Subject: Molecular Biology and Evolution Table of Contents for February 2020 ------=_Part_1346376086.1580756500500 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Molecular Biology and Evolution *** Volume 37, Issue 2, 1 February 2020 Read this issue (https://academic.oup.com/mbe/issue/37/2) ============================= Review ============================More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment Yichen Liu, Laura S Weyrich, Bastien Llamas (https://academic.oup.com/mbe/article/37/2/307/5602326) ============================= Perspective ============================Molecular Biology and Evolution of Cancer: From Discovery to Action Jason A Somarelli, Heather Gardner, Vincent L Cannataro, Ella F Gunady, Amy M Boddy (https://academic.oup.com/mbe/article/37/2/320/5603308) ============================= Discoveries ============================The Universally Conserved Residues Are Not Universally Required for Stable Protein Expression or Functions of Cryptochromes Huachun Liu, Tiantian Su, Wenjin He, Qin Wang, Chentao Lin (https://academic.oup.com/mbe/article/37/2/327/5573121) Tolerance to Selenoprotein Loss Differs between Human and Mouse Didac Santesmasses, Marco Mariotti, Vadim N Gladyshev (https://academic.oup.com/mbe/article/37/2/341/5575079) Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. II. Accumulation of Variation and Evolution of a New Subfamily Watal M Iwasaki, T E Kijima, Hideki Innan (https://academic.oup.com/mbe/article/37/2/355/5580499) Additional Layer of Regulation via Convergent Gene Orientation in Yeasts Jules Gilet, Romain Conte, Claire Torchet, Lionel Benard, Ingrid Lafontaine (https://academic.oup.com/mbe/article/37/2/365/5580500) The Evolutionary History of Ephs and Ephrins: Toward Multicellular Organisms Aida Arcas, David G Wilkinson, M ngela Nieto (https://academic.oup.com/mbe/article/37/2/379/5582654) Human and Nonhuman Primate Lineage-Specific Footprints in the Salivary Proteome Supaporn Thamadilok, Kyoung-Soo Choi, Lorenz Ruhl, Fabian Schulte, A Latif Kazim (https://academic.oup.com/mbe/article/37/2/395/5586967) Along the Indian Ocean Coast: Genomic Variation in Mozambique Provides New Insights into the Bantu Expansion Armando Semo, Magdalena Gayà-Vidal, Cesar Fortes-Lima, Bérénice Alard, Sandra Oliveira (https://academic.oup.com/mbe/article/37/2/406/5583770) Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen Brian Arnold, Mashaal Sohail, Crista Wadsworth, Jukka Corander, William P Hanage (https://academic.oup.com/mbe/article/37/2/417/5582682) Loss of Imprinting in Human Placentas Is Widespread, Coordinated, and Predicts Birth Phenotypes Claudius Vincenz, Jennie L Lovett, Weisheng Wu, Kerby Shedden, Beverly I Strassmann (https://academic.oup.com/mbe/article/37/2/429/5586968) You Will Never Walk Alone: Codispersal of JC Polyomavirus with Human Populations Diego Forni, Rachele Cagliani, Mario Clerici, Uberto Pozzoli, Manuela Sironi (https://academic.oup.com/mbe/article/37/2/442/5583769) Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance Alison Mullis, Zhaolian Lu, Yu Zhan, Tzi-Yuan Wang, Judith Rodriguez (https://academic.oup.com/mbe/article/37/2/455/5582681) Purifying Selection in Corvids Is Less Efficient on Islands Verena E Kutschera, Jelmer W Poelstra, Fidel Botero-Castro, Nicolas Dussex, Neil J Gemmell (https://academic.oup.com/mbe/article/37/2/469/5601620) Dissecting the Transcriptomic Basis of Phenotypic Evolution in an Aquatic Keystone Grazer Dagmar Frisch, Dörthe Becker, Marcin W Wojewodzic (https://academic.oup.com/mbe/article/37/2/475/5613640) Molecular Diversification of the Seminal Fluid Proteome in a Recently Diverged Passerine Species Pair Melissah Rowe, Emma Whittington, Kirill Borziak, Mark Ravinet, Fabrice Eroukhmanoff (https://academic.oup.com/mbe/article/37/2/488/5610084) Eutherian-Specific Gene TRIML2 Attenuates Inflammation in the Evolution of Placentation Xuzhe Zhang, Mihaela Pavlicev, Helen N Jones, Louis J Muglia (https://academic.oup.com/mbe/article/37/2/507/5601622) Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss William H Lewis, Anders E Lind, Kacper M Sendra, Henning Onsbring, Tom A Williams (https://academic.oup.com/mbe/article/37/2/524/5606724) DNA Methylation Profiles Suggest Intergenerational Transfer of Maternal Effects Clare J Venney, Oliver P Love, Ellen Jane Drown, Daniel D Heath (https://academic.oup.com/mbe/article/37/2/540/5607303) ============================= Methods ============================On the Use of Information Criteria for Model Selection in Phylogenetics Edward Susko, Andrew J Roger (https://academic.oup.com/mbe/article/37/2/549/5613171) Living Trees: High-Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees Dalong Hu, Bin Liu, Lei Wang, Peter R Reeves (https://academic.oup.com/mbe/article/37/2/563/5601619) Evolutionary Analyses of Base-Pairing Interactions in DNA and RNA Secondary Structures Michael Golden, Benjamin Murrell, Darren Martin, Oliver G Pybus, Jotun Hein (https://academic.oup.com/mbe/article/37/2/576/5610083) ============================= Resources ============================Computational Framework for High-Quality Production and Large-Scale Evolutionary Analysis of Metagenome Assembled Genomes Boštjan Murovec, Leon Deutsch, Blaz Stres (https://academic.oup.com/mbe/article/37/2/593/5601623) Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data Li-Gen Wang, Tommy Tsan-Yuk Lam, Shuangbin Xu, Zehan Dai, Lang Zhou (https://academic.oup.com/mbe/article/37/2/599/5601621) RASP 4: Ancestral State Reconstruction Tool for Multiple Genes and Characters Yan Yu, Christopher Blair, Xingjin He (https://academic.oup.com/mbe/article/37/2/604/5610535) ============================= Corrigenda ============================Convergent Substitutions in a Sodium Channel Suggest Multiple Origins of Toxin Resistance in Poison Frogs Rebecca D Tarvin, Juan C Santos, Lauren A O'Connell, Harold H Zakon, David C Cannatella (https://academic.oup.com/mbe/article/37/2/607/5610623) The Epigenetic Signature of Colonizing New Environments in Anolis Lizards Juntao Hu, Arash M Askary, Timothy J Thurman, Dave A Spiller, Todd M Palmer (https://academic.oup.com/mbe/article/37/2/608/5612166) ============================= Errata ============================Solving the Riddle of the Evolution of Shine-Dalgarno Based Translation in Chloroplasts Iddo Weiner, Noam Shahar, Pini Marco, Iftach Yacoby, Tamir Tuller (https://academic.oup.com/mbe/article/37/2/609/5614707) Erratum to: Epimutations in Developmental Genes Underlie the Onset of Domestication in Farmed European Sea Bass Dafni Anastasiadi, Francesc Piferrer (https://academic.oup.com/mbe/article/37/2/610/5679975) Unsubscribe (http://cp20.com/unsubscribe) Manage email alerts (https://academic.oup.com/my-account/email-alerts) Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK. Our Privacy Policy (http://global.oup.com/privacy) sets out how Oxford University Press handles your personal information. The content of this email is protected by copyright. Oxford University Press This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1346376086.1580756500500 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Molecular Biology and Evolution  
Volume 37 Issue 2
 
February 2020
 
button-issue.png
 
 
Review
 
 
 
More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment  
 
Yichen Liu; Laura S Weyrich; Bastien Llamas
 
 
 
Perspective
 
 
 
Molecular Biology and Evolution of Cancer: From Discovery to Action border= 
 
Jason A Somarelli ; Heather Gardner; Vincent L Cannataro; Ella F Gunady; Amy M Boddy ...
 
 
 
Discoveries
 
 
 
The Universally Conserved Residues Are Not Universally Required for Stable Protein Expression or Functions of Cryptochromes 
 
Huachun Liu; Tiantian Su; Wenjin He ; Qin Wang; Chentao Lin
 
 
Tolerance to Selenoprotein Loss Differs between Human and Mouse 
 
Didac Santesmasses; Marco Mariotti; Vadim N Gladyshev
 
 
Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. II. Accumulation of Variation and Evolution of a New Subfamily 
 
Watal M Iwasaki; T E Kijima; Hideki Innan
 
 
Additional Layer of Regulation via Convergent Gene Orientation in Yeasts border= 
 
Jules Gilet ; Romain Conte; Claire Torchet; Lionel Benard; Ingrid Lafontaine
 
 
The Evolutionary History of Ephs and Ephrins: Toward Multicellular Organisms border= 
 
Aida Arcas ; David G Wilkinson; M Ángela Nieto
 
 
Human and Nonhuman Primate Lineage-Specific Footprints in the Salivary Proteome border= 
 
Supaporn Thamadilok ; Kyoung-Soo Choi; Lorenz Ruhl; Fabian Schulte; A Latif Kazim ...
 
 
Along the Indian Ocean Coast: Genomic Variation in Mozambique Provides New Insights into the Bantu Expansion border= 
 
Armando Semo ; Magdalena Gayà-Vidal; Cesar Fortes-Lima; Bérénice Alard; Sandra Oliveira ...
 
 
Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen 
 
Brian Arnold; Mashaal Sohail; Crista Wadsworth ; Jukka Corander; William P Hanage ...
 
 
Loss of Imprinting in Human Placentas Is Widespread, Coordinated, and Predicts Birth Phenotypes border= 
 
Claudius Vincenz ; Jennie L Lovett; Weisheng Wu; Kerby Shedden; Beverly I Strassmann
 
 
You Will Never Walk Alone: Codispersal of JC Polyomavirus with Human Populations 
 
Diego Forni; Rachele Cagliani; Mario Clerici ; Uberto Pozzoli; Manuela Sironi
 
 
Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance border= 
 
Alison Mullis ; Zhaolian Lu; Yu Zhan; Tzi-Yuan Wang; Judith Rodriguez ...
 
 
Purifying Selection in Corvids Is Less Efficient on Islands border= 
 
Verena E Kutschera ; Jelmer W Poelstra; Fidel Botero-Castro; Nicolas Dussex; Neil J Gemmell ...
 
 
Dissecting the Transcriptomic Basis of Phenotypic Evolution in an Aquatic Keystone Grazer 
 
Dagmar Frisch; Dörthe Becker; Marcin W Wojewodzic
 
 
Molecular Diversification of the Seminal Fluid Proteome in a Recently Diverged Passerine Species Pair border= 
 
Melissah Rowe ; Emma Whittington; Kirill Borziak; Mark Ravinet; Fabrice Eroukhmanoff ...
 
 
Eutherian-Specific Gene TRIML2 Attenuates Inflammation in the Evolution of Placentation border= 
 
Xuzhe Zhang; Mihaela Pavlicev; Helen N Jones; Louis J Muglia
 
 
Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss border= 
 
William H Lewis ; Anders E Lind; Kacper M Sendra; Henning Onsbring; Tom A Williams ...
 
 
DNA Methylation Profiles Suggest Intergenerational Transfer of Maternal Effects 
 
Clare J Venney; Oliver P Love; Ellen Jane Drown ; Daniel D Heath
 
 
 
Methods
 
 
 
On the Use of Information Criteria for Model Selection in Phylogenetics 
 
Edward Susko; Andrew J Roger
 
 
Living Trees: High-Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees 
 
Dalong Hu; Bin Liu; Lei Wang ; Peter R Reeves
 
 
Evolutionary Analyses of Base-Pairing Interactions in DNA and RNA Secondary Structures border= 
 
Michael Golden ; Benjamin Murrell; Darren Martin; Oliver G Pybus; Jotun Hein
 
 
 
Resources
 
 
 
Computational Framework for High-Quality Production and Large-Scale Evolutionary Analysis of Metagenome Assembled Genomes border= 
 
Boštjan Murovec ; Leon Deutsch; Blaz Stres
 
 
Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data 
 
Li-Gen Wang; Tommy Tsan-Yuk Lam; Shuangbin Xu ; Zehan Dai; Lang Zhou ...
 
 
RASP 4: Ancestral State Reconstruction Tool for Multiple Genes and Characters 
 
Yan Yu; Christopher Blair; Xingjin He
 
 
 
Corrigenda
 
 
 
Convergent Substitutions in a Sodium Channel Suggest Multiple Origins of Toxin Resistance in Poison Frogs 
 
Rebecca D Tarvin; Juan C Santos; Lauren A O'Connell ; Harold H Zakon; David C Cannatella
 
 
The Epigenetic Signature of Colonizing New Environments in Anolis Lizards 
 
Juntao Hu; Arash M Askary; Timothy J Thurman ; Dave A Spiller; Todd M Palmer ...
 
 
 
Errata
 
 
 
Solving the Riddle of the Evolution of Shine-Dalgarno Based Translation in Chloroplasts 
 
Iddo Weiner; Noam Shahar; Pini Marco ; Iftach Yacoby; Tamir Tuller
 
 
Erratum to: Epimutations in Developmental Genes Underlie the Onset of Domestication in Farmed European Sea Bass 
 
Dafni Anastasiadi; Francesc Piferrer
 
 
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