Seascape genetics of Indo-Pacific reef organisms: methodologies and case studies for an emerging discipline

Abstract

Which factors shape population connectivity and the consistency of their influence across species and seascapes is largely unresolved. This thesis takes a comparative genetic approach to investigate the influences of seascape topology (past sea level changes, contemporary oceanography, and geography) and species biology on the genetic connectivity among coral reefs around Australia, the Indo-Australasian Archipelago (IAA), and the wider Indo-Pacific. I focus on a suite of common, codistributed coral reef fishes and invertebrates that differ in life history characteristics. In the introductory chapter of my thesis I discuss population connectivity in marine systems, the contribution of seascape genetics to marine population connectivity research, and the state of our knowledge in the Indian and Pacific Oceans (Chapter One). Chapters Two and Three review the field of seascape genetics and the methodologies used in seascape genetic studies, respectively. My empirical research (Chapters Four-Six) takes a broad, yet integrated approach to describe and understand the processes underlying seascape genetic patterns around Australia, the IAA, and the Indo-Pacific. First, I investigate historical spatial genetic (mitochondrial DNA, mtDNA) patterns and processes using a comparative, multi-species framework (Chapter Four). I extend typical methods of comparative phylogeography to include: a matrix comparison method that allows the quantitative characterization of spatial genetic patterns; and a multiple regression modeling approach to identify the processes underlying the spatial genetic patterns for each species. I find that despite being subjected to common geographic and seascape influences, spatial genetic patterns differ across four common coral reef fishes (Acanthurus triostegus, Dascyllus trimaculatus, Halichoeres hortulanus, Pomacentrus coelestis). Although species with similar dispersal potential (based on egg type and pelagic larval duration) have the most similar spatial genetic patterns, the seascape features and processes (e.g. previous landbridges and oceanographic distances) underlying the genetic patterns are not always shared among species. Second, I characterize the latitude-wide genetic patterns of one species (P. coelestis) and extend methods typically used in such investigations by borrowing concepts and measures more commonly used for analyses of community composition (Chapter Five). Genealogical analyses reveal that levels of population genetic diversity in the core of the species range are elevated by the co-occurrence of two cryptic clades. Furthermore, the application of partitioned β-diversity measures and nestedness analyses reveal that differing demographic processes underlie the genetic patterns observed at the northern and southern latitudinal peripheries of the species range. Last, I focus on edge-of-range genetic patterns for two tropical echinoderm species (Acanthaster planci and Tripneustes gratilla) at a little-studied high latitude peripheral population, Kermadec Islands, New Zealand (Chapter Six). I find surprisingly concordant patterns across species indicating that despite being marginal habitat for tropical species, the Kermadec Islands populations are maintained by self-recruitment and not immigration over contemporary timescales. Through investigating genetic patterns over a range of species and seascapes, I have evaluated several long-standing spatial genetic hypotheses and their relevance to seascape genetics. I have identified shortcomings in our current understanding of seascape genetic patterns and the limitations of our analytical toolset. As such, I demonstrate how novel approaches can effectively identify the processes underlying spatial genetic patterns in marine systems.