Differentiating Chinook salmon with genetic markers

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Differentiating Chinook salmon with genetic
markers
Shawn Narum, Columbia River Inter-Tribal Fish
Commission Bill Arnsberg, Nez Perce Tribe
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Salmonid genome contains 3 billion nucleotides
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Sequencing data
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DNA Sequence Variation

• microsatellite
• di-nucleotide CT repeat
• di- and tetra-nucleotide markers common

• insertion/deletion (indel)
• Ex. 8 bp deletion
• 1 or more nucleotides

• SNP
• Any variation of the 4 nucleotides

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Different Marker Types
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Microsatellite DNA Genotyping
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SNP Genotyping
SNP (C/T)
T
DNA
T
Probes
Enzyme
Components of PCR reaction
Complimentary probe anneals to DNA
Fluorescent tag cleaved and detected
C. Smith
Adapted from C. Smith
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Variation in Functional Genes
Campbell and Narum 2008, Trans. Am. Fish. Soc.
Distinguish signals of adaptive divergence from
random genetic drift
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Clearwater River Chinook Salmon
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Clearwater River

• Watershed comprises 9,654 sq. miles
• Provides approx. 1/3 of the Snake River flow
• Lewiston Dam (Washington Water Power Dam)
• Constructed in 1927
• 4.5 miles upstream of Snake/Clearwater confluence
• Virtually eliminated salmon runs
• Removed in 1973
• Some Chinook may
• have persisted and
• recolonized after dam
• removal

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Chinook Salmon Reintroduced

• Ocean Type
• Successful reintroduction in 1997
• Lyons Ferry Hatchery broodstock
• NPTH production starting 2003
• Stream Type
• Successful reintroduction in 1970s
• Primary stock was Rapid River Hatchery

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Differences between Ocean (O) and Stream (S) Type
Chinook Salmon

• Adult spawning migration
• Ocean type fall
• Stream type spring
• Utilization of freshwater spawning habitat
• Ocean type tidewaters or lower sections of
  large rivers
• Stream type headwater tributaries
• Distinctive juvenile morphology and behavior
• Ocean type migrate to estuaries within three
  months
• Stream type migration to the open sea 1 years
• Genetic
• Genetic markers indicate reproductive isolation

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Can genetic markers identify spring and fall
Chinook juveniles?
Yearling (Stream-Type)
Subyearling (Ocean-Type)
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Distinctive microsatellite locus
Narum et al. 2004, Trans. Am. Fish. Soc.
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(No Transcript)
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Sample Sizes
Lyons Ferry Hat.
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Strong Assignment to Type
Reference samples 99.6 Assignment Success
Narum et al. 2007, Cons. Gen.
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Assignments by Size

• No clear distinction by length
• Proportion of juveniles assigned to stream-type
• 1998 13.0 stream-type
• 2000 20.7 stream-type
• 2002 36.0 stream-type

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Genetic Diversity Higher in Ocean-Type
Lyons F.
Carcass
Juv.
Stream
O
O
O
S
Juv.
Juv.
O
S
O
O
S
O
O
O
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Conclusions

• Reintroduced life history types remain
  reproductively isolated
• Adaption to specific environments
• Colonized habitats represented of each life
  history type
• Variation in fall Chinook life history is diverse
  (i.e., resevoir-type yearling migrants)

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Supplementation Broodstock

• Spring Chinook
• Genetic characteristics
• Lower diversity
• High population differentiation
• Broodstock utilize locally adapted stocks
• Fall Chinook
• Genetic characteristics
• Higher diversity
• Low population differentiation
• Broodstock utilize regional stocks for diversity

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Findings in Relation to Broader Studies

• Throughout Snake and Columbia
• Across the Pacific coast
• Will more genetic markers help differentiate fall
  Chinook stocks?
• Ongoing SNP genotyping

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Diversity Patterns Consistent Throughout Snake
River
Stream-type
Ocean-type
Significant among ocean- and stream-type life
history types (P lt0.001 for both He and AR),
but not within life history type
Stream-type
Ocean-type
Narum et al. 2007, Trans. Am. Fish. Soc.
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Genetic Bottleneck
Stream-type
Ocean-type
Narum et al. 2007, Trans. Am. Fish. Soc.
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Interior Columbia River fall Chinook most similar
to coastal and California populations
Narum et al. 2008, Mol. Ecol.
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Comparison of Genetic Markers
All 50 markers
13 microsatellites
Narum et al. 2008, Mol. Ecol.
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New SNP markers

• 96 SNP markers tested among fall Chinook
  populations
• Preliminary results
• High similarity between LFH and NPTH
• Indicate improved ability to distinguish Snake R.
  from Hanford collections
• Ongoing efforts to evaluate fall Chinook stocks
  Umatilla Hatchery, Deschutes, Methow R., Priest
  Rapids Hatchery
• Testing several other stocks (spring/summer/fall)
  from Columbia Snake River

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Summary

• Powerful suite of markers provides ability
• Parentage analysis to estimate RRS
• Fine scale population structure
• Accurate Genetic Stock ID (GSI)
• Test for natural selection and adaptation
• Marker choice best determined by
• Hypotheses being tested study
• Laboratory specific costs (i.e., available
  equipment)

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Questions?