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Investigating the Genetic Basis of Altered Activity Profiles in the Blind Mexican Cavefish, Astyanax mexicanus

Carlson, Brian M
http://orcid.org/0000-0002-0879-6600
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439282081

Abstract Details

2015, PhD, University of Cincinnati, Arts and Sciences: Biological Sciences.
Organisms that have evolved to exploit extreme ecological niches may alter or abandon survival strategies that no longer provide a benefit, or may even impose a cost, in the environment to which they have adapted. Cave environments are characterized by perpetual darkness, isolation and relatively constant temperature and humidity. Accordingly, cave-adapted species tend to converge on a suite of regressive and constructive morphological, physiological and behavioral alterations, including loss or reduction of eyes and pigmentation, increased locomotor activity and reduction or alteration of behavioral rhythmicity. The cave environment and the associated changes in locomotor behavior make species of cavefish prime natural models in which to examine the complex genetic architecture underlying these behavioral phenotypes. The principal goal of this dissertation was to investigate the genetic basis of altered locomotor activity patterns in the blind Mexican tetra, Astyanax mexicanus. Initially, a custom locomotor assay rig and experimental protocols were developed to assess, characterize and compare activity patterns in surface and Pachon cavefish. The results of these assays clarified differences between the morphotypes, provided evidence that Pachon cavefish retain a weakly-entrainable circadian oscillator with limited capacity to self-sustain entrained rhythms and suggested that patterns in spatial “tank usage” data may be the result of a positive masking effect in response to light stimulus in both morphotypes. In order to facilitate downstream genetic analysis, a high-density genotyping-by-sequencing (GBS) based linkage map was constructed. This map provided much finer mapping ability than any previously published linkage map in this species. Further, the large number of markers enabled the anchoring of ~80% of the total length of the unassembled Astyanax mexicanus draft genome to the newly developed linkage map, which in turn assisted with downstream comparison of linkage groups and quantitative trait loci (QTL) between maps. This greatly facilitated the process of screening for potential candidate genes. Employing the new linkage map and the assay protocols developed for this work, a large F2 surface x Pachon mapping pedigree was assayed and the resulting data was subjected to QTL analysis. QTL results suggest that loci on at least six different linkage groups are associated with patterns in either velocity or tank usage; however, the regions of the genome mediating each of these components are distinct from one another. Further, comparison of linkage groups between maps indicated that the QTL for locomotor activity described here are different than those published in previous studies. Finally, critical genomic intervals underlying activity QTL were screened for candidate genes. A total of 36 potential candidates were identified and genomic and transcriptomic resources were leveraged to highlight several prime candidates for further analysis, as well as to demonstrate that it is unlikely that either catastrophic changes to components of the core molecular clockwork or truncation of members of well-characterized photoreceptor families are behind the altered activity profiles observed in the Pachon cave population.
Joshua Gross, Ph.D. (Committee Chair)
Herman Mays, Ph.D. (Committee Member)
Daniel Buchholz, Ph.D. (Committee Member)
John Layne, Ph.D. (Committee Member)
Kenneth Petren, Ph.D. (Committee Member)
170 p.
Biology
Astyanax mexicanus; QTL; locomotor activity; cave evolution; behavioral genetics; linkage mapping

Recommended Citations

Citations

  • Carlson, B. M. (2015). Investigating the Genetic Basis of Altered Activity Profiles in the Blind Mexican Cavefish, Astyanax mexicanus [Doctoral dissertation, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439282081

    APA Style (7th edition)

  • Carlson, Brian. Investigating the Genetic Basis of Altered Activity Profiles in the Blind Mexican Cavefish, Astyanax mexicanus. 2015. University of Cincinnati, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439282081.

    MLA Style (8th edition)

  • Carlson, Brian. "Investigating the Genetic Basis of Altered Activity Profiles in the Blind Mexican Cavefish, Astyanax mexicanus." Doctoral dissertation, University of Cincinnati, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439282081

    Chicago Manual of Style (17th edition)

ucin1439282081
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This open access ETD is published by University of Cincinnati and OhioLINK.