Evolutionary Biology: Biodiversification from Genotype to Phenotype Evolutionary Biology: Biodiversification from Genotype to Phenotype
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Pierre Pontarotti Editor Evolutionary Biology: Biodiversification from Genotype to Phenotype Evolutionary Biology: Biodiversification from Genotype to Phenotype [email protected] Pierre Pontarotti Editor Evolutionary Biology: Biodiversification from Genotype to Phenotype 123 [email protected] Editor Pierre Pontarotti Evolution Biologique et Modélisation I2M UMR 7373 Aix Marseille Université/CNRS Marseille France ISBN 978-3-319-19931-3 ISBN 978-3-319-19932-0 (eBook) DOI 10.1007/978-3-319-19932-0 Library of Congress Control Number: 2015942234 Springer Cham Heidelberg New York Dordrecht London © Springer International Publishing Switzerland 2015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper Springer International Publishing AG Switzerland is part of Springer Science+Business Media (www.springer.com) [email protected] Preface For the 18th time, the Evolutionary Biology Meeting in Marseille took place from 16 to 19 September 2014. The goal of this annual meeting is to allow scientists of different disciplines, who share a deep interest in evolutionary biology concepts, knowledge and applications, to meet and exchange and enhance interdisciplinary collaboration. The Evolutionary Biology Meeting in Marseille is now recognised internation- ally as an important exchange platform and a booster for the use of evolutionary-based approaches in biology and also in other scientific areas. This year, more than 100 presentations were selected by the evolutionary biol- ogy meeting scientific committee. We have further selected 20 of the most repre- sentative ones for the book. The book will give the reader an overview of the state-of-the-art research in the evolutionary biology field. The book is the eighth one that we have published further to the meeting. We would like to underline that the seven books are com- plementary one to another and should be considered as volumes. The readers of the evolutionary biology books as well as the meeting participants will maybe like us witness years after years during the different meetings and book editions a shift in the evolutionary biology concepts and knowledge. The fact that the chapters of the book are selected from one meeting enables the quick diffusion of the novelties. Concerning the book, the chapters are organised in the following categories Genotype to Phenotype (Chaps. 1–3) Genetic Mechanisms of Diversification (Chaps. 4–8) Evolutionary Mechanisms (Chaps. 9–14) Speciation and Biodiversity (Chaps. 15–20) We would like to thank all the authors, the meeting participants, and the sponsors: Aix Marseille Université (AMU), CNRS, ITMO GGB and BCDE, ECCOREV Federation, Conseil Général 13, Ville de Marseille. We also wish to thank the Springer editing staff and in particular Andrea Schlitzberger for her competence and help. v [email protected] vi Preface We wish also to thank members of the Association pour l’Etude de l’Evolution Biologique (AEEB) for their help in the meeting organisation, as well as AMU for its logistic support. Marseille, France Pierre Pontarotti April 2015 [email protected] Contents Part I Genotype to Phenotype 1 Functional Mapping: How to Map Genes for Phenotypic Plasticity of Development .............................. 3 Lidan Sun, Libo Jiang, Meixia Ye, Xuli Zhu, Jing Wang, Kirk Gosik and Rongling Wu 2 The Genomics of Sexual Ornaments, Gene Identification and Pleiotropy ...................................... 19 Martin Johnsson 3 Life’s Dual Nature: A Way Out of the Impasse of the Gene-Centred ‘Versus’ Complex Systems Controversy on Life .................................. 35 Alexis De Tiège, Koen B. Tanghe, Johan Braeckman and Yves Van de Peer Part II Genetic Mechanisms of Diversification 4 Retrotransposons: Genomic and Trans-Genomic Agents of Change ......................................... 55 David L. Adelson, Reuben M. Buckley, Atma M. Ivancevic, Zhipeng Qu and Lu Zeng 5 Horizontal Transfers and the New Model of TE-Driven Genome Evolution in Eukaryotes ........................ 77 Moaine El Baidouri and Olivier Panaud vii [email protected] viii Contents 6 The Impact of Transposable Elements in the Evolution of Plant Genomes: From Selfish Elements to Key Players....... 93 Beatriz Contreras, Cristina Vives, Roger Castells and Josep M. Casacuberta 7 Sympatric Differentiation and Speciation: Insights from Drosophila Studies .............................. 107 Eugenia Rashkovetsky, Zeev Frenkel, Pawel Michalak and Abraham Korol 8 Mutation-Driven Evolution: Microsatellite Instability Drives Speciation in a Mammalian Taxon ...................... 141 Paul Sequeira, Yen-Shan Chen and Michael A. Weiss Part III Evolutionary Mechanisms 9 Adaptive Diversification in Coevolutionary Systems .......... 167 C. Hui, H.O. Minoarivelo, S. Nuwagaba and A. Ramanantoanina 10 Structure, Interaction, and Evolution: Reflections on the Natural History of Proteins....................... 187 Gavin C. Conant 11 Pollination Syndromes: A Global Pattern of Convergent Evolution Driven by the Most Effective Pollinator ........... 203 Lorena Ashworth, Ramiro Aguilar, Silvana Martén-Rodríguez, Martha Lopezaraiza-Mikel, Germán Avila-Sakar, Víctor Rosas-Guerrero and Mauricio Quesada 12 Altruism, Religion, and Self-Enhancement in a Framework of Ad Hoc Evolutionary Adaptation ..................... 225 Florian Habermacher 13 Investigating Trade-offs in Sexual Populations with Gene Flow .................................... 245 Zachary N. Ardern and Matthew R. Goddard 14 Promoter Order Strategy and Bacterial PspF Regulon Evolution ......................................... 263 Goran Jovanovic, Parul Mehta, Christopher McDonald and Martin Buck [email protected] Contents ix Part IV Speciation and Biodiversity 15 Genomic Admixture and Species Delimitation in Forest Trees ............................................ 287 Amanda R. De La Torre 16 Apomixis as a Facilitator of Range Expansion and Diversification in Plants ........................... 305 Diego Hojsgaard and Elvira Hörandl 17 Elopomorpha (Teleostei) as a New Model Fish Group for Evolutionary Biology and Comparative Genomics......... 329 Jhen-Nien Chen, Sarah Samadi and Wei-Jen Chen 18 Looks Can be Deceiving: Cryptic Species and Phenotypic Variation in Rhodnius spp., Chagas Disease Vectors.......... 345 Márcio G. Pavan, Gustavo B.S. Rivas, Fernando B.S. Dias and Rodrigo Gurgel-Gonçalves 19 Forest Tree Species Traced with a DNA-Based Proof for Illegal Logging Case in Poland....................... 373 Justyna A. Nowakowska, Tomasz Oszako, Anna Tereba and Agata Konecka 20 Domestication and Genetics: What a Comparison Between Land and Aquatic Species Can Bring? ................... 389 Fabrice Teletchea Index ................................................ 403 [email protected] Part I Genotype to Phenotype [email protected] Chapter 1 Functional Mapping: How to Map Genes for Phenotypic Plasticity of Development Lidan Sun, Libo Jiang, Meixia Ye, Xuli Zhu, Jing Wang, Kirk Gosik and Rongling Wu Abstract Functional mapping is a statistical tool derived to map genes or quan- titative trait loci (QTLs) that control the dynamic process of complex traits. In this chapter, we describe an innovative modification of functional mapping to charac- terize the genetic basis of phenotypic plasticity for the developmental pattern of phenotypic traits. Phenotypic plasticity is a phenomenon by which multiple phe- notypes are produced by a single genotype in response to changing environment. Although phenotypic plasticity has been extensively studied in the past decades, new insights into its formation mechanisms can be gained by integrating devel- opmental principles because environmentally induced phenotypes require time to form and build. The new framework for functional mapping enables geneticists to illustrate the genetic architecture of how QTLs cope with environment to regulate the developmental pattern and timing of phenotypic formation. Because of their role in guiding the evolution of complex phenotypes through environmental adaptation, the discoveries of these QTLs facilitate the synthesis of evo-devo and eco-devo. Keywords Functional mapping Á QTL Á Phenotypic plasticity Á Development Á Genetic mapping L. Sun Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University,