Population structure and genetic characteristics of summer steelhead (Oncorhynchus mykiss) in the Deschutes River Basin, Oregon

United States Fish & Wildlife Service Abernathy Fish Technology Center Report

Final Report

January 2011

Prepared by

Denise K. Hawkins1, Kevin S. Williamson1, Andrew P. Matala1,

David Hand2, Doug Olson2, and Howard Schaller2

1U.S. Fish & Wildlife Service, Abernathy Fish Technology Center, Conservation Genetics Program, 1440 Abernathy Creek Road, Longview, WA 98632, TEL: 360-425-6072, FAX: 360-636-1855, ([email protected])

2U.S. Fish & Wildlife Service, Columbia River Fisheries Program Office, 1211 SE Cardinal Ct., Suite 100, Vancouver, WA 98683, TEL: 360-604-2500, FAX: 360-604-2505, ([email protected]), ([email protected]), ([email protected])

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Abstract The Deschutes River Basin represents a region of substantial diversity among anadromous and resident forms of Oncorhynchus mykiss. However, the current distribution and genetic origins of populations throughout the Deschutes River Basin have not been clearly delineated. Using a suite of 17 microsatellite markers, we evaluated genetic structure among Deschutes River Basin populations of steelhead. To provide a broader perspective of diversity and to help assess the Interior Columbia River Technical Recovery Team (ICR-TRT) population delineations, we also compared the steelhead collections to collections of redband trout from the upper basin and the Oak Springs Hatchery rainbow trout stock that was planted in the Deschutes River Basin. Whychus Creek redband trout appeared to be more genetically similar to O. mykiss in the lower mainstem of the Deschutes River than to other collections included in this report, which is inconsistent with the previous population delineation that includes Whychus Creek with Deschutes-Westside populations. Below the Pelton-Round Butte Dam complex mainstem collections were statistically different from tributary collections; however, there were no statistically significant differences between Deschutes-Westside and Deschutes-Eastside populations below the Pelton-Round Butte Dam complex. These data suggest that the previous delineation of populations into Deschutes-Westside and Deschutes-Eastside by the ICR-TRT does not reflect observed genetic relationships.

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Introduction Summer steelhead trout (anadromous form of Oncorhynchus mykiss) in the Deschutes River Basin are part of the Mid-Columbia Steelhead Evolutionarily Significant Unit (ESU) that has been listed as threatened by NOAA-Fisheries since 1999 (NMFS, NOAA 1999 and 2006). In order to evaluate recovery needs and implement a recovery plan for steelhead in the Deschutes River, the Interior Columbia River Technical Recovery Team (ICR-TRT 2003) attempted to characterize population structure and identify discrete populations throughout the basin. The Deschutes River Basin represents a region of substantial biological diversity among O. mykiss (Kostow 1995), likely indicative of multiple colonization events (Currens et al. 1990) and the influence of geologic and hydrologic barriers (Currens et al. 1990; Zimmerman and Ratliff 2003; Stuart et al. 2007). The current distribution and genetic origin of populations throughout the Deschutes River Basin have not been clearly delineated. With a limited amount of genetic information available, the recovery team relied on life- history information and differences in topographic and habitat conditions to describe anadromous O. mykiss (steelhead) populations. Two potentially independent (distinct) populations were identified: 1) Deschutes River eastside tributaries (Deschutes-Eastside), encompassing all of the eastside tributaries below the Pelton-Round Butte Dam complex including the mainstem from its mouth to the confluence of Trout Creek, and 2) Deschutes River westside tributaries (Deschutes-Westside), encompassing all of the westside tributaries below Pelton-Round Butte Dam complex including the mainstem above the confluence of Trout Creek (Figure 1). The recovery team also identified that the areas above Pelton-Round Butte Dam complex likely supported one or more populations historically. The team updated the population delineations in 2005, and clarified that areas likely used historically by anadromous O. mykiss would be included in two of the existing population delineations (NMFS, NOAA 2006). Therefore, the Deschutes-Westside population now includes Whychus Creek and any historically used portions of the Metolius River. The recovery team noted that the lack of comprehensive genetic information limited their ability to infer the relationship among presumed populations, particularly between mainstem and tributary spawners. This lack of information was also recognized as a constraint on fishery managers and on the planning process for reintroductions in the upper sub-basin (Northwest Power and Conservation Council 2004, Deschutes sub-basin

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plan). An analysis of genetic diversity will aid managers and recovery planners by improving understanding of factors influencing the pattern and level of population structure of Deschutes River Basin summer steelhead. Another concern for fishery managers is the impact of within-basin and out-of-basin stray hatchery steelhead on the wild steelhead populations in the lower Deschutes River. Round Butte Hatchery (RBH) originally collected brood stock from unmarked adult steelhead in the Deschutes River and released juvenile hatchery steelhead below Pelton Dam. On average, 47.1% of returning Round Butte Hatchery (RBH) marked steelhead passing Sherars Falls are not captured but remain in the Basin (ODFW 2004). In addition, out-of-basin hatchery strays have accounted for an average of over 60% of the steelhead migrating past Sherars Falls since 1995 (Hand and Olson 2004). The fate of these fish has implications for management, particularly in regard to their presence and reproductive success relative to that of native steelhead on spawning grounds. Genetic analysis may provide evidence of measurable introgression between out-of- basin stray hatchery steelhead and populations of native steelhead in the Deschutes River or its tributaries below the Pelton-Round Butte Dam complex. Although a paucity of information currently exists on the influence of out-of-basin stray hatchery steelhead on local native steelhead populations, Chilcote (2003) used data from the Deschutes River steelhead population as part of an analysis of mixed spawning populations of wild and hatchery steelhead and estimated a reduced level of productivity in populations that had higher proportions of hatchery fish on the spawning grounds. Genetic baseline data for both the hatchery and wild populations in the Deschutes River are necessary prior to an evaluation of the influence of stray hatchery fish on the genetic diversity of the wild steelhead populations. The Warm Springs River system is considered a valuable spawning area for native Deschutes River summer steelhead below the Pelton-Round Butte Dam complex. Only unmarked summer steelhead are provided access to spawning grounds above the barrier at the Warm Springs National Fish Hatchery (WSNFH). Stray wild fish have no identifying marks, are indistinguishable from Warm Springs River native steelhead, and comprise an unknown proportion of the total return. Although the number of stray wild steelhead in the Deschutes River is unknown, marked hatchery stray steelhead comprised an average of 51% of total returns to the Warm Springs River between 1980 and 2003 (Hand and Olson 2004). Most of the hatchery strays that could be identified in the Warm Springs River came from the Snake River

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Basin. There is also a potential for unmarked, hatchery-origin steelhead to stray into the Warm Springs River. In 2003, approximately two million juvenile hatchery steelhead were released in the Columbia River Basin without adipose fin clips. Hence, it is possible that returning unmarked adult hatchery steelhead that stray to the Warm Springs River may be mistaken for native Warm Springs River steelhead and inadvertently provided access to spawning grounds above WSNFH. Genetically characterizing wild fish returning to the Warm Springs River provides a genetic profile of Warm Springs River native summer steelhead and a benchmark to assist in identifying out-of-basin wild or unmarked hatchery origin fish entering the system. Future assessment of strays in the Deschutes basin will be carried out using the 13 microsatellite loci that make up the SPAN baseline (a collection of genotypic data contributed by a consortium of multiple state and federal agencies and Tribes; Stephenson et al. 2009). Representatives of state, federal, and tribal agencies met in The Dalles, Oregon (December 2004) to develop a preliminary study plan addressing the Interior Columbia River Technical Recovery Team (ICR-TRT (2003) conclusion that insufficient information was available to describe the genetic relationships among steelhead in the mainstem Deschutes River, and east and west side tributaries of the Deschutes River below the Pelton-Round Butte Dam complex. The representatives agreed that the study objectives would be: 1) develop an understanding of the population structure and genetic variability among steelhead occupying tributaries and the mainstem Deschutes River downstream of the Pelton-Round Butte Dam complex with a three year genetic sampling protocol, 2) evaluate the effect of out-of-basin strays on the Deschutes River Basin populations (by determining rate of straying and reproductive contribution of strays), and 3) evaluate relationships among resident redband trout and anadromous steelhead in the Deschutes River using genetic characteristics and other life history characteristics. This report represents the completion of Objective 1 – examination of the spatial and temporal aspects of Deschutes River O. mykiss population structure below the Pelton-Round Butte Dam complex. We also evaluate the ICR-TRT population groups (Deschutes- Eastside/Deschutes-Westside), and two other population groupings (Mainstem/Tributary, and Upper mainstem Deschutes/Lower mainstem Deschutes) through a genetic characterization of O. mykiss from five tributaries and two mainstem locations downstream of the Pelton-Round Butte Dam complex.

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Methods The Columbia River Fisheries Program Office (CRFPO) was responsible for coordinating field collections, and sampling protocols were collaboratively developed. Target locations for tributary collections are identified in this report by region: westside, eastside, and Deschutes River mainstem (Figure 1). The Oregon Department of Fish and Wildlife (ODFW) led efforts to collect biological information and genetic samples from three eastside tributaries (Buck Hollow, Bakeoven, and Trout creeks) and the mainstem Deschutes River, while the Confederated Tribes of the Warm Springs Reservation of Oregon (CTWSRO) collected samples from two westside tributaries (Warm Springs River and Shitike Creek; Figure 1). Juvenile steelhead were also collected from the mainstem Deschutes River above the confluence of Trout Creek (upper mainstem) and from the mainstem Deschutes River between Sherars Falls and the confluence of Trout Creek (lower mainstem). Sampling was focused on steelhead juveniles to eliminate the chance of inadvertently collecting either out-of-basin, unmarked stray hatchery, or stray natural origin adults. A target sample size of 50 juvenile steelhead was set for each population sampled from 2005 to 2007. Some areas within the basin are difficult to sample and typically support fewer fish with an anticipated lower yield from sampling. A standard sample size of 50 individuals improves the likelihood of uniform sampling among sites, while meeting cost considerations associated with sample collection and processing. No more than 10 individuals were collected from each 100 meters of stream surveyed to avoid non-random sampling (i.e., sampling of family groups). For each population, field biologists identified sample sites for collection of progeny of anadromous steelhead. Sites and samples were identified based on a combination of factors including: 1) known steelhead spawning areas, 2) stream flow (time of year), 3) size and physical appearance of juveniles, and 4) stream access. Scales were collected and fork lengths and geo-reference information were recorded (when possible) for each sample. Juvenile samples were classified as a) anadromous steelhead (STH) if field crews were reasonably confident of anadromous parentage, b) resident (Omy) if field crews were reasonably confident of resident parentage, or c) unknown (Unk) if the parentage was indeterminate. In nearly all cases, the number of samples collected from each location was close to or exceeded the target of 50. In the three cases where the target was not met, temporal collections were

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combined (Table 1). Samples of adult natural origin (NOR) and hatchery origin (HOR) steelhead were also collected from the Warm Springs River. A detailed description of sample collection for each population is given in Appendix 1. In 2006, fin clip samples were collected from redband trout within the upper Deschutes River sub-basin above the Pelton-Round Butte Dam complex and from Oak Springs Hatchery rainbow trout (n=56; Stock #53; Maupin, Oregon) (Table 1). These collections were obtained, genotyped, and analyzed as part of a separate study to evaluate genetic structure and similarities among Oak Springs Hatchery and Crane Prairie Reservoir stocks and their relationships to redband trout populations in the upper Deschutes River Basin tributaries (Matala et al. 2009). These collections were included in the analyses of Deschutes River native steelhead below the Pelton-Round Butte Dam complex so that a broader picture of genetic diversity could be presented. By including the Whychus Creek and other redband trout collections in the population structure analysis, the National Marine Fisheries Service (2006) update to the independent population group Deschutes-Westside tributaries (containing Whychus Creek) could be evaluated.

Microsatellite Amplification DNA was extracted from all samples in a Chelex 100 (Sigma Chemical Co.) resin solution as described by Miller and Kapuscinski (1996). In total, 22 nuclear loci were amplified by polymerase chain reaction (PCR) assays. Seventeen microsatellite loci were used to analyze genetic diversity. Included among the 17 microsatellite loci used in this study are 13 loci that have been evaluated in the Steven Phelps Allele Nomenclature (SPAN) standardization effort for steelhead trout (Appendix 2). The data are standardized among laboratories and available for sharing among collaborative parties for the benefit of steelhead trout management, conservation, and research. Four additional loci were added to the 13 SPAN loci to provide increased resolution in the population structure analyses. PCRs were carried out in 10 μl volumes containing 2-20 ng of genomic DNA, 1.5-2.0 mM MgCl2, 0.2 mM of each deoxynucleotide triphosphate, 0.2 μM of each primer, and 1X QIAGEN PCR Master Mix containing DNA polymerase (Appendix 2). PTC100 thermal cyclers (MJ Research, San Francisco, California) were programmed with the following conditions to amplify all microsatellite loci examined: one denaturation cycle at 95oC for 15 minutes; 29 amplification cycles of 95oC for 30 seconds,

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primer specific annealing temperatures for 90 sec. (Appendix 2), and 72oC for 60 sec.; and a final extension cycle of 60oC for 20 min. Five diagnostic nuclear markers, OCC35, OCC36, OCC37, OCC42, and OM55 (Ostberg and Rodriguez 2002, 2004), were amplified by PCR to detect cutthroat trout (O. clarki clarki) and O. clarki x O. mykiss hybrids in samples of natural origin fish. PCRs were carried out in 10 μl volumes containing 2-20 ng of genomic DNA, 3.0

mM MgCl2, 0.2 mM of each deoxynucleotide triphosphate, 0.2 μM of each primer, and 1X QIAgen PCR Master Mix containing DNA. PTC100 thermal cyclers were programmed with the following conditions to amplify these five microsatellite loci: one denaturation cycle at 95oC for 15 min.; 20 amplification cycles of 94oC for 30 sec., 58 to 48oC (subtracting 0.5oC /cycle) for 90 sec.; 18 amplification cycles of 94oC for 30 sec., 48oC for 90 sec., and a final extension cycle of 72oC for 10 min. An ABI-3130xl automated DNA Genetic Analyzer and GeneMapper v4.0 software (Applied Biosystems Inc., Foster City, California) were used to resolve and evaluate the size of PCR amplified alleles. Individuals identified as either cutthroat trout or cutthroat x rainbow hybrids were removed from the dataset prior to analyses.

QA/QC: error rate analysis Laboratory error rate was determined through a quality-assessment/quality-control (QA/QC) procedure involving random re-sampling and duplicate genotypic analyses. Original data and replicate data were collected by different laboratory personnel, and data concordance was determined by the lead researcher. DNA from every 10th sample from the complete data set was re-extracted from tissue, re-amplified at 17 loci using PCR, and re-genotyped. The original sample scores were then aligned with the scores generated from the duplicate analysis and an error rate over all loci was calculated as the proportion of mismatches (i.e., differing allelic scores).

Descriptive Statistics – all 21 collections Allele frequencies for each locus were determined with CONVERT v1.3.1 (Glaubitz 2004) and shown in Appendix 3. GENEPOP v4.0.1 (Raymond and Rousset 1995) was used to test for departures from Hardy-Weinberg Equilibrium (HWE) for each locus and collection, and

to test for evidence of linkage disequilibrium (LD) between all pairs of loci. FIS (a measure of departure from random mating) was calculated using FSTAT v2.9.3 (Goudet 2001). Significant

deviations from HWE expectations, extreme values of FIS, and high levels of LD can all indicate

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non-random mating or non-random sampling within a population. Allelic richness and heterozygosity were calculated as measures of genetic diversity within populations. The average number of alleles per locus and allelic richness (the number of alleles per locus corrected for unequal sample sizes among collections) were determined with FSTAT v2.9.3 (Goudet 2001). Observed and expected heterozygosity (Ho and He) were calculated using GDA v1.1 (Lewis and Zaykin 2001).

Tests of population groups –13 juvenile Deschutes collections only Deschutes River NOR steelhead collected from below the Pelton-Round Butte Dam complex were combined into three sets of groups for comparison of summary statistics: 1) Deschutes-Eastside (Bakeoven, Buck Hollow, and Trout creeks, and the lower mainstem Deschutes River) and Deschutes-Westside (Warm Springs River, Shitike Creek, and upper mainstem Deschutes River; NMFS, NOAA 2006), 2) Mainstem (upper and lower mainstem Deschutes) and Tributary (Bakeoven, Buck Hollow, and Trout creeks, Warm Springs River, and Shitike Creek), and 3) Upper and Lower Deschutes. Allelic richness (AR), observed heterozygosity (Ho), gene diversity (Hs; Eq. 8.31 Nei 1987), index of inbreeding (FIS), and FST were compared between population groups using the program FSTAT with 1000 permutations. The proportion of variance among collections within population groups was compared to that between population groups using an analysis of molecular variance (AMOVA) as implemented in ARLEQUIN version 3.1 (Excoffier et al. 2005). Three AMOVAs were performed on the three population groups below the Pelton-Round Butte Dam complex described above.

Population differentiation – all 21 collections and 13 juvenile Deschutes collections

Estimates of pairwise FST and exact tests of genotypic differentiation were carried out to assess genetic relationships. Divergence among all pairs of collections was estimated as FST (θ; Weir and Cockerham 1984) using GENETIX v4.05.2 (Belkhir et al. 2004). Statistical

significance of FST values was evaluated by comparison to a null distribution based on 1000 replicate datasets in which individuals were permuted among the pairs of collections (α = 0.05). Exact tests of genotypic differentiation (differences in allele frequencies) were carried out using GENEPOP v4.0.1 (Raymond and Rousset 1995). Bonferroni corrections (Rice 1989) for multiple tests were applied to P-values when assessing statistical significance of test results. We

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generated a consensus neighbor-joining tree using the program PHYLIP v3.6 (Felsenstein 2005) as a graphical representation of the genetic relationships for all 21 collections and for the subset of 13 juvenile Deschutes collections. The SEQBOOT sub-routine of PHYLIP was used to generate 1000 randomized replicates (boot-strap resampling) of the allele frequency dataset. For each of the 1000 replicates a pairwise genetic distance matrix of Cavalli-Sforza and Edwards

(1967) chord distance measures (DCE) was generated, and an unrooted neighbor-joining tree of genetic distance was calculated from each matrix using the sub-routines GENDIST and NEIGHBOR. The sub-routine CONSENSE was used to calculate the consensus tree. Confidence in the nodes of the consensus tree was based on the percentage of replicate trees that displayed the same topology. The program MEGA4 (Tamura et al. 2007) was used to graphically display the trees.

Test of population assignment – all 21 collections Population assignment testing was used to further investigate genetic distinction among collections of NOR Deschutes River steelhead, as well as between stray (out-of-basin) hatchery steelhead and native Deschutes River populations. To determine how well individual fish could be assigned to their population of origin a jackknife, or leave one out, test was carried out using ONCOR (Kalinowski, downloaded 2010). The jackknife method is carried out by removing individuals one at a time, recalculating the baseline allele frequencies, estimating the probability that the individual came from each baseline collection, and assigning that individual to the population to which it has the highest probability of belonging. Assignment success was evaluated for only those individuals with complete genotypic information at 17 loci, but all individuals were included in the estimation of baseline population allele frequencies.

Results Genotyping The 17 microsatellites examined here exhibited 319 alleles, with individual loci exhibiting between eight and twenty-eight alleles (Appendix 2). We conducted a QA/QC test during each collection year. The total number of samples evaluated was 126, and the number of allelic comparisons made across 17 loci was 3,912 (comparisons with a missing score were excluded). We observed a total of 12 scoring discrepancies, usually associated with weakly

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amplified samples, for a total error rate of 0.31%. Error rates <1% are typically considered acceptable for population structure analyses (Bonin et al. 2004).

Descriptive Statistics There were 9 statistically significant departures from expected genotypic proportions among all 21 collections and 357 total tests of Hardy-Weinberg Equilibrium (HWE). Departures from HWE occurred at Ots1 (n=3), Omy77 (n=2), Omy7iNRA (n=2), Omy1011 (n=1), and Oneμ14 (n=1) (data not shown). All 21 collections had few (0-5 out of 136) statistically significant pairwise linkage disequilibrium (LD) tests. Mean allelic richness (AR) ranged from 5.75 in the Oak Springs collection to 10.09 in the Warm Springs NOR juveniles (Table 2).

Tests of population groups Summary genetic statistics were compared between population groups (Table 3). Comparison of Deschutes River mainstem and tributary population groups indicated that the tributary population group had significantly higher allelic richness, observed heterozygosity, and gene diversity. No significant differences in FIS, or overall FST were detected between mainstem and tributary population groups. Comparison of Deschutes River upper and lower mainstem population groups indicated that the upper mainstem group had significantly higher observed heterozygosity and gene diversity, with no differences detected in the remaining statistics. No statistically significant differences in summary genetic statistics were detected when comparisons were made between eastside and westside Deschutes River tributaries. Analysis of molecular variance provided a second assessment of the Deschutes River steelhead population groups (Table 4). Significant variance was detected between groups of Deschutes River mainstem and tributary (2.09%; P<0.00001), but not between eastside and westside tributary groups (P=0.557), or between lower and upper mainstem (P=0.331) population groups.

Population differentiation Nearly all tests of population differentiation were highly significant. Only two tests of genotypic differentiation based on allele frequency differences between pairs of collections were not statistically significant: the two collections from Trout Creek and the two collections of stray

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adults from the Warm Springs River (data not shown). Similarly, all but five pairwise FST estimates indicated significant differences between population pairs (Appendix 5). The non- significant estimates of FST were temporal samples from Trout Creek, lower Mainstem, and stray adults from Warm Springs River. The collection of Warm Springs NOR adults from 2007 was also not statistically different from either of the two stray adult collections from the Warm

Springs River. Pairwise FST estimates ranged from 0.001 (Warm Springs River adult strays collected in 2005 and 2006) to 0.249 (Oak Springs Hatchery and Whychus Creek). Among the

juvenile collections including Round Butte Hatchery, pairwise FST estimates ranged from 0.005 (temporal collections from Bakeoven Creek) to 0.062 (lower mainstem Deschutes 05 and Bakeoven 05). In the neighbor-joining tree with juvenile and Round Butte Hatchery collections (Figure 2), there was strong bootstrap support for the separation of mainstem and tributary collections and also between upper and lower mainstem collections. Additionally, there was strong support for the separation of the two Westside Deschutes tributaries (Shitike and Warm Springs) from the Eastside Deschutes tributaries (Bakeoven, Buck Hollow, Trout creeks). All of the tributary collections were separated from each other with moderate to high levels of bootstrap support and moderate support for the clustering of the temporal collections, with the exception of Trout Creek (temporal collection bootstrap 74%). The collection from Round Butte Hatchery was most similar to the two Trout Creek collections but with only 40% bootstrap support. In the neighbor-joining tree including all 21 collections (Figure 3), the strong support for the separation of the mainstem Deschutes collections from the tributary collections was still present. However, the Whychus collection clustered with the lower Deschutes mainstem collections with 100% bootstrap support. The other collections above Pelton-Round Butte Dam (Tumalo and Crane Prairie) and the collection from Oak Springs Hatchery were distinctly separated from the below Pelton-Round Butte Dam collections with long branch lengths and high bootstrap support. The clustering of temporal collections from Buck Hollow still had moderate bootstrap support. The 2006 collection of NOR adults from the Warm Springs River clustered with the Warm Springs NOR juveniles with moderate bootstrap support, while the 2007 collection of NOR adults from the Warm Springs River clustered with the Warm Springs River adult strays, separate from the other tributary collections with 100% support.

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Population assignment tests Correct assignment of individuals back to collection of origin was generally low for all collections below Pelton-Round Butte Dam (juvenile collections range: 23% - 67%; adult collections range: 17% - 37%; Table 5). However in general, the largest percentage of misassignments for each collection was to a temporal replicate collection or to a geographically nearby tributary. The Round Butte Hatchery collection had 56% correct assignment with the largest percentage of misassignments going to the Trout Creek 07 collection. The Warm Springs NOR juveniles had 38% correct assignment with the majority of misassignments going to the 2006 Warm Springs River adults. The 2006 Warm Springs River NOR adults had 29% correct assignment with the majority of misassignments going to Trout Creek 07. The 2007 Warm Springs River NOR adults had 17% correct assignment; while the majority of misassignments were to the 2006 Warm Springs River NOR adult collection, a nearly equal number of fish were misassigned to both the Shitike and Warm Springs stray 06 collections (Appendix 4). Collections from above Pelton-Round Butte Dam had very high correct assignment rates with the exception of Whychus Creek. Whychus Creek had 64% correct assignment with the majority of misassignments going to the lower mainstem Deschutes 06 collection.

Discussion The two main objectives of this project were to 1) develop an understanding of the population structure and genetic variability among steelhead occupying tributaries and the mainstem Deschutes River downstream of the Pelton-Round Butte Dam complex and 2) to provide a genetic evaluation of the population groups. The results of this project address the current genetic information gap for Deschutes Basin summer steelhead.

Tests of population groups Differences were detected between the mainstem and tributary groups of collections for both the summary statistics and with the analysis of molecular variation. The increased variation found within the tributary group is consistent with the greater geographic separation of these collections. The neighbor-joining tree mirrored this difference between mainstem and tributary groups. We also detected differences in summary statistics between the upper and lower

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Deschutes mainstem groups, but not with the analysis of molecular variation. The neighbor- joining tree supported the detected differences. The primary ICR-TRT defined management groups are the Eastside and Westside Deschutes groups. These two groups each contain a mix of tributary and mainstem collections, and the Whychus Creek population above Pelton-Round Butte Dam collection has been included in the Westside Deschutes group. We detected no differences between these two groups with either the comparison of summary statistics or with the analysis of molecular variation, and collections within each group were found to be genetically distinct. In the neighbor-joining tree, the Westside Deschutes tributaries are separated from the Eastside Deschutes tributaries, but the cohesiveness of the groups is disrupted by the difference of the mainstem collections from the tributaries. The inclusion of Whychus Creek with the Westside Deschutes group is not supported by our analyses. In the neighbor-joining tree, Whychus Creek clusters with the lower Deschutes mainstem collections which are part of the Eastside Deschutes group. In the jackknife analysis, the majority of misassignments from Whychus Creek go to the lower Deschutes mainstem collection, in agreement with the clustering of these collections on the tree. These combined results do not support the Eastside – Westside Deschutes population groups as currently defined.

Population structure and genetic variability All 21 collections included in this report were found to be genetically distinct with very few non-significant tests of genetic difference. The greatest differences were found between the above and below Pelton-Round Butte Dam collections as would be expected since the above Pelton-Round Butte Dam collections represent resident redband trout. Although there were differences in temporal replicate collections, these differences were relatively small compared to differences between collection locations. In the case of Buck Hollow collections, the 2005 collection was of unknown origin and may have contained resident rainbow trout; additionally, the collection location for the 2005 samples was separated by 12 river kilometers from the 2006 collection. Very few tests of HWE and LD were statistically significant, and all collections had similarly high levels of genetic diversity. Population structure among Deschutes Basin steelhead based on the juvenile collections is driven primarily by differences between mainstem and tributary populations. Within the

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tributary populations, Shitike Creek and Warm Springs River (Westside tributaries) are more similar to each other than to the Eastside tributary collections. Similarly, the Eastside tributary collections are more similar to each other than to the Westside tributary collections. Round Butte Hatchery was most similar to Trout Creek, and specifically to the 2007 collection from Trout Creek. This 2007 Trout Creek collection appears to be genetically similar to many of the other collections, including the Warm Springs strays, and in the jackknife analysis there were many individuals that assigned to various other collections. It is possible that this collection is a mixture of individuals from many populations, although the collection did not show typical signs of this such as elevated levels of LD and departures from HWE. The inclusion of the adult Warm Springs collections provided an initial assessment of Warm Springs NORs and strays. The two collections of strays were most similar to each other. The 2006 collection of adult NOR steelhead from Warm Springs was most similar to the juvenile Warm Springs NOR steelhead. However, the 2007 collection of Warm Springs NOR adults was most similar to the strays. The detailed jackknife results given in Appendix 4 suggest that this collection is likely composed of individuals of both native Warm Springs origin and stray origin. Further analysis of collections of adults and juveniles will be required to obtain a more thorough understanding of the effects of unmarked stray hatchery and natural origin fish in the Warm Springs River, including the assessment of potential introgression between hatchery strays and NORs.

Acknowledgements We extend our appreciation and gratitude to the inter-agency field crew and personnel for their efforts in collecting genetic tissue samples used in these analyses (Oregon Department of Fish and Wildlife, Confederated Tribes of the Warm Springs Reservation of Oregon, NOAA Fisheries-Northwest Fisheries Science Center, and the Columbia River Inter-Tribal Fish Commission). Amanda Matala, Lindsay Godfrey, and Emily Williams of the Abernathy Fish Technology Center provided laboratory processing and microsatellite genotyping. Molly McGlauflin, Christian Smith, Patty Crandell, and Jeff Olsen provided comments on this report. The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the United States Fish and Wildlife Service.

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Figure 1. Deschutes River Basin, Oregon.

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Table 1. All population collections included in report.

Juvenile Smolts Adults Location (collection) 2005 2006 2007 2005 2006 2007 2005 2006 2007 Below Pelton-Round Butte Dam Bakeoven Creek 50,STH 50,STH ------Buck Hollow Creek 45,Unk 42,STH ------Deschutes River: ------Mainstem-Upper -- 38,STH 54,STH ------Mainstem-Lower 50,Unk 96,Unk ------Round Butte Hatchery ------50,STH ------Shitike Creek 30,STHa,b -- -- 39,STHb ------Trout Creek ------56,STH 50,STH ------Warm Springs River 9,STHc ------58,STHc -- -- 61,STH 25,STH Warm Springs R. (strays) ------57,STH 60,STH Above Pelton-Round Butte Dam -- Crane Prairie Reservior ------17, RedBd,e -- -- 34, RedBd,e -- Oak Springs Hatchery ------56, Omyd -- Tumalo Creek ------53, RedBd ------Whychus Creek ------47, RedBd ------a These juveniles are presumed to be steelhead; b These two collections were combined for analysis; c These two collections were combined for analysis; d Genetic data was collected on these fish as part of a separate, complementary sub-project; e These two collections were combined for analysis.

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Table 2. Population descriptive statistics for all 21 collections.

Population HWE LD A AR Ho He FIS Warm Springs strays 05 0 0 11.0 9.18 0.82 0.81 -0.01 Round Butte Hatchery 0 0 9.9 8.89 0.76 0.78 0.03 Shitike juveniles 1 1 12.1 9.59 0.75 0.79 0.04 Buck Hollow juveniles 05 0 2 11.6 10.07 0.80 0.79 -0.01 Mainstem Deschutes lower 05 0 0 10.2 8.43 0.69 0.71 0.03 Bakeoven juveniles 05 1 5 10.6 9.23 0.77 0.79 0.03 Warm Springs NOR adults 06 0 0 12.1 9.81 0.77 0.79 0.02 Warm Springs strays 06 1 0 10.8 9.29 0.77 0.80 0.04 Buck Hollow juveniles 06 1 0 11.3 9.77 0.78 0.80 0.02 Bakeoven juveniles 06 0 1 10.5 9.14 0.76 0.78 0.02 Mainstem Deschutes lower 06 0 0 10.9 8.11 0.70 0.70 0.01 Warm Springs NOR juveniles 1 0 12.4 10.09 0.79 0.79 0.00 Mainstem Deschutes upper 06 1 1 10.1 9.35 0.75 0.78 0.04 Trout Creek juveniles 06 1 0 11.8 9.71 0.77 0.80 0.03 Trout Creek juveniles 07 0 0 11.7 9.84 0.78 0.79 0.02 Warm Springs NOR adults 07 0 0 9.9 9.84 0.79 0.82 0.03 Mainstem Deschutes upper 07 0 5 10.8 9.25 0.77 0.79 0.02 Whychus Creek juveniles 0 1 9.2 7.85 0.70 0.69 -0.01 Crane Prairie Reservoir 0 0 11.1 9.52 0.78 0.81 0.03 Tumalo Creek juveniles 1 0 11.1 9.43 0.75 0.80 0.07 Oak Springs Hatchery adults 1 0 6.4 5.75 0.67 0.69 0.03

HWE: Number of loci statistically out of Hardy-Weinburg Equilibrium expectations after Bonferroni correction. LD: Number of pairs of loci out of 136 tests per population with significant linkage disequilibrium after Bonferroni correction. A: Average number of alleles for the 17 loci observed in this study. AR: Allelic richness based on a minimum sample size of 24 individuals.

Ho: Observed heterozygosity.

He: Expected heterozygosity.

FIS: index of inbreeding (Weir and Cockerham 1984)

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Table 3. Comparison of descriptive statistics between populations groups - juvenile collections only.

Deschutes R. Deschutes R. tributaries Mainstem Deschutes R. Mainstema vs. Tributariesb Eastsidec vs. Westsided Lowere vs. Upperf AR 9.7 < 10.7 (0.012*) 10.5 10.5 (0.973) 9.3 10.1 (0.255)

Ho 0.719 < 0.774 (0.004*) 0.762 0.767 (0.885) 0.693 < 0.762 (0.039*)

Hs 0.736 < 0.790 (0.005*) 0.780 0.787 (0.794) 0.706 < 0.784 (0.025*)

FIS 0.022 0.020 (0.844) 0.024 0.025 (0.864) 0.018 0.028 (0.534)

FST 0.020 0.010 (0.544) 0.018 0.013 (0.808) 0.002 0.008 (0.765) a Lower and upper mainstem of Deschutes River; b Bakeoven, Buck Hollow, Shitike, and Trout Creeks, and Warm Springs River; c All eastside tributaries below Pelton- Round Butte Dam complex including the mainstem from its mouth to the confluence of Trout Creek; d All westside tributaries below Pelton Dam including the mainstem above the confluence of Trout Creek; e From mouth of mainstem Deschutes River to below confluence of Trout Creek; f Mainstem Deschutes River above confluence of Trout Creek to below Pelton-Round Butte Dam.

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Table 4. Analysis of molecular variation (AMOVA) results by population groupings – juvenile collections only.

Percentage of Variation Within Groups Number of Among Among Within Population Groups Groups Populations Groups Populations Populations Mainstema vs. tributaryb populations 2 12 2.09** 1.26** 96.65** Eastsidec vs. westsided Deschutes River populations 2 12 -0.13 2.40** 97.73** Lower e vs. upperf mainstem Deschutes River 2 4 2.28 0.46** 97.26** a Lower and upper mainstem of Deschutes River; b Bakeoven, Buck Hollow, Shitike, and Trout Creeks, and Warm Springs River; c All eastside tributaries below Pelton- Round Butte Dam complex including the mainstem from its mouth to the confluence of Trout Creek; d All westside tributaries below Pelton Dam including the mainstem above the confluence of Trout Creek; e From mouth of mainstem Deschutes River to below confluence of Trout Creek; f Mainstem Deschutes River above confluence of Trout Creek to below Pelton-Round Butte Dam.

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Table 5. Population jackknife summary – all 21 collections.

Population N assigned Percent correct Largest Misassignment Percent assigned Warm Springs strays 05 49 34.70% Warm Springs strays 06 32.70% Round Butte Hatchery 41 56.10% Trout Creek juveniles 07 12.20% Shitike juveniles 67 41.80% Mainstem Deschutes lower 06 10.40% Buck Hollow juveniles 05 44 27.30% Buck Hollow juveniles 06 13.60% Mainstem Deschutes lower 05 50 28.00% Mainstem Deschutes lower 06 48.00% Bakeoven juveniles 05 50 58.00% Trout Creek juveniles 06 10.00% Warm Springs NOR adults 06 58 29.30% Trout Creek juveniles 07 12.10% Warm Springs strays 06 57 36.80% Warm Springs strays 05 19.30% Buck Hollow juveniles 06 39 23.10% Buck Hollow juveniles 05 15.40% Bakeoven juveniles 06 48 39.60% Bakeoven juveniles 05 10.40% Mainstem Deschutes lower 06 93 66.70% Mainstem Deschutes lower 05 8.60% Warm Springs NOR juveniles 65 38.50% Warm Springs NOR adults 06 12.30% Mainstem Deschutes upper 06 36 52.80% Mainstem Deschutes upper 07 16.70% Trout Creek juveniles 06 53 26.40% Trout Creek juveniles 07 18.90% Trout Creek juveniles 07 49 24.50% Buck Hollow juveniles 05 14.30% Warm Springs NOR adults 07 24 16.70% Warm Springs NOR adults 06 16.70% Mainstem Deschutes upper 07 51 37.30% Mainstem Deschutes upper 06 19.60% Whychus Creek juveniles 42 64.30% Mainstem Deschutes lower 06 16.70% Crane Prairie Reservoir 40 100.00% Tumalo Creek juveniles 52 98.10% Warm Springs NOR adults 06 1.90% Oak Springs Hatchery adults 54 100.00%

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Appendix 1. Description of field sampling efforts for collections of resident rainbow trout and steelhead in the Deschutes River basin below the Pelton-Round Butte Dam complex.

Eastside tributary sampling

In Bakeoven and Buck Hollow Creeks, electrofishing was used to collect samples in the fall of both 2005 and 2006. The Bakeoven Creek samples in 2005 (n=50, STH) and 2006 (n=50, STH) were collected from sample sites approximately 12 river kilometers (rkm) upstream from the confluence of the Deschutes River in a stretch of stream that ODFW biologists considered to be predominately inhabited by anadromous steelhead. In 2005, sample sites in Buck Hollow Creek were limited to the lower 200 meters of the creek due to landowner access issues. The 2005 samples (n=50, UNK) were of unknown origin and could potentially contain a mix of resident and anadromous samples. In 2006, samples (n=50, STH) were collected from sites approximately 19 rkm upstream from the confluence of the Deschutes River in a known steelhead spawning area. In 2006 and 2007, samples were collected in Trout Creek at a rotary screw trap, operated by ODFW, located near the mouth of the creek. Scale and fin tissue samples have been collected at the trap for several years as part of a long-term monitoring and evaluation program.

Westside tributary sampling

Due to concerns from NOAA-Fisheries and the CTWSRO, in-stream sample collection from Shitike Creek and the Warm Springs River was attempted using a combination of seining and dip-netting. In 2005, samples (n=30, presumed STH) were collected at rkm 7 of Shitike Creek in an area with both anadromous and resident forms. Samples (n=40, STH) were also collected at rkm 14 in a predominately anadromous spawning area. These 40 samples are classified as smolts in Table 1, but may be either smolts or pre-smolt steelhead. In the Warm Springs River, samples were collected from rkm 10 of Mill Creek (n=4, STH), a tributary to the Warm Springs River, and from the mainstem Warm Springs River at rkm 43 (n=5, STH) for a total of 9 STH samples in 2005. The low sample size was due to the lack of available juveniles in locations where only anadromous steelhead were located.

In the Warm Springs River, steelhead smolt samples (n=58, STH) were collected in 2006 from a trap located near the mouth of the river. Smolts were identified based on out-migration timing, appearance (smolt characteristics), and size. In addition, a collection (n=9, STH) of 2005 juvenile and a collection (n=19, STH) of 2006 adult Warm Springs River were evaluated. For comparison our analyses included samples of adult stray hatchery-origin steelhead sampled at Warm Springs National Fish Hatchery from 2005 and 2006 (n=57 and 102, respectively), and adult natural-origin steelhead (n=25) sampled in the Warm Springs River in 2007.

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Mainstem and Round Butte Hatchery sampling

In 2005, electrofishing was used to collect samples (n=50, Unk) from the lower mainstem Deschutes River to just below the confluence with Trout Creek. Both the lower and upper collections occurred during the fall and may have contained resident, anadromous, or a mix of both life history forms. Electrofishing was used again in the fall of 2006 to collect samples (n=100, Unk) from the mainstem Deschutes River below Trout Creek, between rkm 98 and rkm139. These samples likewise contained resident, anadromous, or a mix of life history forms. The Round Butte Hatchery collection contains samples (n=50, STH) from brood year 2005 steelhead collected from raceways.

In the mainstem Deschutes River (above Trout Creek) 2006 sampling effort, locations were targeted in which predominately anadromous forms were present. A drift boat was used to observe active spawning by adult anadromous steelhead during the springtime and GPS locations were recorded for steelhead redd locations. In early June, field crews returned to the steelhead redd locations and used dip-netting techniques to capture newly emergent fry. Based on the location, timing, and size of the fish collected, field crews were reasonably confident that these samples (n=38, STH) were made up of primarily anadromous origin juveniles. Similar sampling (n=54, STH) was carried out in 2007.

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Appendix 2. Microsatellite loci used in this study. Bold loci are part of the SPAN suite of loci.

Annealing [MgCl2] Number o Locus Reference Temp. ( C) (mM) of Alleles Ssa407 Cairney et al. 2000 60 2.0 23 Omy1001UW Spies et al. 2005 50 1.5 28 Oke4 Buchholz et al. 2001 54 2.0 24 Ots3 Banks et al. 1999 48 2.0 11 Ogo4 Olsen et al. 1998 59 1.5 14 Omy1011UW Spies et al. 2005 59 2.0 23 Omy7iNRA K. Gharbi, and R. Guyomard, INRAa, France 59 2.0 17 Ssa289 McConnell et al.1995 50 2.0 11 Oneμ14 Scribner et al. 1996 60 2.0 14 Ots100 Banks et al. 1999 57 2.0 24 Ots4 Banks et al. 1999 53 2.0 8 Ocl1 Condrey & Bentzen 1998 59 1.5 19 Oki23 Smith et al. 1998 59 2.0 23 Omy77 Morris et al. 1996 59 2.0 21 Ssa408 Cairney et al. 2000 59 2.0 26 Ogo3 Olsen et al. 1998 59 2.0 10 Ots1 Banks et al. 1999 59 2.0 23 a French Institute for Agricultural Research (INRA)

Page 31
Appendix 3. Population allele frequencies – all 21 collections.

0 s 0 0 e t 0 0 0 r l l 5 5 6 6 s 6 s 7 7 s i r r r e t u 0 t e 6 n e l e l s d 0 w e p 7 u p 5 s u 6 e s a w r 6 o v p 0 d p 0 e d 0 y s l il i e l o 6 r 5 0 u u a u l i l a e s j s n o i ry l 0 s s e 0 n s s e s y s i e e e v n e h s l R e R t e e r a e s y n R i v e h c e t il t r t e t v e a e u O v c s O l n u t l r i O u n u s t u u h j s a e i t v e u j e N e a l N n h h j h s c N i n u v k s H e c v c c j s s R e s e H n s s s u u s k g w s v e j e j g v g e e e e t e e g g s n o w u D r ie e i t v l u n j k n n k in r g r l j i o D D r u D i i e r C i u r l e n o r r p j l n e i n m e p a C B p s p e p m r m r r S m o e r H e S e S u S v t S e e P p d e C # v H t C t lo k t s h i k o S e m n s s a s s o t m e l t c m e n t c r a m k m u u i e i n r n e n r u u y n k e a u r c k r i i m o i a a c l z h k a a a l a a a a o a h i M u ro r u o S B a r W R S M O A B B T W T L B W W W M T M W C Ocl1 1 150 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.02830.0000 2 154 0.0000 0.0000 0.0072 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0149 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 3 176 0.0000 0.0100 0.0072 0.0000 0.0000 0.0000 0.0000 0.0083 0.0000 0.0000 0.0053 0.0075 0.0132 0.0091 0.0100 0.0200 0.0093 0.0000 0.0000 0.0094 0.0000 4 184 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0246 0.0000 0.0000 0.0000 0.0000 0.0075 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 5 188 0.0089 0.0000 0.0000 0.0111 0.0000 0.0000 0.0082 0.0333 0.0119 0.0000 0.0000 0.0000 0.0000 0.0091 0.0100 0.0000 0.0000 0.0000 0.0000 0.0943 0.0000 6 192 0.0268 0.0200 0.0145 0.0111 0.0000 0.0400 0.0246 0.0083 0.0119 0.0102 0.0474 0.0522 0.0395 0.0273 0.0500 0.0400 0.0648 0.0000 0.2059 0.0377 0.5625 7 194 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0091 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 8 196 0.1250 0.0200 0.0652 0.1333 0.0300 0.0400 0.1148 0.0583 0.1071 0.0510 0.0263 0.0299 0.2105 0.1455 0.0600 0.1000 0.1296 0.0319 0.0686 0.1038 0.0179 9 198 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 10 200 0.1786 0.1800 0.2971 0.2556 0.4200 0.1600 0.1066 0.1583 0.1310 0.2755 0.3526 0.2239 0.2895 0.1455 0.1500 0.1400 0.3426 0.3404 0.0784 0.1132 0.0000 11 202 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0098 0.0000 0.1429 12 204 0.3750 0.3800 0.2754 0.3222 0.2600 0.3300 0.4508 0.3917 0.4762 0.3878 0.2474 0.3731 0.2500 0.3364 0.3800 0.3400 0.2778 0.1596 0.5196 0.3585 0.1339 13 208 0.0446 0.1600 0.0725 0.0222 0.1900 0.0500 0.0574 0.0417 0.0238 0.0408 0.2000 0.0896 0.1184 0.1364 0.1000 0.1200 0.1111 0.3617 0.0098 0.0566 0.1429 14 212 0.0804 0.0600 0.0797 0.0444 0.0500 0.0600 0.0738 0.1000 0.0238 0.0612 0.0474 0.0746 0.0395 0.0727 0.1100 0.1000 0.0370 0.0745 0.0490 0.1132 0.0000 15 216 0.0000 0.0500 0.0072 0.0000 0.0000 0.0700 0.0082 0.0083 0.0595 0.0102 0.0053 0.0075 0.0132 0.0091 0.0100 0.0400 0.0185 0.0000 0.0294 0.0660 0.0000 16 220 0.0268 0.0300 0.0217 0.0222 0.0300 0.0600 0.0246 0.0167 0.0238 0.0408 0.0158 0.0373 0.0263 0.0364 0.0300 0.0000 0.0000 0.0319 0.0000 0.0094 0.0000 17 224 0.0625 0.0700 0.0942 0.1444 0.0100 0.1700 0.0820 0.1083 0.0952 0.1122 0.0316 0.0373 0.0000 0.0455 0.0700 0.0800 0.0000 0.0000 0.0000 0.0094 0.0000 18 228 0.0446 0.0200 0.0290 0.0222 0.0100 0.0200 0.0246 0.0250 0.0357 0.0102 0.0211 0.0448 0.0000 0.0182 0.0100 0.0000 0.0093 0.0000 0.0294 0.0000 0.0000 19 230 0.0268 0.0000 0.0290 0.0111 0.0000 0.0000 0.0000 0.0417 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # samples:565069455050616042499567385550255447515356

Page 32

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s s 0 t 0 0 5 r e 0 l

0 l r s 0 s e i r u r t t e 5 6 6 6 6 l 7 7 l n e d s e w p s 5 0 e 7 u u p s a e o 6 e p r 0 y l w l v 0 d l d 6 p e r i s 6 0 i y u a i l o u s 5 a 0 e s u i r e n l 0 j s o l s n s e y 0 e e n h e s i s e v s s e l R R t e r a c l e e h v e s y n e R t i v r t s u i t e c t l O v t u e a e n O i u u s t a e j l r h O n u s u j u l i v e a t n c h e N e j i N h H h s u N v s n e s c k j v s c H n w c R e s e s u k g s v s s e e e s u j g o e e t v g j e e s n l g u g e t v e w D n i l r i e u n j k g n n D i r r u u i o k r o j r D i D i l i e C n j r e p r n m r i B l e p a C H n p e r e e m s r S e p o p r m m r S e t e o p d S v u k S S e P # k e s t C l i v H C t S n t o h m t c s a e a n t m s e s i s o e l r u m i t c u m k m n r k u e e r u n n e a o h n k a i u y m M r c r a i a l z i a c B k a a a o l i S a a o h u u r a r R a o W M r O S B W T A W B M T C L B W W T M W Ogo4 1 115 0.0877 0.2041 0.2609 0.2889 0.3400 0.1400 0.2750 0.0750 0.1429 0.2200 0.3474 0.2761 0.3026 0.2636 0.1300 0.1600 0.3426 0.4681 0.2059 0.37740.2411 2 117 0.0263 0.0816 0.0145 0.0444 0.0000 0.0400 0.0250 0.0083 0.0238 0.0200 0.0421 0.0597 0.0395 0.0182 0.0400 0.0000 0.0093 0.0000 0.0588 0.1132 0.0446 3 119 0.0439 0.0204 0.0580 0.1000 0.0200 0.0400 0.0000 0.0417 0.0238 0.0000 0.0053 0.0075 0.0000 0.0182 0.0200 0.0600 0.0093 0.0106 0.0000 0.0283 0.0000 4 121 0.0088 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0075 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 5 123 0.0000 0.0000 0.0072 0.0333 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0566 0.0000 6 125 0.0175 0.0000 0.0145 0.0111 0.0100 0.0000 0.0083 0.0000 0.0238 0.0000 0.0000 0.0149 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 7 127 0.0614 0.1122 0.0072 0.1000 0.0000 0.0300 0.0750 0.1417 0.1310 0.0200 0.0000 0.0597 0.0395 0.0273 0.0800 0.0600 0.0278 0.0106 0.0588 0.0094 0.0446 8 129 0.2895 0.2755 0.3261 0.2222 0.4200 0.3200 0.2333 0.2750 0.2738 0.3400 0.4684 0.2836 0.3158 0.3000 0.4200 0.2800 0.3241 0.3404 0.3725 0.2264 0.1429 9 131 0.2018 0.1020 0.0652 0.0667 0.1300 0.2000 0.1500 0.1500 0.1548 0.0900 0.0842 0.1194 0.2368 0.1545 0.0900 0.2000 0.1296 0.0638 0.1863 0.0189 0.4554 10 133 0.0965 0.0918 0.1087 0.0111 0.0100 0.0100 0.0750 0.1083 0.0833 0.1300 0.0053 0.0373 0.0132 0.0909 0.0800 0.0800 0.0185 0.0106 0.1176 0.1698 0.0714 11 135 0.1404 0.1122 0.1159 0.1111 0.0700 0.1700 0.1167 0.1750 0.1429 0.1800 0.0316 0.1045 0.0395 0.1182 0.1300 0.1400 0.1111 0.0638 0.0000 0.0000 0.0000 12 137 0.0263 0.0000 0.0145 0.0111 0.0000 0.0000 0.0000 0.0250 0.0000 0.0000 0.0158 0.0149 0.0132 0.0091 0.0100 0.0200 0.0278 0.0319 0.0000 0.0000 0.0000 13 139 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0417 0.0000 0.0000 0.0000 0.0000 0.0149 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 14 145 0.0000 0.0000 0.0072 0.0000 0.0000 0.0500 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # samples:574969455050606042509567385550255447515356

Page 33

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

7 6 0 s s 0 t 5 0 0 e r l

0 0 l s r e 6 0 u s i t

r t e l s p d l 0 r n e 5 e p u p s a 5 e 6 e 6 7 7 s l u 6 y s 6 e 0 p d u r r i w v 0 l e d 0 e i y w 0 l l u a i s e n i r o 5 a u s i s o l s o j n e s e e y h l s n 0 e v y n 6 R t e e l h a c v s R e r e e s l i r t s s a 0 R t u v u e i e c t r O v a e j t e v e n t O t u h u s s s t n l l O j u u e a i u i s h N c e j j e e H N u s v s n w h n l N c s s k H i h v R g s s e k e e o c e u s e t g w n c u j g l s e e s n g j e t v l v s e n e g n D i e o i e n r g u u i l e k i r u o D r r i n v n k j j r l r i n i e p D r e C i B u e m H p o D r p C e a r e p j S n v m e e r p r s S S t p d k e H r o k m S o e i m s u P # S t C l n c e S m t a v e C k e s n h a e i t m m r u u t e s l o m k t i s c n t c k h r r e a o M s m u n u e r a i a m e B u y a z n a u r a l S a c i k a n a o u l i R B i a o r h r W o a B r M O S W a W T A W M T C L B W T W

M Omy7i 1 234 0.0702 0.0000 0.0507 0.0444 0.0200 0.0500 0.0667 0.0417 0.0119 0.0500 0.0052 0.0746 0.0000 0.0370 0.0100 0.0600 0.0000 0.0000 0.0392 0.0755 0.1875 2 238 0.0000 0.0400 0.0000 0.0000 0.0000 0.0000 0.0250 0.0000 0.0000 0.0000 0.0000 0.0149 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0196 0.0283 0.0000 3 242 0.0175 0.0200 0.0000 0.0222 0.0000 0.0100 0.0167 0.0333 0.0000 0.0000 0.0000 0.0075 0.0000 0.0093 0.0000 0.0000 0.0000 0.0000 0.0098 0.0000 0.0000 4 244 0.0000 0.0200 0.0725 0.0444 0.2200 0.0400 0.0917 0.0000 0.0476 0.0300 0.1354 0.0522 0.0658 0.0185 0.0300 0.0600 0.1204 0.2222 0.0000 0.0000 0.0000 5 246 0.0789 0.0300 0.1014 0.0667 0.0000 0.0400 0.0833 0.0417 0.0119 0.0800 0.0208 0.0299 0.1053 0.0278 0.0400 0.0400 0.0556 0.0222 0.0196 0.0849 0.1071 6 248 0.1491 0.1000 0.0725 0.1111 0.0400 0.1400 0.1417 0.1333 0.0476 0.0500 0.0312 0.0672 0.1579 0.1667 0.1100 0.2000 0.1574 0.0444 0.3627 0.1415 0.0982 7 250 0.1228 0.2600 0.1377 0.2333 0.1200 0.1900 0.1500 0.1167 0.1548 0.2200 0.1042 0.0970 0.1974 0.1759 0.2100 0.1000 0.1667 0.0333 0.1667 0.1415 0.4554 8 252 0.1228 0.1700 0.0507 0.1000 0.1000 0.1800 0.0250 0.1583 0.3214 0.2000 0.0990 0.0970 0.1184 0.1667 0.1200 0.0800 0.0833 0.1778 0.0196 0.0660 0.0000 9 254 0.2368 0.1800 0.2899 0.2111 0.0600 0.1800 0.2167 0.2917 0.2024 0.2200 0.1250 0.2687 0.1842 0.2500 0.2600 0.2800 0.1944 0.1556 0.0000 0.1509 0.0000 10 256 0.0789 0.1200 0.0580 0.0444 0.1500 0.0400 0.0917 0.0250 0.0238 0.0300 0.1927 0.1194 0.0526 0.0278 0.0900 0.0400 0.0833 0.0556 0.3333 0.2264 0.0000 11 258 0.0702 0.0100 0.1014 0.0222 0.0000 0.0300 0.0083 0.0667 0.0119 0.0300 0.0260 0.0075 0.0132 0.0463 0.0700 0.0800 0.0370 0.0444 0.0000 0.0000 0.0000 12 260 0.0000 0.0000 0.0072 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0149 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 13 262 0.0263 0.0500 0.0507 0.1000 0.2700 0.0800 0.0500 0.0917 0.1667 0.0900 0.2292 0.1269 0.1053 0.0648 0.0300 0.0600 0.1019 0.2444 0.0098 0.0566 0.0179 14 264 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0189 0.0000 15 266 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0094 0.0000 16 268 0.0263 0.0000 0.0072 0.0000 0.0200 0.0000 0.0250 0.0000 0.0000 0.0000 0.0312 0.0075 0.0000 0.0093 0.0300 0.0000 0.0000 0.0000 0.0196 0.0000 0.1339 17 272 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0083 0.0000 0.0000 0.0000 0.0000 0.0149 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # samples:575069455050606042509667385450255445515356

Page 34

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s 0 t 0 e 0 0 0 r l 5 l s 5 s e 6 si 6r 7r r 6 t 7 u 0 t 6 n e l e e l d w s s 0 e p 7 u p 5 u s a 6 e e w o r 6 v p 0 d p l 0 y l d l 0 e s 6 i i r o l y i 5 0 u u a u l a e i r s 0 s j s n o e l s n 0 s e s e s n e y s i e e v h e s l R R t r a e l e e h c e s y n R i v v e t i t r t u e t s e a e l O v c t O n u u l r i O u n u s t a u h j s e j i v e u t e N e a l N n c h h j i h s N n u v k s H e s c v c c j s R s H n w e u e k g s v e s s u s e s j g e j e t o v g e e e e s n e g u g l w n t v D r i e i u n j k g l n n k i r r j i o D D r u D i i i u l e r C o r e n p j r n r l m e a C i B n e p p e s r H p e p m r m r S e m o r e S S t u o p d S v S e e P k e C # k v H s t C t l t h n i o S e m a s t c o n s t m s e l a s e t c r u i m m k i m r u e u e r n u n n k e n k u y m a o h r c a r i i l i a a c z M k a o l i B a a a a o a h u S u r ra o R a r W M O S B W T A W B T C L B W W M T M W Ots1 1 156 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0083 0.0122 0.0000 0.0000 0.0075 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0294 0.13210.0000 2 160 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0053 0.0000 0.0921 0.0000 0.0000 0.0000 0.0377 0.0000 0.0000 0.0000 0.0000 3 162 0.0526 0.1224 0.0870 0.0341 0.0600 0.0700 0.0246 0.0417 0.0366 0.0521 0.0579 0.0000 0.2237 0.0182 0.0400 0.0208 0.1226 0.0532 0.1373 0.1509 0.0625 4 164 0.1842 0.2347 0.1812 0.1250 0.2200 0.2200 0.2869 0.1250 0.1463 0.1562 0.2737 0.3209 0.1842 0.1636 0.2100 0.1667 0.1604 0.1489 0.1471 0.3019 0.1161 5 166 0.2368 0.1939 0.1304 0.2159 0.1800 0.1900 0.1393 0.1250 0.1829 0.1667 0.2105 0.2164 0.0132 0.2273 0.2600 0.0417 0.1509 0.3191 0.0882 0.0283 0.2946 6 168 0.0263 0.0102 0.0145 0.0682 0.0500 0.0000 0.0246 0.0667 0.0000 0.0104 0.0053 0.0075 0.0263 0.0273 0.0300 0.0417 0.0000 0.0000 0.2157 0.0283 0.3750 7 169 0.1491 0.0714 0.1232 0.1250 0.0400 0.0800 0.0984 0.1333 0.1341 0.1250 0.0105 0.0746 0.0658 0.1727 0.1000 0.2292 0.0660 0.0213 0.0588 0.0943 0.0000 8 170 0.0088 0.0102 0.0000 0.0000 0.0000 0.0000 0.0164 0.0083 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0106 0.0784 0.0000 0.0000 9 172 0.0000 0.0306 0.0000 0.0114 0.0000 0.0000 0.0082 0.0083 0.0244 0.0000 0.0000 0.0000 0.0263 0.0091 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 10 174 0.0351 0.0816 0.1304 0.0455 0.2000 0.0400 0.0984 0.0333 0.0976 0.1146 0.2526 0.1269 0.1184 0.0545 0.0400 0.1042 0.0660 0.2128 0.0000 0.0000 0.0000 11 176 0.0000 0.0102 0.0072 0.0000 0.0000 0.0000 0.0082 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0490 0.0000 0.1339 12 180 0.0000 0.0306 0.0507 0.0341 0.0600 0.0000 0.0082 0.0000 0.0122 0.0000 0.0474 0.0149 0.0000 0.0000 0.0100 0.0000 0.0660 0.0638 0.0000 0.0000 0.0000 13 182 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0082 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 14 188 0.0000 0.0000 0.0000 0.0114 0.0100 0.0000 0.0246 0.0000 0.0244 0.0000 0.0000 0.0000 0.0000 0.0091 0.0200 0.0000 0.0094 0.0000 0.0000 0.0000 0.0000 15 190 0.0000 0.0000 0.0000 0.0114 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 16 230 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0377 0.0000 17 234 0.0175 0.0000 0.0362 0.0341 0.0000 0.0300 0.0082 0.0083 0.0000 0.0208 0.0053 0.0000 0.0000 0.0273 0.0100 0.0417 0.0094 0.0000 0.0000 0.0000 0.0089 18 236 0.0088 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0417 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0098 0.0000 0.0000 19 238 0.0526 0.0000 0.0072 0.0227 0.0000 0.0000 0.0082 0.0417 0.0244 0.0000 0.0053 0.0149 0.0789 0.0182 0.0300 0.0000 0.0094 0.0426 0.0000 0.0000 0.0000 20 242 0.2281 0.2041 0.2246 0.2500 0.1400 0.3700 0.2377 0.3583 0.3049 0.3125 0.1211 0.2015 0.0526 0.2636 0.2300 0.3542 0.2830 0.1277 0.0294 0.1981 0.0000 21 244 0.0000 0.0000 0.0072 0.0114 0.0300 0.0000 0.0000 0.0000 0.0000 0.0312 0.0053 0.0075 0.1184 0.0000 0.0000 0.0000 0.0094 0.0000 0.1569 0.0283 0.0000 22 246 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0075 0.0000 0.0091 0.0000 0.0000 0.0094 0.0000 0.0000 0.0000 0.0000 23 248 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0104 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0089 # samples:574969445050616041489567385550245347515356

Page 35

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s 0 0 t e 0 0 0 r l 5 l s 5 s 6 e 6 is r6 7 r7 r t u 0 t 6 n e l e e l d w s s 0 e p 7 u p 5 u 6 s a e w o r e 6 v p 0 d p 0 y d l 0 e l s 6 il i r o l i 5 0 u u a u l a e i s 0 s j s n o ry e l s n 0 s s e s n e y s i e e e v h e s l R R t l e r a e s y n R i v e h c e i r v t u te t e t s e a e l O v c O n u t l r i O u n u s t a u u h j s e i v e u j t e e l n N j a h N c h h i n s u N v H v k s j e s c c c s R H n e s u e k w s e s s u s g s v j e j g e v g e e e e e t o e g g s n w u l D n r i e i t v u n j k l n n k i r g j i o D D r r D i i i u u l e r C o r e n j r n r p l m e a C i B n e p p s r p e p r r S H m o e m m e e r S S t u o p S v S e e P d e C # k v H s t C t l k t h n i o S e m s s a s t c s o n t m e l a m e t c r u i m k i m u e n u r n n k e u n r u y e a r c k r m o h i a i a i c l z k a o a a M a a a o h l i B u a a r u S a r o R r W M O S B W T A W B T C L B W W M T M W Ots100 1 166 0.1273 0.1100 0.0809 0.1444 0.1600 0.1700 0.1083 0.1083 0.1429 0.0500 0.2396 0.1194 0.0946 0.1204 0.0800 0.0400 0.1204 0.4444 0.0588 0.0755 0.0000 2 170 0.2091 0.2000 0.1544 0.1444 0.1100 0.0800 0.1750 0.1583 0.1667 0.1300 0.1302 0.0821 0.0541 0.1019 0.1100 0.2200 0.1389 0.0889 0.2843 0.1887 0.0000 3 172 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0149 0.0000 0.0093 0.0000 0.0000 0.0000 0.0000 0.0000 0.0094 0.0000 4 174 0.0545 0.0300 0.1176 0.0444 0.0600 0.0700 0.0917 0.0417 0.0476 0.0400 0.0208 0.0597 0.0135 0.0093 0.0200 0.1000 0.0926 0.0333 0.0588 0.1132 0.0000 5 178 0.3545 0.2300 0.1618 0.2222 0.0500 0.2100 0.1583 0.3500 0.2024 0.1400 0.0885 0.2015 0.0405 0.3148 0.3000 0.2600 0.0463 0.0889 0.1569 0.0000 0.0982 6 180 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0167 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0093 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 7 182 0.1273 0.0700 0.0882 0.0778 0.0800 0.1200 0.1250 0.2083 0.0952 0.1700 0.0885 0.1119 0.1757 0.0926 0.1300 0.1400 0.0833 0.0222 0.0098 0.0377 0.0000 8 184 0.0091 0.0300 0.0368 0.0333 0.0300 0.0300 0.0833 0.0500 0.0119 0.0500 0.0625 0.0522 0.0811 0.0741 0.0700 0.0400 0.0833 0.0333 0.0490 0.0377 0.1518 9 186 0.0091 0.0600 0.0147 0.0556 0.0100 0.0100 0.0583 0.0167 0.0357 0.0800 0.0000 0.0299 0.0000 0.0556 0.0100 0.0200 0.0000 0.0000 0.0000 0.1415 0.0000 10 188 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0224 0.0000 0.0000 0.0000 0.0000 0.0093 0.0000 0.0000 0.0000 0.0000 11 190 0.0091 0.0900 0.0000 0.0444 0.0100 0.0400 0.0083 0.0333 0.0476 0.0800 0.0104 0.0299 0.0135 0.0278 0.0200 0.0200 0.0093 0.0000 0.0490 0.0472 0.0000 12 192 0.0000 0.0000 0.0000 0.0111 0.0100 0.0100 0.0083 0.0000 0.0119 0.0200 0.0000 0.0075 0.0405 0.0000 0.0000 0.0000 0.0093 0.0000 0.0098 0.0000 0.0000 13 194 0.0273 0.1500 0.2574 0.1556 0.3900 0.1400 0.0750 0.0000 0.1548 0.1200 0.3177 0.1493 0.2432 0.0833 0.1600 0.1400 0.2593 0.2333 0.0294 0.1132 0.0000 14 196 0.0000 0.0000 0.0074 0.0000 0.0200 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0270 0.0000 0.0000 0.0000 0.0370 0.0111 0.0196 0.0189 0.0714 15 198 0.0364 0.0000 0.0441 0.0333 0.0100 0.0400 0.0083 0.0250 0.0119 0.0800 0.0208 0.0522 0.0405 0.0463 0.0600 0.0000 0.0370 0.0333 0.0000 0.0566 0.0000 16 200 0.0091 0.0300 0.0074 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0104 0.0000 0.0270 0.0000 0.0200 0.0000 0.0000 0.0000 0.0980 0.0849 0.4196 17 202 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0583 0.0083 0.0000 0.0000 0.0000 0.0597 0.0000 0.0185 0.0000 0.0200 0.0000 0.0111 0.0098 0.0000 0.0536 18 204 0.0000 0.0000 0.0074 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0196 0.0000 0.0000 19 206 0.0000 0.0000 0.0221 0.0222 0.0100 0.0400 0.0167 0.0000 0.0119 0.0000 0.0000 0.0000 0.0000 0.0278 0.0100 0.0000 0.0185 0.0000 0.0000 0.0660 0.0000 20 209 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0093 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 21 210 0.0273 0.0000 0.0000 0.0000 0.0000 0.0000 0.0083 0.0000 0.0238 0.0000 0.0000 0.0075 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 22 212 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0238 0.0200 0.0000 0.0000 0.0541 0.0000 0.0000 0.0000 0.0000 0.0000 0.1078 0.0000 0.1875 23 216 0.0000 0.0000 0.0000 0.0000 0.0400 0.0000 0.0000 0.0000 0.0000 0.0000 0.0104 0.0000 0.0946 0.0000 0.0000 0.0000 0.0556 0.0000 0.0392 0.0094 0.0179 24 220 0.0000 0.0000 0.0000 0.0111 0.0000 0.0000 0.0000 0.0000 0.0119 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # samples:555068455050606042509667375450255445515356

Page 36

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s s 0 t 5 0 0 r e 0 l

l s 0 0 e r s i u t r t e l r 6 n e d s 5 l w 6 6 7 6 p 7 s 5 e 0 e 7 u a e u p s o 6 y l e 0 l p d r 6 v 0 p l e r i w d s 6 0 i y i l u a s 5 a 0 u u i r e n o e 0 s s o j n l l s e y e 0 e s n h s i e s v s e R e t e l a c R r h v s l e e s y n e R t i v r t s u i e t e c t u e a e l v e O u n u t a j t i h n s s l r u j l v e u i NO i u t n c h e j N H h s n s u s NO c v w h e v k n j s c Re Ha g e s e s u k e e c s v s s e o u j g t e e s n l s v g j e e t v g u g e l w D n e i r i g e u n j k r n n D i r u u i o k r j r D j i i e i n r l C p D n m e i B r l r p C Ho e a r s n p e S e e e m s r p o p r m r S d n e t e o p k k m S v u i e P # i S s S t C l v H S n c e o C t m t a s h e n a t t m s e s r u i o e l m i t c m k m n r k e u n u a h e r k n m e M a i u y r c r a i a l z Bu a c S k a a o l i a a o h u Ro r a o W M r O S Ba W T A W Bu M T Cr L Ba W W T M W Ots3 1 67 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0089 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 2 69 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.1275 0.0000 0.0000 3 71 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0588 0.0000 0.0000 4 73 0.0000 0.0000 0.0217 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0098 0.0000 0.0000 5 75 0.0702 0.0400 0.0217 0.0444 0.0000 0.0500 0.0164 0.0917 0.0238 0.0300 0.0158 0.0152 0.0526 0.0714 0.0200 0.0200 0.0185 0.0106 0.2451 0.1792 0.2232 6 77 0.3772 0.3800 0.4638 0.5333 0.7100 0.4000 0.5164 0.2750 0.3929 0.4900 0.5684 0.4697 0.3684 0.4554 0.4200 0.3200 0.4167 0.5532 0.3333 0.5377 0.2589 7 79 0.3509 0.4200 0.4275 0.2556 0.2800 0.3300 0.3361 0.3500 0.3214 0.3700 0.3526 0.3409 0.5132 0.2500 0.3800 0.4400 0.5000 0.3085 0.1471 0.0943 0.5179 8 81 0.1228 0.0500 0.0580 0.0000 0.0000 0.0200 0.0738 0.1500 0.0714 0.0100 0.0368 0.0909 0.0000 0.0536 0.0600 0.1200 0.0000 0.1064 0.0196 0.0566 0.0000 9 83 0.0614 0.1100 0.0072 0.1556 0.0100 0.1900 0.0492 0.1250 0.1786 0.1000 0.0263 0.0606 0.0658 0.1607 0.1000 0.0800 0.0648 0.0213 0.0588 0.1321 0.0000 10 85 0.0000 0.0000 0.0000 0.0111 0.0000 0.0100 0.0082 0.0083 0.0119 0.0000 0.0000 0.0076 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 11 87 0.0175 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0152 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # samples:575069455050616042509566385650255447515356

Page 37

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s 0 e 0 0 0 5 6 s 6 7 6 l 7 lt 0 5 s i s er t t u 6 er er 0 l l

er 0 w en p 7 p u 6 u 5 es s ad r 6 o v p 0 p w 0 e 0 y es 6 l il i l u l 5 ad 0 u ad u y o es j o i s i 0 n es l 0 l er s s t i es es e v n er es l R es R e t R v ay en u n il i e ch es t t r es ay er v e l u n O u v ch s h O n t l r i O u u j t i v h e s e u c t e es u h N h a j N s c N j l u v k c v c s Hat i j en R en s s H s s u u g n w v j v g j g ee e Des g g e ek t e u s n o w n r n Des k e i t l n j n ri v ju i o Des i Des g r l i i i r l r C u u m r r r n p o l ee a C j e p m eek p B p p s r o en m r m ri S t en e r H S S u e s S v t S e e P o p C d v H t C t k s k n S s e# m n i o s t s e l m t m ch t c m k eo m u e u i ai u u y n e c mal c ar u l ze o h ar o ar a ak l ar ak ar o h i ak u r r u o B M r R S S W B Main W T O L A B W W B W Main T T Main W C Ots4 1 105 0.1579 0.1327 0.1765 0.0778 0.0800 0.0500 0.1066 0.1186 0.1429 0.1000 0.0789 0.1343 0.2237 0.1727 0.1000 0.1000 0.1296 0.1702 0.5000 0.3302 0.2857 2 113 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 3 117 0.1754 0.1224 0.0662 0.1889 0.0700 0.1500 0.1721 0.1356 0.2024 0.1800 0.0211 0.1194 0.1579 0.1364 0.1400 0.2000 0.1574 0.0106 0.1569 0.0189 0.5625 4 119 0.0789 0.1837 0.0882 0.0667 0.0500 0.1600 0.0246 0.0847 0.0357 0.1400 0.0789 0.0746 0.0789 0.0636 0.0700 0.0800 0.1204 0.0319 0.0196 0.1321 0.0536 5 121 0.0088 0.0306 0.0147 0.0111 0.0200 0.0500 0.0246 0.0508 0.0119 0.0500 0.0158 0.0224 0.0789 0.0182 0.0100 0.0400 0.0463 0.0532 0.0588 0.0377 0.0000 6 123 0.3421 0.3980 0.5294 0.5444 0.7200 0.2400 0.4836 0.4068 0.4167 0.3000 0.7263 0.4627 0.4342 0.4273 0.5100 0.2200 0.5000 0.6064 0.0490 0.2547 0.0982 7 125 0.2281 0.1224 0.1176 0.1111 0.0600 0.3400 0.1803 0.1864 0.1905 0.2200 0.0737 0.1716 0.0132 0.1727 0.1500 0.3400 0.0463 0.1277 0.2059 0.2170 0.0000 8 127 0.0088 0.0102 0.0074 0.0000 0.0000 0.0100 0.0082 0.0169 0.0000 0.0100 0.0053 0.0149 0.0132 0.0091 0.0100 0.0200 0.0000 0.0000 0.0098 0.0094 0.0000 # samples:574968455050615942509567385550255447515356

0 s 0 e 0 0 0 t 5 6 6 ls 6 7 7 er l 5 0 s i s t t u 6 n er er 0 w l l wer e p p o 0 6 7 u 5 s u es s ad l r 6 o v p 0 p l 0 e 0 y e s 6 l i i l u l 5 ad 0 u ad u y e j o i s i 0 n es 0 l er s s t i es es e v n er es l h t es l e en u n i v e h ay es t i t c ay er r e u u c v OR l n n OR v t les r i OR u u j i v e s es u ch t e es u j N N j at l s s ch N u v v k s i j en s ch ch Hat e en s R s s s s u s e H e u g w v j j v g e g e e e D g g e t en u s n o w n r i u n D k eek i t n j n r v j i o D D g r ll i i C i r l ek e ri u u r r r n l p j o e e a C i em p p s B p en p r r r S t en o em r H S S u e s S v t S em em P o p C # d v H t C t k s h n S s e m n i o s t s e al n t m c l t m m eo m ck e n n u i ai u u y k e ck k m cu ar u k ai l ze o h ar o ar an a l ar a ar ai o ai h i a u r r u o B M r R S S W B M W T O L A B W W B W M T T M W C Ogo3 1 77 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0132 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 2 79 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0167 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 3 81 0.0000 0.0300 0.0290 0.0111 0.0100 0.0200 0.0082 0.0083 0.0119 0.0100 0.0052 0.0299 0.0132 0.0000 0.0000 0.0600 0.0000 0.1196 0.3039 0.2547 0.0000 4 83 0.2456 0.3100 0.1884 0.3000 0.1300 0.2000 0.2131 0.1750 0.2143 0.2600 0.1458 0.2463 0.1316 0.2321 0.3000 0.2600 0.1481 0.1522 0.0686 0.3396 0.1250 5 85 0.0000 0.0100 0.0217 0.0000 0.0100 0.0000 0.0082 0.0000 0.0238 0.0000 0.0104 0.0149 0.0658 0.0000 0.0100 0.0000 0.0000 0.0326 0.0000 0.0000 0.0089 6 87 0.3158 0.2400 0.3406 0.4444 0.1500 0.3100 0.2377 0.3167 0.2381 0.2500 0.1146 0.2388 0.1842 0.3661 0.2800 0.2400 0.1852 0.0326 0.3039 0.2264 0.2143 7 89 0.0088 0.0300 0.0507 0.0333 0.2500 0.0600 0.0410 0.0417 0.0595 0.0600 0.1562 0.0299 0.1053 0.0536 0.0200 0.0600 0.2407 0.1739 0.1765 0.0849 0.3571 8 91 0.4035 0.3800 0.3406 0.2111 0.3500 0.3500 0.3770 0.4167 0.4167 0.3800 0.4688 0.4030 0.4474 0.3393 0.3800 0.3600 0.3981 0.4457 0.0588 0.0566 0.2857 9 93 0.0175 0.0000 0.0290 0.0000 0.0900 0.0500 0.0902 0.0250 0.0357 0.0300 0.0990 0.0373 0.0395 0.0000 0.0000 0.0200 0.0278 0.0435 0.0000 0.0000 0.0000 10 95 0.0088 0.0000 0.0000 0.0000 0.0100 0.0100 0.0246 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0089 0.0000 0.0000 0.0000 0.0000 0.0882 0.0377 0.0089 # samples:575069455050616042509667385650255446515356

Page 38

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s 0 t 0 e 0 0 0 r l 5 l s 5 s 6 e 6 si r6 7 r7 r t u 0 t 6 n e l e e l d w s s 0 e p 7 u p 5 u 6 s a e w o r e 6 v p 0 d p l 0 y l d l 0 e s 6 i i r o l y i 5 0 u u a u l a e i r s 0 s j s n o e l s n 0 s s e s n e y s i e e e v h s l R e R t r e l e e h a c e s y n R i v e t i t r v t u e t s e a e l O v c t O n u l r i O u n u s t a u u h j s e j i v e u t e e l n h N h j a h N c i n s u N v s H k j e s c v c c s R H n e s u e k g w s e s s u s s v j e j g e o v g e e e e e n t e g g s w u t l D n r i e i v u n j k l n n k i r g r j i o D D r u D i i i u l e r C o r e n p j r n r l m e a C i B n e p p e s r H p e p m r m r S e m o r e S S t u o p d S v S e e P e C # k v H s t C t l k t h n i o S e m s s a s t c s o n t m e l m e t c r u i a m k i m r u e u e r n u n n k e n k u y m a o h r c a r i i c l i k a a a z M a l i B a a a a o a h u S u ro r o R a r W M O S B W T A W B T C L B W W M T M W Oki23 1 112 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0882 0.0000 0.0000 2 116 0.0263 0.0306 0.0145 0.0778 0.0000 0.0000 0.0246 0.0417 0.0238 0.0200 0.0000 0.0373 0.0405 0.0179 0.0900 0.0200 0.0648 0.0426 0.2059 0.0943 0.4286 3 120 0.0439 0.0408 0.0145 0.0111 0.0500 0.0200 0.0246 0.0500 0.0119 0.0300 0.0469 0.0000 0.0270 0.0714 0.0600 0.0200 0.0556 0.0638 0.0000 0.0189 0.0000 4 122 0.0088 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 5 124 0.4035 0.5000 0.3406 0.2444 0.2600 0.5000 0.3033 0.3417 0.4524 0.4400 0.3281 0.2761 0.3649 0.3125 0.3400 0.3800 0.2407 0.4894 0.0000 0.0566 0.0000 6 128 0.2018 0.1633 0.2391 0.2444 0.2000 0.1600 0.1967 0.1583 0.1548 0.2400 0.1771 0.1418 0.1216 0.1875 0.1300 0.1400 0.2037 0.1170 0.3922 0.3113 0.0536 7 132 0.0614 0.0408 0.0290 0.0778 0.0000 0.0300 0.0410 0.0500 0.0595 0.0400 0.0052 0.0224 0.0541 0.0089 0.0400 0.0200 0.0278 0.0106 0.0196 0.0849 0.0000 8 136 0.0526 0.0204 0.0507 0.0444 0.0000 0.0500 0.0246 0.0667 0.0238 0.0100 0.0104 0.0448 0.0000 0.0625 0.0400 0.0600 0.0741 0.0213 0.0000 0.0849 0.0000 9 140 0.0526 0.0102 0.0217 0.0778 0.0000 0.0400 0.0410 0.0833 0.0357 0.0100 0.0156 0.0448 0.1216 0.0625 0.0700 0.0400 0.0185 0.0213 0.0588 0.0377 0.0000 10 144 0.0702 0.0612 0.0652 0.0333 0.0300 0.0600 0.0902 0.0833 0.0833 0.0700 0.0260 0.1343 0.0135 0.0714 0.0700 0.1600 0.1111 0.0638 0.0000 0.0189 0.0000 11 148 0.0526 0.0306 0.0145 0.0444 0.0200 0.0100 0.0164 0.0583 0.0000 0.0500 0.0104 0.0448 0.0000 0.0179 0.0100 0.0200 0.0093 0.0000 0.0098 0.0566 0.0000 12 152 0.0175 0.0306 0.1377 0.0444 0.2000 0.0000 0.0984 0.0000 0.0357 0.0400 0.1771 0.0896 0.0541 0.0446 0.0400 0.0200 0.0833 0.0851 0.0196 0.0472 0.0000 13 156 0.0000 0.0714 0.0290 0.0444 0.0900 0.0000 0.0328 0.0000 0.0952 0.0300 0.1042 0.0075 0.0270 0.0268 0.0300 0.0000 0.0093 0.0638 0.0000 0.0094 0.0000 14 160 0.0000 0.0000 0.0290 0.0111 0.0900 0.0300 0.0246 0.0000 0.0000 0.0200 0.0677 0.0373 0.0135 0.0536 0.0300 0.0000 0.0370 0.0106 0.0000 0.0283 0.0000 15 164 0.0000 0.0000 0.0000 0.0000 0.0100 0.0300 0.0328 0.0167 0.0000 0.0000 0.0052 0.0746 0.0000 0.0089 0.0100 0.0400 0.0093 0.0106 0.0098 0.0094 0.0000 16 168 0.0000 0.0000 0.0000 0.0111 0.0200 0.0100 0.0246 0.0000 0.0000 0.0000 0.0104 0.0075 0.0270 0.0089 0.0000 0.0200 0.0278 0.0000 0.0000 0.0094 0.0000 17 172 0.0088 0.0000 0.0072 0.0000 0.0100 0.0200 0.0082 0.0083 0.0119 0.0000 0.0156 0.0224 0.0541 0.0179 0.0000 0.0200 0.0000 0.0000 0.0294 0.0283 0.0000 18 176 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0098 0.0472 0.0179 19 180 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0089 0.0100 0.0000 0.0000 0.0000 0.0294 0.0000 0.0714 20 184 0.0000 0.0000 0.0000 0.0111 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0811 0.0089 0.0100 0.0000 0.0093 0.0000 0.0686 0.0000 0.2946 21 188 0.0000 0.0000 0.0072 0.0000 0.0200 0.0000 0.0082 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0185 0.0000 0.0098 0.0472 0.0000 22 192 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0083 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0179 23 196 0.0000 0.0000 0.0000 0.0222 0.0000 0.0200 0.0082 0.0333 0.0119 0.0000 0.0000 0.0149 0.0000 0.0089 0.0100 0.0400 0.0000 0.0000 0.0490 0.0094 0.1161 # samples:574969455050616042509667375650255447515356

Page 39

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s 0 0 t e 0 0 0 r l l 5 5 6 s 6 7 s 6 e i r 7 r r ts u 0 t 6 n e l e e l d w s s 0 e p 7 u p 5 u 6 s a e w o r e 6 v p 0 d p l 0 y d l 0 e l s 6 i i r o l y i 5 0 u u a u l a e i s 0 s j s n o r e l s n 0 s s e s n e y s i e e e v h e s l R R t e l e r a e s y n R i v e h c e i r v t u t t e t s e a e l O v c O n u t l r i O u n u s t a u u h j e i v e u s j t e n e N j a l h N c h h i n s u N v v k s H j e s c c c s R H n e s u e k w s e s s u s g s v j e j g e v g e e e e e t o e g g s n w u l D n r i e i t v u n j k l n n k i r g j i o D D r r D i i i u u l e r C r e n o r n r p j l m e a C i B n e p p s r p e p r r S H m o e m m e e r S S t u o p S v S e e P d e C # k v H s t C t l k t h n i o S e m s s a s t c s o n t m e l a m e t c r u i m k i m u e n u r n n k e u n r u y e a r c k r m o h i a i a i c l z k a o a a M a a a o h l i B u a a r u S a r o R r W M O S B W T A W B T C L B W W M T M W Omy10 1 134 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0053 0.0075 0.1316 0.0000 0.0000 0.0000 0.0648 0.0000 0.0196 0.0000 0.1786 2 138 0.0089 0.0000 0.0000 0.0111 0.0000 0.0000 0.0082 0.0083 0.0000 0.0000 0.0000 0.0299 0.0000 0.0089 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 3 146 0.0268 0.0600 0.0072 0.0000 0.0100 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0075 0.0000 0.0268 0.0100 0.0000 0.0093 0.0000 0.0000 0.0094 0.0000 4 150 0.0089 0.0300 0.0362 0.0000 0.0000 0.0300 0.0410 0.0167 0.0000 0.0100 0.0053 0.0149 0.0132 0.0089 0.0200 0.0400 0.0648 0.0000 0.0098 0.1132 0.0000 5 154 0.0625 0.0300 0.0145 0.1222 0.0100 0.0900 0.0738 0.0583 0.0119 0.0900 0.0000 0.0970 0.0000 0.0536 0.0800 0.1200 0.0278 0.0000 0.0000 0.0566 0.0000 6 158 0.1250 0.0900 0.0507 0.0333 0.0200 0.0900 0.0820 0.0750 0.0595 0.0800 0.0316 0.1119 0.0526 0.0268 0.0800 0.1800 0.0833 0.0109 0.1275 0.0472 0.3929 7 162 0.0089 0.0500 0.0290 0.0667 0.0200 0.0300 0.0574 0.0417 0.0714 0.0300 0.0263 0.0075 0.0789 0.0268 0.0500 0.0000 0.0370 0.1196 0.0588 0.0660 0.0714 8 166 0.0804 0.1200 0.1449 0.1333 0.1600 0.0800 0.1148 0.0750 0.0476 0.0800 0.1632 0.0746 0.0789 0.1071 0.0500 0.1600 0.0741 0.1957 0.0784 0.2264 0.0000 9 170 0.2411 0.1400 0.1739 0.1556 0.1700 0.2500 0.2049 0.2417 0.2500 0.2400 0.1421 0.2239 0.1316 0.1607 0.1500 0.1200 0.1389 0.2391 0.0784 0.1887 0.0000 10 174 0.0982 0.2200 0.1159 0.0889 0.0300 0.1500 0.1393 0.1083 0.1071 0.1400 0.0526 0.1418 0.0658 0.1607 0.2400 0.1000 0.1296 0.0000 0.1176 0.1887 0.0000 11 178 0.1339 0.0900 0.0362 0.0111 0.0500 0.0300 0.0656 0.1750 0.0595 0.0200 0.0526 0.0224 0.0132 0.1607 0.0900 0.0400 0.0556 0.0543 0.1275 0.0660 0.2143 12 182 0.0000 0.0100 0.0507 0.0667 0.1200 0.0100 0.0492 0.0083 0.0238 0.0400 0.1053 0.0448 0.0263 0.0179 0.0100 0.0600 0.0370 0.1304 0.0490 0.0000 0.1250 13 186 0.0536 0.0700 0.1304 0.1333 0.2600 0.0800 0.0492 0.0417 0.2500 0.0900 0.2316 0.0448 0.1842 0.0446 0.0700 0.0400 0.1574 0.1304 0.0686 0.0000 0.0179 14 190 0.0536 0.0400 0.0435 0.0556 0.0500 0.0500 0.0492 0.0500 0.0357 0.0800 0.0474 0.0746 0.1184 0.0893 0.0200 0.0600 0.0463 0.0761 0.0784 0.0283 0.0000 15 194 0.0357 0.0200 0.0652 0.0222 0.0500 0.0200 0.0246 0.0167 0.0238 0.0400 0.0684 0.0448 0.0526 0.0179 0.0800 0.0200 0.0556 0.0217 0.0882 0.0000 0.0000 16 198 0.0000 0.0300 0.0217 0.0444 0.0100 0.0300 0.0328 0.0250 0.0476 0.0500 0.0105 0.0224 0.0395 0.0357 0.0300 0.0200 0.0000 0.0109 0.0392 0.0094 0.0000 17 202 0.0625 0.0000 0.0507 0.0444 0.0200 0.0100 0.0000 0.0583 0.0119 0.0100 0.0526 0.0299 0.0132 0.0536 0.0100 0.0200 0.0185 0.0109 0.0000 0.0000 0.0000 18 206 0.0000 0.0000 0.0000 0.0000 0.0000 0.0300 0.0082 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 19 210 0.0000 0.0000 0.0290 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 20 218 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0196 0.0000 0.0000 21 230 0.0000 0.0000 0.0000 0.0111 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0053 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 22 258 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0098 0.0000 0.0000 23 274 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0294 0.0000 0.0000 # samples:565069455050616042509567385650255446515356

Page 40

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s s 0 t 0 5 0 e r 0 l l 0 s 0 e r s i u t r t e r 6 l l n e d s 5 6 w 6 6 7 7 e p s 5 0 e 7 u a e u p s o 6 e y l p r 0 l v 0 d l i w d 6 p e r s 6 0 i y u a i l u i r s e n o 5 a 0 e s u 0 j s o l n l s e y e 0 e s n h s i e s v s t e R e e l h a c v s R l r e s y n R i e r e t v t s e u i t e c t u e a e l O v t n t a e j O i h u u s l r O n u s l j u i v e u t n c h e N e j i N H h s n s u s N c v h e v k n w j s c R Ha g e s e s u k e c s v s s e e o u j g e t l s g e j s n v e e e t v g u g i l w D n i e e n j r g u k i r u u n n D k r r o j i o D i i e r i n j r l C p D n e i B r l m r C H e p a n p e r S e e e m s r p o p r m r S d n e t o p k m S v e k e u P i S s S t C l # i H n e v o C t S m t c h a s a e t n t m s e s u i o e l r m i t c s k n k e m m r u a h e r u n n e M k a i u y m r c r a i a l z Bu a c k a a o l i S a a o h u Ro r a o W M r O S Ba W T A W Bu M T Cr L Ba W W T M W Omy77 1 84 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0196 0.0000 0.0000 2 96 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0980 0.0000 0.0000 3 98 0.0091 0.0000 0.0000 0.0000 0.0800 0.0000 0.0000 0.0000 0.0000 0.0000 0.0158 0.0000 0.2237 0.0000 0.0000 0.0000 0.1574 0.0000 0.2647 0.0472 0.6875 4 102 0.0273 0.0000 0.0290 0.0556 0.0100 0.0000 0.0082 0.0417 0.0250 0.0000 0.0000 0.0076 0.0000 0.0273 0.0204 0.0400 0.0185 0.0222 0.0294 0.1132 0.0000 5 110 0.0000 0.0521 0.0652 0.0000 0.0100 0.0000 0.0246 0.0083 0.0125 0.0000 0.0000 0.0076 0.0000 0.0091 0.0000 0.0000 0.0278 0.0000 0.0490 0.1132 0.0804 6 112 0.0091 0.0104 0.0000 0.0222 0.0100 0.0000 0.0082 0.0083 0.0125 0.0700 0.0000 0.0227 0.0000 0.0091 0.0204 0.0200 0.0093 0.0667 0.0000 0.0566 0.0089 7 114 0.0364 0.0000 0.0000 0.0222 0.0200 0.0400 0.0000 0.0333 0.0125 0.0000 0.0368 0.0152 0.0132 0.0182 0.0204 0.0200 0.0093 0.0111 0.0686 0.0000 0.1071 8 116 0.1091 0.1354 0.1159 0.0667 0.1300 0.0600 0.1393 0.2000 0.0500 0.0900 0.1368 0.0758 0.0526 0.0909 0.0918 0.0800 0.0833 0.1444 0.3137 0.0566 0.0000 9 118 0.0273 0.1771 0.0797 0.0667 0.1500 0.1300 0.0820 0.0333 0.0125 0.0900 0.1316 0.1212 0.1184 0.0545 0.0612 0.0800 0.1204 0.1222 0.0196 0.0472 0.0000 10 120 0.0455 0.0312 0.0145 0.0333 0.0200 0.0500 0.0656 0.0500 0.0375 0.0300 0.0211 0.0379 0.0000 0.0273 0.0816 0.0400 0.0000 0.0111 0.0000 0.0377 0.0000 11 122 0.2182 0.0208 0.0435 0.0667 0.0000 0.1000 0.0328 0.1583 0.1250 0.1100 0.0000 0.0909 0.0132 0.0636 0.1327 0.1800 0.0093 0.0000 0.0000 0.0849 0.0000 12 124 0.0818 0.1458 0.1087 0.1778 0.0200 0.1000 0.0902 0.0750 0.1625 0.1500 0.0368 0.1364 0.0526 0.2364 0.1429 0.0600 0.1019 0.0667 0.0098 0.0755 0.0000 13 126 0.1364 0.0833 0.1884 0.1333 0.1100 0.1300 0.0902 0.1167 0.0625 0.1300 0.0684 0.1136 0.1053 0.1182 0.0816 0.2000 0.0278 0.0111 0.0294 0.2642 0.0000 14 128 0.0273 0.1667 0.0435 0.0556 0.0600 0.0600 0.0984 0.0500 0.0875 0.0800 0.0737 0.0909 0.0789 0.1000 0.1939 0.0200 0.1389 0.0444 0.0000 0.0943 0.0089 15 130 0.0364 0.0521 0.0797 0.0667 0.1200 0.0100 0.0902 0.0333 0.1375 0.0600 0.1789 0.1212 0.0395 0.0636 0.0000 0.1200 0.1296 0.2444 0.0196 0.0000 0.0000 16 132 0.1909 0.0938 0.1884 0.1333 0.2300 0.2100 0.1721 0.1833 0.1375 0.1200 0.2211 0.1212 0.1974 0.1545 0.0816 0.1000 0.1481 0.1889 0.0098 0.0000 0.0000 17 134 0.0182 0.0104 0.0362 0.0778 0.0300 0.0400 0.0902 0.0083 0.0125 0.0000 0.0737 0.0303 0.0658 0.0000 0.0612 0.0200 0.0185 0.0111 0.0000 0.0000 0.0000 18 136 0.0000 0.0104 0.0000 0.0222 0.0000 0.0500 0.0000 0.0000 0.0875 0.0500 0.0000 0.0076 0.0395 0.0000 0.0102 0.0000 0.0000 0.0556 0.0000 0.0000 0.0000 19 138 0.0091 0.0104 0.0072 0.0000 0.0000 0.0100 0.0082 0.0000 0.0250 0.0200 0.0000 0.0000 0.0000 0.0273 0.0000 0.0000 0.0000 0.0000 0.0098 0.0000 0.0000 20 140 0.0182 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0053 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0588 0.0094 0.1071 21 146 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 # samples:554869455050616040509566385549255445515356

Page 41

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

7 6 0 s s t 5 0 5 0 0 r l e

0 0 l s 0 r e u s i t r s r t e l p d l n e 5 e e p u p s a 7 s l u 6 e y 6 6 6 7 e 0 i 6 p d u r r w 0 e w d 0 v l y 0 i l u a i s e n 0 r a o u s i o 5 s o s l e l j n y h s e e s 6 s n 0 e v y R t e a c v s e l h s R e 0 e r e l r t s a i s l R t u v c u e e i t r O e v a e j i s t t t e O u n h s t u s l l O n n e j u a i s u e N c u i h e j H N l e s e s n w i h N c v h n s s k H v R g s v s e k e e o n c u c e e t l g s u j g s e s n s g u e t v l v e j e i n j g n D e i e g e n re r u u i v k i o u D r r i n k j j r r n u e i p r D i C i B D w e m H j C p o r p a r e S p e n o m r p re s d S l S t p k k H n m re o m e S e i l s u P n S t C l # c a e e S m t e v C k s n h a e i t t r u u m v t m e s o l m s i s r c n t r c k e h M m a o o u n u e r i a m e B a u n u a y a z n r l S e a c k a i a o u l i R i a o r h r W B k M O o a a r S W W T A W a M T C L B W T W M B Ssa289 1 99 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0093 0.0000 0.0000 0.0000 0.0000 2 103 0.0000 0.0000 0.0072 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 3 105 0.0000 0.0000 0.0000 0.0222 0.0400 0.0000 0.0000 0.0333 0.0119 0.0200 0.0104 0.0149 0.0921 0.0000 0.0000 0.0000 0.0926 0.0000 0.0700 0.0566 0.2857 4 107 0.5625 0.7500 0.7464 0.7444 0.8600 0.8000 0.7705 0.6500 0.6667 0.8600 0.9115 0.8209 0.6974 0.7455 0.7400 0.6600 0.7130 0.9043 0.4300 0.6509 0.0357 5 109 0.2857 0.1000 0.1014 0.1556 0.0400 0.1600 0.1967 0.1667 0.2262 0.0800 0.0156 0.0597 0.0395 0.1727 0.1300 0.1200 0.0926 0.0213 0.1800 0.0943 0.5446 6 111 0.0000 0.0400 0.0217 0.0111 0.0200 0.0000 0.0000 0.0000 0.0119 0.0100 0.0312 0.0075 0.0263 0.0273 0.0200 0.0000 0.0093 0.0000 0.0200 0.0094 0.0089 7 113 0.0357 0.0000 0.0217 0.0556 0.0000 0.0300 0.0164 0.0750 0.0357 0.0100 0.0000 0.0299 0.0000 0.0364 0.0600 0.0800 0.0093 0.0000 0.0000 0.0000 0.0000 8 115 0.1071 0.0500 0.0290 0.0111 0.0200 0.0100 0.0164 0.0667 0.0357 0.0200 0.0208 0.0597 0.1316 0.0182 0.0400 0.1400 0.0556 0.0745 0.1400 0.1132 0.1250 9 117 0.0000 0.0500 0.0507 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0052 0.0000 0.0132 0.0000 0.0100 0.0000 0.0185 0.0000 0.0800 0.0283 0.0000 10 119 0.0089 0.0100 0.0217 0.0000 0.0000 0.0000 0.0000 0.0083 0.0119 0.0000 0.0052 0.0075 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0500 0.0472 0.0000 11 121 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0300 0.0000 0.0000 # samples:565069455050616042509667385550255447505356

Page 42

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s 0 0 e t 0 0 0 r l l 5 5 6 6 is 6 s 7 7 s e r r r t u 0 t 6 n e l e e l s d w 0 e p 7 u p 5 s u 6 s a e w o r e 6 v p 0 d p 0 y d l 0 e l s 6 il i o l y r 5 0 u u a u i l a e i s 0 s j s n o r e l s 0 n s s e s n e y s i e e e v h s l R e R t e l e r a e s y n R i v e h c e t i t r v t u e t e a e l O v c s O n u t l r i O u n u s t a u u h j s e i t v e u j e N e a l N n c h h j h s N i n u v k s H e s c v c c j s R e s H n s s s u s e k g w s v e u j g e v g j e e e g g e e e s n t o e u w n r i t l u n D e i v n j n k l k i r g r j i o D D r u D i i e r C i u r l e n o r n r p j l m e a C i n e p B p s r p e p m r m r S H m o e r e e S S t u p S v S e e P d e C # k v H s t C t lo k t h i o S e m n s s a s s o n t m e l t c m e t c r u i a m k i m u e n u r n n k e u n r u y e a r c k r i i m o h i a a c l z k a o a l M a a a a o a h u i B u r ra o S a r R W M O S B W T A W B T C L B W W M T M W Ssa407 1 159 0.0000 0.0300 0.0000 0.0000 0.0000 0.0000 0.0082 0.0000 0.0119 0.0000 0.0052 0.0000 0.0000 0.0273 0.0200 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 2 163 0.0179 0.0000 0.0074 0.0000 0.0300 0.0000 0.0000 0.0083 0.0000 0.0200 0.0000 0.0149 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0094 0.0000 3 167 0.0714 0.0600 0.0368 0.0556 0.0400 0.0600 0.0328 0.0833 0.1310 0.0900 0.0521 0.0448 0.0263 0.0455 0.0400 0.0600 0.0556 0.0000 0.0000 0.0094 0.0000 4 171 0.1071 0.1700 0.1544 0.1889 0.2400 0.1600 0.1475 0.1833 0.1786 0.1700 0.2969 0.1269 0.1447 0.1273 0.1900 0.1000 0.1019 0.3617 0.0000 0.0094 0.0000 5 175 0.1518 0.0600 0.1176 0.0778 0.0600 0.1500 0.0492 0.1833 0.0714 0.1100 0.0365 0.0821 0.0395 0.1545 0.1500 0.1200 0.0926 0.0106 0.1600 0.1038 0.2054 6 179 0.1875 0.1300 0.1029 0.1778 0.1100 0.1200 0.2131 0.1750 0.1905 0.1600 0.0573 0.0896 0.1316 0.0818 0.1800 0.2000 0.1204 0.0745 0.0600 0.0472 0.0268 7 183 0.1786 0.2200 0.2059 0.1667 0.2400 0.0900 0.2131 0.1333 0.1310 0.1700 0.1615 0.1343 0.2763 0.2000 0.1300 0.1200 0.2870 0.2128 0.2700 0.3585 0.2321 8 187 0.1339 0.0800 0.1691 0.1111 0.1300 0.1400 0.1557 0.0833 0.1071 0.1000 0.1615 0.2910 0.1316 0.0909 0.0600 0.2400 0.1019 0.0638 0.1200 0.1698 0.0000 9 191 0.0268 0.0400 0.0147 0.0333 0.0100 0.0300 0.0328 0.0250 0.0238 0.0300 0.0260 0.0299 0.0395 0.0364 0.0500 0.0000 0.0000 0.0106 0.0200 0.1132 0.0000 10 195 0.0446 0.0300 0.0147 0.0556 0.0100 0.0900 0.0164 0.0167 0.0357 0.0500 0.0104 0.0149 0.0395 0.0182 0.0200 0.0200 0.0648 0.0957 0.1700 0.0283 0.0000 11 199 0.0179 0.0300 0.0441 0.0222 0.0300 0.0300 0.0082 0.0500 0.0119 0.0100 0.0156 0.0522 0.0395 0.0455 0.0100 0.0000 0.0093 0.0106 0.0400 0.0000 0.0000 12 201 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0200 0.0093 0.0000 0.0000 0.0000 0.0000 13 203 0.0089 0.0000 0.0000 0.0111 0.0100 0.0100 0.0164 0.0000 0.0238 0.0200 0.0000 0.0224 0.0132 0.0000 0.0100 0.0000 0.0093 0.0000 0.0100 0.0283 0.0625 14 207 0.0089 0.0100 0.0147 0.0333 0.0100 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0273 0.0000 0.0000 0.0278 0.0000 0.0600 0.0755 0.2054 15 209 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 16 211 0.0179 0.0200 0.0147 0.0111 0.0200 0.0500 0.0328 0.0333 0.0357 0.0000 0.0417 0.0149 0.0395 0.0000 0.0300 0.0200 0.0000 0.0106 0.0100 0.0094 0.0893 17 215 0.0089 0.0900 0.0662 0.0111 0.0500 0.0000 0.0246 0.0000 0.0119 0.0200 0.1042 0.0448 0.0526 0.0455 0.0600 0.0200 0.1204 0.0638 0.0500 0.0094 0.0000 18 219 0.0000 0.0000 0.0221 0.0000 0.0100 0.0600 0.0328 0.0083 0.0238 0.0200 0.0052 0.0299 0.0000 0.0273 0.0000 0.0200 0.0000 0.0319 0.0100 0.0000 0.1786 19 223 0.0089 0.0300 0.0074 0.0111 0.0000 0.0000 0.0082 0.0000 0.0000 0.0100 0.0156 0.0075 0.0263 0.0727 0.0300 0.0200 0.0000 0.0213 0.0000 0.0094 0.0000 20 227 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0104 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0319 0.0000 0.0000 0.0000 21 231 0.0089 0.0000 0.0000 0.0000 0.0000 0.0000 0.0082 0.0167 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0094 0.0000 22 235 0.0000 0.0000 0.0000 0.0333 0.0000 0.0000 0.0000 0.0000 0.0119 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0000 0.0094 0.0000 23 247 0.0000 0.0000 0.0074 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # samples:565068455050616042509667385550255447505356

Page 43

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s 0 0 e 0 0 t 5 6 ls 6 7 0 6 r 7 l 5 s i r s r u r t t 6 n e e 0 l l s d 0 we e p 7 p u 6 u 5 s e s a v l r 6 o p 0 d p e we d 0 e 0 y s 6 l i i l u l y r o 5 a 0 u a u i e j o i r s l l 0 s s e 0 s s es s en n y n i e e v e h s s l l s y t e e r a e n i v e c e e t i t r e a e v t e l u OR u v ch t OR n n t l r i OR u u j s u i v h e s es u t e e u j N n h N h j at l n s c N h u v v k i e c c s Ha j s s R e s e H c s s s u u s k g n w v j s v j g e e De g g g e e t e u s n o w n r i l u n De e i t v n j n r g j i o De De r r l i i C i u m l ek ek ri u r r r n p o l n j e n m e e p a C i B p p p s t e m r m r r S e o e r e H S S u s S v t S e e P o p C d v H t C t k s n o S s e# n i o s s al m i t t m ch e l t m e n r ck m m u u a e i n r n e i r u u y n k e r ck r i i m a u a c l z o h a o a a a ak a a o a h i u r r u o B M ak r R S S W B M W T Oa L Al B W W B W M T T M W C Ssa408 1 169 0.0000 0.0000 0.0000 0.0556 0.0000 0.0000 0.0000 0.0167 0.0119 0.0100 0.0000 0.0000 0.0395 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 2 173 0.0526 0.2021 0.1159 0.0333 0.0100 0.0700 0.0656 0.1167 0.0714 0.1400 0.0260 0.0896 0.0395 0.0727 0.1100 0.0400 0.0278 0.0106 0.0100 0.0000 0.0000 3 177 0.1316 0.0957 0.0725 0.1444 0.0200 0.0600 0.0328 0.1500 0.0476 0.1200 0.0521 0.0970 0.1316 0.1091 0.0800 0.1000 0.0556 0.0213 0.0000 0.0094 0.0000 4 181 0.0351 0.0213 0.0217 0.0111 0.0200 0.0200 0.0492 0.0833 0.0238 0.0200 0.0156 0.0448 0.0658 0.0091 0.0200 0.0600 0.0370 0.0319 0.0100 0.0189 0.0357 5 185 0.1228 0.0851 0.0217 0.1333 0.0900 0.1600 0.0656 0.0833 0.1786 0.0900 0.0833 0.0746 0.0263 0.1182 0.1000 0.1600 0.0648 0.0532 0.1200 0.0000 0.1964 6 189 0.0351 0.0426 0.1232 0.0667 0.0600 0.1100 0.0410 0.0500 0.0714 0.0800 0.0521 0.1045 0.1316 0.0364 0.0500 0.0800 0.1574 0.1383 0.1500 0.1604 0.0714 7 193 0.0965 0.1383 0.1449 0.1000 0.1200 0.0100 0.1639 0.1083 0.0476 0.0600 0.1667 0.0672 0.1184 0.0364 0.0800 0.1200 0.1111 0.0532 0.1500 0.1604 0.1339 8 197 0.1053 0.0532 0.1014 0.1222 0.2400 0.0900 0.0656 0.0500 0.1429 0.0900 0.1823 0.1343 0.1184 0.1091 0.0900 0.0800 0.0463 0.1596 0.1800 0.2075 0.0000 9 201 0.0789 0.0319 0.0362 0.0444 0.0000 0.0100 0.0410 0.0250 0.0595 0.0300 0.0104 0.0597 0.0132 0.0727 0.0800 0.0000 0.0463 0.0106 0.0000 0.0472 0.0000 10 203 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 11 205 0.2105 0.1489 0.1087 0.0778 0.0100 0.2500 0.0902 0.2083 0.0833 0.1100 0.0104 0.0597 0.0000 0.1727 0.0900 0.0800 0.0556 0.0000 0.0100 0.0094 0.0000 12 207 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 13 209 0.0614 0.0000 0.0217 0.0111 0.0300 0.0000 0.0492 0.0250 0.0476 0.0000 0.0156 0.0224 0.0132 0.0636 0.0200 0.0200 0.0741 0.0745 0.0700 0.1038 0.1161 14 213 0.0000 0.0319 0.0217 0.0111 0.0100 0.0000 0.0492 0.0167 0.0476 0.0300 0.0052 0.0448 0.0000 0.0273 0.0800 0.0400 0.0000 0.1064 0.0300 0.0377 0.0089 15 217 0.0088 0.0106 0.0145 0.0111 0.0000 0.0000 0.0164 0.0333 0.0238 0.0300 0.0000 0.0224 0.0000 0.0000 0.0700 0.0000 0.0370 0.0426 0.0500 0.0377 0.2589 16 219 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 17 221 0.0088 0.0638 0.0507 0.0111 0.1100 0.1100 0.0574 0.0167 0.0119 0.0700 0.1302 0.0299 0.0526 0.0182 0.0400 0.1000 0.1204 0.1383 0.0100 0.0472 0.0000 18 225 0.0439 0.0106 0.0507 0.0556 0.0700 0.0000 0.0410 0.0167 0.0238 0.0400 0.0573 0.0000 0.0263 0.0273 0.0500 0.0000 0.0093 0.0532 0.0300 0.0472 0.0268 19 227 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0119 0.0100 0.0000 0.0000 0.0000 0.0455 0.0000 0.0000 0.0000 0.0106 0.0000 0.0000 0.0000 20 229 0.0088 0.0638 0.0797 0.0667 0.1900 0.0900 0.1148 0.0000 0.0833 0.0600 0.1719 0.0522 0.1447 0.0364 0.0000 0.0800 0.1389 0.0851 0.0000 0.0000 0.0000 21 233 0.0000 0.0000 0.0072 0.0333 0.0100 0.0000 0.0492 0.0000 0.0119 0.0000 0.0208 0.0597 0.0395 0.0273 0.0000 0.0000 0.0185 0.0106 0.1500 0.0755 0.0982 22 237 0.0000 0.0000 0.0000 0.0111 0.0100 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0075 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0283 0.0000 23 241 0.0000 0.0000 0.0072 0.0000 0.0000 0.0000 0.0082 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0094 0.0000 24 245 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0299 0.0395 0.0091 0.0000 0.0000 0.0000 0.0000 0.0300 0.0000 0.0179 25 249 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0357 26 253 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0091 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # samples:574769455050616042509667385550255447505356

Page 44

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s s 0 0 t 0 e 0 0 r l 5 l r s s e i r 0 r5 6 6 t 7 u t 6 e 7 6 n l e e l d s w p s 5 0 e 7 u p u 6 s a e o e w p r 0 y 6 v 0 d p l l d l 0 e s 6 i i r i o u a l y 5 0 u u s l a e i r e 0 s j s n o n l s 0 s e y s i e e s v n h e s e e s t e l R a R l e r e h c e s y n R i v v e t i r t u t e c s t e a e l O v t O u n u u l r i O n u s t a e u h j s j i v e u l t h e N e a n c h j i h N n s u N v s H e s c v k j s c n c R H w e s s u e k g s v e s u s e s j g e e j e t o v g e e e s n l e g u g t v w D n r i e i u n j l n n k i g r D k r r u u j i o D D i i e r C i o r l e n p j r n r i l m e p a C B n e p e m s r S H p e p r m r e m o r e S S v t e u o p d S S e P # k e t C l k v H s C t n i t o h S m s a s e t c o n t m s e l a s m e t c r u i k i n u m m r k u e e r u n n e a n k i u y m o h r c a r i l z i a a a c M k a a o l i B a a a o h u S u r a r o R a r W M O S B W T A W B M T C L B W W T M W Oke4 1 234 0.0088 0.0000 0.0362 0.0222 0.0100 0.0000 0.0167 0.0086 0.0000 0.0000 0.0052 0.0075 0.0000 0.0185 0.0200 0.0400 0.0000 0.0111 0.0521 0.09430.0000 2 236 0.0526 0.1735 0.0362 0.0444 0.0000 0.0900 0.0333 0.0172 0.0357 0.0900 0.0000 0.0299 0.0270 0.0370 0.0500 0.0000 0.0556 0.0111 0.0000 0.0000 0.0000 3 240 0.0000 0.0000 0.0072 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0573 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0111 0.0104 0.0000 0.0089 4 242 0.1053 0.2551 0.2029 0.2444 0.3100 0.2100 0.3167 0.1552 0.2143 0.1600 0.3542 0.3284 0.2703 0.1667 0.1600 0.1200 0.2963 0.3667 0.1250 0.2642 0.0000 5 244 0.1842 0.1429 0.1739 0.1111 0.1600 0.3400 0.1750 0.2931 0.1190 0.2300 0.0833 0.1119 0.1081 0.2593 0.2400 0.2200 0.1296 0.0556 0.0521 0.1509 0.0000 6 245 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0119 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0104 0.0189 0.0000 7 246 0.0702 0.1531 0.0942 0.0889 0.0900 0.0900 0.1083 0.0603 0.1071 0.1000 0.0625 0.1119 0.0270 0.1852 0.0800 0.1400 0.0648 0.0111 0.0000 0.0000 0.0000 8 248 0.1404 0.0918 0.1812 0.1444 0.3600 0.0300 0.1083 0.0603 0.1905 0.1900 0.3333 0.1642 0.2973 0.1019 0.0900 0.1400 0.1204 0.4667 0.0625 0.2453 0.0000 9 250 0.1316 0.0510 0.0580 0.0556 0.0100 0.0500 0.0250 0.1379 0.0833 0.0300 0.0052 0.0224 0.0135 0.0370 0.0900 0.0600 0.0463 0.0000 0.1354 0.0094 0.6607 10 252 0.0000 0.0000 0.0145 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0104 0.0000 0.0000 11 254 0.2456 0.1224 0.1739 0.2222 0.0000 0.1500 0.1917 0.1983 0.2262 0.1400 0.0677 0.1194 0.0270 0.1481 0.1800 0.1800 0.1111 0.0444 0.0208 0.1038 0.0000 12 255 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0208 0.0000 0.0000 13 256 0.0000 0.0000 0.0072 0.0111 0.0000 0.0100 0.0167 0.0000 0.0000 0.0300 0.0000 0.0597 0.0000 0.0093 0.0300 0.0200 0.0278 0.0000 0.0312 0.0377 0.0446 14 257 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0104 0.0373 0.0000 0.0000 0.0000 0.0200 0.0000 0.0111 0.0000 0.0189 0.0000 15 258 0.0439 0.0000 0.0145 0.0000 0.0000 0.0300 0.0083 0.0517 0.0000 0.0100 0.0000 0.0000 0.0000 0.0185 0.0500 0.0400 0.0093 0.0000 0.0312 0.0000 0.0446 16 262 0.0000 0.0000 0.0000 0.0111 0.0000 0.0000 0.0000 0.0000 0.0119 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1875 0.0000 0.0089 17 264 0.0175 0.0102 0.0000 0.0333 0.0000 0.0000 0.0000 0.0172 0.0000 0.0100 0.0052 0.0075 0.0541 0.0093 0.0000 0.0000 0.0278 0.0000 0.0625 0.0094 0.0893 18 266 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0521 0.0000 0.0357 19 267 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0833 0.0094 0.0000 20 268 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0208 0.0000 0.0000 21 270 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0093 0.0000 0.0000 0.0000 0.0000 0.0000 0.0377 0.0179 22 272 0.0000 0.0000 0.0000 0.0111 0.0400 0.0000 0.0000 0.0000 0.0000 0.0100 0.0052 0.0000 0.0676 0.0000 0.0000 0.0000 0.0556 0.0000 0.0312 0.0000 0.0893 23 274 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0104 0.0000 0.1081 0.0000 0.0000 0.0000 0.0556 0.0000 0.0000 0.0000 0.0000 24 276 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0111 0.0000 0.0000 0.0000 # samples:574969455050605842509667375450255445485356

Page 45

Appendix 3 (cont.). Population allele frequencies – all 21 collections.

0 s e 0 5 06 6 s 60 7 70 t l er l 0 s i s 5 er t t u 6 er er 0 w l l en p p 0 w 6 7 u 5 o u es s ad r l 6 o v p 0 p l 0 e 0 y es 6 l i i u l l 5 ad 0 u ad u y es j o i i 0 s 0 l er es s i es es en v n er t es l R es l R es t R v ay en u i i e ch es t t er r es ay en u v O l O u v ch t l r i O u u j i t v en u s at es u ch en es j N N j at l s u ch N v ch v ch s i j en R H es en s s s s u u H v es j g w v j g eek e g g g es es e en D s n t w u r i o u n D n eek i t l n j n r v j i o D i D g i i i r r l l r C u u m r r r n l p o eek eek a C i j p m p s B e p p m m r o en r r r S t en e H S S u e S v t S e e P o p s C d v H t C t s k n S s e# s s al m n i t t m ch e l m m eo n m t ck eo n n u i u u y e ck m cu l ar u ar an ze o h ar ar ar o o h ak l u ak r u o i ak r r B Mai R S S W B Mai W T O L A B W W B W Mai T T Mai W C Omy10 1 166 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0377 0.0000 2 168 0.0263 0.0204 0.0074 0.0222 0.0000 0.0000 0.0169 0.0431 0.0000 0.0000 0.0052 0.0075 0.0000 0.0089 0.0000 0.0000 0.0093 0.0000 0.0000 0.0000 0.0000 3 172 0.0000 0.0000 0.0000 0.0000 0.0000 0.0300 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 4 174 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0364 5 176 0.0439 0.0510 0.0147 0.0444 0.0000 0.1100 0.0000 0.0862 0.0119 0.0400 0.0052 0.0522 0.0658 0.0000 0.0400 0.0000 0.0463 0.0444 0.0111 0.0283 0.0000 6 178 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0111 0.0000 0.0000 7 180 0.0351 0.0102 0.0074 0.0333 0.0400 0.0800 0.0000 0.0517 0.0357 0.0400 0.0052 0.0149 0.1447 0.0179 0.0100 0.0600 0.0370 0.0000 0.0444 0.0660 0.0636 8 182 0.0351 0.0612 0.0882 0.1000 0.1200 0.1600 0.0593 0.0517 0.0357 0.0800 0.2135 0.0448 0.0658 0.0893 0.0600 0.1200 0.0926 0.2222 0.0000 0.0094 0.0000 9 184 0.1140 0.0306 0.0809 0.0778 0.0400 0.0300 0.0508 0.0776 0.0476 0.0900 0.0312 0.1269 0.0658 0.0982 0.1100 0.0800 0.0926 0.0333 0.2222 0.1887 0.3182 10 186 0.0088 0.0612 0.0221 0.0333 0.0600 0.0000 0.0508 0.0086 0.0238 0.0300 0.0208 0.0299 0.0395 0.0089 0.0100 0.0400 0.0000 0.0333 0.0000 0.0472 0.0000 11 188 0.1404 0.0918 0.1103 0.1111 0.1300 0.0700 0.1441 0.1207 0.1905 0.1100 0.1302 0.1269 0.0921 0.2054 0.1300 0.1600 0.1574 0.1000 0.1000 0.0755 0.0182 12 190 0.1140 0.0612 0.1176 0.1444 0.0000 0.1800 0.1271 0.0948 0.1310 0.1300 0.0469 0.0746 0.1447 0.1161 0.1600 0.0800 0.1389 0.0111 0.0000 0.0000 0.0000 13 192 0.0965 0.0306 0.1103 0.0333 0.0500 0.0200 0.0339 0.0690 0.0357 0.0600 0.0312 0.0448 0.0263 0.1250 0.1400 0.0600 0.0926 0.0333 0.0000 0.0094 0.0000 14 194 0.0088 0.0204 0.0221 0.0111 0.0600 0.0200 0.0169 0.0259 0.0238 0.0500 0.0208 0.0075 0.0000 0.0268 0.0200 0.0000 0.0000 0.0222 0.1333 0.1604 0.0000 15 196 0.1316 0.1122 0.0882 0.0556 0.0500 0.0300 0.1695 0.0862 0.1071 0.1200 0.0104 0.0597 0.0526 0.0893 0.0800 0.1400 0.0370 0.0111 0.0778 0.0377 0.0818 16 198 0.0263 0.0408 0.0074 0.0778 0.0300 0.0100 0.0085 0.0345 0.0714 0.0100 0.0000 0.0299 0.0000 0.0357 0.0300 0.0400 0.0185 0.0000 0.0778 0.0094 0.1273 17 200 0.0351 0.1939 0.0147 0.0222 0.0100 0.0100 0.0339 0.0517 0.0357 0.0100 0.0312 0.0597 0.0526 0.0179 0.0200 0.1200 0.0278 0.0111 0.1333 0.0943 0.2727 18 202 0.0263 0.0000 0.1544 0.0444 0.2300 0.0300 0.1356 0.0345 0.0238 0.0700 0.3125 0.0597 0.1053 0.0179 0.0400 0.0000 0.1019 0.3667 0.0000 0.0000 0.0000 19 204 0.0877 0.1122 0.0441 0.0444 0.0400 0.0900 0.0508 0.0862 0.0833 0.0600 0.0312 0.1269 0.0789 0.0625 0.0600 0.0600 0.0093 0.0778 0.0778 0.1415 0.0000 20 206 0.0000 0.0000 0.0147 0.0000 0.0800 0.0100 0.0000 0.0000 0.0119 0.0000 0.0312 0.0224 0.0395 0.0089 0.0000 0.0000 0.0741 0.0000 0.0000 0.0000 0.0000 21 208 0.0088 0.0714 0.0662 0.0556 0.0100 0.0300 0.0508 0.0345 0.0476 0.0900 0.0104 0.0373 0.0263 0.0179 0.0500 0.0200 0.0370 0.0000 0.0222 0.0566 0.0000 22 210 0.0000 0.0306 0.0074 0.0556 0.0400 0.0000 0.0254 0.0000 0.0238 0.0000 0.0521 0.0373 0.0000 0.0000 0.0200 0.0000 0.0185 0.0333 0.0000 0.0000 0.0000 23 212 0.0088 0.0000 0.0000 0.0222 0.0000 0.0400 0.0169 0.0000 0.0119 0.0000 0.0000 0.0224 0.0000 0.0089 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 24 214 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0104 0.0000 0.0000 0.0000 0.0000 0.0000 0.0093 0.0000 0.0111 0.0000 0.0364 25 216 0.0000 0.0000 0.0074 0.0000 0.0000 0.0000 0.0000 0.0000 0.0119 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0111 0.0189 0.0000 26 220 0.0088 0.0000 0.0074 0.0000 0.0000 0.0400 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0667 0.0000 0.0364 27 222 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0094 0.0091 28 224 0.0439 0.0000 0.0074 0.0111 0.0100 0.0000 0.0085 0.0431 0.0357 0.0000 0.0000 0.0149 0.0000 0.0446 0.0000 0.0200 0.0000 0.0000 0.0000 0.0094 0.0000 # samples:574968455050595842509667385650255445455355

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Appendix 3 (cont.). Population allele frequencies – all 21 collections.

7 6 0 s s t 5 0 5 0 0 r l e 0 0 0 l s e r u s i t r s r t e l p d l n e 5 e e p u p s a e 7 s l u 6 6 6 7 y 6 e 0 i 6 p d u r r w 0 e w d 0 v l y 0 i l 0 u a i s e n o s i r o 5 a u s s o l l j e s e n e y h s 6 s n 0 e v y R t e a v s e l h c s R e 0 e r e l r t s s a R i l e t u v c u e i e t r i O v a e j e s t t t O u n h t u s s l l n n e O j u a i s u e N c u i h e j H N l e s e w i v s n h h N c n s s k H v R g v e k e e o s n c s u c e e t g s g l s u j e s n s g u e e t v v j e l j D e i n g n e e i e g n v r r u u o u i k i n D r r j i r k r n j u e i p r D i C i B D w e m H p o j r p C e a r e p e S n o m e r p r s d S l S t p k k e H n m e r o m S l i s u P l # S t C n c a e e S m t e v C k t s n h a e i t m r u u v t m e s l o m s i s r c n t c k e h r a o M o m u n u e r i a m e B a n u y a z n u r a l S e a c k a i a o u l i R i a o r h r W B k a M O o a r S W W T A W a M T C L B W T W M B One14 1 146 0.1842 0.0000 0.1014 0.0778 0.0200 0.1000 0.0750 0.1121 0.0952 0.0500 0.0365 0.1045 0.0000 0.0727 0.1200 0.0600 0.0481 0.0745 0.0000 0.0288 0.0000 21500.1053 0.0300 0.0580 0.0333 0.0200 0.1600 0.1083 0.0776 0.0476 0.1300 0.0104 0.0896 0.0658 0.0636 0.0500 0.1800 0.0577 0.0106 0.0116 0.0481 0.0000 31520.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0083 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 41540.2281 0.4300 0.2246 0.2111 0.0700 0.1900 0.2000 0.2845 0.2262 0.1800 0.1094 0.2313 0.0526 0.3000 0.2900 0.3000 0.2019 0.0426 0.2791 0.2019 0.3818 51560.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0083 0.0000 0.0119 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0096 0.0000 61580.4649 0.5400 0.5870 0.6222 0.8700 0.5200 0.5750 0.5086 0.5119 0.6100 0.8073 0.5299 0.7763 0.5364 0.4900 0.4200 0.6635 0.8511 0.4535 0.4712 0.0000 71600.0088 0.0000 0.0072 0.0111 0.0100 0.0200 0.0083 0.0086 0.0119 0.0000 0.0208 0.0149 0.0921 0.0091 0.0300 0.0000 0.0288 0.0106 0.1512 0.1731 0.2182 81620.0088 0.0000 0.0217 0.0222 0.0100 0.0100 0.0083 0.0086 0.0952 0.0100 0.0156 0.0224 0.0132 0.0091 0.0100 0.0000 0.0000 0.0106 0.0000 0.0481 0.0000 91640.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0075 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0465 0.0000 0.3909 10 166 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0091 0.0000 0.0000 0.0000 0.0000 0.0000 0.0192 0.0091 11 168 0.0000 0.0000 0.0000 0.0111 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 12 172 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0581 0.0000 0.0000 13 180 0.0000 0.0000 0.0000 0.0111 0.0000 0.0000 0.0083 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 14 246 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 # samples:575069455050605842509667385550255247435255

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Appendix 4. Population jackknife results – all 21 collections.

5 0 6 es 6 7 s 06 0 0 7 0 t 0 l r i l s r s r r e 5 t n e t e u 6 l e l s 0 e d 0 w p 6 7 p u u e s v l r a 5 w 6 o p 0 p s d 0 d i s 6 l i e 0 o 5 0 u u u l y e a j a y l e s s n o i r l s l 0 s r s 0 s s s i i e e e v e e e n e R s e l l R e r y n t s y t R v h n t i i t e h a e a e e e u e u u r c l O r l O u n n O u s v c t i j t s v h i t v h e t h e h e u a N n N j s e u c n s c N a u c v v c k l j s j e e s s s e R s H i s s s u u s k H e j v v e j g e g n g g g e e e e w s e u w u r i n t e D n n D n k n e o j j D k D r i t i i o i i g v l e C i r r r r l r e r u l l n n u m n e e a C i p p p m p p s j o e m r m r r e e o r B e S u S t S S S e e o v v t P p e H H t C C t s s h l d o s s k o t e a S n t m c m n i k m m k e n m i e n n r t r r i r u u r y n u c c k i i m k i a k a a a a a o o a h a u a a a a o h a u r r r u Assigned Population S B M B M W T O W R B W W B W M T T M W C Warm Springs strays 0517102012162002042000000 Round Butte Hatchery 0230010101312125100000 Shitike juveniles 4128450312171054010000 Buck Hollow juveniles 050121211356313023100000 Mainstem Deschutes lower 0500101400000242300042000 Bakeoven juveniles 05 0014029032300052010000 Warm Springs NOR adults 063242121732135037200010 Warm Springs strays 0611311011214303033200000 Buck Hollow juveniles 06440601209602021101000 Bakeoven juveniles 06 0231052131902034300000 Mainstem Deschutes lower 060220802020622400027000 Warm Springs NOR juveniles2220128223325045220000 Mainstem Deschutes upper 060001100022221900061000 Trout Creek juveniles 0664120044110501410100000 Trout Creek juveniles 075137015431010512100000 Warm Springs NOR adults 07103002430201012410000 Mainstem Deschutes upper 0703511011031110020193000 Whychus Creek juveniles0000200010722000127000 Crane Prairie Reservoir 0000000000000000004000 Tumalo Creek juveniles0000001000000000000510 Oak Springs Hatchery adults0000000000000000000054

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Appendix 5. Pairwise FST values – all 21 collections. Bold loci are not statistically significant.

5 6 6 s 6 7 7 0 0 0 e 0 0 0 l i r s r r s r e t e n e t e 5 l 6 l s e p p 0 w u 0 w 6 7 u e v l s 5 6 p 0 0 p r s o d s o d i i 0 l 5 0 6 l u u u e y e a e j a n l y r s s o i s l s 0 s l 0 s s s r i i e e e v e l l n e y e s R y s e R e R e v r h n t n t t i i t e a e a e e h e e u r c u l O r l u O u n n O u j s v c t t i t i s v h v h h e e h e u t s a n N s n N N j e u c u c c v v c k a j j s l s e s s e s s s s s e R H i u u k H e v v e e j j e e g n g g g g e e e w w r n u n n u n n i s t e D j j D D k k D r e i t o i i o i i C i r g r v l r r l r e e r u l n l n e e a n p u m p p m p m p m s C i j o e o e r r r B u r S e S S e S e S e t v v t t C C t P o p e H H h l d s o o s s s k t t c e a S m n i k n e m m k e n m n m n r t i r r i r i u u r i y n u c k c k m k i a o o a a a a a a o h u a u a r r r u

Wa R S B M B W Wa B B M Wa M T T Wa M Wh C T O Warm Springs strays 05 0.0000 Round Butte Hatchery 0.0182 0.0000 Shitike juveniles 0.0164 0.0136 0.0000 Buck Hollow juveniles 05 0.0160 0.0161 0.0072 0.0000 Mainstem Deschutes lower 05 0.0705 0.0538 0.0277 0.0379 0.0000 Bakeoven juveniles 05 0.0129 0.0162 0.0197 0.0176 0.0620 0.0000 Warm Springs NOR adults 06 0.0133 0.0121 0.0067 0.0076 0.0373 0.0162 0.0000 Warm Springs strays 06 0.0005 0.0165 0.0177 0.0172 0.0715 0.0111 0.0149 0.0000 Buck Hollow juveniles 06 0.0081 0.0120 0.0154 0.0093 0.0495 0.0114 0.0097 0.0097 0.0000 Bakeoven juveniles 06 0.0130 0.0083 0.0068 0.0085 0.0419 0.0047 0.0078 0.0121 0.0057 0.0000 Mainstem Deschutes lower 06 0.0691 0.0484 0.0269 0.0410 0.0017 0.0604 0.0360 0.0689 0.0487 0.0427 0.0000 Warm Springs NOR juveniles 0.0169 0.0122 0.0072 0.0103 0.0351 0.0167 0.0040 0.0183 0.0120 0.0077 0.0311 0.0000 Mainstem Deschutes upper 06 0.0407 0.0313 0.0200 0.0288 0.0294 0.0391 0.0260 0.0419 0.0309 0.0250 0.0321 0.0254 0.0000 Trout Creek juveniles 06 0.0066 0.0103 0.0100 0.0056 0.0512 0.0109 0.0084 0.0070 0.0080 0.0069 0.0517 0.0094 0.0344 0.0000 Trout Creek juveniles 07 0.0068 0.0065 0.0091 0.0085 0.0530 0.0122 0.0083 0.0062 0.0078 0.0061 0.0487 0.0081 0.0338 0.0021 0.0000 Warm Springs NOR adults 07 0.0030 0.0137 0.0129 0.0178 0.0667 0.0075 0.0096 0.0044 0.0093 0.0074 0.0656 0.0106 0.0348 0.0086 0.0096 0.0000 Mainstem Deschutes upper 07 0.0311 0.0194 0.0082 0.0165 0.0233 0.0276 0.0136 0.0305 0.0214 0.0160 0.0260 0.0144 0.0080 0.0197 0.0187 0.0233 0.0000 Whychus Creek juveniles 0.0784 0.0615 0.0428 0.0548 0.0188 0.0698 0.0509 0.0789 0.0571 0.0530 0.0126 0.0442 0.0435 0.0616 0.0645 0.0767 0.0399 0.0000 Crane Prairie Reservoir 0.0654 0.0739 0.0764 0.0723 0.1129 0.0838 0.0703 0.0724 0.0765 0.0796 0.1223 0.0746 0.0754 0.0682 0.0740 0.0648 0.0720 0.1332 0.0000 Tumalo Creek juveniles 0.0497 0.0460 0.0400 0.0379 0.0728 0.0557 0.0383 0.0554 0.0518 0.0436 0.0819 0.0374 0.0537 0.0405 0.0475 0.0422 0.0468 0.0890 0.0402 0.0000 Oak Springs Hatchery 0.1586 0.1767 0.1851 0.1799 0.2314 0.1867 0.1781 0.1696 0.1769 0.1897 0.2365 0.1807 0.1724 0.1729 0.1704 0.1664 0.1655 0.2489 0.1201 0.1737 0.0000

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