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Dammed Rivers: Genetic Signatures of Altered Flow Regimes in a River Breeding Frog (Rana boylii)


Ryan Peek

PhD Candidate, Ecology

2017/10/25 09:45am


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Acknowledgements

  • Mike Miller & Sean O'Rourke

  • Center for Watershed Sciences

  • Brad Shaffer

  • Amy Lind

  • Corey Luna, many field helpers, SYRCL, Sierra Streams Institute

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California Rivers

N. American freshwater species projected extinction rate is 5x higher than terrestrial animals (Ricciardi and Rasmussen, 1999)

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CA Anthropogenic Legacy: Mining

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CA Anthropogenic Legacy: Mining

Permanently changed the geomorphology/ecology of CA watersheds

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CA Anthropogenic Legacy: Mining

Permanently changed the geomorphology/ecology of CA watersheds

Estimated 8x more material excavated from Yuba/Bear/American Watersheds than during construction of entire Panama Canal

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CA Dammed Rivers

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CA Dammed Rivers

  • Over 1,400 large dams (NID 2007)

  • Residential energy demands expected to increase by 24% by 2035 (US EIA 2010)

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Foothill yellow-legged frogs (Rana boylii)

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Foothill yellow-legged frogs (Rana boylii)

  • Obligate river breeding frog, uses wide range of habitat, but has disappeared from over 50% of historical range

  • Being evaluated as candidate for state and federal listing under ESA

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Foothill yellow-legged frogs (Rana boylii)

  • Obligate river breeding frog, uses wide range of habitat, but has disappeared from over 50% of historical range

  • Being evaluated as candidate for state and federal listing under ESA

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BUT: Frogs Are Still Here!

Indian Creek, NF American watershed

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And Here:

Mainstem River, NF American watershed

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But barely holding on here: (Slate Ck: North Yuba)

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Frogs As Hydrologic Indicators

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Frogs As Hydrologic Indicators

  • R. boylii strongly linked with local hydrology, and thus the watershed history

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Frogs As Hydrologic Indicators

  • R. boylii strongly linked with local hydrology, and thus the watershed history

  • Spawning timing & habitat selection is tied to receding flow cues & increasing water temperatures

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Case Study

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Case Study

Has river (flow) regulation caused genetic fragmentation in R. boylii?

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Case Study

Has river (flow) regulation caused genetic fragmentation in R. boylii?

Can we quantify this genetic signature with specific hydrologic metrics of flow impairment?

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Case Study

Has river (flow) regulation caused genetic fragmentation in R. boylii?

Can we quantify this genetic signature with specific hydrologic metrics of flow impairment?

Use genome-wide methods (RADSeq/RAPTURE)1

[1] Ali et al. 2016

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Study Area

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Study Area: American Watershed

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Hydrographs: Unimpaired

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Hydrographs: Unimpaired

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Hydrographs: Impaired (Hydropeaking)

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Hydrographs: Impaired (Hydropeaking)

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RESULTS

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PCA: Assessing Population Structure

N. Sierra Nevada samples mostly show structure by watershed (n=7,548 SNPs)

-0.10-0.050.000.050.10-0.2-0.10.0
N. Sierra Nevada: PC1 (2.1%) / PC2 (1.37%)(BEA,REG)(MFA,REG)(MFY,REG)(NFA,UNREG)(NFF,REG)(NFY,UNREG)(SFA,REG)(SFY,REG)PC1PC2Riverreg
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PCA: Unimpaired Watershed

Limited structure, greater similarity across subpops. (n=8,739 SNPs)

-0.4-0.3-0.2-0.10.00.1-0.4-0.20.0
North Fork American: PC1 (1.59%) / PC2 (1.5%)NFANFA-BUNCNFA-EUCHDSNFA-EUCHUSNFA-INDCNFA-NFNFANFA-PONDNFA-ROBRNFA-SAICNFA-SHICNFA-SLARPC1PC2Pop
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PCA: Impaired (hydropeaking) Watershed

Strong structure, greater divergence across subpops. (n=8,854 SNPs)

-0.10.00.10.20.3-0.2-0.10.00.10.2
Middle Fork American: PC1 (6.14%) / PC2 (3.15%)MFA-AMECMFA-GASCMFA-TODCMFA-US-RNFMFA-SCRUB-LC-USRUB-USPHSFA-CAMIPC1PC2Pop
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FST (Wright 1950):

a measure of population differentiation due to genetic structure

  • Scaled 0=(panmixis) to 1=(completely different)

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FST vs. River Distance

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FST vs. Stream Order

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Genomic Variation

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Loss of genetic diversity in regulated systems >> unregulated

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Are metrics of flow strongest factor in genomic patterns?

Can we integrate genomics with environmental flow management?

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Boosted Regression Tree Models

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Summary:

Flow alteration is having a direct impact on a hydrologically sensitive species at a genomic level

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Summary:

Flow alteration is having a direct impact on a hydrologically sensitive species at a genomic level

The current population trajectory is highly concerning in Sierras

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Summary:

Flow alteration is having a direct impact on a hydrologically sensitive species at a genomic level

The current population trajectory is highly concerning in Sierras

Flow management and listing distinct population segments may afford some protection...

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Summary:

Flow alteration is having a direct impact on a hydrologically sensitive species at a genomic level

The current population trajectory is highly concerning in Sierras

Flow management and listing distinct population segments may afford some protection...

RAPTURE/RADSeq is a powerful & effective method

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Thank you!

Slides : ryanpeek.github.io/presentations

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Acknowledgements

  • Mike Miller & Sean O'Rourke

  • Center for Watershed Sciences

  • Brad Shaffer

  • Amy Lind

  • Corey Luna, many field helpers, SYRCL, Sierra Streams Institute

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