<p> Coral reefs on Florida&rsquo;s Reef Tract (FRT) are susceptible to many anthropogenic influences including controlled freshwater discharges and agricultural runoff as well as high natural environmental variability from seasonal rainfall, runoff and upwelling. To better understand coral population structure and responses to sublethal stressors, populations of the scleractinian coral <i> Montastraea cavernosa</i> in the northern FRT were examined using a combination of genomic and transcriptomic techniques. Microsatellite genetic markers identified high local retention among sites and a slight southward gene flow. An _in-situ temporal gene expression analysis utilizing a tag-based sequencing transcriptomic approach was used to analyze baseline coral health at St. Lucie Reef (SLR), off Stuart, FL. Temporal variation had the greatest influence of differential gene expression among <i>M. cavernosa</i> at SLR. Results will be shared with local resource managers and coupled with a complementary <i> ex-situ</i> experimental trial.</p><p>

<p> The predominant method to quantify reef fish populations is the Open Circuit SCUBA (OC) <i>in-situ</i> fish survey. However, there are many biases associated with these surveys including the expelled OC exhaust which can cause visual and audible disturbances. This study aims to evaluate the bias created by OC exhaust utilizing closed-circuit rebreather (CCR) surveys, along surveys were conducted in protected areas and fished areas. The three sites in the main Hawaiian Islands were Kealakekua Bay (KK), Old Kona Airport (OA), and P&umacr;p&umacr;kea (PK) marine life conservation district. This study found that the total fish biomass and species richness from all sites pooled showed no significant differences between gear types. However, there was a significant interaction between the gear type and the protection status (Pr(>|t|) = 0.025), indicating that there are greater differences between OC and CCR in the fished areas than the protected areas. The difference between the gear types showed a greater magnitude of OC having a higher biomass in the fished areas opposed to the protected areas where that difference was smaller. When fished species (Table 4 &ndash; a, b) were examined, significant differences between gear types were shown (Pr(>|t|) = 0.010). The OC surveys showed more fished biomass than the CCR surveys which could mean that the attraction to the exhaust within the protected areas were greater than the repulsion of the exhaust in the fished areas. Differences in the fished species biomass while having no difference in the all fish biomass supports the previous studies findings that fishing pressure is very influential on the magnitude of difference between the gear types. For researchers, estimating fishing pressure is of high importance in order to assess the level of bias associated with OC exhaust on surveys. These biases need to be accounted for in population estimations for protected areas and non-protected areas in order to get more accurate biological fish data.</p><p>

Two rare Banksia species, B. chamaephyton A.S. George and B. elegans Meissner, were the subject of this study. B. chamaephyton is gazetted as rare under the Wildlife Conservation Act of Western Australia and B. elegans has been recorded by various authors as restricted in range and habitat.Data were collected on the distribution, habitat, reproduction and fire responses of each species. Both were found to occur predominantly in the Irwin Botanical District. B. chamaephyton is found in low heath on sand over laterite and B. elegans in scrub or thickets on deep, yellow sands. Data on species co-occurring with B. chamaephyton were gathered for the purpose of identifying habitats with actual or potential populations of the rare species. Several species appeared to be reliable indicators.Both species are represented in areas set aside for conservation although some populations are vulnerable and their loss would considerably reduce the range of each species. Of particular concern are the southernmost populations of B. chamaephyton and the northernmost populations of B. elegans. The latter appears to represent a size variant within the species. Although neither species is currently endangered, it is recommended that B. chamaephyton remain a gazetted rare species and that consideration be given to the gazettal of B. elegans.Both species are xenogamous and probably bird-pollinated although pollination by small mammals is a possibility. Both also have very low fruit and seed set. In B. chamaephyton, this is probably related to resource availability but B. elegans possesses a malformed stigma which may prevent the normal reproductive process from taking place. Most populations of B. elegans are sterile. Further research into the sexual reproduction and propagation of B. elegans is recommended.Fire is important to both species. In B. chamaephyton, fire, together with subsequent ++ / wet/dry cycles, is necessary for seed release from the follicles. Seedling recruitment is negligible in B. elegans. Mature individuals of both species survive fire and in B. elegans fire stimulates root suckering. Autumn burns appear to be most suitable for recruitment in both species, preferably at a minimum interval of ten years.

<p> River-associated birds may be valuable indicators of environmental change in riverine ecosystems because they are predators of fishes and therefore often top predators in the aquatic food web. To evaluate the likely scope of one form of change - river restoration through dam removal and the expected return of abundant diadromous fish prey - we: 1) developed an appropriate river bird survey protocol; 2) documented the relative importance of sea-run fish in the diet of four river bird species, bald eagle (<i>Haliaeetus leucocephalus</i>), osprey (<i>Pandion haliaetus</i>), belted kingfisher (<i>Megaceryle alcyon</i>), and tree swallow (<i> Tachycineta bicolor</i>); 3) documented nest distribution and brood size of osprey; and 4) investigated the relationships between river bird abundance and various habitat parameters. We expect these measures will reflect changes to the river system post-dam removal as diadromous fish populations recover, proliferate, and integrate into the food web. Based on species accumulation curves and first-order Jacknifes, we concluded that biweekly or triweekly I5 minute surveys are sufficient to meet our objectives. Within the Penobscot River, stable isotope analysis of river bird diets indicated that marine nutrients are consumed by bald eagle, osprey, and belted kingfishers that reside below the lowermost dam, but not tree swallows. Despite greater connectivity for and abundance of spawning diadromous fishes (particularly river herring), in the Kennebec and Sebasticook Rivers as compare to the Penobscot River, osprey brood size was not significantly larger. We suspect other factors such as competition with bald eagles may be limiting the benefit of large river herring runs to nesting osprey. Finally, an ordination of 26 river bird species and 5 single-species (invertivore - spotted sandpiper, piscivore - osprey; piscivore - bald eagle; insectivore - tree Swallow; and omnivore - American black duck) generalized linear models, I revealed associations between estimated species abundance and water flow, water level, distance from the river mouth (river kilometer), site position in relation to a dam (e.g. above, below, or not at a dam), and adjacent land cover composition.</p>

<p> Marine resources are characteristically patchy and concealed beneath the surface of a "featureless" ocean, which makes facilitative species interactions especially advantageous to seabirds. My research addresses how behavioral mechanisms accommodate prey availability, or more specifically, how common (<i>Sterna hirundo</i>) and roseate terns (<i>S. dougallii </i>) locate and access food when it is not easily detectable. I study their foraging behavior and ecology from pre- to post-breeding, offshore in the pelagic realm (chapter 1), around the colony (chapter 2), and in nearshore waters (chapter 3). My first chapter tests the hypothesis that, as broadly-ranging seabirds, common and roseate terns forage over habitat where marine mammals and predatory fish help to find and access prey. I quantify the spatial association among foraging terns, tunas, dolphins, and their habitat, using Bayesian hierarchical models, and tests of behavioral community interactions. Facilitation explains how terns benefit from subsurface predators through local enhancement and commensal relationships: foraging tunas improve the detection and availability of prey by signaling their presence, and driving them to the surface. Chapter 2 evaluates the link between resource utilization and foraging strategy, measured by nest provisioning and patterns among foraging routes or feeding flocks. I propose that the opportunistic generalists, common terns, depend more on social cues than the specialists, roseate terns, which rely more heavily on spatial memory to find predictable prey. The results support this and suggest that increased breeding and foraging success in roseate terns relates to higher quality and abundance in their preferred prey, sandlance (<i>Ammodytes </i> spp.); in contrast, common terns seem to endure prey limitation through their use of local enhancement. In my third chapter, I hypothesize that habitat variability and prey availability predict interspecific differences in tern foraging. Behavioral tests and density-surface models, with distance sampling, show that foraging common and roseate terns respond positively to the distribution and abundance of each other and their preferred prey. Clearly, common and roseate terns use conspecifics, heterospecifics and subsurface predators to encounter prey via facilitation: such interactions create dynamic hotspots that need to be considered in an ecosystem approach to marine spatial planning.</p>

<p> Abstract As invasive predators spread across landscapes, their sudden presence may have significant effects on the behavior patterns of their new found prey. Here, I examined how predator-naive foxes responded to colonization by non-native golden eagles on Santa Cruz Island, California. First, using radio-telemetry, I investigated the effects of this diurnal, aerial predator on fox activity patterns. In 1992, just prior to the arrival of golden eagles, foxes showed substantial diurnal activity, but diurnal activity was 37.0% lower in 2003-7, after golden eagle colonization; concurrently, overall activity declined and nocturnal activity increased. Moreover, on nearby Santa Catalina Island, where golden eagles were absent but where the fox population recently crashed due to a disease epidemic, remaining foxes were significantly more diurnally active than were those on Santa Cruz Island. The weight of evidence suggested that the change in activity pattern was a response to predation, not to low population density, and that this was probably a heritable, rather than a learned, behavioral trait. Second, I used radio-telemetry, camera traps, sightings to investigate spatial patterns and habitat use in the wake of eagle colonization. When comparing pre- and post-colonization conditions, foxes demonstrated an inverse home range-density relationship, as fox core areas and home ranges expanded significantly in the low-density conditions following eagle colonization. I found that diurnal ranges were 11% smaller than nocturnal home ranges in post-colonization conditions, perhaps reflecting restricted diurnal movement as a form of predator avoidance of the diurnally hunting eagles. In terms of habitat preference, foxes preferred shrubland &ndash; a habitat which provides cover from aerial predators &ndash; over other habitat types. This suggested a way in which foxes may have mitigated golden eagle predation risk. Finally, I examined changes in fox diet before and after colonization using scat analysis. Because this invasion reduced the endemic fox population by 95% in a decade, these dietary changes could have been be attributed to behavioral change (e.g., reduced diurnal activity and movement), demographic change (e.g., reduced intra-specific density), and/or community level change (e.g., increased intra-specific competition with island spotted skunks), all of which were shifts associated with eagle predation. Concurrently, there were marked changes in the island's vegetation community, with the removal of introduced grazers and the subsequent increase in recruitment of shrubland. I hypothesized that these effects would cause fox diets to differ from historic diets, as indicated by scat analysis. I also evaluated seasonal differences and dietary breadth in the post-eagle colonization period. Although I did not observe an overall large scale modification of fox dietary patterns, statistically significant dietary changes were observed before and after eagle colonization. Results suggested that all four factors may have had an effect on fox diet, although evidence suggested that grazer removal may have had a more pronounced effect. Seasonal patterns and dietary breadth reflected the seasonal availability of fruiting shrubs in the dry season, and an emphasis on other food items, primarily mice and insects, in the wet season, as expected. While this fox population has subsequently rebounded successfully, understanding how animals respond to the sudden arrival of an invasive predator is crucial to improving approaches to conserving endangered species in the future.</p>

<p> Identity and intensity of parasitism have been shown to be correlated to the host genotype at the major histocompatibility complex (MHC), a genomic region involved in the adaptive immune response. However, the evolutionary mechanisms by which parasites exert a selective force on host immune systems are unknown. This thesis investigates the relationship between parasitism and MHC genotype in two bear populations in Southcentral Alaska. We diagnosed infection using the polymerase chain reaction (PCR), targeting the ribosomal subunit of 18S of common blood parasites. Parasitism was detected in half of brown bears and 75% of black bears. We detected <i>Eimeria</i> spp. and several species of apicomplexan and nematode parasites, and we report here the first finding of <i>Trypanosoma cruzi</i> in Alaskan bears. We found no association between MHC genotype and identity or intensity of infection, suggesting that other loci or even non-genetic factors are important covariates in predicting infection status.</p>

<p> Noise associated with human activity is widespread and expanding rapidly in terrestrial environments, but there is still much to learn about its effects on animals. To determine the effect of introduced noise on lek attendance and strutting behavior, I played back recorded continuous and intermittent anthropogenic sounds associated with natural gas drilling and roads at leks of Greater Sage-Grouse (<i>Centrocercus urophasianus</i>). For 3 breeding seasons, I monitored sage-grouse abundance at leks with and without noise. Peak male attendance (i.e., abundance) at leks experimentally treated with noise from natural gas drilling and roads decreased 29% and 73% respectively relative to paired controls. Decreases in abundance at leks treated with noise occurred in the first year of the study and were sustained throughout the experiment. There was limited evidence for an effect of noise playback on peak female attendance during the experiment or on male attendance the year after the experiment ended. These results suggest that sage-grouse avoid leks with anthropogenic noise and that intermittent noise has a greater effect on attendance than continuous noise. To quantify the potential for noise from natural gas infrastructure to mask sage-grouse vocalizations over both long and short distances, I analyzed both the individual notes of mating vocalizations produced by male sage-grouse and recordings of such noise. Noise produced by natural gas infrastructure is predicted to mask sage-grouse vocalizations substantially, reducing the active space of detection and discrimination of all vocalization components, particularly impacting notes that are low frequency and low amplitude. Such masking could increase the difficulty of mate assessment for lekking sage-grouse. Significant impacts to sage-grouse populations have been measured at noise levels that predict little to no masking. I investigated whether male sage-grouse adjust the repetition and timing of their strut displays in response to playback of noise associated with natural gas development. I compared the signaling behavior of male sage-grouse on leks with long-term drilling and road noise playback to that of males on similar leks with no noise playback. Males exposed to long-term drilling noise playback strutted at higher rates and in longer bouts than males on control leks, while males on road noise leks strutted at lower rates and in shorter bouts than males on control leks; these differences were only observed during close courtship, when strut rate is most important in influencing female mate choice. I did a short-term playback of intermittent traffic noise and compared the strut timing of individuals during noisy and quiet periods. Males performed fewer struts overall during noisy periods, but male strutting behavior was related to female proximity. Males that were not closely approached by females strutted less during noisy periods than quiet periods and males that engaged in close courtship with females strutted at similar rates during noisy and quiet periods, even when females were far away. Introduced noise associated with natural gas development causes large declines in sage-grouse lek attendance and is likely to cause substantial masking of sage-grouse vocalizations. However, masking is not likely to be the only mechanism of noise impact on this species. Sage-grouse may at least partially reduce masking impacts through behavioral plasticity, adjusting the timing of their signals in a manner that may reduce the impacts of masking on communication.</p>

<p> I theorize and offer some evidence that humans inadvertently risk exacerbating the loss of maintenance-dependent species on private land by using species-based land-use regulation to seek other benefits. Drawing evidence primarily from the US, I argue that such regulation poses a risk to maintenance-dependent species, that humans routinely disregard this risk, and that this disregard widely serves to defend the power of individuals and organizations to use such regulation to seek other benefits. I suggest this implies that with constraints on public funding, humans might improve the survival of some species by clarifying the purpose of such regulation and considering openly refraining from such regulation for some species. I also suggest such change might depend on articulating the issue as whether the survival of a species could ever depend on individuals having a right to conserve or maintain it without selectively incurring harm from regulation intended to save it.</p>

<p> Levee Lake is a forested wetland system located within a Mississippi River oxbow meander scar in the American Bottom of the Northern Section of the Lower Mississippi River Bottomlands Division (White 1978) that has not been developed or converted to agricultural land. Because of its relatively undisturbed status, Levee Lake is representative of a presettlement wetland. In 1976, Levee Lake was documented with a 93-acre Grade B shrub swamp/marsh/pond (SSMP) community, qualifying for the Illinois Natural Areas Inventory (INAI). Additionally, 129 acres of Grade C wet floodplain forest surrounding the SSMP community was recorded (Nyboer and Reeves 1976). </p><p> Nyboer and Reeves (1976) described Levee Lake as the largest complex of marsh, pond, and swamp communities representing presettlement American Bottom conditions. They also identified potential draining efforts at site perimeters. Based on regulatory agency and Illinois Natural History Survey (INHS) documents as well as historical aerial photographs, perimeter portions of the forested wetland system and adjoining properties were subjected to decades of clearing and draining efforts prior to and following the 1976 survey. </p><p> This study involved evaluating the current floristic composition, natural communities, and the overall quality of the Levee Lake wetland system. The information from the current evaluation was then compared to the 1976 survey to examine how recorded disturbances have affected the condition, communities, and quality of the Levee Lake wetland system. The hypothesis of this study was that documented clearing, draining, and subsequent hydrologic alterations would likely cause changes in plant composition and natural communities since the 1976 INAI survey. </p><p> To accomplish this task, the transect (Transect 1 or T1) that was used for vegetative sampling in 1976 was re-created and used as a benchmark for 2012 vegetative sampling. To compare the plant composition from 1976 to 2012, twenty 0.25 meter (m)2 sampling plots were established along Transect 1. At each plot (T1P1 through T1P20), the relative cover of each vascular plant species was recorded and the resulting species data evaluated. To provide additional plant data for the site, herbaceous, shrub, and tree sampling was conducted via the <i>Critical Trends Assessment Program</i> (CTAP) protocols. Vegetative sampling was conducted in late summer/fall of 2012. </p><p> To evaluate the overall plant quality of Levee Lake and the existing natural communities, existing vegetation outside of the aforementioned transects was also recorded in late summer/fall of 2012. The overall site conditions and natural communities were observed and recorded during site visits in 2011, 2012, and 2014. The current natural communities were determined by the vegetative sampling, the overall site observations, as well as available aerial photographs and images. </p><p> Based on the research and field work, the native plant composition suffered a reduction in quality. Additionally, communities suffered a reduction in quality and a shift in community type. A reduction in water levels caused severe woody encroachment of the SSMP community identified in 1976. Today, only approximately 0.58-acre [0.23 hectare (ha)] of Grade C marsh/pond community remains. In 1976, the pond community was considered an exceptional feature with the surrounding shrub swamp/marsh community considered a significant feature. Although most of the former 93-acre Grade B SSMP community suffered from severe woody encroachment, recent wetland restorations to the north and to the south appear to have aided in returning hydrology to this community. Herbaceous, shrub, and tree vegetation data collected in the CTAP plots provided further evidence of wetland and swamp conditions. The former SSMP community has evolved into a Grade C swamp/marsh/pond (SMP) community. An approximate 11.73-acre (4.75 ha) Grade D marsh/wet meadow has evolved in the southwestern region that was subjected to decades of clearing and draining disturbance (White 1978; White and Madany 1978). Further evidence of a shift in plant composition and communities between species along Transect 1 in 1976 and in 2012 was shown through the NMDS ordination and an ANOSIM test which showed that plot communities distinctly differ between the two years (Minchin 2013). (Abstract shortened by UMI.) </p><p> </p>