Population genomic inference of ecology, conservation, evolution, and demographic history of Atlantic seahorses and pipefishes (Syngnathidae)

In the Atlantic Ocean powerful directional ocean currents can play a significant role in the formation and persistence of marine species. Syngnathidae fishes have a sparse fossil record, high morphological plasticity, and many of these species are difficult to observe in the wild, therefore they frequently lack life history information and the status of regional lineages and species designations are often obscure. In this dissertation I explore the ecology, evolution, and conservation of primarily Atlantic seahorses (Hippocampus) and pipefish (Syngnathus) in four core chapters, using differing genetic datasets ranging from mitochondrial DNA to genome-wide RAD sequences. Most Synganthids have the potential to disperse passively by rafting on floating vegetation, and are direct developers, which is thought to limit their active mobility, yet many species have widespread distributions. The majority of genetic research on Syngnathids fishes has focused on Indo-Pacific species, however the Atlantic Ocean is home to dozens of species of pipefishes from nine genera and roughly 1/5th of the world\u27s seahorses species. In Chapter 1, I use six loci to infer the species tree for all Atlantic seahorses and infer the demographic history and evolution of the Hippocampus erectus complex. The results of this study support the establishment of an ancestral population of the H. erectus complex in the Americas, followed by the Amazon River outflow splitting it into Caribbean/North American H. erectus and South American H. patagonicus at a time of increased sedimentation and outflow. Following this split, colonization occurred across the Atlantic via the Gulf Stream currents with subsequent trans-Atlantic isolation. Based on the results of Chapter 1, the species H. erectus exhibited a panmictic genetic structure from Latin America to temperate New York waters. However, inhabitants of the temperate region are considered by some ecologists to be tropical vagrants that only arrive during warm seasons from the southern provinces and perish as temperatures decline. Contrary to the findings of Chapter 1, in Chapter 2, I use thousands of RADseq loci and show strong support that temperate inhabitants are genetically diverged from southern populations and are composed of an isolated and persistent ancestral gene pool. The aim of Chapter 3 is to investigate how major current forces as well as climatic and geographic processes have shaped the evolutionary and demographic history of western Atlantic seahorses (Hippocampus) and pipefishes (Syngnathus). This Chapter takes a comparative approach across five codistributed species (two seahorses and three pipefishes). Genomic patterns of subpopulation divergence and post-divergence gene flow may be shared amongst fish species with similar life history traits, however ecological differences (i.e., macroclimatic tolerance and rafting propensity) may impact the rates of gene exchange and/or isolation times between subpopulations. The result of this study show how directional ocean currents and the life history trait of rafting propensity impacts population divergence and connectivity, and predicts gene flow directionality and magnitude in four out of five of the focal taxa. Lastly in Chapter 4, I use a molecular forensics approach to track the U.S. dried seahorse trade. Due to global exploitation, the genus Hippocampus are the only fish to have all species listed under the Convention of International trade of endangered species (CITES). Millions of individuals are traded each year for the use in traditional Chinese medicine as well as for souvenirs and crafts. Using DNA barcoding, while mentoring high school and undergraduate students, we identified and compared specimens collected from two primary U.S. dried seahorse end-markets: 1) traditional Chinese medicine and, 2) Internet and coastal souvenir retailers. The results of this study found a significant contrast in both the species composition and size of individuals being sold between each market