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

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## Ryan Peek
### PhD Candidate, Ecology
### *2017/10/25 09:45am*
 
![](images/CWS_logo_small.png)
]

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## Acknowledgements

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- ### 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

### 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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- **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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- ### 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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![](images/rabo_range_poly.png)

]

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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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- ### *R. boylii* strongly linked with local hydrology, and thus the watershed history
]
--
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- ### Spawning timing & habitat selection is tied to receding flow cues & increasing water temperatures
]

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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

.footnote[
*[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)

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RAP860","PC1: 9.087438e-03 PC2: 0.0383067810 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP617","PC1: 9.395610e-03 PC2: 0.0311144752 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP801","PC1: 8.972926e-03 PC2: 0.0300795628 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP855","PC1: 1.280345e-02 PC2: 0.0126175617 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP809","PC1: 1.158714e-02 PC2: 0.0204643098 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP810","PC1: 1.343271e-02 PC2: 0.0252595507 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP805","PC1: 3.767045e-02 PC2: 0.0595503876 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP814","PC1: 7.509123e-03 PC2: 0.0400970742 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP846","PC1: 1.240047e-02 PC2: 0.0297817456 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP650","PC1: 1.068796e-02 PC2: 0.0303956052 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP827","PC1: 1.757084e-02 PC2: 0.0127110201 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP811","PC1: 9.925282e-03 PC2: 0.0224278574 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP804","PC1: 3.286912e-02 PC2: 0.0526840177 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP813","PC1: 1.075094e-02 PC2: 0.0447547578 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP771","PC1: 1.458599e-02 PC2: 0.0189155505 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP852","PC1: 1.375676e-02 PC2: 0.0305127104 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP799","PC1: 1.590755e-02 PC2: 0.0296383130 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP803","PC1: 1.171609e-02 PC2: 0.0409756932 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP798","PC1: 8.229187e-03 PC2: 0.0359447382 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP808","PC1: 1.751558e-02 PC2: 0.0300614053 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP806","PC1: 1.062543e-02 PC2: 0.0211972712 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP807","PC1: 6.742092e-05 PC2: 0.0373263855 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP800","PC1: 1.171601e-02 PC2: 0.0212335991 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP802","PC1: 3.065475e-02 PC2: 0.0506730604 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP868","PC1: 2.752680e-02 PC2: 0.0554634215 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP876","PC1: 1.284803e-02 PC2: 0.0447855238 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - AAA793","PC1: 2.384273e-02 PC2: 0.0450887238 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - AAA835","PC1: 1.641850e-03 PC2: 0.0427679539 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP-331","PC1: 3.276049e-02 PC2: 0.0648150366 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP871","PC1: 3.610712e-02 PC2: 0.0703360066 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP880","PC1: 1.188100e-02 PC2: 0.0396949694 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - AAA841","PC1: 2.143880e-02 PC2: 0.0572507166 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP869","PC1: 3.822726e-02 PC2: 0.0708362656 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP879","PC1: 2.367678e-02 PC2: 0.0476726386 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - AAA836","PC1: 1.272667e-02 PC2: 0.0504348168 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP-330","PC1: 3.370166e-02 PC2: 0.0687203212 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP870","PC1: 2.929014e-02 PC2: 0.0682443217 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP873","PC1: 6.882362e-03 PC2: 0.0512923358 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - AAA839","PC1: 2.726426e-02 PC2: 0.0709304642 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP874","PC1: 1.542383e-02 PC2: 0.0516451505 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - AAA840","PC1: 4.037148e-02 PC2: 0.0760965884 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP878","PC1: 1.004484e-02 PC2: 0.0532748842 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - AAA814","PC1: 3.167602e-02 PC2: 0.0656950127 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP877"],"type":"scatter","mode":"markers","marker":{"autocolorscale":false,"color":"rgba(39,127,142,1)","opacity":0.8,"size":11.3385826771654,"symbol":"triangle-up","line":{"width":1.88976377952756,"color":"rgba(39,127,142,1)"}},"hoveron":"points","name":"(NFA,UNREG)","legendgroup":"(NFA,UNREG)","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[-0.0327975819993901,-0.0378559160118753,-0.0319694922848234,-0.0441198222544484],"y":[-0.0798742626999417,-0.0826491602091805,-0.0712190108165439,-0.0868127488532363],"text":["PC1: -3.279758e-02 PC2: -0.0798742627 reg: REG River: NFF paste(River, \"-\", ID): NFF - RAP1616","PC1: -3.785592e-02 PC2: -0.0826491602 reg: REG River: NFF paste(River, \"-\", ID): NFF - RAP1568","PC1: -3.196949e-02 PC2: -0.0712190108 reg: REG River: NFF paste(River, \"-\", ID): NFF - RAP1592","PC1: -4.411982e-02 PC2: -0.0868127489 reg: REG River: NFF paste(River, \"-\", ID): NFF - RAP1604"],"type":"scatter","mode":"markers","marker":{"autocolorscale":false,"color":"rgba(31,161,135,1)","opacity":0.8,"size":11.3385826771654,"symbol":"circle","line":{"width":1.88976377952756,"color":"rgba(31,161,135,1)"}},"hoveron":"points","name":"(NFF,REG)","legendgroup":"(NFF,REG)","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[-0.071302012833613,-0.0742692354315407,-0.0780617711431095,-0.0810462324064236,-0.0798214298307373,-0.0808751453176241,-0.0742302535512652,-0.0680204986104853,-0.0610899612801079,-0.0692868606823704,-0.0605727290037246,-0.0754100853351571,-0.0751418553002866,-0.0785708758335312,-0.0843795678732264,-0.0893771579828917,-0.090302034795884,-0.0722578339204725],"y":[-0.025737121833031,-0.0311879796964974,-0.0334487975991232,-0.0361933714494161,-0.0378893098419771,-0.0446117689584891,-0.046756557946975,-0.0243715182826709,-0.0204013027008413,-0.0404689903206885,-0.0270178019662332,-0.0324412598319476,-0.0260959033420183,-0.0394054058727455,-0.0374088826072097,-0.0314976807506423,-0.0485995578757966,-0.0286003999391051],"text":["PC1: -7.130201e-02 PC2: -0.0257371218 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - RAP1697","PC1: -7.426924e-02 PC2: -0.0311879797 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - RAP1716","PC1: -7.806177e-02 PC2: -0.0334487976 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - RAP921","PC1: -8.104623e-02 PC2: -0.0361933714 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - RAP918","PC1: -7.982143e-02 PC2: -0.0378893098 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - RAP922","PC1: -8.087515e-02 PC2: -0.0446117690 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - RAP919","PC1: -7.423025e-02 PC2: -0.0467565579 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - RAP920","PC1: -6.802050e-02 PC2: -0.0243715183 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - RAP1683","PC1: -6.108996e-02 PC2: -0.0204013027 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - RAP1656","PC1: -6.928686e-02 PC2: -0.0404689903 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - RAP1689","PC1: -6.057273e-02 PC2: -0.0270178020 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - RAP1676","PC1: -7.541009e-02 PC2: -0.0324412598 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - AAA808","PC1: -7.514186e-02 PC2: -0.0260959033 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - AAA830","PC1: -7.857088e-02 PC2: -0.0394054059 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - AAA798","PC1: -8.437957e-02 PC2: -0.0374088826 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - AAB850","PC1: -8.937716e-02 PC2: -0.0314976808 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - AAA797","PC1: -9.030203e-02 PC2: -0.0485995579 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - AAA799","PC1: -7.225783e-02 PC2: -0.0286003999 reg: UNREG River: NFY paste(River, \"-\", ID): NFY - AAA800"],"type":"scatter","mode":"markers","marker":{"autocolorscale":false,"color":"rgba(74,193,109,1)","opacity":0.8,"size":11.3385826771654,"symbol":"triangle-up","line":{"width":1.88976377952756,"color":"rgba(74,193,109,1)"}},"hoveron":"points","name":"(NFY,UNREG)","legendgroup":"(NFY,UNREG)","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[0.113246501600054,0.12035726950368,0.122577354552341,0.119633869091745,0.124276859337525,0.116026994919435],"y":[-0.241005210336161,-0.23170686872412,-0.256365931678616,-0.254067135801777,-0.273030236886487,-0.245516104920138],"text":["PC1: 1.132465e-01 PC2: -0.2410052103 reg: REG River: SFA paste(River, \"-\", ID): SFA - RAP776","PC1: 1.203573e-01 PC2: -0.2317068687 reg: REG River: SFA paste(River, \"-\", ID): SFA - RAP781","PC1: 1.225774e-01 PC2: -0.2563659317 reg: REG River: SFA paste(River, \"-\", ID): SFA - RAP779","PC1: 1.196339e-01 PC2: -0.2540671358 reg: REG River: SFA paste(River, \"-\", ID): SFA - RAP778","PC1: 1.242769e-01 PC2: -0.2730302369 reg: REG River: SFA paste(River, \"-\", ID): SFA - RAP777","PC1: 1.160270e-01 PC2: -0.2455161049 reg: REG River: SFA paste(River, \"-\", ID): SFA - RAP780"],"type":"scatter","mode":"markers","marker":{"autocolorscale":false,"color":"rgba(159,218,58,1)","opacity":0.8,"size":11.3385826771654,"symbol":"circle","line":{"width":1.88976377952756,"color":"rgba(159,218,58,1)"}},"hoveron":"points","name":"(SFA,REG)","legendgroup":"(SFA,REG)","showlegend":true,"xaxis":"x","yaxis":"y","hoverinfo":"text","frame":null},{"x":[-0.0718768253589441,-0.0703076596161376,-0.0752047558492672,-0.064422314367479,-0.0669530005850492,-0.076459397595631,-0.0708155917764339,-0.0758623598350467,-0.0689873353367451,-0.0731358277772785,-0.0655938596008074,-0.0685930350548577,-0.0708563447880125,-0.0729719274508115,-0.0692007517254551,-0.0712516808956968,-0.0748569120199301,-0.07793449819612,-0.074366345515202,-0.0694612979544548,-0.0822879378866432,-0.0747208683008326,-0.0634611470729596,-0.0683608280594821,-0.0704476505766437,-0.0754082019668433,-0.0709154428073134,-0.0751086555171977,-0.0764666171826645,-0.0832777882048488,-0.0731452294371264,-0.0832843844479267,-0.0727494918128467,-0.0760508697626552,-0.0669551875092761,-0.0706018138945643,-0.0760269783017964,-0.0658775049534087,-0.0752258291017255],"y":[-0.00650054597826699,-0.0476775188282311,-0.0213715525837014,-0.0474130922354335,-0.0124567436380168,-0.0150106192301851,-0.018642444122637,-0.0267771257476557,-0.00580057226537476,-0.0223540032353169,-0.0157006624378648,-0.0372994491252885,-0.0170323419671984,-0.0201244829543685,-0.0185494467750898,-0.014387263554891,-0.0224058089263293,-0.0164046992894648,-0.0274867005823991,-0.0396390083588749,-0.0424716617722098,-0.0124715594415771,-0.0120283804495414,-0.0132398696744053,-0.0433970189287369,-0.0370935845675415,-0.020053448581255,-0.0243357375645866,-0.0223862241191893,-0.00897497723660082,-0.0183214203806525,-0.00230987203454451,-0.0198731355498498,-0.0187079226964053,-0.0062465815249342,0.000679597712126058,-0.0142053608999515,-0.0210732858246203,-0.00933023315067756],"text":["PC1: -7.187683e-02 PC2: -0.0065005460 reg: REG River: SFY paste(River, \"-\", ID): SFY - RAP-121","PC1: -7.030766e-02 PC2: -0.0476775188 reg: REG River: SFY paste(River, \"-\", ID): SFY - RAP-131","PC1: -7.520476e-02 PC2: -0.0213715526 reg: REG River: SFY paste(River, \"-\", ID): SFY - RAP-130","PC1: -6.442231e-02 PC2: -0.0474130922 reg: REG River: SFY paste(River, \"-\", ID): SFY - RAP-132","PC1: -6.695300e-02 PC2: -0.0124567436 reg: REG River: SFY paste(River, \"-\", ID): SFY - RAP-123","PC1: -7.645940e-02 PC2: -0.0150106192 reg: REG River: SFY paste(River, \"-\", ID): SFY - RAP-275","PC1: -7.081559e-02 PC2: -0.0186424441 reg: REG River: SFY paste(River, \"-\", ID): SFY - RAP-128","PC1: -7.586236e-02 PC2: -0.0267771257 reg: REG River: SFY paste(River, \"-\", ID): SFY - RAP-135","PC1: -6.898734e-02 PC2: -0.0058005723 reg: REG River: SFY paste(River, \"-\", ID): SFY - RAP-100","PC1: -7.313583e-02 PC2: -0.0223540032 reg: REG River: SFY paste(River, \"-\", ID): SFY - RAP-134","PC1: -6.559386e-02 PC2: -0.0157006624 reg: REG River: SFY paste(River, \"-\", ID): SFY - RAP-274","PC1: -6.859304e-02 PC2: -0.0372994491 reg: REG River: SFY paste(River, \"-\", ID): SFY - 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---

### PCA: Unimpaired Watershed
Limited structure, greater similarity across subpops. (n=8,739 SNPs)

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---

### PCA: Impaired (hydropeaking) Watershed
Strong structure, greater divergence across subpops. (n=8,854 SNPs)

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---
class: inverse, middle

## FST (Wright 1950):

### a measure of population differentiation due to genetic structure

- ### Scaled 0=(panmixis) to 1=(completely different)

---
background-image: url(images/fst_vs_meandist_regunreg.png)
background-size: 910px
background-position: 55% 15%
class: left, top

## FST vs. River Distance

---
background-image: url(images/fst_vs_streamorder.png)
background-size: 910px
background-position: 55% 15%
class: left, top

## FST vs. Stream Order

---
class: center, middle, inverse

# Genomic Variation

---
background-image: url(images/theta_boxplot_signif_annotated.png)
background-size: 850px
background-position: 65% 15%
class: center, bottom

### Loss of genetic diversity in regulated systems >> unregulated

---
class: inverse

## Are metrics of flow strongest factor in genomic patterns?

### Can we integrate genomics with environmental flow management?

---
background-image: url(images/relinf_brt_simple.png)
background-size: 900px
background-position: 55% 15%
class: left, bottom

## Boosted Regression Tree Models
---
class: left, top, inverse

# Summary:

.pull-left[
<img src="images/gray_fylf.png" height="220" width="300">
]

### 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

---
background-image: url(images/nfy_recession_bar.png)
background-size: cover
class: inverse

# Thank you!

.footnote[

### *Slides* : ryanpeek.github.io/presentations

]