Subject: Molecular Biology and Evolution Table of Contents for October 2018 ------=_Part_664110577.1539892246175 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_664110577.1539892246175 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Molecular Biology and Evolution  
Volume 35 Issue 10
 
October 2018
 
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Fast Track
 
 
 
Biophysical Inference of Epistasis and the Effects of Mutations on Protein Stability and Function 
 
Jakub Otwinowski
 
 
Exon-Capture-Based Phylogeny and Diversification of the Venomous Gastropods (Neogastropoda, Conoidea) 
 
Jawad Abdelkrim; Laetitia Aznar-Cormano; Alexander E Fedosov; Yuri I Kantor ; Pierre Lozouet ...
 
 
 
Discoveries
 
 
 
Recurrent Amplification of the Heterochromatin Protein 1 (HP1) Gene Family across Diptera border= 
 
Quentin Helleu; Mia T Levine
 
 
Evolution on the Biophysical Fitness Landscape of an RNA Virus border= 
 
Assaf Rotem; Adrian W R Serohijos; Connie B Chang ; Joshua T Wolfe; Audrey E Fischer ...
 
 
Duplication of hsp-110 Is Implicated in Differential Success of Globodera Species under Climate Change border= 
 
Laura M Jones; Sebastian Eves-van den Akker ; Patricija van-Oosten Hawle; Howard J Atkinson; Peter E Urwin
 
 
Specificity of the DNA Mismatch Repair System (MMR) and Mutagenesis Bias in Bacteria 
 
Hongan Long; Samuel F Miller; Emily Williams; Michael Lynch
 
 
Functional Shifts in Bat Dim-Light Visual Pigment Are Associated with Differing Echolocation Abilities and Reveal Molecular Adaptation to Photic-Limited Environments 
 
Eduardo de A Gutierrez; Gianni M Castiglione; James M Morrow ; Ryan K Schott; Livia O Loureiro ...
 
 
Novel Bioinformatics Approach Identifies Transcriptional Profiles of Lineage-Specific Transposable Elements at Distinct Loci in the Human Dorsolateral Prefrontal Cortex border= 
 
Guia Guffanti ; Andrew Bartlett; Torsten Klengel; Claudia Klengel; Richard Hunter ...
 
 
Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops border=  
 
Joshua T Trujillo; Arun S Seetharam; Matthew B Hufford ; Mark A Beilstein; Rebecca A Mosher
 
 
Rapid Viral Symbiogenesis via Changes in Parasitoid Wasp Genome Architecture 
 
Gaelen R Burke; Tyler J Simmonds; Barbara J Sharanowski; Scott M Geib
 
 
Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It border= 
 
Paulina Bolívar ; Carina F Mugal; Matteo Rossi; Alexander Nater; Mi Wang ...
 
 
Within-Gene Shine'Dalgarno Sequences Are Not Selected for Function 
 
Adam J Hockenberry; Michael C Jewett; Luís A N Amaral; Claus O Wilke
 
 
Patterns of Ancestral Animal Codon Usage Bias Revealed through Holozoan Protists border=  
 
Jade Southworth; Paul Armitage; Brandon Fallon ; Holly Dawson; Jarosław Bryk ...
 
 
Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex border= 
 
Yuttapong Thawornwattana; Daniel Dalquen ; Ziheng Yang
 
 
Xenacoelomorph Neuropeptidomes Reveal a Major Expansion of Neuropeptide Systems during Early Bilaterian Evolution border=  
 
Daniel Thiel; Mirita Franz-Wachtel; Felipe Aguilera ; Andreas Hejnol
 
 
Limited Evidence for Parallel Molecular Adaptations Associated with the Subterranean Niche in Mammals: A Comparative Study of Three Superorders border= 
 
Kalina T J Davies ; Nigel C Bennett; Chris G Faulkes; Stephen J Rossiter
 
 
 
Methods
 
 
 
A Maximum-Likelihood Approach to Estimating the Insertion Frequencies of Transposable Elements from Population Sequencing Data border= 
 
Xiaoqian Jiang ; Haixu Tang; Wazim Mohammed Ismail; Michael Lynch
 
 
A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences border=  
 
Timothy E Schlub; Jan P Buchmann; Edward C Holmes
 
 
 
Resources
 
 
 
MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons border= 
 
Vincent Ranwez; Emmanuel J P Douzery; Cédric Cambon; Nathalie Chantret; Frédéric Delsuc
 
 
 
Protocols
 
 
 
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent border= 
 
TomáÅ¡ Flouri; Xiyun Jiao ; Bruce Rannala; Ziheng Yang
 
 
 
Corrigenda
 
 
 
Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids 
 
 
 
Undersampling Genomes has Biased Time and Rate Estimates Throughout the Tree of Life 
 
 
 
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