Graduation Year

2022

Document Type

Dissertation

Degree

Ph.D.

Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Biology (Integrative Biology)

Major Professor

Christina L. Richards, Ph.D.

Co-Major Professor

Aaron W. Schrey, Ph.D.

Committee Member

Kathleen Scott, Ph.D.

Committee Member

John Parkinson, Ph.D.

Committee Member

Eric Hoffman, Ph.D.

Keywords

Conservation Genetics, ddRADseq, Density Estimates, Connectivity, Symbiodiniaceae

Abstract

The giant Caribbean sea anemone Condylactis gigantea is a long-lived, conspicuous, and phenotypically diverse species native to the western Atlantic Ocean (from Bermuda to southeast Brazil), Caribbean Sea, and southeastern Gulf of Mexico. This sea anemone is an important benthic community member that provides habitat to numerous species, including cleaner shrimp. This relationship makes these animals desirable to aquarists for both enjoyment and the service provided by the shrimp for the overall health of an aquarium, and which is why they are sought.

The extraction of about 3.3 million C. gigantea individuals in Florida over a 23-year period for the aquarium trade and an unprecedented cold-water mortality event in 2010 are suspected to have led to declines in abundance. In an attempt to reverse local declines in abundance of this anemone, Florida state managers suspended harvest of this popular aquarium organism in late 2012. This provided the motivation for this dissertation. Major goals of this dissertation were to monitor the effect of the closure on the stock and to obtain information on the genetic characteristics of C. gigantea in this region in order to provide recommendations to facilitate the management of this species.

To assess the recovery of C. gigantea (Chapter 1), we monitored relative abundance at 45 fixed locations from 2013 to 2016. Densities at only four of 17 established marine life industry collection sites increased, while nearby non-collection sites remained unchanged over this period. In addition, we conducted an examination of genome-wide single nucleotide polymorphism (SNP) data to assess genetic diversity and population structure of 82 individuals from seven locations (three collection and four non-collection locations) across South Florida. Observed genetic diversity was comparable in all locations. However, the eastern Gulf of Mexico location showed a significant FIS value suggesting inbreeding that might be attributed to a small number of occupants. Condylactis gigantea is generally well-mixed across the region (FST = 0.069), though a relatively weak pattern of genetic differentiation was detected. These results suggest limited reproductive success, and that dispersal is restricted by hydrological and geographical barriers at larger scales.

Condylactis gigantea hosts photosynthetic dinoflagellates in the family Symbiodiniaceae. This symbiosis enables these organisms to flourish in oligotrophic environments. However, when conducting genetic studies, especially at the population level, this symbiosis proves problematic due to a mixture of host and symbiont DNA. To increase confidence in having host-only DNA for population-level analyses (Chapter 2), I bleached three C. gigantea individuals, sequenced them, and then created a reference index using the individual with the highest number of sequence reads. I then mapped individuals from Chapter 1 to the C. gigantea reference index and re-analyzed those data to test the hypothesis that using a bleached reference index would improve results. Although induced bleaching did not completely remove all symbionts, overall, I recovered roughly similar diversity estimates and summary statistics suggesting that there are few, if any, symbiont loci in the two datasets. Although I cannot conclude that all ddRADseq loci belong to C. gigantea, this study suggests that induced symbiont bleaching does not improve population genetic inferences.

In Chapter 3, I conducted a broad-scale genomic sequencing analysis of C. gigantea throughout its range using SNPs to test the hypothesis that C. gigantea is a single panmictic species. Additionally, I genotyped endosymbionts to evaluate their association with C. gigantea. I discovered that C. gigantea is generally well mixed range wide (FST = 0.077) and primarily a panmictic species with signatures of weak differentiation. Also, C. gigantea associated with Symbiodinium spp. range wide and Breviolum spp. at the extremes of its range. I found mild levels of inbreeding at a few locations. The patterns found here will aid those who manage this species and for future conservation efforts.

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