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020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
020213 wfsr 2012 johnson et al
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020213 wfsr 2012 johnson et al

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  1. The genetic structure of steelhead and spring Chinook salmon in the upper Willamette River, Oregon Marc A. Johnson1, Thomas A. Friesen1, David J. Teel2, Donald M. Van Doornik2 1Oregon Department of Fish and Wildlife,Corvallis Research Laboratory, 28655 Highway 34, Corvallis, OR 97333 2NOAA Fisheries, Northwest Fisheries Science Center, Manchester Research Laboratory, PO Box 130, Manchester, WA 98353
  2. Upper Willamette River Chinook and Steelhead Chinook salmon •Spring Chinook are native to the basin •Hatchery stocks founded from local, wild stocks •Integrated hatcheries •Minimize genetic divergence •Reduce consequences of HxW interactions introduction methods results summary questions Steelhead •Winter steelhead are native to some subbasins •Hatchery summer steelhead are not a native UWR stock •Segregated hatcheries •Reduce frequency of HxW interactions •Minimize natural production and interbreeding “One of the most serious problems faced by wild and hatchery populations is the permanent loss of genetic material. Not only can such losses affect the immediate performance of a stock, but they also limit its flexibility to respond to changing conditions in the future.” -Waples et al. 1990. Fisheries 15:19-25
  3. Willamette River Spring Chinook introduction methods results summary questions
  4. Objectives introduction methods results summary questions Describe how genetic diversity is distributed within and among hatchery and wild spring Chinook populations Evaluate how alternate wild integration and hatchery straying (migration) rates could affect genetic diversity
  5. Sampling introduction methods results summary questions Fin tissue collected from adult hatchery and wild spring Chinook •MF Willamette (H & W) •McKenzie (H & W) •Calapooia (W) •South Santiam (H & W) •North Santiam (H & W) •Molalla (W) •Clackamas (H & W) •Catherine Cr., Grande Ronde (H) “Wild” determined by adipose fin and no otolith thermal mark
  6. In the Lab Isolated genomic DNA Amplified and scored 17 microsatellites • 13 GAPS markers • 4 “immune-relevant” markers* An electrophoretogram for a single microsatellite locus from a Willamette River Chinook salmon. This individual is a heterozygote, with two major “peaks” representing the two different alleles, or character states, for this marker. *Tonteri et al. (2008) Molecular Ecology Resources 8:1486-1490 introduction methods results summary questions
  7. Data Analyses Describe how genetic diversity is distributed within and among hatchery and wild spring Chinook populations Estimated • Mean heterozygosity1 • Allelic richness2 • Pairwise θ1 Inferred • Phylogenetic relationships among hatchery and wild populations3 Tested • Locus-specific signatures of selection with FST outlier4 Evaluate how alternate wild integration and hatchery straying (migration) rates could affect genetic diversity Simulated • Effects of alternate migration rates on heterozygosity, θ, total allele count5 1 GENETIX – Belkhir et al. 2004. Available at http://kimura.univ-montp2.fr/genetix/ 2 FSTAT – Goudet. 1995.Journal of Heredity 86:485-486 3 CONTML – Felsenstein. 2009. Available at http://evolution.genetics.washington.edu/phylip/doc/ 4 LOSITAN – Antao et al. 2008. Bioinformatics 9: 323 5 NEMO – Guillaume & Rougemont. 2006. Bioinformatics 22:2556-2557 introduction methods results summary questions
  8. Samples introduction methods results summary questions Subbasin n wild n hatchery Clackamas 51 80 Molalla 8 - North Santiam 72 95 South Santiam 62 94 Calapooia - - McKenzie 67 95 Middle Fork Willamette 12 144 Catherine Creek - 33 Total 272 541 Total of 813 samples included in statistical analyses
  9. Heterozygosity & Allelic Richness • Higher heterozygosities in hatchery populations • No pattern of difference for allelic richness introduction methods results summary questions Subbasin Wild Ho Hatchery Ho Clackamas 0.752 0.815 Molalla 0.823 North Santiam 0.777 0.820 South Santiam 0.746 0.813 McKenzie 0.788 0.805 Middle Fork Willamette 0.620 0.818 Catherine Creek 0.735
  10. Heterozygosity and Allelic Richness RANK Population He Ho AR 1Lewis Hatchery (spring) 0.866 0.87 15.2 2Cowlitz Hatchery (spring) 0.861 0.853 14.9 3Klickitat River (spring) 0.864 0.846 15.9 4Kalama Hatchery (spring) 0.865 0.837 15.1 5McKenzie Hatchery (spring) 0.817 0.812 12.9 6North Santiam Hatchery (spring) 0.82 0.812 13.1 7Winthrop Hatchery, Carson stock (spring) 0.792 0.809 12.5 8Wenatchee River (spring) 0.795 0.803 13.4 9Tucannon River (spring)a 0.791 0.803 11.6 10Battle Creek (spring) 0.841 0.801 15 11Cle Elum Hatchery (spring) 0.816 0.796 13.2 12Red River (spring)a 0.795 0.795 13 13Entiat Hatchery (spring) 0.782 0.793 11.7 14Imnaha River (spring)a 0.783 0.793 12.7 15Sawtooth Hatchery (spring)a 0.79 0.793 13 16Dworshak Hatchery (spring)a 0.793 0.792 13.5 17Pahsimeroi River (spring)a 0.78 0.79 11.5 18Lochsa River–Powell Trap (spring)a 0.788 0.789 13.1 19Methow River (spring) 0.793 0.788 13.4 20Minam River (spring)a 0.79 0.788 13.5 21South Fork Clearwater (spring)a 0.785 0.782 12.8 22Big Creek-b (spring)a 0.76 0.782 11.3 23West Fork Yankee Fork (spring)a 0.758 0.779 10.3 24Marsh Creek (spring) 0.782 0.777 12.1 25Catherine Creek (spring)a 0.775 0.776 12.7 26Johnson Creek supplementation (spring)a 0.779 0.776 12.2 27Johnson Creek (spring)a 0.776 0.775 11.9 28Lolo Creek (spring)a 0.787 0.767 13.6 29Rapid River Hatchery (spring)a 0.762 0.767 11.3 30Big Creek-a (spring)a 0.754 0.764 11.7 31Lostine River (spring)a 0.754 0.763 11 32Secesh River (spring)a 0.773 0.763 12.1 33Newsome Creek (spring)a 0.765 0.76 12 34Shitike Creek (spring) 0.763 0.757 12.2 35East Fork Salmon River (spring)a 0.769 0.757 12 36John Day River (spring) 0.78 0.755 13.5 37Warm Springs Hatchery (spring) 0.725 0.728 10.9 Narum et al. 2010. Transactions of the American Fisheries Society 139:1465-1477 RANK Population He Ho AR 1Klickitat River (spring) 0.864 0.846 15.9 2Lewis Hatchery (spring) 0.866 0.87 15.2 3Kalama Hatchery (spring) 0.865 0.837 15.1 4Battle Creek (spring) 0.841 0.801 15 5Cowlitz Hatchery (spring) 0.861 0.853 14.9 6Lolo Creek (spring)a 0.787 0.767 13.6 7Dworshak Hatchery (spring)a 0.793 0.792 13.5 8Minam River (spring)a 0.79 0.788 13.5 9John Day River (spring) 0.78 0.755 13.5 10Wenatchee River (spring) 0.795 0.803 13.4 11Methow River (spring) 0.793 0.788 13.4 12Cle Elum Hatchery (spring) 0.816 0.796 13.2 13North Santiam Hatchery (spring) 0.82 0.812 13.1 14Lochsa River–Powell Trap (spring)a 0.788 0.789 13.1 15Red River (spring)a 0.795 0.795 13 16Sawtooth Hatchery (spring)a 0.79 0.793 13 17McKenzie Hatchery (spring) 0.817 0.812 12.9 18South Fork Clearwater (spring)a 0.785 0.782 12.8 19Imnaha River (spring)a 0.783 0.793 12.7 20Catherine Creek (spring)a 0.775 0.776 12.7 21Winthrop Hatchery, Carson stock (spring) 0.792 0.809 12.5 22Johnson Creek supplementation (spring)a 0.779 0.776 12.2 23Shitike Creek (spring) 0.763 0.757 12.2 24Marsh Creek (spring) 0.782 0.777 12.1 25Secesh River (spring)a 0.773 0.763 12.1 26Newsome Creek (spring)a 0.765 0.76 12 27East Fork Salmon River (spring)a 0.769 0.757 12 28Johnson Creek (spring)a 0.776 0.775 11.9 29Entiat Hatchery (spring) 0.782 0.793 11.7 30Big Creek-a (spring)a 0.754 0.764 11.7 31Tucannon River (spring)a 0.791 0.803 11.6 32Pahsimeroi River (spring)a 0.78 0.79 11.5 33Big Creek-b (spring)a 0.76 0.782 11.3 34Rapid River Hatchery (spring)a 0.762 0.767 11.3 35Lostine River (spring)a 0.754 0.763 11 36Warm Springs Hatchery (spring) 0.725 0.728 10.9 37West Fork Yankee Fork (spring)a 0.758 0.779 10.3
  11. Pairwise θ Values Small but significant values among subbasins Pairwise θ values among hatchery (H) and wild (W) origin spring Chinook populations from the Willamette River and Catherine Creek Hatchery (Grande Ronde River), estimated from genotypic data for 13 GAPS microsatellite loci. Values not significantly different from zero (p > 0.05) are indicated in bold. introduction methods results summary questions Clackamas Hatchery Clackamas Wild Willamette Hatchery McKenzie Hatchery McKenzie Wild N.Santiam Hatchery N. Santiam Wild S. Santiam Hatchery S. Santiam Wild Catherine Cr. H 0.111 0.106 0.106 0.107 0.102 0.100 0.110 0.099 0.104 Clackamas H 0.007 0.012 0.013 0.013 0.010 0.012 0.010 0.009 Clackamas W 0.004 0.003 0.003 0.004 0.005 0.002 0.001 Willamette H 0.007 0.006 0.008 0.009 0.003 0.004 McKenzie H 0.000 0.003 0.006 0.004 0.005 McKenzie W 0.004 0.006 0.004 0.003 N. Santiam H 0.002 0.005 0.005 N. Santiam W 0.005 0.005 S. Santiam H 0.000
  12. Phylogenetic Relationships Hatchery populations most similar to local wild populations introduction methods results summary questions Maximum likelihood trees depicting genetic relationships among hatchery (H) and wild origin (W) spring Chinook populations from the Willamette River and (right) Catherine Creek Hatchery population. Phylogeny inferred from genotypic data for 13 microsatellite loci. Branch lengths represent Cavalli-Sforza chord measures of genetic distances (Cavalli-Sforza and Edwards 1967). Bootstrap values are indicated for nodes with >50% support (left tree only). Branch lengths of the South Santiam H- South Santiam W-MF Willamette H clade are not significantly different from zero (95% confidence interval).
  13. Evidence of Selection • Among UWR populations: NO • UWR populations & Catherine Cr: YES introduction methods results summary questions Overall FST values for 17 microsatellite loci (markers) plotted against heterozygosity, as characterized from the Catherine Creek hatchery and nine Willamette River spring Chinook populations. Gray shaded area defines the 99.5% CI of expected FST values for all possible heterozygosities, constructed from 50,000 data simulations. Shaded areas indicate regions associated with positive (red) and balancing (yellow) selection.
  14. Simulations of Migration and Diversity Migration: Represents symmetrical pHOS and pNOB introduction methods results summary questions Generation 0 5 10 15 20 25 30 35 Heterozygosity 0.94 0.95 0.96 0.97 0.98 m = 0.00 m = 0.02 m = 0.05 m = 0.10 Generation 0 5 10 15 20 25 30 35 Theta -0.005 0.000 0.005 0.010 0.015 0.020 0.025 0.030 0.035 m = 0.00 m = 0.02 m = 0.05 m = 0.10 Migration of 5% preserves similar level of diversity as 10% Simulated change in mean heterozygosity and theta for 17 neutral microsatellite loci in hatchery and wild populations of McKenzie River spring Chinook. Data were simulated under four migration rates (m) across 30 generations.
  15. Simulations of Migration and Diversity Migration: Represents symmetrical pHOS and pNOB introduction methods results summary questions Migration of 5% preserves similar level of diversity as 10% Generation 0 5 10 15 20 25 30 35 MeanNumberofAlleles 29 30 31 32 33 34 35 36 37 m = 0.00 m = 0.02 m = 0.05 m = 0.10 Simulated change in total allele count for 17 neutral microsatellite loci in hatchery and wild populations of McKenzie River spring Chinook. Data were simulated under four migration rates (m) across 30 generations.
  16. introduction methods results summary questions Key Points • Heterozygosity in hatchery populations higher than in wilds • Genetic structure is weak but present among subbasins • Hatchery populations are genetically most similar to local wild populations • No evidence for locus-specific selection among Willamette populations • Selection appears to drive divergence between UWR and Catherine Creek populations at two of the loci examined • Symmetrical migration of 5% appeared to preserve most (neutral) genetic diversity – nearly as well as 10%
  17. Willamette River Steelhead introduction methods results summary questions
  18. Objectives introduction methods results summary questions Describe genetic structure among Oncorhynchus mykiss populations Estimate the proportion of summer steelhead among natural origin O. mykiss smolts sampled at Willamette Falls and other locations (subbasins) of the upper Willamette River Estimate the proportion of summer steelhead hybrids among natural origin O. mykiss smolts sampled at Willamette Falls and various locations (subbasins) of the upper Willamette River
  19. Sampling and Data Collection Sample Collections • Samples of known type– baseline and phylogeny • Unmarked juvenile and some adult O. mykiss • Juveniles • Willamette Falls (2009-2011) • Subbasins (2011; McKenzie 2005 & 2011) Data Collection • All samples genotyped at 15 GAPS microsatellite loci introduction methods results summary questions
  20. Analyses Describe genetic structure among Oncorhynchus mykiss populations Estimate the proportion of summer steelhead among natural origin O. mykiss smolts sampled at Willamette Falls and other locations (subbasins) of the upper Willamette River Genetic Stock Identification (GSI) • Constructed phylogeny to identify reporting groups1 • Unknown samples assigned with a Bayesian GSI approach2 Estimate the proportion of summer steelhead hybrids among natural origin O. mykiss smolts sampled at Willamette Falls and various locations (subbasins) of the upper Willamette River Introgression Analysis • Bayesian clustering method3 • Samples classified to group or hybrid group 1PHYLIP - Felsenstein. 2009. Available at http://evolution.genetics.washington.edu/phylip/doc/ 2ONCOR – Kalinowski. 2007. Available at http://www.montana.edu/kalinowski/Software/ONCOR.htm 3STRUCTURE – Pritchard et al. 2000. Genetics 155: 945-959. introduction methods results summary questions
  21. Introgression Analyses (continued) Introgression Analysis Based on a four-group stock structure, we estimated the proportion (q) of each individual’s genome descended from each group We then used q values to classify individual samples into the following general categories: introduction methods results summary questions Pure: q > 0.50 for a single population and q < 0.20 for all other populations Two-way hybrid: 0.20 < q < 0.80 for exactly two populations Three-way hybrid: 0.20 < q < 0.80 for exactly three populations S EW RB WW SxEW SxRB Percentq 0 20 40 60 80 100 SUMMER EAST-SIDE WINTER WEST-SIDE WINTER RAINBOW
  22. Willamette Oncorhynchus mykiss Van Doornik & Teel 2010 introduction methods results summary questions Neighbor-joining dendrogram of Cavalli-Sforza Edwards genetic distances among Willamette River steelhead populations. Bootstrap values (%) greater than 50% are shown. The last two digits of the brood year for the earliest samples are included in the sample names. Major groupings, which also correspond to the reporting groups used for GSI analyses, are circled.
  23. GSI of unmarked juvenile Oncorhynchus mykiss: Willamette Falls VanDoornik & Teel 2010, 2011, 2012 Location Year n EW S WW RB Willamette Falls 2009 240 88.3% 7.5% 4.2% 0.0% Willamette Falls 2010 287 78.0% 13.2% 8.7% 0.0% Willamette Falls 2011 56 89.3% 5.4% 5.4% 0.0% introduction methods results summary questions
  24. GSI of unmarked juvenile Oncorhynchus mykiss: Willamette River subbasins VanDoornik & Teel 2010, 2011, 2012 Location Year n EW S WW RB Willamette R., various mainstem 2011 29 58.6% 13.8% 0.0% 27.6% Santiam R., mouth 2011 11 90.9% 9.1% 0.0% 0.0% North Santiam R. 2011 36 94.4% 2.8% 0.0% 2.8% South Santiam R. 2011 27 100.0% 0.0% 0.0% 0.0% McKenzie R., Leaburg Bypass 2005 72 25.0% 75.0% 0.0% 0.0% McKenzie R., Leaburg Bypass 2011 91 27.5% 68.1% 0.0% 4.4% introduction methods results summary questions
  25. Genetic introgression introduction methods results summary questions KnownsUnknowns East-side Winter Rainbow Summer West-side Winter
  26. Genetic introgression: Juveniles Year Location n S EW RB WW SxWW SxEW SxRB WWxEW WWxRB EWxRB 3x Hybrid 2009 Willamette Falls 240 19 126 1 34 1 23 1 31 0 1 3 2010 Willamette Falls 287 39 144 1 37 4 29 0 25 0 3 5 2011 Willamette Falls 56 3 29 0 13 1 3 0 5 0 0 2 Percent of Total 10.5 51.3 0.3 14.4 1.0 9.4 0.2 10.5 0.0 0.7 1.7 2005 McKenzie R., Leaburg 72 56 1 0 0 1 11 1 1 0 0 1 2011 McKenzie R., Leaburg 91 63 2 4 0 1 11 6 0 0 2 2 Percent of Total 73.0 1.8 2.5 0.0 1.2 13.5 4.3 0.6 0.0 1.2 1.8 2010 Mainstem Willamette R. 30 3 10 10 0 1 1 0 0 0 5 0 Percent of Total 10.0 33.3 33.3 0.0 3.3 3.3 0.0 0.0 0.0 16.7 0.0 2011 N. Santiam R. 36 0 25 0 1 0 4 0 4 0 1 1 Percent of Total 0.0 69.4 0.0 2.8 0.0 11.1 0.0 11.1 0.0 2.8 2.8 2011 Santiam R., Mouth 11 0 6 2 0 0 1 0 1 0 0 1 Percent of Total 0.0 54.5 18.2 0.0 0.0 9.1 0.0 9.1 0.0 0.0 9.1 2011 S. Santiam R. 27 0 20 0 1 0 4 0 2 0 0 0 Percent of Total 0.0 74.1 0.0 3.7 0.0 14.8 0.0 7.4 0.0 0.0 0.0 introduction methods results summary questions
  27. Summer steelhead introgression introduction methods results summary questions q 0.0 0.2 0.4 0.6 0.8 1.0 Proportion 0.0 0.2 0.4 0.6 0.8 1.0 Willamette Falls 2009 n = 240 q 0.0 0.2 0.4 0.6 0.8 1.0 Proportion 0.0 0.2 0.4 0.6 0.8 1.0 Willamette Falls 2011 n = 56
  28. Summer steelhead introgression introduction methods results summary questions q 0.0 0.2 0.4 0.6 0.8 1.0 Proportion 0.0 0.2 0.4 0.6 0.8 1.0 North Santiam 2011 n = 36 q 0.0 0.2 0.4 0.6 0.8 1.0 Proportion 0.0 0.2 0.4 0.6 0.8 1.0 South Santiam 2011 n = 27 q 0.0 0.2 0.4 0.6 0.8 1.0 Proportion 0.0 0.2 0.4 0.6 0.8 1.0 McKenzie 2011 n = 91 q 0.0 0.2 0.4 0.6 0.8 1.0 Proportion 0.0 0.2 0.4 0.6 0.8 1.0 McKenzie 2005 n = 72
  29. introduction methods results summary questions Key Points • About ~10% of naturally produced juvenile steelhead sampled at Willamette Falls were summer-run type • Little evidence for natural production of pure summer steelhead in the Santiam rivers, but most juveniles from the McKenzie River were summer steelhead • Evidence for some genetic introgression from summer steelhead detected at all locations
  30. Questions? introduction methods results summary questions Acknowledgments ODFW Rich Carmichael, Hatchery managers, Field crews et al. Sample collections WDFW Jeffrey Grimm Otolith analyses OSU Michael Banks, Kathleen O’Malley, Amelia Whitcomb, Dave Jacobson et al. Genetic laboratory services USACE David Griffith, Rich Piaskowski, David Leonhardt et al. Funding
  31. Genetic introgression: Adults Year Location n S EW RB WW SxWW SxEW SxRB WWxEW WWxRB EWxRB 3x Hybrid 2009 S. Santiam R., Foster 50 0 42 0 0 0 5 0 2 0 1 0 Percent of Total 0.0 84.0 0.0 0.0 0.0 10.0 0.0 4.0 0.0 2.0 0.0 2004 N. Santiam R., Bennett 28 2 7 0 0 0 16 0 1 0 1 1 2009 N. Santiam R., Minto 11 0 8 0 0 0 2 0 1 0 0 0 2010 N. Santiam R., Minto 1 0 1 0 0 0 0 0 0 0 0 0 Percent of Total 5.0 40.0 0.0 0.0 0.0 45.0 0.0 5.0 0.0 2.5 2.5 2005 Mainstem Willamette R. 1 0 1 0 0 0 0 0 0 0 0 0 2010 Willamette R., Fall Cr. 19 0 16 0 0 0 0 0 0 0 3 0 2011 Willamette R., Fall Cr. 16 0 16 0 0 0 0 0 0 0 0 0 Percent of Total 0.0 91.7 0.0 0.0 0.0 0.0 0.0 0.0 0.0 8.3 0.0 2005 McKenzie R., Mohawk R. 1 0 1 0 0 0 0 0 0 0 0 0 2011 McKenzie R., Leaburg 6 3 0 1 0 0 1 1 0 0 0 0 Percent of Total 42.9 14.3 14.3 0.0 0.0 14.3 14.3 0.0 0.0 0.0 0.0 introduction methods results summary questions

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