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University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2009 Hybridization, ancestral polymorphism, and cryptic species in Nothonotus darters (Teleostei: Percidae: Etheostomatinae) Benjamin Paul Keck University of Tennessee Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Keck, Benjamin Paul, "Hybridization, ancestral polymorphism, and cryptic species in Nothonotus darters (Teleostei: Percidae: Etheostomatinae). " PhD diss., University of Tennessee, 2009. https://trace.tennessee.edu/utk_graddiss/5992 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Benjamin Paul Keck entitled "Hybridization, ancestral polymorphism, and cryptic species in Nothonotus darters (Teleostei: Percidae: Etheostomatinae)." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Ecology and Evolutionary Biology. Thomas J. Near, Major Professor We have read this dissertation and recommend its acceptance: Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) To the Graduate Council: I am submitting herewith a dissertation written by Benjamin Paul Keck entiltled “Hybridization, ancestral polyporphism, and cryptic species in Nothonotus darters (Teleostei: Percidae: Etheostomatinae).” I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Ecology and Evolutionary Biology. ____Thomas J. Near________________ Thomas J. Near, Major Professor We have read this dissertation and recommend its acceptance: ____Benjamin M. Fitzpatrick_____ Benjamin M. Fitzpatrick ____James A. Fordyce___________ James A. Fordyce ____David A. Etnier_____________ David A. Etnier ____J. Larry Wilson______________ J. Larry Wilson Accepted for the Council: ____Carolyn R. Hodges_____________ Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official student records.) HYBRIDIZATION, ANCESTRAL POLYMORPHISM, AND CRYPTIC SPECIES IN NOTHONOTUS DARTERS (TELEOSTEI: PERCIDAE: ETHEOSTOMATINAE) A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Benjamin Paul Keck May 2009 To Julie for having faith in my resolve to complete this study and Elizabeth for reminding me of the exuberance of discovering the beasts around us. ii ACKNOWLEDGMENTS Many people have guided and influenced the direction of my doctoral research through many years and I am thankful and indebted to all. During my undergraduate days at Centre College, Mike and Christine Barton and Jean Porterfield inspired me to continue down the academic path to study fish and after my graduation still encourage my development as a colleague. My parents and my wife Julie have provided the support and motivation that are required for such an investment of time and effort. My daughter Elizabeth reinvigorated my research and continually reminds me of the joys of exploration and discovery, and the personal gratification of sharing knowledge. Tom Near, my advisor, has helped me develop confidence and focus in my research and taught me a great deal about fish and phylogenetics. He has also been a role model in his commitment to the advancement and dissemination of knowledge above the cliquish competition that is occasionally encountered in academe. My committee members, Dave Etnier, Ben Fitzpatrick, Jim Fordyce, and Larry Wilson, have provided fresh perspectives and guidance that improved the quality and clarity of the product. The fieldwork for this research was completed thanks to considerable help from my labmates, Christen Bossu, Rich Harrington, Phillip Hollingsworth, and Jacob Kendrick. Our field experiences have been some of the highlights of these past years. Many others provided insights and help in the field during this research, including: Bruce Bauer, Monica Beals, Rebecca Blanton, Gideon Bradbund, Rose Carlson, Todd Crail, Gerald Dinkins, Mike Doosey, Rachael Goodman, Darrin Hulsey, Kristen Kuhn, Dave Mathews, Sean McMahon, Pat Rakes, Morgan Raley, Charlie Saylor, Kevin Smith, J.R. Shute, Todd Sink, Wayne Starnes, David Tank, and Justin Walguarnery. I am grateful for all of the support provided by the Department of Ecology and Evolutionary Biology at the University of Tennessee, Knoxville (UT). The majority of my research was conducted at UT, I received a teaching assistant position for two years, and the faculty provided a great environment conducive to research and academic development. The Department of Ecology and Evolutionary Biology at Yale University and the Cornell University Museum of Vertebrates provided lab space and materials when I was away from the UT. I greatly appreciate those at museums that provided data and specimens, including: ANSP, M. Sabaj Perez; AUM, J. Armbruster; CU, C. Dardia; FMNH, R. Robbins; INHS, M. Retzer; JFBM, A. Simons; Morehead State University, D. Eisenhour; NCSM, W. Starnes; OKMNH, S. Cartwright; OSUM, M. Kibbey; RC, R. Jenkins; ROM, E. Holm; SIUC, J. Stewart; TNHC, J. Rosales; TU, N. Rios; UAIC, B. Kuhajda; UMMZ, D. Nelson; UT, J. Joice; YPM, G. Watkins-Colwell. I received gifts of specimens, tissues, or DNA alloquots from: Conservation Fisheries, Inc. (N. wapiti), H. Bart (N. vulneratus), R. Johnson (N. moorei), B. Porter (N. chuckwachatte, N. etowahae, and N. maculatus), and C. Taylor (N. rubrus). All other samples were collected under permits in the authors name, including: AL, KY, MS, NC, OH, PA, TN, WV. I obtained locality data from several agencies and organizations including: Conservation Fisheries, Inc., Great Smoky Mountains National Park, Kentucky Department of Fish and Wildlife Resources, North American Native Fishes Association, Tennessee Valley Authority, and Tennessee Wildlife Resources Agency. All pictures were taken by members of the Near Lab, except for N. chlorobranchius that was taken by R.T. Bryant. iii ABSTRACT Darters (Teleostei: Percidae: Etheostomatinae) are a diverse group of charismatic fish endemic to North America and many of their characteristics combined with the fact that diversity within the clade is relatively well known makes them an attractive system for studying evolutionary patterns. I used molecular and morphological data to identify patterns of hybridization in darters, introgression in Nothonotus darters, and small geographic scales of diversification in two Cumberland River drainage Nothonotus species. I compiled records of hybrid Etheostomatinae museum specimens and found that over one quarter of darter species were involved in hybrid specimens, species most frequently involved had large range sizes, and involvement was negatively correlated with phylogenetic distance. I created a Nothonotus phylogeny based on mitochondrial and nuclear DNA sequence data and morphological data, and the observed relationships were largely consistent with previous hypotheses; however, better resolution and sampling in this phylogeny identified novel relationships and paraphyly. I expanded genetic sampling of N. camurus, N. chlorobranchius, and N. rufilineatus, the three Nothonotus most frequently involved in hybrid specimens, to search for introgression. I found extensive mitochondrial replacement in N. rufilineatus, with those in the upper Tennessee River drainage having mitochondrial haplotypes similar to haplotypes observed in N. chlorobranchius and those in the Cumberland River drainage having mitochondrial haplotypes similar to haplotypes observed in N. camurus. Additionally, N. rufilineatus has acted as a ‘conduit species’ in the upper Tennessee River drainage by transferring N. chlorobranchius like haplotypes into N. camurus. I also expanded genetic sampling of N. microlepidus and N. sanguifluus, two Cumberland River drainage Nothonotus whose sister relationship had not previously been hypothesized, to identify the number of lineages within the Cumberland River drainage. I preformed Discriminant Analysis using meristic characters based on the lineages indicated by the genetic analyses and found that there were four distinct lineages. By comparing the diversity in these two ‘species’ to diversity in another subclade of darters, barcheeks, I concluded that the isolating mechanisms in the Cumberland River drainage occur at small geographic scales, as found in the barcheeks, have been persistent through significant evolutionary time, and across multiple darter subclades. iv TABLE OF CONTENTS 1. Introduction and overview ….……………………………………………………..1 2. Patterns of natural hybridization in darters (Percidae: Etheostomatinae) Abstract ……………………………………………………………....4 Introduction …………………………………………………………..4 Methods ………………………………………………………………6 Results ………………………………………………………………..6 Discussion ……………………………………………………………10 Conclusions …………………………………………………………..15 3. Assessing phylogenetic resolution among mitochondrial,
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