“It is also obvious that the individuals of the same species, though now inhabiting distant and isolated regions, must have proceeded from one spot, where their parents were first produced.” – Darwin 1859, On the Origin of Species “Quod nullus proiceat lastadien in deep hujus civitatis, sub pena vite” “That no one throws ballast in the deep of this town, by loss of his life” – Wismar (Germany) statute, 1345 “Picture the mouth of the muddy, narrow River Tyne, jammed with four or five hundred keels and two or three hundred ships…” – John Nef, 1558 Evolution in the North Atlantic: processes shaping spatial patterns of genetic diversity in introduced intertidal invertebrates by Anthony Leon Einfeldt B.Sc. UBC 2008 A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in the Graduate Academic Unit of Biology Supervisor: Jason Addison, PhD, Biology, UNB Examining Board: Gary Saunders, PhD, Biology, UNB Adrian Reyes-Prieto, PhD, Biology, UNB Tony Diamond, PhD, Forestry, UNB External Examiner: Sean Rogers, PhD, University of Calgary This dissertation is accepted by the Dean of Graduate Studies THE UNIVERSITY OF NEW BRUNSWICK March, 2018 ©Anthony Einfeldt, 2018 ABSTRACT The movement of individuals and their genes across geographic space influences a species’ ecology and evolution, but it is often not possible to observe past or present movement directly. Molecular tools provide a means of inferring past movement and contemporary barriers to movement, because the known modes of mutation and inheritance underlying genetic variation provide clear predictions for patterns arising from movement and subdivision. In this thesis, I investigate how contemporary and historic patterns of movement shape evolutionary trajectories by investigating distributions of genetic variation in focal intertidal invertebrates of the North Atlantic. To determine how movement is affected by the interaction of currents with life-history traits, I sequenced mitochondrial and nuclear DNA of the intertidal amphipod Corophium volutator from discrete patches of mudflat habitat throughout the Northwest Atlantic. I detected patterns of genetic subdivision and gene flow concordant with hydrological patterns, demonstrating that currents shape evolution by determining dispersal pathways and cause fine-scale subdivision in marine communities. To test how C. volutator colonized the Northwest Atlantic coast, I investigated spatial genetic variation in populations from across its entire range using the same markers. I found that diversity in Northwest Atlantic populations was subsampled from more genetically diverse populations in the Northeast Atlantic, consistent with historic human-mediated introduction from the Northeast to the Northwest. To investigate how human-mediated dispersal affects species’ evolutionary trajectories, I characterized genomic variation in C. volutator and a co-occurring annelid Hediste diversicolor in populations from the Northeast and Northwest Atlantic coasts. I found extensive genetic divergence between ii the introduced and native ranges and genetic patterns consistent with historic admixture between populations within each range, providing evidence that human-mediated movement can create new allopatric lineages and erase ancestral genetic structure by promoting gene flow between otherwise isolated populations. Together, my results suggest that the increasing reach, magnitude, and frequency of global human movement will change the evolutionary trajectories of species associated with human vectors of transport. While contemporary connectivity will continue to be affected by regional processes (such as currents), uncurbed human activity will likely disrupt diversification arising from barriers at regional scales while promoting the formation of new lineages at a global scale. iii DEDICATION I dedicate this thesis to my parents, Sandra and Flemming Einfeldt, who instilled in me a deep appreciation for the natural world and a desire to understand the forces behind it. I have many fond memories of how they fostered my curiosity, creativity, and confidence. Amongst the first of these memories are the weekly walks they would take me on through the woods to find a rare species of plant, which when in bloom would produce individually wrapped chocolates. The world turns out to be full of things much like the Chocolate Tree, and I thank my parents for introducing me to the thrill of discovering their true nature. iv ACKNOWLEDGEMENTS This research grew from an initial project conceived by Jason Addison to assess connectivity amongst mudflats in the Bay of Fundy, funded by NSERC through a Strategic Project Grant to Myriam Barbeau and a Discovery Grant to Jason Addison. Additional funding for the projects in this thesis was provided by a Canadian Foundation for Innovation grant to Jason Addison, a New Brunswick Innovation Foundation grant to Jason Addison and scholarship to myself, a New Brunswick Wildlife Trust Fund grant to Jason Addison and myself, and fellowships from the Fredrik and Catherine Eaton Foundation, ACENET, and the Marguerite and Murray Vaughan Foundation awarded to myself. Many thanks to my supervisor Jason Addison and committee member Linley Jesson for their guidance and support on projects in and beyond this thesis. Thanks to my other committee member Myriam Barbeau, who gave helpful feedback on my proposals and thesis. Thanks also to Mark Forbes for direction and funding at a key point. The broad geographic scope of this research was made possible with the help of many people. Sampling trips in North America were aided by Jeremy Doucet and Felix Zhou during their B.Sc. Honours in Jason Addison’s lab, Brian Nason, Jarrett Starkey- Seto, and my parents Sandra and Flemming Einfeldt. I thank the researchers who collected and sent me Corophium volutator specimens, including Myriam Barbeau, David Drolet, Guy Bachelet, Anne-Laure Barillé, Jérôme Jourde, Chloé Dancié, Julia Sigwart, Rob Hughes, Martin Solan, Annelies Debacker, Sander Wijnhoven, Ines Heisterkamp, Birgit Hussel, K. Thomas Jensen, Jacob Strand, and Andreas Bick. Thanks to Jim Provan for hosting me at Queen’s University Belfast, and to Julia Sigwart, Christine Maggs, Siobhan Rose Vye, Thomas Prebble, Nessa O’Connor, Lauren Sumner- v Rooney, Julia Calderwood, and many others for facilitating both scientific and social endeavours in Northern Ireland and Ireland. Laboratory work was helped immensely by Jin-Hong Kim Jana Gruettner, who first implemented and troubleshot the genome reduction methods used in Chapter 4. Sara Edwards was a reliable sounding board (and rubber duck) for the many coding, analysis, and writing problems that I encountered. Stephen Heard and his Nerds (particularly Chandra Moffat, Julia Mlynarek, Allyson Heustis, and Mallory MacDonnell, Ken Dearborn, and Rylee Isett) were really good at Boggle, and along with Dan Quiring and Rob Johns provided stimulating weekly presentations, discussions, constructive comments, and collaboration. The mudflat ecology group (particularly David Drolet, Diana Hamilton, Kelan Kennedy, and Trevor Bringloe) provided many discussions. This thesis was strengthened by my involvement in projects and systems not directly mentioned elsewhere in this document, which was made possible by the strong community in the UNB Biology Department. Thanks to Gary Saunders and his lab (particularly Amanda Savoie, Lesleigh Kraft, and Meghann Bruce) for ideas and discussions throughout my degree, and for spearheading a 2014 arctic sampling expedition. Thanks to Tony Diamond and his lab (particularly Kevin Kelly, Sarah Hudson, Kirsten Bowser, and Lauren Scopel) for the annual migrations to and from Machias Seal Island and the opportunities they presented. Helen Tai generously provided assistance and resources for RNA work on a project in progress that stems from the research presented here. By no means least, thank you to the graduate students at UNB and friends in Fredericton, who gave me the strength and motivation to continue this research and kept me in touch with what is truly important. vi Table of Contents ABSTRACT ........................................................................................................................ ii DEDICATION ................................................................................................................... iv ACKNOWLEDGEMENTS ................................................................................................ v Table of Contents .............................................................................................................. vii List of Tables ..................................................................................................................... xi List of Figures .................................................................................................................. xiii Chapter 1 – General introduction ........................................................................................ 1 Inferring movement from distributions of variation ....................................................... 1 Inferring movement from molecular variation ............................................................... 3 Movement and evolution in North Atlantic intertidal invertebrates ............................... 6 References ..................................................................................................................... 10 Chapter 2 – Hydrology influences population genetic structure