background-image: url(images/P1070160_frog.jpg) background-size: cover background-position: 50% 75% class: center, inverse, title-slide # River Regulation Decreases Genetic Health of a Sensitive Frog, *Rana boylii* .pull-left[ <br> ## Ryan Peek ### PhD Candidate, Ecology ### *2018/02/15* <br>  ] ??? ??? - 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. --- background-image: url(images/frogcatcher_connor.png) background-size: 450px background-position: 100% 15% class: left, inverse ## Acknowledgements .pull-left[ - ### Mike Miller & Sean O'Rourke - ### Center for Watershed Sciences - ### Brad Shaffer - ### Amy Lind - ### Corey Luna, many field helpers, SYRCL, Sierra Streams Institute ] --- background-image: url(https://photos.smugmug.com/Nature/Landscapes/Via-Ryan/Panoramas/i-ztXFpBQ/0/bbc3f297/XL/IMG_5190-XL.jpg) background-position: 10% 10% class: inverse, bottom ### "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*) ??? - 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) - 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. - North American freshwater species projected extinction rate is 5x higher than terrestrial animals (Ricciardi and Rasmussen, 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) --- background-image: url(https://photos.smugmug.com/Nature/Landscapes/Via-Ryan/Panoramas/i-cpNnd8s/0/4d5b3bff/XL/IMG_0709-XL.jpg) background-position: 10% 0% class: inverse, bottom, left ## The abridged history of Sierra Nevada Rivers -- - ### Rivers flow largely uninterrupted for 20,000+ years -- - ### Hydraulic Mining begins in 1853, banned in 1884. -- - ### Regulation via dams/diversion/hydropower (1930's-today) --- background-image: url(images/hydraulicMining.png) background-size: cover class: goldslide # 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** - Hydraulic mining removes 8x as much sediment as was excavated from Panama Canal. -First used by Edward Matteson near Nevada City, California in 1853 during the California Gold Rush. - Sawyer Decision in 1884, enjoined operation in tributaries to navigable streams and rivers. - Small scale mining recommences with Camminetti Act 1893 if small sediment dams built. Most mining of this type wiped out by 1891 flood. 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 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. --- background-image: url(images/dams_in_west.png) background-size: 500px background-position: 100% class: left # 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) -- .pull-left[ - **Over 1,400 large dams (NID 2007)** - **Residential energy demands expected to increase by 24% by 2035 (US EIA 2010)** ] --- background-image: url(images/MFA_11433500_1911_1986_facet1964.png) background-size: 820px background-position: 100% class: middle, center ### Unreg. flow patterns, high seasonality & predictability --- background-image: url(images/MFA_11433500_1911_1986_facet1968.png) background-size: 820px background-position: 100% class: middle, center ### Reg. flow patterns limit connectivity, disrupt predictability ??? **These altered flow regimes have affected freshwater species that evolved under natural flow patterns by limiting connectivity, reducing flow cues, and eliminating habitat.** --- background-image: url(images/pre_cowplot_predic_seas.png) background-size: 820px background-position: 100% class: top, center ### Pre-Dam Data from USGS --- background-image: url(images/post_cowplot_predic_seas.png) background-size: 820px background-position: 100% class: top, center ### Post-Dam Data from USGS --- background-image: url(images/IMGP0349.jpg) background-size: cover class: top, center, inverse ### Small populations with limited connectivity may have reduced adaptive potential, or genetic health ??? thus difficulty responding to current conditions as well as future environmental change... Populations in highly regulated rivers have strong genetic differentiation and evidence of bottlenecking --- class: inverse, left, top # Foothill yellow-legged frogs (*Rana boylii*) -- .pull-left[ - ### 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[  ] --- background-image: url(images/P1070476.JPG) background-size: cover class: top, inverse # *FYLF* make excellent hydrologic indicators -- .pull-right[ - ### *R. boylii* strongly linked with local hydrology, and thus the <span style="color:#FFD700;">hydrologic history</span> ] -- .pull-right[ - ### Spawning timing & habitat selection is tied to receding <span style="color:#1E90FF;">flow cues</span> & increasing <span style="color:#00BFFF;">water temperatures</span> ] ??? - ### 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** --- background-image: url(images/rabo_A_P1060730.jpg) background-size: 350px background-position: 95% 0% class: left, middle, inverse # Study ### Has river (flow) regulation caused genetic fragmentation in *R. boylii*? ### Can we quantify this genetic signature for specific hydrologic flow regimes? -- - ### Use genome-wide methods RADSeq/RAPTURE (*Ali et al. 2016*) ??? 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. - 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 --- background-image: url(images/fig_01_map_regtype_v3_resize_1-5c.png) background-size: cover background-position: 97% class: left, top ## Study Area --- background-image: url(images/fig_02_mean_ann_discharge_combined_noRUB_labs_AB.png) background-size: 900px background-position: 90% 95% class: left, top ## Annual and Hourly Flows by Regulation Type -- .pull-left[ <img src="images/eggs_closeup.png" height="100" width="120"> ### Egg Deposition Timing Matters... ] -- .pull-right[ <img src="images/desiccated_tads_crop.png" height="100" width="120"> ### To avoid scour or dessication ] ??? 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)` --- class: inverse, center, middle # RESULTS: Anomolous genetic pattern in highly regulated MF American watershed --- background-image: url(images/fig_03a_pca_sierra_thresh_vir.png) background-size: 850px class: left, bottom ### PCA: Northern Sierra Nevada <br> ??? Why does structure matter? Indicates loss of variation, potential limited connectivity, small population sizes, isolation, divergence, etc. --- background-image: url(images/fig_03b_pca_nfa_thresh_vir.png) background-size: 850px class: center, bottom ### PCA: Unimpaired NF American <br> ??? Limited structure, greater similarity across subpops. (n=8,739 SNPs) --- background-image: url(images/fig_03c_pca_mfa_thresh_vir.png) background-size: 900px class: center, middle ### PCA: Regulated MF American --- background-image: url(images/fig_03c_pca_mfa_thresh_vir_annot.png) background-size: 900px class: center, middle .pull-left[ ### Hydropeaking sites in MF American are strongly divergent ] <br> <br> <br> ??? Strong structure, greater divergence across subpops. (n=8,854 SNPs) --- class: inverse, middle ## Assessing Population Connectivity using F_ST (Wright 1950): ### a measure of population differentiation due to genetic structure - ### Scaled 0=(panmixis) to 1=(completely different) --- background-image: url(images/fig_04_fst_vs_dist_by_flowtype_mfa_nfmfa_resize.png) background-size: 880px background-position: 55% 15% class: right, top ## Mean F_ST vs. River Distance ??? Populations in highly regulated rivers have strong genetic differentiation and evidence of bottlenecking --- class: center, middle, inverse # Evidence of Bottlenecks/Limited Genetic Variation for Impaired Flow Types  --- background-image: url(images/fig_05b_theta_boxplot_regtype_bysite_facet_wsiteID_noY.png) background-size: 600px background-position: 0% 90% class: right, top <br> <br> <br> -- .pull-right[ ### Most populations in N Sierra show pattern of bottleneck ] <br> -- .pull-right[ ### Greater loss of genetic diversity in regulated systems ] <br> --- background-image: url(images/fig_05_theta_boxplot_signif_regtype_flipped_annot.png) background-size: 780px background-position: 50% 5% class: left, bottom <br> <br> ### Genetic differences between regulation types are significant. Wilcoxon rank-sum: bonferroni p<0.01 ??? Sample sizes at 100k: - NFA: 110 (50k=123), mainstem 36 - NFY: 18 (50k=22) - MFY: 25 (50k=31) - SFY: 39 (50k=49) - MFA-Hydro: 23 (50k=37) - FEA: 94 - BEAR: 33 (50k=49) - NFMFA: 18 (same) - RUB: 20 (same) - --- background-image: url(images/slate_ck_aerial_v2.png) background-size: 450px background-position: 100% 15% class: inverse, left .pull-left[ ## River regulation is the strongest predictor of population isolation, NOT distance! ] --- background-image: url(images/fig_06_relinf_brt_simple_v2.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 ] --- background-image: url(images/pca_fea_thresh_locality_colorblind.png) background-size: 900px class: middle, center ## PCA: Feather --- background-image: url(images/pca_rasi_all_25k_1v2_thresh_ANNOT.png) background-size: 900px class: top, left <br> ## PCA: Hybrids are RARE and Likely F1