'Number of fish analyzed; ifeonibmed with previous sample (indicated in "Location" column), number indicates the 



combined sample size; if present, the number in () is the average number successt'ull) ;uialyzed per locus (some 



individuals do not amplify for all marker loci). 



'dumber of markers analyzed that are diagnostic for the non-native species. 



'Codes: WSCT = wcstslope cutthroat trout (Oncorhyiic litis clarki lewisi); RB 1= rainbow trout (O. mykiss); YSCT= 



Yellowstone cutthroat trout (O. clarki houvien). Only one ta.\on code is listed when the entire sample possessed alleles 



from only that tavon. However, it should be noted that m such cases vvc cannot completely rule out the possibility that 



some or all of the individuals are hybrids; we merely have not detected any non-native alleles at the limited number of 



loci e.xamined (see Power % column). Codes separated by "x" indicate hybridization between the ta.\a. 



■"Number corresponds to the percent chance we have to detect 1% hybridization given the number of individuals 



successfullv' analyzed and the number of diagnostic markers used (e.g., 25 individuals are required to yield a 95% 



chance to detect l"o hybridization of rainbow or Yellowstone cutthroat trout into a westslope trout population using 6 



markers). Not reported when hybridization is detected. 



'Indicates the genetic contribution of westslope cutthroat trout to the sample assuming Hardy- Weinberg proportions. 



This number is reported only if the sample appears to come from a random mating population. 



"^Indicates number of individuals with genotypes corresponding to the ta\on in the code column when the sample does 



not appear to have come from a random mating hybrid swarm. 



'Longitudinal sample, see the "Sample Details" section below. 



Brief Description of Methods: 



Polymerase chain reaction (PCR) amplification of paired interspersed nuclear DNA 

 elements (PINEs) was used to determine each fish's genetic characteristics at multiple 

 regions of the nuclear DNA. This method produces DNA fragments that can be used to 

 distinguish between various cuttluoat trout subspecies {Oncorhynchus clarki spp.), 

 rainbow trout {O. mykiss) and their hybrids, and between bull trout {Salvelimis 

 conjhieniiis), brook trout {S. fontinalis), and their hybrids. The presence of a PINE 

 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 conform 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 1 997). 



