A report in partial fulfillment of: agreement # 165/04 state of wyoming




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MOLECULAR GENETIC INVESTIGATION OF YELLOWSTONE CUTTHROAT TROUT AND FINESPOTTED SNAKE RIVER CUTTHROAT TROUT



A REPORT IN PARTIAL FULFILLMENT OF:




AGREEMENT # 165/04

STATE OF WYOMING

WYOMING GAME AND FISH COMMISSION: GRANT AGREEMENT




PREPARED BY:




MARK A. NOVAK AND JEFFREY L. KERSHNER

USDA FOREST SERVICE

AQUATIC, WATERSHED AND EARTH RESOURCES DEPARTMENT

UTAH STATE UNIVERSITY




AND




KAREN E. MOCK

FOREST, RANGE AND WILDLIFE RESOURCES DEPARTMENT

UTAH STATE UNIVERSITY




TABLE OF CONTENTS





MOLECULAR GENETIC INVESTIGATION OF YELLOWSTONE CUTTHROAT TROUT AND FINESPOTTED SNAKE RIVER CUTTHROAT TROUT 1

A REPORT IN PARTIAL FULFILLMENT OF: 1

AGREEMENT # 165/04 1

STATE OF WYOMING 1

WYOMING GAME AND FISH COMMISSION: GRANT AGREEMENT 1

PREPARED BY: 1

MARK A. NOVAK AND JEFFREY L. KERSHNER 1

USDA FOREST SERVICE 1

AQUATIC, WATERSHED AND EARTH RESOURCES DEPARTMENT 1

UTAH STATE UNIVERSITY 1

AND 1

KAREN E. MOCK 1



FOREST, RANGE AND WILDLIFE RESOURCES DEPARTMENT 1

UTAH STATE UNIVERSITY 1

TABLE OF CONTENTS ii

LIST OF TABLES iv

LIST OF FIGURES vi

ABSTRACT viii

EXECUTIVE SUMMARY ix

INTRODUCTION 1

Yellowstone Cutthroat Trout Phylogeography and Systematics 2

Cutthroat Trout Distribution in the Snake River Headwaters 6

Study Area Description 6

Scale of Analysis and Geographic Sub-sampling 8

METHODS 9

Sample Collection 9

Stream Sample Intervals 10

Stream Sampling Protocols 10

Fish Species Identification 10

Fish Metrics, Photographs, and Tissue Samples 13

Genetic Analysis 13

Extraction of DNA 13

Methods by Objective 14

Objective 1 – Develop cost-effective, reliable, and repeatable molecular tools that will answer the study questions 14

Objective 2a – Determine morphological differences between the two morphotypes of cutthroat trout (YSC & SRC) in the study landscape 18

Objective 2b – Determine genetic differentiation between the two morphotypes of cutthroat trout (YSC & SRC) in the study landscape 19

Objective 3 – Describe patterns of genetic variation in cutthroat trout within and among major drainages in the study landscape 19

Objective 4 – Assess introgression with rainbow trout using both morphologic and genetic tools 20

Results 20

Survey Results 20

Genetic Structuring 22

Results by Study Objective 22

Objective 1 – Develop cost-effective, reliable, and repeatable molecular tools that will answer the study questions 22

Objective 2b – Determine genetic differentiation between the two morphotypes of cutthroat trout (YSC & SRC) in the study landscape 26

Objective 3 – Describe patterns of genetic variation in cutthroat trout within and among major drainages in the study landscape 36

Objective 4 – Detection of Rainbow Trout Introgression 41

Discussion 44

Develop cost-effective, reliable, and repeatable molecular tools that will answer the study questions 44

Genetic Differentiation among Morphotypes 45

Genetic Differentiation among Major Drainages 46

Detection of Rainbow Trout Introgression 47

Management Recommendations 48

References Cited 49

APPENDIX A 55

APPENDIX B 64



LIST OF TABLES





Table 1 Common and scientific names1 of fishes and amphibians in the Snake Headwaters basin of Wyoming, and species abbreviations as identified by the Wyoming Game and Fish Department. 12

Table 2 Polymerase chain reaction (PCR) primers used to amplify and sequence the ND1-2 region in cutthroat trout. Unpublished primer sources are noted: IDFG = Idaho Fish & Game Eagle Fish Health Lab; USU = Utah State University. 15

Table 3 Sample subset used to assess landscape-scale sequence variation in the mitochondrial ND1-2 region and to design internal primers to capture this variation. 16

Table 4 Polymerase chain reaction (PCR) primers used to amplify and assess polymorphism at nDNA microsatellite loci in cutthroat trout. Unpublished primer sources are noted by place of origin: GIS = Genetic Identification Services. 17

Table 5 Summary by river drainage for numbers of streams and stream reaches, and stream length (km) surveyed for cutthroat trout presence/absence between 1998 and 2003 in the Snake River headwaters of northwest Wyoming. River drainages are listed as they flow into the Snake River proceeding upstream from Palisades Reservoir. 21

Table 6 Number of streams with cutthroat, brook, and rainbow trout present and the stream length (km) occupied, based on presence/absence surveys between 1998 and 2003 in the Snake River headwaters, Wyoming. 21

Table 7 Presence of Yellowstone cutthroat trout (large spotted morphotype) and Snake River cutthroat trout (fine spotted morphotype) in streams surveyed, and stream length (km) occupied in the Snake River headwaters, Wyoming. 22

Table 8 Average pairwise genetic distances (and standard errors) between individuals within (along diagonal) and between morphotypic groups of cutthroat trout in the upper Snake River drainage, Wyoming. Samples were pooled across all drainages. Distances within and between groups are expressed as average number of mutational differences (below diagonal, italicized) or average percent of mutational differences (above diagonal). 26

Table 9 Average pairwise genetic distances (and standard errors) between individuals within (along diagonal) and between morphotypic groups of cutthroat trout in the Jackson Hole segment of the Snake River, Wyoming. Distances within and between groups are expressed as average number of mutational differences (below diagonal, italicized) or average percent of mutational differences (above diagonal). 26

Table 10 Average pairwise genetic distances (and standard errors) between individuals within (along diagonal) and between morphotypic groups of cutthroat trout in the Gros Ventre River drainage, Wyoming. Distances within and between groups are expressed as average number of mutational differences (below diagonal, italicized) or average percent of mutational differences (above diagonal). 27

Table 11 Average pairwise genetic distances (and standard errors) between individuals within (along diagonal) and between morphotypic groups of cutthroat trout in the Hoback River, Wyoming. Distances within and between groups are expressed as average number of mutational differences (below diagonal, italicized) or average percent of mutational differences (above diagonal). 27

Table 12 Average pairwise genetic distances (and standard errors) between individuals within (along diagonal) and between morphotypic groups of cutthroat trout in the Snake River Canyon segment of the Snake River, Wyoming. Distances within and between groups are expressed as average number of mutational differences (below diagonal, italicized) or average percent of mutational differences (above diagonal). 27

Table 13 Average pairwise genetic distances (and standard errors) between individuals within (along diagonal) and between morphotypic groups of cutthroat trout in the Greys River, Wyoming. Distances within and between groups are expressed as average number of mutational differences (below diagonal, italicized) or average percent of mutational differences (above diagonal). 28

Table 14 Average pairwise genetic distances (and standard errors) between individuals within (along diagonal, shaded) and between geographic groups of cutthroat trout in the Snake River headwaters, Wyoming. Distances within and between groups are expressed as average number of mutational differences (below diagonal, italicized) or average percent of mutational differences (above diagonal). 36

Table 15 Genetic diversity indices for cutthroat trout in Snake River headwaters drainages. Nucleotide diversity (), haplotype diversity (Hd), and number of haplotypes are presented for each drainage. 37

Table 16 Genetic differentiation among cutthroat trout in Snake River headwaters drainages, based on haplotype distributions, characterized using the GST statistic (Nei 1987; Hudson et al. 1992). 37

Table 17 Locations and fish metrics for five rainbow trout (RBT) and seven rainbow-cutthroat trout hybrids (RXC) captured in the Snake River headwaters, Wyoming. 42

Table 18 Summary of the number of records, by river drainage, of individual fish, and the approximate number of those fish that were photographed and/or a caudal fin clip collected. River drainages are listed as they generally occur from north to south. 55

Table 19 Total genomic DNA extractions for several streams1 in each of five geographic areas. The number of extractions per stream varied due to stream length, numbers of fish captured over the minimum size (>150 mm), and number of samples available for each putative cutthroat trout morphotype1. The geographic areas are arranged as they generally occur from north to south. A history of cutthroat trout stocking in each stream is provided. 56

Table 20 Lists the streams and samples, by geographic area1, selected for sequencing the mtDNA ND2 gene region. Contiguous sequences (~1,100 bp) of n=324 samples were completed. 59

Table 21 Number of cutthroat trout1 of the haplotypes A-M, per stream, within five geographic areas in the Snake River study area. The Snake River is split into two geographic areas, Jackson Hole and Snake River Canyon. The geographic areas are arranged as they generally occur from north to south. 61



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