A L Andersson, Kerry Reid, Taylor Hains, Leo Joseph ...
 
 
 
Tree Sequences as a General-Purpose Tool for Population Genetic Inference border=  
 
Logan S Whitehouse, Dylan D Ray, Daniel R Schrider
 
 
 
Convergent Degenerated Regulatory Elements Associated with Limb Loss in Limbless Amphibians and Reptiles border= 
 
Chenglong Zhu, Shengyou Li, Daizhen Zhang, Jinjin Zhang, Gang Wang ...
 
 
 
Methods
 
 
 
 
RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution border= 
 
Ruby Redlich, Amanda Kowalczyk, Michael Tene, Heather H Sestili, Kathleen Foley ...
 
 
 
Gentrius: Generating Trees Compatible With a Set of Unrooted Subtrees and its Application to Phylogenetic Terraces border= 
 
Olga Chernomor, Christiane Elgert, Arndt von Haeseler
 
 
 
Five-leaf Generalizations of the D -statistic Reveal the Directionality of Admixture border= 
 
Kalle Leppälä, Flavio Augusto da Silva Coelho, Michaela Richter, Victor A Albert, Charlotte Lindqvist
 
 
 
Integrating Contact Tracing Data to Enhance Outbreak Phylodynamic Inference: A Deep Learning Approach border= 
 
Ruopeng Xie, Dillon C Adam, Shu Hu, Benjamin J Cowling, Olivier Gascuel ...
 
 
 
The Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches border= 
 
Frédéric Lemoine, Olivier Gascuel
 
 
 
Brief Communications
 
 
 
 
Further Evidence for Strong Nonneutrality of Yeast Synonymous Mutations border= 
 
Xukang Shen, Siliang Song, Chuan Li, Jianzhi Zhang
 
 
 
Correction
 
 
 
 
Correction to: Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications border= 
 
 
 
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