Demographic modeling of conservation strategies for the Yosemite toad (Anaxyrus canorus)

The Yosemite toad (Anaxyrus canorus) is an anuran species endemic to the Sierra Nevada in California that, like many amphibians globally, has suffered population declines. The documented decline in A. canorus populations across their historic range highlights the need for an effective management strategy to protect the species from future extirpation. For this study, I estimated survival rates of A. canorus using a Cormack-Jolly-Seber model populated with data from a demographic study. I then used a female-only post-birth pulse stochastic Lefkovitch matrix model using vital rates I estimated and from the literature to simulate the effect of different management scenarios and to optimize a supplementation or reintroduction management plan. Without any management action, small populations of A. canorus populations have ≥50% risk of quasi-extinction over the next 13 years. The implementation of effective management strategies is critical to prevent further extinction of existing small populations. My results suggest that the effectiveness of a supplementation or a reintroduction management plan is dependent on the initial population size of the receiving population, life stage at release and number of individuals released into a wild population. I found that supplementing small toad populations with female adults is the most effective supplementation strategy to increase the stochastic growth rate and minimize the risk of quasi-extinction. This thesis suggests that modeling A. canorus population dynamics and trends of extant populations can help inform conservation strategies

Complex Consequences of Herbivory and Interplant Cues in Three Annual Plants

Information exchange (or signaling) between plants following herbivore damage has recently been shown to affect plant responses to herbivory in relatively simple natural systems. In a large, manipulative field study using three annual plant species (Achyrachaena mollis, Lupinus nanus, and Sinapis arvensis), we tested whether experimental damage to a neighboring conspecific affected a plant's lifetime fitness and interactions with herbivores. By manipulating relatedness between plants, we assessed whether genetic relatedness of neighboring individuals influenced the outcome of having a damaged neighbor. Additionally, in laboratory feeding assays, we assessed whether damage to a neighboring plant specifically affected palatability to a generalist herbivore and, for S. arvensis, a specialist herbivore. Our study suggested a high level of contingency in the outcomes of plant signaling. For example, in the field, damaging a neighbor resulted in greater herbivory to A. mollis, but only when the damaged neighbor was a close relative. Similarly, in laboratory trials, the palatability of S. arvensis to a generalist herbivore increased after the plant was exposed to a damaged neighbor, while palatability to a specialist herbivore decreased. Across all species, damage to a neighbor resulted in decreased lifetime fitness, but only if neighbors were closely related. These results suggest that the outcomes of plant signaling within multi-species neighborhoods may be far more context-specific than has been previously shown. In particular, our study shows that herbivore interactions and signaling between plants are contingent on the genetic relationship between neighboring plants. Many factors affect the outcomes of plant signaling, and studies that clarify these factors will be necessary in order to assess the role of plant information exchange about herbivory in natural systems

Chapter Ten - Informing marine spatial planning decisions with environmental DNA

Marine management areas provide a key tool for efforts towards sustainable development, reconciling socio-economic goals with those for biodiversity conservation. Decisions about where and when to establish spatial management areas in the oceans are currently hampered by the uncertainties of incomplete, or overly general, information about biodiversity. The analysis of environmental DNA (eDNA) provides a potentially powerful tool to overcome this lack of data in the future. Here we present directions to develop robust approaches to integrate eDNA and spatial planning processes, aiming to provide guidance to underpin tool development. The potential of eDNA use in conservation is widely recognised, although direct applications almost exclusively focus on detection of invasive or threatened species and not spatial management decisions. The implementation of broader interaction between the fields of conservation science and eDNA analysis could create substantial benefits to biodiversity conservation and management. In particular, eDNA analysis can provide information on biodiversity over spatial-temporal scales that are currently prohibitive in spatial planning studies. Here, we provide an overview of how eDNA is currently used in conservation practice, in addition to understanding its limitations and benefits within the context of spatial planning. With the goal to harness rapid technological developments in both molecular and conservation sciences, we provide a horizon scan of the future of eDNA analysis and its application to inform biodiversity conservation in a rapidly changing world

Adapting molecular techniques in wilderness management and restoration in the Sierra Nevada

Analysis of aquatic environmental DNA (eDNA) is a promising tool for monitoring invasive species and determining population density. Previous applications of this method have been hindered by the inability to distinguish whether sources are alive or dead and whether quantities can reliably reflect population size. In part one of this study, we analyzed how the detection of eDNA from dead model organisms differs depending on collection method. In part two, we analyzed how the quantity of DNA collected over time and space relates to population density of trout. We sampled 15 microcosms containing dead or live goldfish using different filter membrane types and pore sizes and at varying depths. We detected DNA from dead individuals less frequently and in lower quantities compared with live individuals. DNA from dead individuals was found only at the bottom of the water column. As pore size increased, the quantity of DNA captured decreased for both treatments. Because dead individuals were associated with less DNA, using filters with larger pore sizes decreased detection of dead individuals. We applied our findings to restoration sites where non-native fish were being removed. We sampled completed restoration sites (sites containing only dead fish, N = 21) as well as active restoration sites (sites containing dead and live fish, N = 9) with 1.2 µm PCTE iv filters. Our field sampling accurately indicated the status of each site, with the exception of one likely false positive (low-level) and one false negative at a low-density site. Our results highlight that collection methods for eDNA can be tailored to maximize the utility of eDNA techniques in aquatic conservation. In part two of the study, we collected eDNA samples once a month for 4 months at 6 active restoration sites and 3 control sites containing populations of trout. We found that the density of DNA collected was related to the density of fish or biomass of fish removed the month prior. Small increases in eDNA density corresponded to large increases in trout density, therefore inherent variation in eDNA collection may provide an upper limit to the precision that can be obtained for abundance estimates

Asymmetric Information Measures: How to Extract Knowledge from an Expert So That the Expert\u27s Effort is Minimal

Knowledge acquisition is when we ask experts questions, and put the answers into the computer system. Since this is a very time-consuming task, it is desirable to minimize the effort of an expert. As a crude estimate for this effort, we can take a number of binary (yes-no) questions that we ask. The procedure that minimizes this number is binary search. This approach does not take into account that people often feel more comfortable answering yes than answering no . So, to make our estimates more realistic, we will take into consideration that for a negative answer the effort is bigger. This paper describes a procedure that minimizes the effort of an expert. We also estimate the effort of this optimal search procedure

Complex consequences of herbivory and interplant cues in three annual plants.

Information exchange (or signaling) between plants following herbivore damage has recently been shown to affect plant responses to herbivory in relatively simple natural systems. In a large, manipulative field study using three annual plant species (Achyrachaena mollis, Lupinus nanus, and Sinapis arvensis), we tested whether experimental damage to a neighboring conspecific affected a plant's lifetime fitness and interactions with herbivores. By manipulating relatedness between plants, we assessed whether genetic relatedness of neighboring individuals influenced the outcome of having a damaged neighbor. Additionally, in laboratory feeding assays, we assessed whether damage to a neighboring plant specifically affected palatability to a generalist herbivore and, for S. arvensis, a specialist herbivore. Our study suggested a high level of contingency in the outcomes of plant signaling. For example, in the field, damaging a neighbor resulted in greater herbivory to A. mollis, but only when the damaged neighbor was a close relative. Similarly, in laboratory trials, the palatability of S. arvensis to a generalist herbivore increased after the plant was exposed to a damaged neighbor, while palatability to a specialist herbivore decreased. Across all species, damage to a neighbor resulted in decreased lifetime fitness, but only if neighbors were closely related. These results suggest that the outcomes of plant signaling within multi-species neighborhoods may be far more context-specific than has been previously shown. In particular, our study shows that herbivore interactions and signaling between plants are contingent on the genetic relationship between neighboring plants. Many factors affect the outcomes of plant signaling, and studies that clarify these factors will be necessary in order to assess the role of plant information exchange about herbivory in natural systems