Lyme_Study_Dataset_README

Lyme_Study_Dataset_READM

Prey Sample by OTU

Sequence counts in individual scat samples matching reference sequences of extant vertebrates (potential prey species of mesocarnivores) in the Santa Cruz Mountains. Scat samples were collected by citizen scientists on trails in seven Midpeninsula Open Space preserves and were all less than one week old

Predator Sample by OTU

Sequence counts in individual scat samples matching reference sequences of extant carnivores in the Santa Cruz Mountains. Scat samples were collected by citizen scientists on trails in seven Midpeninsula Open Space preserves and were all less than one week old

Environmental DNA from Residual Saliva for Efficient Noninvasive Genetic Monitoring of Brown Bears (<i>Ursus arctos</i>)

<div><p>Noninvasive genetic sampling is an important tool in wildlife ecology and management, typically relying on hair snaring or scat sampling techniques, but hair snaring is labor and cost intensive, and scats yield relatively low quality DNA. New approaches utilizing environmental DNA (eDNA) may provide supplementary, cost-effective tools for noninvasive genetic sampling. We tested whether eDNA from residual saliva on partially-consumed Pacific salmon (<i>Oncorhynchus</i> spp.) carcasses might yield suitable DNA quality for noninvasive monitoring of brown bears (<i>Ursus arctos</i>). We compared the efficiency of monitoring brown bear populations using both fecal DNA and salivary eDNA collected from partially-consumed salmon carcasses in Southeast Alaska. We swabbed a range of tissue types from 156 partially-consumed salmon carcasses from a midseason run of lakeshore-spawning sockeye (<i>O</i>. <i>nerka</i>) and a late season run of stream-spawning chum (<i>O</i>. <i>keta</i>) salmon in 2014. We also swabbed a total of 272 scats from the same locations. Saliva swabs collected from the braincases of salmon had the best amplification rate, followed by swabs taken from individual bite holes. Saliva collected from salmon carcasses identified unique individuals more quickly and required much less labor to locate than scat samples. Salmon carcass swabbing is a promising method to aid in efficient and affordable monitoring of bear populations, and suggests that the swabbing of food remains or consumed baits from other animals may be an additional cost-effective and valuable tool in the study of the ecology and population biology of many elusive and/or wide-ranging species.</p></div

Stock recruitment relationships for study systems, fit with the Ricker stock-recruitment model.

<p>The difference between recruitment and the replacement line is considered surplus production that can be sustainably harvested. This difference is maximized at <i>E_MSY</i>, but the lower and upper target escapements are often well below estimates of <i>E_MSY</i>. The escapement in the absence of the fishery, <i>E_m</i>, is estimated at the steady state of the Ricker model, which is best visualized at the intersection of the Ricker and replacement lines.</p

Relative Success of Different Salmon Swabbing Techniques.

<p>Braincases and bite holes were encountered most frequently, and also amplified at proportionally higher rates than other swabbing techniques.</p

Using bears to quantify the importance of salmon to wildlife.

<p>Mature salmon are (A) important prey to orcas, pinnipeds, salmon sharks, humans, and other predators in the marine domain before they (B) reach terrestrial and aquatic systems, where they supply annual pulses of marine-derived nutrients and are the dominant prey of grizzly bears. By leaving uneaten carcass remains in riparian areas, bears serve as vectors of salmon to terrestrial and aquatic systems, supplying nutrients and food to riparian vegetation, invertebrates, and vertebrate scavengers including canids, gulls, eagles, and mustelids. The importance of salmon to bears can be quantified with (C) the relationship between salmon density and salmon consumption by bears as determined by stable isotope analysis of 18 grizzly bear populations from British Columbia (BC) <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001303#pbio.1001303-Mowat1" target="_blank">[36]</a>. (D) Predicted salmon consumption by bears (gray bars with 95% confidence intervals) closely matches measured salmon consumption (green bars) as estimated by stable isotope analysis in bears from Rivers Inlet and Quesnel Lake in interior BC, and for the Ugashik and Egegik stocks combined in Bristol Bay, Alaska.</p

Detections by Sample Type.

<p>Number of detections by sample type for 12 individual brown bears identified from both saliva samples and scat swab samples collected in the Chilkoot valley near Haines, AK. Age classes, where noted, were determined based on scat diameter (for juveniles) or sightings of known individuals (for immature bears and adults).</p

Using bears for ecosystem-based management in Chilko and Quesnel.

<p>(A) The relative bear density (solid) and relative fisheries yield (hatched) across a range of sockeye salmon escapements in Chilko and Quesnel (Fraser River) systems from British Columbia (BC), Canada. Ecosystem-based escapement goals, <i>E_EBM</i>, occur where the curves meet, indicating that bears and fishery yields are equally reduced from their maxima (double-sided arrows). Increases in escapement from <i>E_MSY</i> (maximum sustainable yield escapements; dashed arrows) to <i>E_EBM</i> (dotted arrows) reduce harvests to some fraction of <i>MSY</i>. (B) Tradeoffs between loss in fisheries yield and increase in grizzly bear densities for escapements greater than those corresponding to MSY. Green dots indicate proposed ecosystem-based management escapements (<i>E_EBM</i>) for each system. Reduction in fishery yields can result in substantial increases in bear density. (C) However, increased salmon allocations to bears (gray) under <i>E_EBM</i> provide much higher nutrient subsidies to terrestrial and aquatic systems than either the percent increase in bear densities (red) or decrease in fishery yields (yellow), which we suggest is due to the shape of the stock-recruitment relationships.</p

Accounting for bears when setting escapement goals in Bristol Bay and Rivers Inlet.

<p>(A) Bear density as a function of sockeye salmon escapement relative to the expected bear density at the maximum observed escapement (solid blue line). Vertical black dashed lines indicate <i>E_MSY</i>. The lower and upper escapement goals are highlighted by green dotted lines. (B) Increasing escapements from the lower to upper goals can substantially increase bear density (lower dark-red bar). Further increases in escapement to <i>E_MSY</i> continue to increase bear density (upper light-red bar), but the benefit is somewhat less due to the saturating relationship between escapement and percent salmon in diet. Importantly, there is no expected tradeoff to increasing escapement; yields are expected to be higher at upper escapement goals (lower dark-yellow bar) and increase further until <i>E_MSY</i> (upper light-yellow bar). Although <i>E_MSY</i> and the response in fisheries yields are uncertain, especially for the Egegik stock, bear success can still be assessed at the tangible lower and upper escapement goals and beyond.</p