Population Genomics Editor-in-Chief: Om P. Rajora Marjorie F. Oleksiak Om P. Rajora Editors Population Genomics: Marine Organisms Population Genomics Editor-in-Chief Om P. Rajora Faculty of Forestry and Environmental Management University of New Brunswick Fredericton, NB, Canada This pioneering Population Genomics Series deals with the concepts and approaches of population genomics and their applications in addressing fundamental and applied topics in a wide variety of organisms. Population genomics is a fast emerging discipline, which has created a paradigm shift in many fields of life and medical sciences, including population biology, ecology, evolution, conservation, agricul- ture, horticulture, forestry, fisheries, human health and medicine. Population genomics has revolutionized various disciplines of biology including population, evolutionary, ecological and conservation genetics, plant and animal breeding, human health, genetic medicine, and pharmacology by allowing to address novel and long-standing intractable questions with unprecedented power and accu- racy. It employs large-scale or genome-wide genetic information across individuals and populations and bioinformatics, and provides a comprehensive genome-wide perspective and new insights that were not possible before. Population genomics has provided novel conceptual approaches, and is tremen- dously advancing our understanding the roles of evolutionary processes, such as mutation, genetic drift, gene flow, and natural selection, in shaping up genetic variation at individual loci and across the genome and populations, disentangling the locus-specific effects from the genome-wide effects, detecting and localizing the functional genomic elements, improving the assessment of population genetic parameters or processes such as adaptive evolution, effective population size, gene flow, admixture, inbreeding and outbreeding depression, demography, and bioge- ography, and resolving evolutionary histories and phylogenetic relationships of extant and extinct species. Population genomics research is also providing key insights into the genomic basis of fitness, local adaptation, ecological and climate acclimation and adaptation, speciation, complex ecologically and economically important traits, and disease and insect resistance in plants, animals and/or humans. In fact, population genomics research has enabled the identification of genes and genetic variants associated with many disease conditions in humans, and it is facilitating genetic medicine and pharmacology. Furthermore, application of popu- lation genomics concepts and approaches facilitates plant and animal breeding, forensics, delineation of conservation genetic units, understanding evolutionary and genetic impacts of resource management practices and climate and environmen- tal change, and conservation and sustainable management of plant and animal genetic resources. The volume editors in this Series have been carefully selected and topics written by leading scholars from around the world. More information about this series at http://www.springer.com/series/13836 Marjorie F. Oleksiak • Om P. Rajora Editors Population Genomics: Marine Organisms Editors Marjorie F. Oleksiak Om P. Rajora Marine Biology and Ecology Faculty of Forestry and Environmental Rosenstiel School of Marine and Management Atmospheric Science, University of Miami University of New Brunswick Miami, FL, USA Fredericton, NB, Canada ISSN 2364-6764 ISSN 2364-6772 (electronic) Population Genomics ISBN 978-3-030-37935-3 ISBN 978-3-030-37936-0 (eBook) https://doi.org/10.1007/978-3-030-37936-0 © Springer Nature Switzerland AG 2020 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, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Population Genomics Book Series This Population Genomics book series is dedicated with love to my wife Malti and children Apoorva, Anu, and Maneesha. Om P. Rajora Population Genomics: Marine Organisms This book is dedicated with love to my granddaughter Ashna Persaud, whose early passion for marine life/biology is both inspiring and captivating. Om P. Rajora This book is dedicated with love to my parents Robert and Melinda, my husband Douglas, and my daughter Samantha. Marjorie F. Oleksiak Preface Genomics has revolutionized biology and is providing powerful approaches and impetus to address common questions across diverse biological fields. Although this commonality has existed previously, now, genomics can be used across biological disciplines and fields to define and more accurately address common questions about the genetic basis underlying a biological trait or function and the evolutionary history, adaptive trajectory, conservation, and management of a population or species. Never before the recent advances in genomics has it been possible to address such common inquires with such power and accuracy, and never before has it been so easy to generate and incorporate genomic information to answer diverse and intractable biological questions. Thus, even though marine sciences encompass the vast breadth of biology, genomics has the potential to provide key insights into diverse biological topics relevant to life in the world’s oceans. This potential and the insights gained from genomics approaches are expanding the biological questions being addressed in the marine sciences and driving research in new directions. For populations of marine organisms, many of which have characteristics that make them quite difficult to study, population genomics approaches provide an exciting potential to generate and integrate knowledge at different levels of organi- zation, from the molecular up through to the ecosystem, to gain a greater under- standing of how life in our oceans exists and works. Understanding and integrating this knowledge across different levels of organization and within complex marine environments is also one of the greatest challenges of marine population genomics. Multidisciplinary approaches, already common in the marine sciences, will be integral to this data analysis and integration. Population genomics approaches are making significant, unprecedented advances in both basic and applied research. Many population genomics studies of marine organisms focus on figuring out which species are present in water columns and gaining some understanding of those species at both the individual and population levels. In the world’s oceans, where organisms are difficult to observe and sample, this information is still not known for many species and ecosystems. Undoubtedly, these studies build upon each other, and as we gain a greater understanding of life vii viii Preface forms and organisms present in oceans, we next can ask: When are they there and what are they doing? Population genomics approaches, similar to previous molecular genetic studies, are also being used to figure out population demography and basic population and evolutionary genetic parameters of different marine populations. These basic population parameters include such attributes as genetic diversity and structure, effective population size (Ne), inbreeding and outbreeding depression, historic bottlenecks, natural selection, and gene flow. Historically, these population genetic parameters have been studied using molecular genetic markers (e.g., allozymes, microsatellites, or a few hundred SNPs). New population genomics approaches, which enable easy and inexpensive sequencing of genomes, transcriptomes, and proteomes for any species, often provide similar information but with much greater resolution and are particularly useful for the many extant marine species, which lack prior genetic and genomic data. In addition to basic research questions to better understand marine species and their populations, population genomics approaches also have practical uses for marine studies, particularly when it comes to understanding local adaptation of marine species and populations and managing and protecting marine resources. Basic needs for marine species management that are well addressed with population genomic data include defining populations and population connectivity because managing fishery species effectively and defining management units depend on knowing what constitutes a population. Population genomics