Document Type



Doctor of Philosophy (PhD)



First Advisor's Name

Heather D. Bracken-Grissom

First Advisor's Committee Title

committee chair

Second Advisor's Name

Jose M. Eirin-Lopez

Second Advisor's Committee Title

committee member

Third Advisor's Name

Jessica U. Liberles

Third Advisor's Committee Title

committee member

Fourth Advisor's Name

Demian Chapman

Fourth Advisor's Committee Title

committee member

Fifth Advisor's Name

Dean Whitman

Fifth Advisor's Committee Title

committee member

Sixth Advisor's Name

Eric S. Cole

Sixth Advisor's Committee Title

committee member


anchialine, crustacea, genetics, genomics, population dynamics, phylogeography, taxonomy, shrimp, decapod, conservation

Date of Defense



This research investigates the distribution and population structure of crustaceans, endemic to anchialine systems in the tropical western Atlantic focusing on cave-dwelling shrimp from the family Barbouriidae. Taxonomic and molecular tools (genetic and genomic) are utilized to examine population dynamics and the presence of phenotypic hypervariation (PhyV) of the critically endangered species Barbouria cubensis (von Martens, 1872). The presence of PhyV and its geographic distribution is investigated among anchialine populations of B. cubensis from 34 sites on Abaco, Eleuthera, and San Salvador, Bahamas. Examination of 54 informative morphological characters revealed PhyV present in nearly 90% (n=463) of specimens with no identifiable geographic distribution. Updated range descriptions of Macrobrachium lucifugum Holthuis, 1974, Parhippolyte sterreri (Hart & Manning, 1981) and B. cubensis in the western Atlantic are provided with observations on the behavior of B. cubensis from nearly 10 years of work. Molecular phylogenetic analyses of a combination of two mitochondrial and five nuclear gene regions is used for molecular barcoding, to further investigate PhyV and re-examine the current classification of the family Barbouriidae. The results find no evidence of cryptic speciation, or differentiation among individuals of B. cubensis (n=72). Morphological and molecular evidence supports synonymizing Janicea within Parhippolyte and the recognition of the sub-families Calliasmatinae Ditter et al., 2020 and Barbouriinae Christoffersen, 1987. Connectivity among anchialine systems and population structure of B. cubensis across the tropical western Atlantic was examined using a combination of next generation molecular tools. Genomic analyses suggest a single highly connected population of B. cubensis with low genetic diversity and effective population size, which conflicts with the generally accepted isolation paradigm of anchialine systems. Our findings support the value added to genomic studies by generating a partial draft genome constructed using de novo hybrid assembly of short read RADseq and Nanopore long read sequencing data through the investigation of the anchialine isolation paradigm.



Previously Published In

Ditter, R. E., Erdman, R. B., Goebel, A. M., and Bracken-Grissom, H. D. 2019. Widespread phenotypic hypervariation in the enigmatic anchialine shrimp Barbouria cubensis (Decapoda: Barbouriidae). Zootaxa, 4648(1): 1–26. [Reproduced with permission from copyright holder, Magnolia Press]

Ditter, R. E., Snyder, A. P., Schulman, S. E., and Bracken-Grissom, H. D. 2019. Notes on the behavior and first records of three enigmatic anchialine shrimps (Decapoda: Caridea: Barbouriidae, Palaemonidae) in the Bahamas. Journal of Crustacean Biology, 39(6): 684–688. [Reproduced with permission from copyright holder, Oxford University Press]

Ditter, R. E., Mejía-Ortíz, L. M., and Bracken-Grissom, H. D. 2020. Anchialine adjustments: an updated phylogeny and classification for the family Barbouriidae Christoffersen, 1987 (Decapoda: Caridea). Journal of Crustacean Biology, 40(4): 401– 411. [Reproduced with permission from copyright holder, Oxford University Press]

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Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.



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