System analysis of the spread of introgressive hybridization in salmonid population through an agent-based simulation model

Abstract

Using the specific example of introgressive hybridization between native cutthroat trout (Oncorhynchus clarkii sp., CTT) and introduced rainbow trout (O. mykiss, RBT), I have designed and developed an individual-based model that mimics the spread of introgressive hybridization in a river network inhabited by salmonids accounting for realistic population demographics, genetics, and stochasticity. As a tool capable of providing mechanistic explanations for observed patterns of introgression, the model is used in Chapter 2 to show that network bifurcations act as semi-permeable barriers to the spread of introgression across river network by decreasing (a) the rate of spread of non-native alleles and (b) the predictability of such spread. As a tool to test the effects of realistic population demographics and realistic mechanisms for the passage of alleles from one generation to the next the model is used in Chapters 3 and 4 to show that commonly used sampling and analysis methods greatly overestimate the power to detect and the precision to quantify introgression in populations.