'Number ol's;implc> anaK/cd. il prcsciil. ihc nunibcr m () is the averaiji; niinibi;r siicccssrullv aiuil_\ /i;d per locus (somi; 

 individuals do noi amplilv I'or all marker loci) 



""Number ol' markers anal.w.ed dial are diagnosue for the non-native speeies. 



Xodes: V\ SCT = iveslslope eultliroal trout [Oncorhynchus clarki lewisi): RBT= raidbou trout (O myhss): 'l'SCT= 

 Yello\vstone cutthroat trout (O clarki boiivien). Only one species code is listed when the entire sample possessed 

 alleles from that species oiil\. However, it must be noted that in such cases we cannot definitively rule out the 

 possibiliiv that some or all of the individuals are hybrids; wc merely have not detected any non-native alleles at the 

 limited number of loci examined (see Power "io column). Species codes separated by ".n" indicate hybridi:<:ation 

 between those species. 



""Number corresponds to the percent chance we have to detect l°l) hybridization given the number of individuals 

 successfully anaU zed and the number of diagnostic markers used (e.g., 25 individuals are required to yield a 95% 

 chance to detect l°b hybridization of rainbow or Yellowstone cutthroat trout into a vvestslope trout population). 

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

 This number is reported only if samples appear to come from a random mating population and can be analyzed at the 

 population level. 



Indicates number of individuals vvith genotypes corresponding to the species code column \\hen the sample can be 

 analyzed on the individual level only; this occurs when alleles are not randomly distributed and hybridization appears 

 to be recent and/or if the sample appears to consist of an admixture of populations. 

 *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 cutthroat trout subspecies {Oncorhynchus clarki spp.), 

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

 confliientus), 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 species. Backcrossed (F2+) individuals will 

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

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

 marker, which precludes us from directly calculating allele frequencies. However, in 

 order to provide comparative values, we have assumed the samples conform to random 

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

 species. 



It is critical to note that in all hybrid swarms, regardless of the percent contribution from 

 the non-native species, 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 swarms (Boecklen and Howard 1997). 



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. 



