CURRENT RESEARCH
We seek to identify the genetic bases involved in vertebrate evolution in extreme environments across the Tree of Life. We also quantify the physical expression of these genomic traits through morphology and behavioral experiments. Our research is driven by a passion to conserve the biodiversity of extremophiles, and we utilize ecology in an evolutionary context to support conservation efforts. Our work on cavefish sensory systems opens an innovative avenue for studying human disease. We have ongoing collaborations examining the biodiversity of anglerfishes.
Sensory Convergence in Extremophiles.
Lateral Line Enhancement in Cavefishes
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Human Applications from Cavefish Sensory Systems |
Regressive or degenerative characters like eye loss have received much attention in cave organisms; however, much less research has been done on constructive or additive characters. Constructive traits are thought to be adaptive and key innovations for the survival of cave-obligate organisms. A hypertrophied lateral line in cavefishes is one of the characters hypothesized to be an adaptive trait. Variability in cavefish lateral lines is known but has rarely been quantified. We use different visualization techniques to examine the mechanosensory cells on cavefishes and compare distribution and sensitivity of these cells. This work was previously funded by the NSF Postdoctoral Research Fellowship in Biology and is in collaboration with Dr. Dahiana Arcila at the University of Oklahoma and Dr. Daphne Soares at New Jersey Institute of Technology.
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Studying the morphology of the lateral line system in cavefishes expands far beyond evolutionary biology: Cavefish lateral line sensory cell morphology has inspired biotechnology including flow-sensing for intravenous applications, human auditory technology, object detection and avoidance in submersible vehicles, oceanographic imaging, disaster prevention, and seismic monitoring. My examinations into the cavefish lateral line have implications for both biotechnology and human disease. Examining the genomic basis for cavefish lateral line enhancement may open a new avenue to explore candidate genes related to vestibular system diseases in humans. Additionally, studying the morphology and physiology of the lateral line may give insights into the regenerative ability of sensory hair cells and provide new morphologies for sensor network designs.
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Evolutionary History.
Evolutionary History of Anglerfishes (Lophiiformes)
The macroevolutionary consequences of evolving in the deep-sea remain poorly understood and compounded by the fact that convergent adaptations for living in the dark makes elucidating phylogenetic relationships difficult. The Lophiiform anglerfishes exhibit extreme habitat and predator specializations, including the adaptation of a bioluminescent lure, and unique reproductive habits where parasitic males attach and fuse to females. Despite their notoriety, evolutionary relationships among these fishes remain unclear. We sought to clarify the evolutionary history of Lophiiformes using data from ultraconserved elements and phylogenomic inference methods with particular interest paid to the Ceratioidei (deep-sea anglerfishes) and Antennarioidei (frogfishes and handfishes). This work has been published in Molecular Phylogenetics and Evolution. We described three new frogfish families based on molecular and morphological data and re-assessed Antennariidae. Dr. Rachel Arnold at US Fish and Wildlife, Dr. Fernando Alda at the University of Tennessee at Chattanooga, Dr. Ted Pietsch at the University of Washington, Dr. Chris Kenaley from Boston College, Destinee Hutchinson (undergraduate researcher) and Dr. Prosanta Chakrabarty from Louisiana State University were collaborators on this work.
We are currently collaborating with Dr. Liz Miller, Dr. Dahiana Arcila, Dr. Ted Pietsch, Dr. Rachel Arnold, Dr. Luke Tornabene, Dr. Ricardo Betancur, and Zach Heiple on additional anglerfish research.
We are currently collaborating with Dr. Liz Miller, Dr. Dahiana Arcila, Dr. Ted Pietsch, Dr. Rachel Arnold, Dr. Luke Tornabene, Dr. Ricardo Betancur, and Zach Heiple on additional anglerfish research.
PAST RESEARCH.
Evolutionary History of North American Cavefishes
The multiple modes animals use to colonize subterranean habitats is poorly understood despite fascinating scientists for centuries. I use genomic techniques to examine the possible ways the North American amblyopsid cavefishes have invaded and adapted to cave environments. This research has been published in Evolution. Collaborators included Drs. Edward Burress, Matthew Niemiller, Jonathan Armbruster, William Ludt, and Prosanta Chakrabarty. Our work was supported by the Society for Systematic Biology and the Linnean Society and Systematic Research Fund (awarded to Dr. Hart).
Population Genomics & Conservation of the Southern Cavefish
The Southern Cavefish, Typhlichthys subterraneus, is one of the most fascinating cave-adapted North American fishes because it has one of the widest ranges of any subterranean fish. Recent molecular research suggests the Southern Cavefish is a species complex consisting of as many as 15 different lineages. The taxonomic status of this species complex remains unresolved. We used population genomic analyses on a dataset of single nucleotide polymorphisms harvested from ultraconserved elements to examine genetic diversity and structuring of the Southern Cavefish species complex. Five strongly delineated genetic clusters were identified with little to no genetic exchange between clusters, indicative of highly restricted distributions and low connectivity among clusters. Low genetic diversity, low genetic distances, and short branch lengths imply incomplete lineage sorting due to recent divergence. Low genetic diversity estimates and highly restricted ranges are greatly concerning for the conservation of these cavefishes. Population genomics analyses are strong tools for understanding cryptically diverse species complexes and can be used to inform conservation management. This project was completed in collaboration with Drs. Matthew Niemiller, Jonathan Armbruster, and Prosanta Chakrabarty. Funding for this work was awarded to Dr. Hart from the Cave Research Foundation, the National Speleological Society, the North American Native Fish Association, and Sigma Xi Scientific Honors Society. This study has been published in the journal Conservation Genetics.
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Evolutionary History of Loaches
The evolutionary relationships among balitorid loaches remains uncertain. Using Ultraconserved Element genetic markers, I examined the relationships among these East-Asian endemic fishes with particular interest in the placement of the waterfall-climbing cave angel loach, Cryptotora thamicola. We published two papers with Dr. Callie Crawford in the Journal of Morphology and the Journal of Experimental Biology on the pelvic morphology and walking kinematics of loaches in a phylogenetic context. This is in collaboration with Drs. Prosanta Chakrabarty, Brooke Flammang, Larry Page and was supported by an NSF RoL Grant.
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List of Publications
(13) Heiple, Z., J.M. Huie, A.P. Medeiros, P.B. Hart, C.H.R. Goatley, D. Arcila, and E.C. Miller. Many Ways to Build an Angler: Diversity of Feeding Morphologies in a Deep-Sea Evolutionary Radiation. Biology Letters.
(12) Arcila, D., W.F.H. Regan, V. Gonzalez, P.B. Hart, M.E. Bichuette, and R. Betancur-R. A De Novo Transcriptome for the Brazilian Blind Characid Offers Insight into Characid Cavefish Convergence. In review at Frontiers in Ecology and Evolution.
(11) Hart, P.B., M.L. Niemiller, J.W. Armbruster, and P. Chakrabarty. Conservation Implications for the World’s Most Widely Distributed Cavefish, Typhlichthys subterraneus, Based on Population Genomics. Conservation Genetics.
(10) Elías D.J., C.D. McMahan, F. Alda, C. García-Alzate; P.B. Hart, P. Chakrabarty. (2023) Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 and colonization patterns of Middle America. PLOS One.
(9) Hart, P.B., R.J. Arnold, F. Alda, C.P. Kenaley, T.W. Pietsch, D. Hutchinson*, and P. Chakrabarty. (2022) Evolutionary Relationships of Anglerfishes (Lophiiformes) Reconstructed using Ultraconserved Elements. Molecular Phylogenetics and Evolution 10.1016/j.ympev.2022.107459
*Undergraduate Student
(8) Hart, P.B. Review of: Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China: Systematics, Biology, Biogeography and Cave Adaptation. In review at Ichthyology & Herpetology.
(7) Crawford, C. H., A. Webber-Schultz, P. B. Hart, Z. S. Randall, C. Cerrato-Morales, A. B.
Kellogg, H. E. Amplo, A. Suvarnaraksha, L. M. Page, P. Chakrabarty, and B. E. Flammang. (2022) They Like to Move it (Move it): Walking Kinematics of Balitorid Loaches of Western Thailand. Journal of Evolutionary Biology https://doi.org/10.1242/jeb.242906
(6) Santiago-Rosario, L.Y., B.D. Elderd, K. Harms, P.B. Hart, and M. Dassanayake. (2021) No escape: The influence of Sodium Substrate on Plant Growth and Tissue Sodium Responses. Ecology and Evolution. DOI: 10.1002/ece3.8138
(5) Hart, P.B., M.L. Niemiller, E.D. Burress, W.B. Ludt, J.W. Armbruster, and P. Chakrabarty. (2020) Cave-adapted evolution in the North American amblyopsid fishes inferred using phylogenomics and geometric morphometrics. Evolution. doi:10.1111/evo.13958
(4) Crawford, C.H., Z.S. Randall, P.B. Hart, L.M. Page, P. Chakrabarty, and B.E. Flammang. (2020) Skeletal and muscular pelvic morphology of hillstream loaches (Cypriniformes: Balitoridae). Journal of Morphology. DOI: 10.1002/jmor.21247
(3) Burress, P.B.H., E.D. Burress, J.W. Armbruster (2017) Body shape variation within the Southern Cavefish, Typhlichthys subterraneus (Percopsiformes: Amblyopsidae). 2017. Zoomorphology. DOI: 10.1007/s00435-017-0360-0
(2) Armbruster, J.W., M.L. Niemiller, and P.B. Hart (2016) Morphological evolution of the Cave-, Spring- and Swampfishes of the Amblyopsidae (Percopsiformes). Copeia. 104: 763-777. DOI: 10.1643/CI-15-339
(1) Niemiller, M.L., K.S. Zigler, P.B. Hart, B.R. Kuhajda, J.W. Armbruster, B.N. Ayala, and A.S. Engel (2016) First record of a stygobiotic fish (Percopsiformes: Amblyopsidae: Typhlichthys) from the Appalachians karst region in the eastern United States. Subterranean Biology. Subterranean Biology 20: 39-50. DOI: 10.3897/subtbiol.20.9693
(12) Arcila, D., W.F.H. Regan, V. Gonzalez, P.B. Hart, M.E. Bichuette, and R. Betancur-R. A De Novo Transcriptome for the Brazilian Blind Characid Offers Insight into Characid Cavefish Convergence. In review at Frontiers in Ecology and Evolution.
(11) Hart, P.B., M.L. Niemiller, J.W. Armbruster, and P. Chakrabarty. Conservation Implications for the World’s Most Widely Distributed Cavefish, Typhlichthys subterraneus, Based on Population Genomics. Conservation Genetics.
(10) Elías D.J., C.D. McMahan, F. Alda, C. García-Alzate; P.B. Hart, P. Chakrabarty. (2023) Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 and colonization patterns of Middle America. PLOS One.
(9) Hart, P.B., R.J. Arnold, F. Alda, C.P. Kenaley, T.W. Pietsch, D. Hutchinson*, and P. Chakrabarty. (2022) Evolutionary Relationships of Anglerfishes (Lophiiformes) Reconstructed using Ultraconserved Elements. Molecular Phylogenetics and Evolution 10.1016/j.ympev.2022.107459
*Undergraduate Student
(8) Hart, P.B. Review of: Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China: Systematics, Biology, Biogeography and Cave Adaptation. In review at Ichthyology & Herpetology.
(7) Crawford, C. H., A. Webber-Schultz, P. B. Hart, Z. S. Randall, C. Cerrato-Morales, A. B.
Kellogg, H. E. Amplo, A. Suvarnaraksha, L. M. Page, P. Chakrabarty, and B. E. Flammang. (2022) They Like to Move it (Move it): Walking Kinematics of Balitorid Loaches of Western Thailand. Journal of Evolutionary Biology https://doi.org/10.1242/jeb.242906
(6) Santiago-Rosario, L.Y., B.D. Elderd, K. Harms, P.B. Hart, and M. Dassanayake. (2021) No escape: The influence of Sodium Substrate on Plant Growth and Tissue Sodium Responses. Ecology and Evolution. DOI: 10.1002/ece3.8138
(5) Hart, P.B., M.L. Niemiller, E.D. Burress, W.B. Ludt, J.W. Armbruster, and P. Chakrabarty. (2020) Cave-adapted evolution in the North American amblyopsid fishes inferred using phylogenomics and geometric morphometrics. Evolution. doi:10.1111/evo.13958
(4) Crawford, C.H., Z.S. Randall, P.B. Hart, L.M. Page, P. Chakrabarty, and B.E. Flammang. (2020) Skeletal and muscular pelvic morphology of hillstream loaches (Cypriniformes: Balitoridae). Journal of Morphology. DOI: 10.1002/jmor.21247
(3) Burress, P.B.H., E.D. Burress, J.W. Armbruster (2017) Body shape variation within the Southern Cavefish, Typhlichthys subterraneus (Percopsiformes: Amblyopsidae). 2017. Zoomorphology. DOI: 10.1007/s00435-017-0360-0
(2) Armbruster, J.W., M.L. Niemiller, and P.B. Hart (2016) Morphological evolution of the Cave-, Spring- and Swampfishes of the Amblyopsidae (Percopsiformes). Copeia. 104: 763-777. DOI: 10.1643/CI-15-339
(1) Niemiller, M.L., K.S. Zigler, P.B. Hart, B.R. Kuhajda, J.W. Armbruster, B.N. Ayala, and A.S. Engel (2016) First record of a stygobiotic fish (Percopsiformes: Amblyopsidae: Typhlichthys) from the Appalachians karst region in the eastern United States. Subterranean Biology. Subterranean Biology 20: 39-50. DOI: 10.3897/subtbiol.20.9693