Delineating population units is essential for the conservation and management of a species. Applying a genetic approach to delineate units, this study identifies genetic population structure, and landscape resistance to gene flow, of the nationally threatened boreal woodland caribou (Rangifer tarandus caribou) across the ecotypes’ southern range in Saskatchewan. Three genetic clusters were delineated across the study area, with moderate genetic connectivity identified with Manitoba. Isolation-by-distance was found to be significant across Saskatchewan, and within each genetic cluster. Gene flow across clusters in Saskatchewan was high (FST = ~0.01), with genetic connectivity being lowest for the south-central cluster surrounding Prince Albert National Park (FST = ~0.03). Resistance to gene flow was identified with the following landscape variables: water, forestry, roads, wildfire, and low suitability habitat. Careful consideration of these variables in range planning will help to maintain genetic connectivity of boreal caribou across its southern range in Saskatchewan. / May 2016

The encrusting sponge Terpios hoshinota is a cyanobacteriosponge with symbiotic photosynthetic cyanobacteria. It covers live corals causing their death. Corals at Green Island were suspected to be infected by Terpios hoshinota in 2006, and field investigations indicated there was massive propagation of the species in both Green Island (Lyudao) and Orchid Island (Lanyu) in 2008 to 2010. We propose two hypotheses, either by Self-Seeding or by Long-Range Dispersal, that explain the fast propagation of Terpios hoshinota in the islands offshore of southeastern of Taiwan. We use ribosomal DNA and mitochondria DNA as molecular markers to investigate how the sponge disperses locally and in a greater geographic scale. A total of 110 samples, from Taiwan: Green Island, Orchid Island, and Kenting (Wanlitong). Japan: Okinawa, Nakijin, Miyako, Bise, Shiraho, Arahama Kumeshima, Yakomo (Okinoerabu), San (Takunoshima), and Xisha Island of China, were collected. Internal Transcribed Spacer 2 (ITS2) from ribosomal DNA and cytochrome oxidase I (COI) from mitochondria DNA are used as markers to infer population structure of Terpios hoshinota. No genetic variation within COI sequence over all sponges from Taiwan to Japan and China was found, although the only sponge sample from Wanlitong in Kenting had three variable sites, which suggest different species of Terpios hoshinota. Based on ITS2 analysis, haplotype diversity (h) is commonly high among most populations, but with different single haplotype found at Green Island and Arahama (Japan). Pairwise population differentiations (FST) are usually high and significant among populations supporting self-seeding, although Bise, Shiraho and Lanyu populations showed no significant differentiation that supports long-range dispersal. Analysis of Molecular Variance (AMOVA) shows no population subdivision; however, genetic differentiations among populations are significantly greater than within populations. TCS analysis indicates that single haplotype in Green Island is originated from Lanyu, and populations in Bise are widely dispersed over other sponge populations in Taiwan and Japan regions. By evidence of TCS analysis with nucleotide diversity, haplotype diversity and field investigation, Bise is the origin of Terpios hoshinota among populations within this study. Frequency of sequence haplotypes indicates one dominant haplotype is shared among most of the sponge populations, and the dominated sponge haplotype takes highest proportions of local populations. The existence of dominant haplotype may result from better dispersal or reproduction ability than other haplotype in populations. Nested clade analysis shows that populations mainly have restricted gene flow with some clade have contiguous range expansion. We suggest that populations of Terpios hoshinota propagate mainly by self-seeding method with occasional long-range dispersal event that leading to genetic connection among populations and obscuring evidence of isolation by distance in these populations. In Green Island, we consider local populations as undergoing explosion within past several years and propagate by self-seeding method coming from single lineage of Lanyu. Populations in Lanyu may come from Bise, Shiraho, and Yakomo, yet may still in status of population explosion. Populations in Japan may underwent founder effect with rapid population growth, while most populations are rarely interact with each other showing deep genetic differentiation among islands, and Bise is the origin of Terpios hoshinota in this study. Not all of the sponge individuals have ability to dominate local populations, expect for one special haplotype of Terpios hoshinota is capable of dominating local population in both range and quantity, which also has capability of spreading across islands as larger distances than its habitats range in Taiwan and Japan.

Discerning the extent and patterns of genetic connectivity and understanding population demographic processes is essential for framing proper management and conservation measures for species of concern. Although genetic connectivity may be influenced by numerous biotic and abiotic factors, habitat utilization and dispersal potential are often key factors driving connectivity, especially in marine fishes. While dispersal potential is of key importance with respect to shaping connectivity, other extrinsic (e.g., oceanographic processes) and intrinsic (e.g., reproductive behavior) factors may also influence connectivity; however, the relative influence of such factors is immensely variable across species and life-stages. This dissertation explores genetic connectivity and demographic history in marine fishes with diverse dispersal potentials to determine which processes, in addition to the known dispersal potential of the species, may be shaping connectivity. Genetic connectivity and demographic history is assessed for four marine fishes: two shark species with juxtaposing dispersal potentials, the highly migratory tiger shark (Galeocerdo cuvier) and the reef associated Caribbean reef shark (Carcharhinus perezi), which possess high and low dispersal potentials, respectively, and two teleost species, the pelagic roundscale spearfish (Tetrapturus georgii) and the Nassau grouper (Epinephelus striatus), which possess high and low adult dispersal potentials, respectively. This work demonstrates that dispersal potential does, in fact, play a key role in delineating genetic structure for these species; however, other factors, such as contemporary oceanographic currents (e.g., upwelling and temperature), habitat availability (e.g., coral cover), and historical events, such as cyclical glacial cycles, also influence genetic connectivity across variable spatial scales, thereby creating complex patterns of genetic population structure, requiring composite management strategies to ensure the persistence of these species.