GENE FLOW & DISPERSAL AS FACTORS MEDIATING POPULATION DIVERGENCE, ADMIXTURE AND SPECIATION IN FISHES by RyanP Walter B.Sc, SUNY Brockport, NY, 2000 M.Sc, SUNY Brockport, NY, 2002 A Dissertation Submitted to the Faculty of Graduate Studies through the Great Lakes Institute for Environmental Research in partial fulfillment of the Requirements for the Degree of Doctor of Philosophy at the University of Windsor Windsor, Ontario, Canada 2009 © 2009 Ryan Walter Library and Archives Bibliotheque et 1*1 Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington OttawaONK1A0N4 Ottawa ON K1A 0N4 Canada Canada Your file Votre re'terence ISBN: 978-0-494-82070-4 Our file Notre reference ISBN: 978-0-494-82070-4 NOTICE: AVIS: The author has granted a non­ L'auteur a accorde une licence non exclusive exclusive license allowing Library and permettant a la Bibliotheque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par I'lnternet, preter, telecommunication or on the Internet, distribuer et vendre des theses partout dans le loan, distribute and sell theses monde, a des fins commerciales ou autres, sur worldwide, for commercial or non­ support microforme, papier, electronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in this et des droits moraux qui protege cette these. Ni thesis. Neither the thesis nor la these ni des extraits substantiels de celle-ci substantial extracts from it may be ne doivent etre imprimes ou autrement printed or otherwise reproduced reproduits sans son autorisation. without the author's permission. In compliance with the Canadian Conformement a la loi canadienne sur la Privacy Act some supporting forms protection de la vie privee, quelques may have been removed from this formulaires secondaires ont ete enleves de thesis. cette these. While these forms may be included Bien que ces formulaires aient inclus dans in the document page count, their la pagination, il n'y aura aucun contenu removal does not represent any loss manquant. of content from the thesis. 1+1 Canada Declaration of Co-Authorship / Previous Publication I. Co-Authorship Declaration I hereby declare that this thesis incorporates material that is result of joint research, as follows: Chapter 2 contains material from a manuscript entitled "Gene flow increases temporal stability of Chinook salmon (Oncorhynchus tshayvytscha) populations in the Upper Fraser River, British Columbia, Canada" that has been accepted in the Canadian Journal of Fisheries and Aquatic Sciences. This manuscript is co-authored by RP Walter, T Aykanat, DW Kelly, JM Shrimpton and DD Heath. Chapter 3 contains material from the paper entitled "Dispersal and population genetic structure of Telmatherina antoniae, an endemic freshwater Sailfin silverside from Sulawesi, Indonesia" published in The Journal of Evolutionary Biology. This manuscript is co-authored by RP Walter, GD Haffner and DD Heath. Chapter 4 contains material from a manuscript entitled "No barriers to gene flow among sympatric colour-morphs of "small" Telmatherina antoniae from Indonesia's Lake Matano" that has been submitted to The Journal of Fish Biology. This manuscript is coauthored by RP Walter, GD Haffner and DD Heath. The Appendix contains the manuscript "Characterization of four tetranucleotide and six dinucleotide microsatellite markers for use in the tropical freshwater fish Telmatherina antoniae and related species" published in Molecular Ecology Notes. This manuscript is co-authored by RP Walter, JR Ovenden and DD Heath. In all cases, the key ideas, primary contributions, experimental designs, data analysis and interpretation, were performed by the author, and the contribution of co-authors was primarily through the provision of guidance with field and lab work. I am aware of the University of Windsor Senate Policy on Authorship and I certify that I have properly acknowledged the contribution of other researchers to my thesis, and have obtained written permission from each of the co-author(s) to include the above material(s) in my thesis. I certify that, with the above qualification, this thesis, and the research to which it refers, is the product of my own work. II. Declaration of Previous Publication This thesis includes four original papers that have been previously published/submitted for publication in peer reviewed journals, as follows: Thesis Chapter Publication title/full citation Publication status* Chapter 2 Walter RP, Aykanat T, Kelly D, Shrimpton JM, In press Heath DD. Gene flow increases temporal stability of Chinook salmon {Oncorhynchus tshawytscha) populations in the Upper Fraser River, British Columbia, Canada. Canadian Journal for Fisheries and Aquatic Science Chapter 3 Walter RP, GD Haffner GD, Heath DD (2008) Published Dispersal and population genetic structure of iii Telmatherina antoniae, an endemic freshwater Sailfin silverside from Sulawesi, Indonesia. Journal of Evolutionary Biology. DOI: 10.HH/j.1420-9101.2008.01645.x Chapter 4 Walter RP, Haffner GD, Heath DD. No barriers Submitted to gene flow among sympatric colour morphs of Telmatherina antoniae from Indonesia's Lake Matano. In review at Journal of Fish Biology. Appendix Walter RP, Ovenden JR, Heath DD (2007) Published Characterization of four tetranucleotide and six dinucleotide microsatellite markers for use in the tropical freshwater fish Telmatherina antoniae and related species. Molecular Ecology Notes 7: 651-653. DOI: 10.111 l/j.l471-8286.2006.01664.x I certify that I have obtained a written permission from the copyright owner(s) to include the above published material(s) in my thesis. I certify that the above material describes work completed during my registration as graduate student at the University of Windsor. I declare that, to the best of my knowledge, my thesis does not infringe upon anyone's copyright nor violate any proprietary rights and that any ideas, techniques, quotations, or any other material from the work of other people included in my thesis, published or otherwise, are fully acknowledged in accordance with the standard referencing practices. Furthermore, to the extent that I have included copyrighted material that surpasses the bounds of fair dealing within the meaning of the Canada Copyright Act, I certify that I have obtained a written permission from the copyright owner(s) to include such material(s) in my thesis. I declare that this is a true copy of my thesis, including any final revisions, as approved by my thesis committee and the Graduate Studies office, and that this thesis has not been submitted for a higher degree to any other University or Institution. IV ABSTRACT Understanding how species persist and how they arise are among the most fundamental objectives of ecology and evolutionary biology. Genetic markers coupled with population genetic theory are frequently employed in the study of animal dispersal and gene flow, two parameters central to understanding the genetic structure underlying natural populations. This thesis presents novel examples of the temporally-stabilizing effect of low to moderate levels of gene flow (Chapter 2), population admixture or evidence of sympatric divergence (Chapter 3), a lack of genetic structure among phenotypes with no reproductive barriers (Chapter 4), river effects on genetic structure of endemic populations (Chapter 5), and parallelism in ecological diversification (Chapter 6). Throughout this thesis, dispersal also plays a fundamental role in the observed genetic structure, taking on a number of forms given the life history of the species under study. For homing salmonids, straying from natal spawning sites is dispersal. In Chapter 2,1 argue that low levels of gene flow can elevate effective population sizes and preserve genetic variability highlighting the importance of considering gene flow acting to temporally stabilize populations. The genetic data presented here overwhelmingly suggests that dispersing individuals are likely reproductively successful members of the populations into which they stray (Chapter 2). For the Malili Sailfin silversides, larval dispersal most likely accounts for the sympatric population structure of an endemic fish in Lake Matano (Chapter 3, 4). Population genetic structure in the presence of substantial dispersal provides a unique perspective on the evolution of reproductive isolation. Genetic analyses using novel microsatellite markers revealed significant population-level v structure consisting of 4-6 sympatric clusters resolving the apparent paradox of population genetic structure coupled with frequent dispersal. Despite an ontogenetic predisposition to dispersal, geographic and other environmental factors also encourage or retard dispersal. Rivers act to facilitate the movement of individuals between lacustrine populations but biasing one lake as a new exporter of migrants (Chapter 5), or they can completely block passage leading to isolation and the independent evolution of similar feeding strategies (Chapter 6). In all these cases, dispersal (or a lack of) influences the underlying population genetic structure. VI For my Grandparents Bucky and Suzanne ACKNOWLEDGEMENTS I thank my primary supervisor Daniel Heath. His breadth