Northern Michigan University NMU Commons All NMU Master's Theses Student Works 2013 GENETIC INVESTIGATION OF BROOK TROUT (SALVELINUS FONTINALIS) POPULATION STRUCTURE IN LAKE SUPERIOR TRIBUTARIES LOCATED IN PICTURED ROCKS NATIONAL LAKESHORE, MICHIGAN, USA Jonathan J. Pearce Northern Michigan University Follow this and additional works at: https://commons.nmu.edu/theses Recommended Citation Pearce, Jonathan J., "GENETIC INVESTIGATION OF BROOK TROUT (SALVELINUS FONTINALIS) POPULATION STRUCTURE IN LAKE SUPERIOR TRIBUTARIES LOCATED IN PICTURED ROCKS NATIONAL LAKESHORE, MICHIGAN, USA" (2013). All NMU Master's Theses. 482. https://commons.nmu.edu/theses/482 This Open Access is brought to you for free and open access by the Student Works at NMU Commons. It has been accepted for inclusion in All NMU Master's Theses by an authorized administrator of NMU Commons. For more information, please contact [email protected],[email protected]. GENETIC INVESTIGATION OF BROOK TROUT (SALVELINUS FONTINALIS) POPULATION STRUCTURE IN LAKE SUPERIOR TRIBUTARIES LOCATED IN PICTURED ROCKS NATIONAL LAKESHORE, MICHIGAN, USA By Jonathan J. Pearce THESIS Submitted to Northern Michigan University In partial fulfillment of the requirement For the degree of MASTERS OF SCIENCE Office of Graduate Education and Research 2013 ABSTRACT GENETIC INVESTIGATION OF BROOK TROUT (SALVELINUS FONTINALIS) POPULATION STRUCTURE IN LAKE SUPERIOR TRIBUTARIES LOACTED IN PICTURED ROCKS NATIONAL LAKESHORE, MICHIGAN, USA By Jonathan J. Pearce This study focused on four tributaries located in Pictured Rocks National Lakeshore: Miners River, Mosquito River, Sevenmile Creek, and Hurricane River. Eight microsatellite loci were used to examine genetic diversity and structure between groups of brook trout. Brook trout were sampled in Open and Restricted sections from each tributary for wider comparisons between groups. Open designated sections are the downstream portion of the tributary with access to Lake Superior, whereas each Restricted section is the upstream portion above a barrier to fish movement (i.e. waterfall). Adfluvial brook trout were classified from PIT tag movement data from two of the streams (MOS and SVN). Abundance of classified adfluvial (coaster) brook trout, individuals that utilize both stream and lake environments, varied between streams (MOS=35 to SVN= 106). The results showed that adfluvial brook trout were more closely related to the fluvial brook trout from their stream of capture than to other designated adfluvial groups. All Restricted sections of rivers were most closely related to their Open section counterparts, with the exception of Hurricane Restricted which was most closely related to Sevenmile Open. Within the Restricted sections there was moderate genetic differentiation between all tributaries. Miners River was the most genetically distinct population overall followed by Mosquito River, which showed levels consistent with higher interaction rates between other tributaries. Sevenmile Creek and i Hurricane River are the most genetically similar populations. This suggests that there is more movement of brook trout between Sevenmile Creek and Hurricane River than between the other sites in PIRO. I suggest that the movement of adfluvial brook trout between systems is the most likely explanation for these patterns and inter-stream movement is driving the genetic dynamics found across the population. ii Copyright by JONATHAN J. PEARCE 2013 iii DEDICATION This thesis is dedicated to all those who have supported me in my decisions, my parents, Don and Melinda Pearce, my brother, Benjamin Pearce who I always strived to be and helped make me the person I am today. iv ACKNOLEDGEMENTS I thank my advisor Dr. Katherine Teeter for all of the support and guidance whether it be laboratory or analytical techniques. Her support during the thesis process was invaluable, and pushed me to stay on track. I also thank Dr. Jill Leonard for allowing me to work with her brook trout in PIRO and Dr. Alec Lindsay for his guidance with Athena. I thank the National Park Service, The Greater Lake Superior Foundation and Northern Michigan University for their financial support. Thanks to my parents, Don and Melinda Pearce who supported and allowed me to make decisions and follow my dreams in all aspects of my life. Thank you to my loving partner, Emily Spagnoli for her unconditional support throughout my education and always willing to participate in and support my adventures. This thesis follows the format prescribed by the Journal of Great Lakes Research. v TABLE OF CONTENTS LIST OF TABLES……………………………………………………………………….vii LIST OF FIGURES………………………………………….…………………...……...xii LIST OF ABBREVIATIONS…………………………….……………………...……..xiii CHAPTER ONE: LITERATURE REVIEW……………………………………………...1 CHAPTER TWO: GENETIC POPULATION STRUCTURE OF BROOK TROUT (SALVELINUS FONTINALIS) IN LAKE SUPERIOR TRIBUTARIES LOCATED IN PICTURED ROCKS NATIONAL LAKESHORE, MICHIGAN, USA………………….………………………...................................................…11 CHAPTER OVERVIEW……………….………………………….…………………..11 INTRODUCTION…………………………………………………………………..…12 METHODS…………………………………………………………………………….14 RESULTS……………………………………………………………………………...18 DISCUSSION………………………………………………………………………….22 CHAPTER THREE: GENETIC INVESTIGATION OF ADFLUVIAL BROOK TROUT (SALVELINUS FONTINALIS) LOCATED IN LAKE SUPERIOR TRIBUTARIES IN PICTURED ROCKS NATIONAL LAKESHORE, MICHIGAN…………………………………………………………………...…36 CHAPTER OVERVIEW………………………………………………………………36 INTRODUCTION…………………………………………………………………..…36 METHODS………………………………………………………………………….…40 RESULTS……………………………………………………………………….……..43 DISCUSSION………………………………………………………………………….46 CHAPTER FOUR: CONCLUSIONS……………………………………………….…..54 REFERENCE LIST…………………………………………………………………...…57 APPENDICES……………………………………………………………..…………….65 vi LIST OF TABLES Table 2.1: Physical characteristics of six study streams located within PIRO, MI……...27 Table 2.2: Summary of physical parameters of brook trout captured. N = Sample Size, TL = total length (mm), STD = standard deviation from the mean……………...27 Table 2.3: Characteristics of microsatellite primers used……………………………..…28 Table 2.4: Summary of PCR protocol conditions for eight microsatellites……………...28 Table 2.5: Sample distribution of brook trout collected in PIRO during 2011 and 2012 season………………………………………………………………………….…28 Table 2.6: Microsatellite loci and descriptions of allelic variation across eight populations of brook trout from four tributaries located in Pictured Rocks National Lakeshore………………………………………………………………………...29 Table 2.7: Genetic diversity measures for all ten sampled groups of brook trout from four Lake Superior Tributaries located in Pictured Rocks National Lakeshore, Michigan. All populations were genotyped at eight loci; Open = below barrier, Restricted = above barrier, N = the sample size, and diversity measures for microsatellite DNA loci (observed [H₀] versus expected [Hₑ] heterozygosity), and A = the mean number of alleles per locus…………………………..……….…..29 Table 2.8: Private allele list with number found at each loci across all populations of brook trout found in PIRO………………………………………..………….......30 Table 2.9: F-statistics for sections of tributaries of Lake Superior in PIRO. Fis = inbreeding coefficient, Fit = Heterozygosity of individuals to population, Fst = fixation index………………………………………………………….…....30 vii Table 2.10: F-statistics for Open and Restricted sections of four tributaries of Lake Superior in PIRO. Fis = inbreeding coefficient, Fit = Heterozygosity of individual to population, Fst = fixation index……………………………………….…...…..30 Table 2.11: Pairwise Fst values for both Open and Restricted. Fst on below diagonal, probability shown on above diagonal……………………………….……..…….31 Table 2.12: Pairwise Fst values for Open section, Fst on below diagonal, Probability shown on above diagonal………………………………………………………...31 Table 2.13: Pairwise Fst values for Restricted section, Fst on below diagonal, Probability shown on above diagonal………………………………………………………...31 Table 2.14: Nei’s Genetic Distance for Open populations of four Lake Superior Tributaries located in Pictured Rocks National Lakeshore………..…………..…31 Table 2.15: Nei’s Genetic Distance of Restricted populations of four Lake Superior Tributaries located in Pictured Rocks National Lakeshore………………………32 Table 2.16: Nei’s Genetic Distance for Open and Restricted Populations of four Lake Superior tributaries located in Pictured Rocks National Lakeshore……………..32 Table 2.17: Accuracy of Assignment between Open sections of four Lake Superior tributaries in Pictured Rocks National Lakeshore. N = sample size, As = number assigned to self, A₀ = number assigned to other…………………………………32 Table 2.18: Accuracy of Assignment between Restricted sections of four Lake Superior tributaries in Pictured Rocks National Lakeshore. N = sample size, As = number assigned to self, A₀ = number assigned to other…………………………..……..32 viii Table 2.19: Accuracy of Assignment between Open and Restricted sections of four Lake Superior tributaries in Pictured Rocks National Lakeshore. N = sample size, As = number assigned to self, A₀ = number assigned to other…………….….……….33 Table 2.20: Percentage of brook trout assigned between each site of the four major tributaries of Lake Superior located in Pictured Rocks National Lakeshore….....33 Table 2.21: Percentage of brook trout assigned between each site of the four Restricted sections located in Pictured Rocks National Lakeshore…………………………33 Table 2.22: Pairwise Fst values for Open and Restricted Sections of PIRO including Sullivan’s Creek……………………………………………………………….…34