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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)
]

???
???
 - Here to tell a story about rivers, and an organism which has evolved within these watersheds and yet what we see today is largely a very different ecosystem than what these species experienced 200+ years ago.

- As freshwater systems and biota are rapidly declining globally, conservation efforts will require assessment of the adaptive capacity of populations to rapid environmental change.

- Small populations with limited genetic diversity may have reduced adaptive potential and difficulty responding to future environmental change.

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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)*

???
**The face of the water, in time, became a wonderful book--a book that was a dead language to the uneducated passenger, but which told its mind to me without reserve… And it was not a book to be read once and thrown aside, for it had a new story to tell every day”
–Mark Twain (Two Views of the Mississippi, 1883)**

- Humans rely on freshwater systems not only for drinking water, but also for agriculture, transportation, energy production, industrial processes, waste disposal, and the extraction of fish and other products.

- Human settlements worldwide are concentrated near freshwater ecosystems &#8212; over half of the world’s population lives within 20 km of a permanent river (Small and Cohen, 1999).

- Freshwater fisheries valued globally at $5.58 billion/year and ecosystem services of wetlands valued $70 billion/year (IUCN Review, Darwall et al. 2008)

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# CA Anthropogenic Legacy: Mining

???
Hydraulic mining originated out of ancient Roman techniques that used water to excavate soft underground deposits.  Romans invented “hushing”, certain landscapes in Spain still bear marks of this highly invasive mining technique. called “hydraulicking” by miners of CA, technique still used to remove hillsides
--

### 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

???
First used by Edward Matteson near Nevada City, California in 1853 during the California Gold Rush.

By the mid-1880s, it is estimated that 11 million ounces of gold (worth approximately US$7.5 billion at mid-2006 prices) had been recovered by hydraulic mining in the California Gold Rush.

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# CA Dammed Rivers

???

Hydroelectric power generation comprises over half of all renewable energy generation in California (California Energy Commission 2010

Majority (84%) of dams are for:
47% Irrigation (n=709)
23% Water supply (n=342)
14% Hydroelectric (n=207)

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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

]

.pull-right[

![](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
]
--
.pull-right[
- ### Spawning timing & habitat selection is tied to receding flow cues & increasing water temperatures
]

???

- ### 90% of eggs observed in Sierras were in shallow, sheltered waters (n=147) (Bondi et al. 2013)
 - **< 0.67 m total depth**
 - **< 0.15 m/s velocity**

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# Case Study

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

???

Expect flow regulation to limit connectivity between populations, thus causing loss of genetic variation/diversity, inbreeding risk goes up and pop bottlenecks, risk of extirpation increases in small populations.

### 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*
]

???

- Methods like **RADSeq** leverage genome-wide genetic variation to provide insight into ecological/population health
- Many amphibian species cryptic/lack data, Large genome size, assessment and monitoring hard to do
- *restriction site-associated DNA sequencing*, highly efficient genotyping across thousands of individual samples for targeted loci
- For frogs, can sample with non-invasive methods using mouth swabs, or tadpole tail clips

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## Study Area

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### Study Area: American Watershed

???
These are already small populations! Mainstem may have been the source, or the highway that connected these tributary sites.

using the mean pairwise comparison value for Fst and mean river distance, so if 11 sites, approx 55 possible combinations `combn(11, m = 2)`

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### Hydrographs: Unimpaired

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<img src="images/eggs_closeup.png" height="100" width="120">
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### Hydrographs: Unimpaired

???
Flow management will become even more critical and difficult under warming climate (more rain/less snow, more extreme events and less predictable patterns)

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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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RAP911","PC1: 1.395101e-02 PC2: 0.0284895456 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP816","PC1: 1.457560e-02 PC2: 0.0474487103 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP866","PC1: 1.353053e-02 PC2: 0.0179743747 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP820","PC1: 1.057090e-02 PC2: 0.0171849024 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP843","PC1: 1.304478e-02 PC2: 0.0373853866 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP914","PC1: 7.497813e-03 PC2: 0.0465436003 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP912","PC1: 7.489201e-03 PC2: 0.0291600612 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP818","PC1: 1.778834e-02 PC2: 0.0398820618 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP863","PC1: -4.314430e-03 PC2: 0.0223230656 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP819","PC1: 1.369715e-02 PC2: 0.0475488868 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - RAP822","PC1: 7.551738e-03 PC2: 0.0279553933 reg: UNREG River: NFA paste(River, \"-\", ID): NFA - 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 - 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???
Why does structure matter? Indicates loss of variation, potential limited connectivity, small population sizes, isolation, divergence, etc.
---

### 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

???

- (i.e., small pops. with limited connectivity, low diversity)
- *RAPTURE/RADSeq* is a powerful and effective method
- Genomics should be an integral component in assessments & **monitoring** in future conservation efforts
- Targeted research assessing environmental flows & ecological traits across taxa (fish, BMI, frogs)

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

# Thank you!

.footnote[

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

]