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Molecular Evolutionary Routes That Lead to Innovations International Journal of Evolutionary Biology Molecular Evolutionary Routes That Lead to Innovations Guest Editors: Frédéric Brunet, Hideki Innan, Ben-Yang Liao, and Wen Wang Molecular Evolutionary Routes That Lead to Innovations International Journal of Evolutionary Biology Molecular Evolutionary Routes That Lead to Innovations Guest Editors: Fred´ eric´ Brunet, Hideki Innan, Ben-YangLiao, and Wen Wang Copyright © 2012 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “International Journal of Evolutionary Biology.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Editorial Board Giacomo Bernardi, USA Kazuho Ikeo, Japan Jeffrey R. Powell, USA Terr y Burke, UK Yoh Iwasa, Japan Hudson Kern Reeve, USA Ignacio Doadrio, Spain Henrik J. Jensen, UK Y. Satta, Japan Simon Easteal, Australia Amitabh Joshi, India Koji Tamura, Japan Santiago F. Elena, Spain Hirohisa Kishino, Japan Yoshio Tateno, Japan Renato Fani, Italy A. Moya, Spain E. N. Trifonov, Israel Dmitry A. Filatov, UK G. Pesole, Italy Eske Willerslev, Denmark F. Gonzalez-Candelas,´ Spain I. Popescu, USA Shozo Yokoyama, Japan D. Graur, USA David Posada, Spain Contents Molecular Evolutionary Routes That Lead to Innovations,Fred´ eric´ Brunet, Hideki Innan, Ben-Yang Liao, and Wen Wang Volume 2012, Article ID 483176, 2 pages Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome,P.C.Sharma,ManishRoorkiwal,andAtulGrover Volume 2012, Article ID 970920, 8 pages New Insights into Ligand-Receptor Pairing and Coevolution of Relaxin Family Peptides and Their Receptors in Teleosts, Sara Good, Sergey Yegorov, Joran Martijn, Jens Franck, and Jan Bogerd Volume 2012, Article ID 310278, 14 pages In with the Old, in with the New: The Promiscuity of the Duplication Process Engenders Diverse Pathways for Novel Gene Creation, Vaishali Katju Volume 2012, Article ID 341932, 24 pages Genetic Innovation in Vertebrates: Gypsy Integrase Genes and Other Genes Derived from Transposable Elements, Domitille Chalopin, Delphine Galiana, and Jean-Nicolas Volff Volume 2012, Article ID 724519, 11 pages Evolution of the FGF Gene Family, Silvan Oulion, Stephanie Bertrand, and Hector Escriva Volume 2012, Article ID 298147, 12 pages Mechanisms of Gene Duplication and Translocation and Progress towards Understanding Their Relative Contributions to Animal Genome Evolution, Olivia Mendivil Ramos and David E. K. Ferrier Volume 2012, Article ID 846421, 10 pages The Ecology of Bacterial Genes and the Survival of the New, M. Pilar Francino Volume 2012, Article ID 394026, 14 pages Polyploidy and the Evolution of Complex Traits, Lukasz Huminiecki and Gavin C. Conant Volume 2012, Article ID 292068, 12 pages Transposon Invasion of the Paramecium Germline Genome Countered by a Domesticated PiggyBac Transposase and the NHEJ Pathway, Emeline Dubois, Julien Bischerour, Antoine Marmignon, Nathalie Mathy, Vinciane Regnier,´ and Mireille Betermier´ Volume 2012, Article ID 436196, 13 pages Why Chromosome Palindromes?, Esther Betran,´ Jeffery P. Demuth, and Anna Williford Volume 2012, Article ID 207958, 14 pages The Role of Reticulate Evolution in Creating Innovation and Complexity, Kristen S. Swithers, Shannon M. Soucy, and J. Peter Gogarten Volume 2012, Article ID 418964, 10 pages Repeated Evolution of Testis-Specific New Genes: The Case of Telomere-Capping Genes in Drosophila, Raphaelle¨ Dubruille, Gabriel A. B. Marais, and Benjamin Loppin Volume 2012, Article ID 708980, 11 pages Novel Genes from Formation to Function, Rita Ponce, Lene Martinsen, Lu´ıs M. Vicente, and Daniel L. Hartl Volume 2012, Article ID 821645, 9 pages Alternative Splicing: A Potential Source of Functional Innovation in the Eukaryotic Genome,LuChen, Jaime M. Tovar-Corona, and Araxi O. Urrutia Volume 2012, Article ID 596274, 10 pages Where Do Phosphosites Come from and Where Do They Go after Gene Duplication?, Guillaume Diss, Luca Freschi, and Christian R. Landry Volume 2012, Article ID 843167, 8 pages The Evolution of Novelty in Conserved Gene Families, Gabriel V. Markov and Ralf J. Sommer Volume 2012, Article ID 490894, 8 pages What Can Domesticated Genes Tell Us about the Intron Gain in Mammals?,Dusanˇ Kordisandˇ Janez Kokosarˇ Volume 2012, Article ID 278981, 7 pages Hindawi Publishing Corporation International Journal of Evolutionary Biology Volume 2012, Article ID 483176, 2 pages doi:10.1155/2012/483176 Editorial Molecular Evolutionary Routes That Lead to Innovations Fred´ eric´ Brunet,1 Hideki Innan,2 Ben-Yang Liao,3 and Wen Wang4 1 Institut de G´enomique Fonctionnelle de Lyon, Ecole Normale Sup´erieure de Lyon, 32-34 Avenue Tony Garnier, 69007 Lyon, France 2 Hayama Center for Advanced Studies, The Graduate University for Advanced Studies, Kanagawa 240-0193, Japan 3 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 350, Taiwan 4 Max-Planck Junior Scientist Group on Evolutionary Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Yunnan, Kunming 650223, China Correspondence should be addressed to Fred´ eric´ Brunet, [email protected] Received 9 September 2012; Accepted 9 September 2012 Copyright © 2012 Fred´ eric´ Brunet et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In biology, it is always fascinating to observe the continuous performed in-depth reviews of these submissions to ensure changes occurring at different levels in living organisms. In the articles would be of the highest quality. Among the 18 demonstration of this interest, one question we regularly ask articles that went through this reviewing process, 17 were is the following: accepted. We feel that this represents the high quality of the work offered to us by the invited authors. “What are the events that contribute to the evo- Above all, we are immensely grateful to all authors and lution of new functions and adaptive evolutionary reviewers who contributed to this special issue. We would innovations?” like to take the chance to express our sincerest gratitude to Deep down at the molecular level, we are referring to the each and every person involved in this project. The effort they various genetic and molecular mechanisms that occasionally have put forth is an expression of the dedicated passion we all either duplicate preexisting genes, or lead to the origination share for this field of research. Additionally, we deeply hope of new sequences. Altogether, these new and duplicated genes that everyone will enjoy reading each and every one of these represent a substantial fraction of every genome sequenced. excellent articles as much as we did. They are of multiple origins ranging from whole-genome D. Kordisˇ and J. Kokosar examined the intron dynamics duplications, which are documented in many eukaryotes, to in the domesticated genes of eutherians, showing some various other modes of duplication—mostly single full or gained with positional bias. partial gene duplications—by DNA-based or retroposition K. S. Swithers et al. reviewed the functional role of events. reticulate evolution, focusing on horizontal gene transfers, in Each month, new and exciting articles dealing with these creating novelties and complexities. topics are published in different journals, and it has now been R. Ponce et al. reviewed novel genes, mostly in Drosophila several years since a special issue collecting this research into and primates, providing details of the chimeric gene Sdic. a single volume has been published. Our belief is that it is L. Chen et al. reviewed and discussed the important now the time for the publication of a new special issue that role alternative splicing may have in generating transcrip- would bring together researchers working in this field, and tome and organism complexity during eukaryotic evolu- provide up-to-date research on the subject. For this special tion. issue, we allowed these authors the liberty to offer either R. Dubruille et al. reviewed and presented their latest review papers or pure research articles. Others were also results on the evolution of the hiphop/K81 telomere capping encouraged to use a rather unconventional format, bringing genes in Drosophila. together a review of their published work, but updated with L. Huminiecki and G. C. Conant demonstrated the rise new insights into their latest discoveries. Experts in the field to complex innovations in cellular networks that can only be 2 International Journal of Evolutionary Biology evolved from whole-genome duplications using examples in fungi and vertebrates. G. V. Markov and R. J. Sommer reviewed the evolution of novelties among conserved gene families in insects and nematodes genomes. P. C. Sharma et al. provided a nice example of the potential evolution of microsatellites in duplicated regions of the rice genome. E. Dubois et al. discussed the impact the domestication of the transposase of a piggyBac had on the spread of Tc1/mariner elements throughout the germline of a Parame- cium. G. Diss et al. provided some evidence that posttransla- tional regulatory control on a function might influence the divergence between paralogous genes. O. M. Ramos and D. Ferrier
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