"Number of fish analyzed; if combined vviih previous sample (indieaied in "Location" column), number indicates the combined sample size; if 



present, tlie number in i; is the average number successfully analyzed per locus (some individuals do not amplify for all marker loci;. 



""Number of markers analysed that are diagnostic for the non-native species. 



'Codes: WSCT = vvestslope cutthroat trout {Oncorhynchus ciarki lewist). RBT= rainbow trout (O. mykiss); \'SCT= Yellowstonecutihroat trout 



(O ciarki bouvien). Only one la.xon code is listed when the entire sample possessed alleles from only that txxon. However, it should be noted 



that in such cases we 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 examined (see Power ".o column). Codes separated by "x" indicate hybridization between the ta.xa. 



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



number of diagnostic markers used (e.g., 25 individuals are required to yield a 95% chance to detect 1% 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 w ith genotypes corresponding to the taxon in the code column when the sample does not appear to have come 



from a random mating hybrid swarm. 



'See the "Sample Details" section below. 



Brief Description of Methods: 



Polymerase chain reaction (PCR) amphfication of paired interspersed nuclear DNA elements (PINEs) was used to 

 determine each fish's genetic between various cuttliroat trout subspecies {Oncorhynchus ciarki spp), rainbow trout {0. 

 mykiss) and their hybrids, and between bull trout {Salvdinus confluentus), brook trout {S. fontinalis characteristics at 

 multiple regions of the nuclear DNA. This method produces DNA fragments that can be used to distinguish), 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 ta:<.a. Most backcrossed individuals will possess some, but not 

 all, markers characteristic of both parental ta.xa. 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 (Table 2), we assume genot\'pes in the sample conform to 

 random mating e.xpectations and we can estim.ate the average genetic contribution of each taxon to such hybrid 

 swarms. Regardless of the percent contribution from the non-native taxon, m 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 reshuftling 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 these 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. 

 ^a^/o^^wS (8) pp. 2611-2616. 



