Advances in Experimental Medicine and Biology 781 Christian R. Landry Nadia Aubin-Horth Editors Ecological Genomics Ecology and the Evolution of Genes and Genomes Advances in Experimental Medicine and Biology Volume 781 For further volumes: http://www.springer.com/series/5584 Advances in Experimental Medicine and Biology Series Editor: JOHN D. LAMBRIS, University of Pennsylvania, Philadelphia, PA, USA Editorial Board: IRUN R. COHEN, The Weizmann Institute of Science, Rehovot, Israel ABEL LAJTHA, N.S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA RODOLFO PAOLETTI, University of Milan, Milan, Italy Recent Volumes in this Series Volume 782 PROGRESS IN MOTOR CONTROL Michael A. Riley, Michael J. Richardson and Kevin D. Shockley Volume 783 THE NEW PARADIGM OF IMMUNITY TO TUBERCULOSIS Maziar Divangahi Volume 784 KISSPEPTIN SIGNAING IN REPRODUCTIVE BIOLOGY Alexander S. Kauffman and Jeremy T. Smith Volume 785 CROSSROADS BETWEEN INNATE AND ADAPTIVE IMMUNITY IV Bali Pulendran, Peter D. Katsikis and Stephen P. Schoenberger Volume 786 TRANSCRIPTIONAL AND TRANSLATIONAL REGULATION OF STEM CELLS Gary Hime and Helen Abud Volume 787 BASIC ASPECTS OF HEARING Brian CJ Moore Volume 788 NEUROBIOLOGY OF RESPIRATION Mieczyslaw Pokorski Volume 789 OXYGEN TRANSPORT TO TISSUE XXXV Sabine Van Huffel, Gunnar Nualaers, Alexander Caicedo, Duane F. Bruley and David K. Harrison Volume 790 VIRAL ENTRY INTO HOST CELLS Stefan Pöhlmann and Graham Simmons A Continuation Order Plan is available for this series. A continuation order will bring delivery of each new volume immediately upon publication. Volumes are billed only upon actual shipment. For further information please contact the publisher. Christian R. Landry • Nadia Aubin-Horth Editors Ecological Genomics Ecology and the Evolution of Genes and Genomes 123 Editors Christian R. Landry Nadia Aubin-Horth Département de Biologie Département de Biologie Local 3110 Institut de Biologie Local 1241 Institut de Biologie Intégrative et des Systèmes Intégrative et des Systèmes Université Laval Université Laval Québec, QC Québec, QC Canada Canada ISSN 0065-2598 ISSN 2214-8019 (electronic) ISBN 978-94-007-7346-2 ISBN 978-94-007-7347-9 (eBook) DOI 10.1007/978-94-007-7347-9 Springer Dordrecht Heidelberg New York London Library of Congress Control Number: 2013954790 © Springer Science+Business Media Dordrecht (outside the USA) 2014 Chapter 13 was created within the capacity of an US government employment. US copyright protection does not apply. © Springer Science+Business Media Dordrecht 2014 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. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. 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. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Contents 1 Recent Advances in Ecological Genomics: From Phenotypic Plasticity to Convergent and Adaptive Evolution and Speciation.......................................... 1 Christian R. Landry and Nadia Aubin-Horth 2 Trait Transitions in Explicit Ecological and Genomic Contexts: Plant Mating Systems as Case Studies ............ 7 Vincent Castric, Sylvain Billiard, and Xavier Vekemans 3 Revisiting Mortimer’s Genome Renewal Hypothesis: Heterozygosity, Homothallism, and the Potential for Adaptation in Yeast...................................... 37 Paul M. Magwene 4 Ecological Genomics of Adaptation and Speciation in Fungi .. 49 Jean-Baptiste Leducq 5 Integrating Phenotypic Plasticity Within an Ecological Genomics Framework: Recent Insights from the Genomics, Evolution, Ecology, and Fitness of Plasticity................ 73 Matthew Morris and Sean M. Rogers 6 Eco-Evo-Devo: The Time Has Come....................... 107 Ehab Abouheif, Marie-Julie Favé, Ana Sofia Ibarrarán-Viniegra, Maryna P. Lesoway, Ab Matteen Rafiqi, and Rajendhran Rajakumar 7 Evolutionary and Ecological Genomics of Developmental Plasticity: Novel Approaches and First Insights From the Study of Horned Beetles.............................. 127 Armin P. Moczek, Teiya Kijimoto, Emilie Snell-Rood, Guilherme Rocha, Melissa Pespeni, and Karen Kafadar 8 Neurogenomics of Behavioral Plasticity.................... 149 Rayna M. Harris and Hans A. Hofmann 9 Ecological Genomics of Host Behavior Manipulation by Parasites............................................ 169 François Olivier Hébert and Nadia Aubin-Horth v vi Contents 10 Ecological Epigenetics................................... 191 Holly J. Kilvitis, Mariano Alvarez, Christy M. Foust, Aaron W. Schrey, Marta Robertson, and Christina L. Richards 11 The Reproducibility of Adaptation in the Light of Experimental Evolution with Whole Genome Sequencing. 211 Guillaume Achaz, Alejandra Rodriguez-Verdugo, Brandon S. Gaut, and Olivier Tenaillon 12 Ecological Genomics of Host Shifts in Drosophila mojavensis.................................... 233 Luciano M. Matzkin 13 The Genomics of an Adaptive Radiation: Insights Across the Heliconius Speciation Continuum...................... 249 Megan Supple, Riccardo Papa, Brian Counterman, and W. Owen McMillan 14 Merging Ecology and Genomics to Dissect Diversity in Wild Tomatoes and Their Relatives............................. 273 David C. Haak, Jamie L. Kostyun, and Leonie C. Moyle 15 Integrated Genomics Approaches in Evolutionary and Ecological Endocrinology............................ 299 Jun Kitano, Asano Ishikawa, and Sean C. Lema 16 Evolutionary Genomics of Environmental Pollution ......... 321 Andrew Whitehead 17 Signatures of Natural Selection and Ecological Differentiation in Microbial Genomes................................... 339 B. Jesse Shapiro Recent Advances in Ecological Genomics: From Phenotypic Plasticity 1 to Convergent and Adaptive Evolution and Speciation Christian R. Landry and Nadia Aubin-Horth Abstract Biological diversity emerges from the interaction between genomes and their environment. Recent conceptual and technological developments allow dissecting these interactions over short and long time-scales. The 16 contributions to this book by leaders in the field cover major re- cent progresses in the field of Ecological Genomics. Altogether, they illustrate the interplay between the life-history and genomic architecture of organisms, how the interaction of the environment and the genome is shaping phenotypic variation through phenotypic plasticity, how the process of adaptation may be constrained and fueled by internal and external features of organisms and finally, how species formation is the result of intricate interactions between genomes and the ecological conditions. These contributions also show how fundamental questions in biology transcend the boundaries of kingdoms, species and environments and illustrate how integrative approaches are powerful means to answer the most important and challenging questions in ecology and evolution. Keywords Phenotypic plasticity • Ecological genomics • Life history • Speciation • Adaptation that have shaped genotype frequencies in nat- 1.1 Introduction to Ecological ural populations (Pavey et al. 2012). Meeting Genomics this challenge requires the use of integrative ap- proaches, as different techniques and combina- One of the major challenges in biology is to tion of disciplines are needed to understand pro- connect genotypes to phenotypes and to iden- cesses that act at different levels of organizations, tify the ecological and demographic parameters from ecosystems to genes. These integrative ap- proaches have given rise to the field of ecological C.R. Landry ( ) • N. Aubin-Horth genomics (Feder and Mitchell-Olds 2003). The Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 Avenue de la chapters contributed to this book reflect the most Médecine, Québec, QC G1V 0A6, Canada recent and exciting progress in this young field of e-mail: [email protected] research. C.R. Landry and N. Aubin-Horth (eds.), Ecological Genomics: Ecology and the Evolution 1 of Genes and Genomes,