marker is dominant to absence. First-generation (Fi) hybrids will have all the diagnostic 

 markers characteristic of the two hybridizing taxa. Most backcrossed individuals will 

 possess some, but not all, markers characteristic of both parental taxa. The appearance of 

 a marker indicates the individual is either heterozygous or homozygous for that marker, 

 which precludes us from directly calculating allele frequencies. 



Unless the distribution of markers indicates otherwise, we assume genotypes in the 

 sample confonn to random mating expectations and we can estimate the average genetic 

 contribution of each taxon to such hybrid swarms. Regardless of the percent contribution 

 from the non-native taxon, 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, some individuals will appear pure for 

 one or the other parental taxa due to the limited number of marker loci used. It has been 

 shown that 6 markers are adequate to provide adequate power for detection of 

 hybridization at the population level, but upwards of 70 markers are required to 

 discriminate between pure individuals, if they exist, and backcrossed individuals in 

 hybrid swarms (Boecklen and Howard 1997). 



The distribution of non-native markers may not be randomly distributed among the fish 

 in a sample primarily because hybridization has only recently begun in the population, 

 the sample contains individuals from two or more genetically divergent populations, or 

 both. Such collections can be analyzed at the individual level only. Since such samples 

 do not come from hybrid swarms, the proportion of native and non-native markers cannot 

 reliably be estimated. In these cases, the sample may contain some non-hybridized 

 individuals. Rather than reporting percent genetic contributions we report the number of 

 individuals in the sample, based on the fragments they possessed that may be non- 

 hybridized. 



Literature Cited: 



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

 markers and power of resolution. Ecology 78 (8) pp. 261 1-2616. 



Sample Details : 



Blackfoot River Telemetry 2003: All twenty successfully amplified individuals in this 

 sample displayed PfNE fragments diagnosfic of westslope cutthroat trout. 



• Eighteen of these individuals displayed only PINE fragments diagnostic of 

 westslope cutthroat trout. 



o Sample #: 17-21, 17-28, 17-43, 17-44, 17-45, 18-16, 18-50, 18-51, 

 18-52, 18-53, 18-55, 18-56, 19-06, 19-07, 19-61, 19-62,19-64 and 

 19-65. 



• Two individuals also displayed PfNE fragments diagnostic of rainbow 

 trout. 



o Sample # 1 7-22 and 1 7-41 each showed that they are post-first 

 generation hybridized fish. Both of these fish came from 

 designated Reach 1 (North Fork to Nevada Creek, n = 7). 



