Assessing Biodiversity, Evolution, and Biogeography in Bonefishes (Albuliformes): Resolving Relationships and Aiding Management

Abstract

Bonefishes (Albuliformes: Albula) are tropical marine fishes that are the focus of a valuable recreational fishery. Despite substantial research interest, their global diversity, fishery composition, and phylogenetic relationships remain uncertain. Bonefishes exhibit significant morphological conservatism; cryptic species have been identified, complicating conservation efforts. My research addresses these lingering questions to ensure effective management. In the first chapter of this dissertation, I resurrect Albula goreensis (Valenciennes 1847) from synonymy with Albula vulpes (Linnaeus 1758) and apply the name to a cryptic sympatric congener based on an integrated taxonomic approach, using multilocus molecular, ecological, and behavioral evidence. Genetic assignment tests based on microsatellites correctly diagnose A. goreensis from congeners (posterior probabilities=0.97-1.0). Phylogenetic analyses based on cytochrome b yielded substantial divergence among Atlantic lineages (d=0.08-0.10), and five nucleotides were diagnostic for A. goreensis. Microhabitat use, pelagic larval duration, and growth rate differences have been documented between A. goreensis and A. vulpes. Phylogenetic distinctiveness in sympatry, and ecological and behavioral differences are considered strong evidence that A. goreensis is valid and distinct from congeners.In regions with intensive fisheries, information is needed on species ranges and stock structure. In Chapter 2, I explore the distributions, genetic structure, and occurrence of hybrids among three members of the Atlantic bonefish (Albula sp.) complex, using 19 microsatellite loci. Samples were analyzed from 14 locations across the Caribbean Sea and western Atlantic region, with one external sample from the eastern Atlantic. The species in the complex were broadly sympatric across the region; though local level overlap was variable, likely due to habitat partitioning. Analyses identified Albula vulpes as the species predominantly supporting the coastal flats recreational fishery. Unexpected population partitioning was identified within all three species, but the partitions co-occurred within most geographic locations. No clear geographic or temporal patterns were revealed. A strong, consistent identification of two A. vulpes genetic populations was further supported by hypothesis testing for migration patterns between them. Hybrids occurred at low frequency, and results suggested a combination of intrinsic and extrinsic semi-permeable barriers to gene flow exist among these divergent species. Lastly, advanced phylogenetic methods can clarify evolutionary relationships and offer insights into the potential geographic drivers of diversity. In the third chapter I present a multilocus phylogenetic assessment of Albuliformes. The results support recognition of all known members of Albula as distinct species, including several morphological cryptics that occur in sympatry. The broader phylogenetic relationships inferred between Albuliformes and other elopomorphs suggest the genus Pterothrissus is not a member of Albuliformes, warranting additional revisions to the order. Estimated dates of divergence within Albuliformes further suggest up to four invasions of the Atlantic Ocean through multiple historical routes. Two pairs of transisthmian geminate species were identified, though divergence well predates final closure of the Isthmus of Panama. Each chapter of this dissertation will be submitted to a specific scientific journal. Variations in formatting within chapters, such as citation styles, reflect the different journals requirements.