POPULATION STRUCTURE AND HYBRIDIZATION OF ALASKAN CARIBOU AND REINDEER: INTEGRATING GENETICS AND LOCAL KNOWLEDGE By Karen H. Mager RECOMMENDED: APPROVED: Paul W. Layer Dean, College · ce and Mathematics La ce K. Duffy Dean ofthe Graduate School ~ 27, ~'2- Date POPULATION STRUCTURE AND HYBRIDIZATION OF ALASKAN CARIBOU AND REINDEER: INTEGRATING GENETICS AND LOCAL KNOWLEDGE A DISSERTATION Presented to the Faculty of the University ofAlaska Fairbanks in Partial Fulfillment ofthe Requirements for the Degree of DOCTOR OF PHILOSOPHY By Karen H. Mager, B.A. Fairbanks, Alaska May 2012 iii Abstract Alaskan caribou (Rangifer tarandus granti) are a valued game species and a key grazer in Alaska's terrestrial ecosystem. Caribou herds, defined by female fidelity to calving grounds, are management units. However, the extent to which herds constitute genetic populations is unknown. Historical fluctuations in herd size, range, and distribution suggest periods ofcontact and isolation between herds. Likewise, historical contact between caribou and introduced domestic reindeer (R.t. tarandus) created opportunities for hybridization, but its extent is not known. I conducted an interdisciplinary study to understand how historical processes influence genetic identity and population structure ofcaribou and reindeer. Interviews with herders and hunters in Barrow, Alaska, revealed that many reindeer migrated away with caribou in the 1940s despite herder efforts to prevent mixing. Local observations of reindeer-like animals in caribou herds today suggest feral reindeer may survive and interbreed. Using genetic analysis ofNorth Slope caribou and Seward Peninsula reindeer (n = 312) at 19 microsatellite loci, I detected individuals with hybrid ancestry in all four caribou herds and in reindeer. Selective hunting of reindeer-like animals, along with herd size and natural selection, may remove reindeer from caribou herds over time. I used genetics ~s well to describe caribou population structure and determine how it is influenced by geography, historical demography, and ecotypes. I found that Alaskan caribou from 20 herds (n = 655) are subdivided into two genetic clusters: the Alaska Peninsula and the mainland. Alaska Peninsula herds are genetically distinct, while many mainland herds are not. I hypothesize that Alaska Peninsula herds have diverged due to post-glacial founder effects and recent bottlenecks driven by constraints to population size from marginal habitat and reduced gene flow across a habitat barrier at the nexus of the peninsula. I hypothesize that mainland herds have maintained genetic connectivity and large effective population size via range expansions and shifts over time. However, I find evidence that herds ofdifferent ecotypes (migratory, sedentary) can remain differentiated despite range overlap. Genetic evidence provides information for iv herd-based management, while also demonstrating the importance of spatial connectivity of herds and their habitats over the long-term. v Table of Contents Page Signature Page....................................................................................................................i Title Page............................................................................................................................ ii Abstract............................................................................................................................. iii Table of Contents .............................................................................................................. v List of Figures................................................................................................................... ix List of Tables .................................................................................................................... xi List ofAppendices........................................................................................................... xii General Acknowledgments ........................................................................................... xiii Chapter 1 General Introduction ...................................................................................... 1 1.1 Research Topic and Conceptual Framework ................................................................ 1 1.2 Study System ................................................................................................................ 2 1.2.1 Background ............................................................................................................ 2 1.3 Objectives, Methodology, and Outline ......................................................................... 6 1.4 References Cited ........................................................................................................... 9 Chapter 2 "I'd Be Foolish to Tell You They Were Caribou:" Local Knowledge of Historical Interactions between Reindeer and Caribou in Barrow, Alaska••.••••••••••. 19 2.1 Abstract ....................................................................................................................... 19 2.3 Introduction................................................................................................................. 20 2.3.1 Background on Barrow Reindeer Herds .............................................................. 22 2.4 Methods....................................................................................................................... 24 2.4.1 Interview Participants and Procedures ................................................................. 24 2.4.2 Methodological Approach and Limitations ......................................................... 26 2.5 Role of Caribou in the Barrow Reindeer Decline ....................................................... 27 2.5.1 Reindeer Herder Responses to Caribou ............................................................... 29 2.5.2 Fluctuations in Caribou Population Size .............................................................. 30 2.5.3 Perceptions ofCaribou in the Reindeer Administration ...................................... 31 2.6 The Fate of Lost Reindeer and their Impact on Caribou Herds .................................. 35 Vl 2.6.1 Distinguishing Characteristics ofCaribou and Reindeer ..................................... 35 2.6.2 Persistence ofFeral Reindeer and Hybridization with Caribou ........................... 36 2.6.3 Cultural Implications of a Heritage with Reindeer and Caribou ......................... 40 2.7 Discussion ...............................................•................................................................... 42 2.8 Acknowledgments....................................................................................................... 46 2.9 Endnotes...................................................................................................................... 47 2.10 References Cited ....................................................................................................... 49 Chapter 3 Genetic Connectivity Between Caribou Herds and Hybridization with Domestic Reindeer in Northern Alaska ........................................................................ 66 3.1 Abstract ....................................................................................................................... 66 3.2 Introduction................................................................................................................. 66 3.3 Materials and Methods ................................................................................................ 70 3.3.1 Genetic Sampling ................................................................................................. 70 3.3.2 Geo-Spatial Data .................................................................................................. 71 3.3.3 Marker Selection and Genotyping ....................................................................... 71 3.3.4 Statistical Analysis - Herd Differentiation and Diversity .................................... 72 3.3.5 Analysis ofGenetic Population Structure ............................................................ 73 3.3.6 Landscape Genetic Analyses ............................................................................... 73 3.3.7 Hybridization and Reindeer Introgression Analysis ............................................ 74 3.4 Results......................................................................................................................... 75 3.4.1 Herd Differentiation and Diversity ...................................................................... 75 3.4.2 Overall Genetic Population Structure .................................................................. 75 3.4.3 Hybridization and Reindeer Introgression ........................................................... 76 3.5 Discussion ................................................................................................................... 77 3.5.1 Herd Differentiation ............................................................................................. 77 3.5.2 Genetic Population Structure ............................................................................... 78 3.5.3 Reindeer-Caribou Hybridization .......................................................................... 79 3.5.4 Constraints on Gene Flow and Hybridization in Large Populations ................... 82 3.5.5 Conclusions.........................................................................................................