Unless the distribution of markers dictates otherwise, we assume the samples conform to 

 random mating expectations in order to estimate the average genetic contribution from 

 each species. In these cases, we report the percent genetic contribution from each species 

 present in the population. When hybridization is present in these situations, the 

 population is considered a hybrid swarm. Regardless of the percent contribution from the 

 non-native species, in hybrid swarms, all individuals are of hybrid origin, even those that 

 appear '"pure" at our diagnostic loci. It is not possible to rescue pure individuals from 

 these populations, as they likely do not exist. Due to the random reshuffling of alleles 

 during sexual reproduction, many individuals will appear pure for one or the other 

 parental species due to the limited number of marker loci used. It has been shown that 6 

 markers are adequate to provide coarse classification of hybridization, but upwards of 70 

 markers are required to discriminate between pure individuals, if they exist, and 

 backcrossed individuals in hybrid swanns (Boecklen and Howard 1997). 



However, when the distribution of non-native markers appears to be non-random, it is not 

 valid to report genetic contributions of the component species at the population level, as 

 they do not come from a randomly mating population. It is likely that the individuals in 

 these samples either come from populations where hybridization is recent or are from 

 admixtures of populations. Samples can be analyzed at the individual level only. These 

 samples are not considered to come from hybrid swarms and some pure individuals may 

 exist. In these cases, we report the number of individuals with genotypes corresponding 

 to each species and/or the types of hybrids detected and do not report genetic contribution 

 percentages. 



Literature Cited: 



Boecklen WJ, and Howard DJ (1997) Genetic analysis of hybrid zones: numbers of 



markers and pov/er of resolution. Ecology 78 (8) pp. 261 1-2616. 



Sample Details: 



West Fork Bitterroot: All individuals in this sample exhibited fragments diagnostic of 

 westslope cutthroat trout. However, a single first generation (Fi) westslope 

 cutthroat/rainbow trout hybrid was detected indicating that an extremely low level of 

 hybridization has recently occurred. Assuming random mating proportions, the genetic 

 contribution of westslope cutthroat trout and rainbow trout is 97.3% and 2.7%, 

 respectively. 



Main Stem Bitterroot: All individuals in this sample displayed all PINE fragments 

 diagnostic of westslope cutthroat trout. One fish in this sample also exhibited a single 

 diagnostic rainbow trout marker at 1 locus (telemetry code 40.442). The individual that 



