No description available.

No description available.

Beluga whales in Canadian waters are subdivided into at least six genetically distinct stocks maintained by geographic separation and philopatry to estuaries in summer. Belugas in eastern and western Hudson Bay have previously been shown to be compose genetically distinct populations using mitochondrial restriction analysis. It is not known whether these stocks are further subdivided on the basis of specific estuarine use. Mitochondrial DNA control region sequences were used to investigate variation among belugas sampled at several sites along eastern Hudson Bay, Hudson Strait and Ungava Bay. 320 bp were sequenced, including the highly variable 5' region of control region, in 126 belugas. 17 variable sites and 17 haplotypes, which clustered into 2 related groups, were detected among the whales sequenced. Haplotypes of group A were found mostly in eastern Hudson Bay sites, while B group haplotypes were predominant in northern populations. Significant differences in frequencies of haplotype groups were found between eastern Hudson Bay and Southern Hudson Strait/Ungava Bay populations, indicating they are genetically distinct populations. Haplotype distribution patterns also suggested possible differences between belugas using different estuaries along eastern Hudson Bay. The presence of both groups in each population indicated some exchange of individuals between populations, and/or between eastern and western Hudson Bay. Multilocus DNA fingerprinting was used to investigate the extent of gene flow between eastern and western Hudson Bay belugas via interbreeding on common wintering grounds in Hudson Strait. Belugas from St. Lawrence estuary and the Mackenzie Delta were also analyzed to measure their genetic relatedness to Hudson Bay whales as well as for purposes of comparison to earlier fingerprinting analyses. While results supported lower genetic diversity within the St. Lawrence population, the range of bandsharing within and between populations was otherwise low (0.09 -0.17 for Jeffreys 33.15 and 0.12-0.22 for Jeffreys 33.6). Mantel tests showed differences among St. Lawrence, Hudson Bay, and Mackenzie Delta populations, but not within Hudson Bay. The conflicting nature of the data did not allow conclusions regarding gene flow. Therefore, DNA fingerprinting was not considered to have provided sufficient resolution in addressing this issue. / Thesis / Master of Science (MS)

The endangered St. Lawrence beluga (Delphinapterus leucas) population is not recovering from severe depletion despite its protected status over the past 20 years. DNA fingerprinting analysis of St. Lawrence beluga whales with three minisatellite probes (Jeffreys 33.6, 33.15 and Ml3) indicate a reduced level of genetic variability compared to Mackenzie Delta animals. The average band-sharing between individuals of the St. Lawrence beluga population for the three probes (0.534, 0.573, 0.478) was significantly higher than the average band-sharing of the Mackenzie Delta beluga population for the same probes (0.343, 0.424, 0.314). Higher levels of mean homozygosity in the isolated St. Lawrence belugas (0.33 vs 0.21) as well as a high degree of relatedness suggest that this population is inbred and that inbreeding depression is a factor in the lack of recovery of the St. Lawrence beluga population. Because sampling of some beluga populations may be biased, there is the need of alternative sampling procedures such as biopsy darting. To evaluate the impact of biopsy darting on beluga whales, different combinations of dart and stop sizes were tested on fresh beluga carcasses and the effect of different factors on the success of retrieval and the extent of wounding were evaluated. Tips with smaller diameters were more likely to retrieve a sample than those with larger diameters (p <0.05) and longer tips were also more likely to retrieve a sample than shorter tips (p < 0.10). The force of impact, a function of draw weight and distance, had a significant effect on the severity of wounding (p<0.05). The samples obtained from all biopsy darts tested yielded sufficient amounts of DNA for genetic analysis. / Thesis / Master of Science (MS)

No description available.

The detection and localization of important acoustic events in a complex urban environment, such as gunfire and explosions, is critical to providing effective surveillance of military and civilian areas and installations. In a complex environment, obstacles such as terrain or buildings introduce multipath propagations, reflections, and diffractions which make source localization challenging. This dissertation focuses on the problem of source localization in three-dimensional (3D) realistic urban environments. Two different localization techniques are developed to solve this problem: a) Beamforming using a few microphone phased arrays in conjunction with a high fidelity model and b) Fingerprinting using many dispersed microphones in conjunction with a low fidelity model of the environment. For an effective source localization technique using microphone phased arrays, several candidate beamformers are investigated using 2D and corresponding 3D numerical models. Among them, the most promising beamformers are chosen for further investigation using 3D large models. For realistic validation, localization error of the beamformers is analyzed for different levels of uncorrelated noise in the environment. Multiple-array processing is also considered to improve the overall localization performance. The sensitivity of the beamformers to uncertainties that cannot be easily accounted for (e.g. temperature gradient and unmodeled object) is then investigated. It is observed that evaluation in 3D models is critical to assess correctly the potential of the localization technique. The enhanced minimum variance distortionless response (EMVDR) is identified to be the only beamformer that has super-directivity property (i.e. accurate localization capability) and still robust to uncorrelated noise in the environment. It is also demonstrated that the detrimental effect of uncertainties in the modeling of the environment can be alleviated by incoherent multiple arrays. For efficient source localization technique using dispersed microphones in the environment, acoustic fingerprinting in conjunction with a diffused-based energy model is developed as an alternative to the beamforming technique. This approach is much simpler requiring only microphones rather than arrays. Moreover, it does not require an accurate modeling of the acoustic environment. The approach is validated using the 3D large models. The relationship between the localization accuracy and the number of dispersed microphones is investigated. The effect of the accuracy of the model is also addressed. The results show a progressive improvement in the source localization capabilities as the number of microphones increases. Moreover, it is shown that the fingerprints do not need to be very accurate for successful localization if enough microphones are dispersed in the environment. / Ph. D.

Legacy cyber-physical systems (CPSs) were designed without considering cybersecurity as a primary design tenet especially when considering their evolving operating environment. There are many examples of legacy systems including automotive control, navigation, transportation, and industrial control systems (ICSs), to name a few. To make matters worse, the cost of designing and deploying defenses in existing legacy infrastructure can be overwhelming as millions or even billions of legacy CPS systems are already in use. This economic angle, prevents the use of defenses that are not backward compatible. Moreover, any protection has to operate efficiently in resource constraint environments that are dynamic nature. Hence, the existing approaches that require ex- pensive additional hardware, propose a new protocol from scratch, or rely on complex numerical operations such as strong cryptographic solutions, are less likely to be deployed in practice. In this dissertation, we explore a variety of lightweight solutions for securing different existing CPSs without requiring any modifications to the original system design at hardware or protocol level. In particular, we use fingerprinting, crowdsourcing and deterministic models as alternative backwards- compatible defenses for securing vehicles, global positioning system (GPS) receivers, and a class of ICSs called supervisory control and data acquisition (SCADA) systems, respectively. We use fingerprinting to address the deficiencies in automobile cyber-security from the angle of controller area network (CAN) security. CAN protocol is the de-facto bus standard commonly used in the automotive industry for connecting electronic control units (ECUs) within a vehicle. The broadcast nature of this protocol, along with the lack of authentication or integrity guarantees, create a foothold for adversaries to perform arbitrary data injection or modification and impersonation attacks on the ECUs. We propose SIMPLE, a single-frame based physical layer identification for intrusion detection and prevention on such networks. Physical layer identification or fingerprinting is a method that takes advantage of the manufacturing inconsistencies in the hardware components that generate the analog signal for the CPS of our interest. It translates the manifestation of these inconsistencies, which appear in the analog signals, into unique features called fingerprints which can be used later on for authentication purposes. Our solution is resilient to ambient temperature, supply voltage value variations, or aging. Next, we use fingerprinting and crowdsourcing at two separate protection approaches leveraging two different perspectives for securing GPS receivers against spoofing attacks. GPS, is the most predominant non-authenticated navigation system. The security issues inherent into civilian GPS are exacerbated by the fact that its design and implementation are public knowledge. To address this problem, first we introduce Spotr, a GPS spoofing detection via device fingerprinting, that is able to determine the authenticity of signals based on their physical-layer similarity to the signals that are known to have originated from GPS satellites. More specifically, we are able to detect spoofing activities and track genuine signals over different times and locations and propagation effects related to environmental conditions. In a different approach at a higher level, we put forth Crowdsourcing GPS, a total solution for GPS spoofing detection, recovery and attacker localization. Crowdsourcing is a method where multiple entities share their observations of the environment and get together as a whole to make a more accurate or reliable decision on the status of the system. Crowdsourcing has the advantage of deployment with the less complexity and distributed cost, however its functionality is dependent on the adoption rate by the users. Here, we have two methods for implementing Crowdsourcing GPS. In the first method, the users in the crowd are aware of their approximate distance from other users using Bluetooth. They cross validate this approximate distance with the GPS-derived distance and in case of any discrepancy they report ongoing spoofing activities. This method is a strong candidate when the users in the crowd have a sparse distribution. It is also very effective when tackling multiple coordinated adversaries. For method II, we exploit the angular dispersion of the users with respect to the direction that the adversarial signal is being transmitted from. As a result, the users that are not facing the attacker will be safe. The reason for this is that human body mostly comprises of water and absorbs the weak adversarial GPS signal. The safe users will help the spoofed users find out that there is an ongoing attack and recover from it. Additionally, the angular information is used for localizing the adversary. This method is slightly more complex, and shows the best performance in dense areas. It is also designed based on the assumption that the spoofing attack is only terrestrial. Finally, we propose a tandem IDS to secure SCADA systems. SCADA systems play a critical role in most safety-critical infrastructures of ICSs. The evolution of communications technology has rendered modern SCADA systems and their connecting actuators and sensors vulnerable to malicious attacks on both physical and application layers. The conventional IDS that are built for securing SCADA systems are focused on a single layer of the system. With the tandem IDS we break this habit and propose a strong multi-layer solution which is able to expose a wide range of attack. To be more specific, the tandem IDS comprises of two parts, a traditional network IDS and a shadow replica. We design the shadow replica as a deterministic IDS. It performs a workflow analysis and makes sure the logical flow of the events in the SCADA controller and its connected devices maintain their expected states. Any deviation would be a malicious activity or a reliability issue. To model the application level events, we leverage finite state machines (FSMs) to compute the anticipated states of all of the devices. This is feasible because in many of the existing ICSs the flow of traffic and the resulting states and actions in the connected devices have a deterministic nature. Consequently, it leads to a reliable and free of uncertainty solution. Aside from detecting traditional network attacks, our approach bypasses the attacker in case it succeeds in taking over the devices and also maintains continuous service if the SCADA controller gets compromised. / Doctor of Philosophy / Our lives are entangled with cyber-physical systems (CPSs) on a daily basis. Examples of these systems are vehicles, navigation systems, transportation systems, industrial control systems, etc. CPSs are mostly legacy systems and were built with a focus on performance, overlooking security. Security was not considered in the design of these old systems and now they are dominantly used in our everyday life. After numerous demonstration of cyber hacks, the necessity of protecting the CPSs from adversarial activities is no longer ambiguous. Many of the advanced cryptographic techniques are far too complex to be implemented in the existing CPSs such as cars, satellites, etc. We attempt to secure such resource constraint systems using simple backward compatible techniques in this dissertation. We design cheap lightweight solutions, with no modifications to the original system. In part of our research, we use fingerprinting as a technique to secure passenger cars from being hacked, and GPS receivers from being spoofed. For a brief description of fingerprinting, we use the example of two identical T-shirts with the same size and design. They will always have subtle differences between them no matter how hard the tailor tried to make them identical. This means that there are no two T-shirts that are exactly identical. This idea, when applied to analog signalling on electric devices, is called fingerprinting. Here, we fingerprint the mini computers inside a car, which enables us to identify these computers and prevent hacking. We also use the signal levels to design fingerprints for GPS signals. We use the fingerprints to distinguish counterfeit GPS signals from the ones that have originated from genuine satellites. This summarizes two major contributions in the dissertation. Our earlier contribution to GPS security was effective, but it was heavily dependent on the underlying hardware, requiring extensive training for each radio receiver that it was protecting. To remove this dependence of training for the specific underlying hardware, we design and implement the next framework using defenses that require application-layer access. Thus, we proposed two methods that leverage crowdsourcing approaches to defend against GPS spoofing attacks and, at the same time, improve the accuracy of localization for commodity mobile devices. Crowdsourcing is a method were several devices agree to share their information with each other. In this work, GPS users share their location and direction information, and in case of any discrepancy they figure that they are under attack and cooperate to recover from it. Last, we shift the gear to the industrial control systems (ICSs) and propose a novel IDS to protect them against various cyber attacks. Unlike the conventional IDSs that are focused on one of the layers of the system, our IDS comprises of two main components. A conventional component that exposes traditional attacks and a second component called a shadow replica. The replica mimics the behavior of the system and compares it with that of the actual system in a real-time manner. In case of any deviation between the two, it detects attacks that target the logical flow of the events in the system. Note that such attacks are more sophisticated and difficult to detect because they do not leave any obvious footprints behind. Upon detection of attacks on the original controller, our replica takes over the responsibilities of the original ICS controller and provides service continuity.

External fertilization makes male anurans susceptible to direct intrasexual competition for fertilization opportunities at the egg mass. The red-eyed treefrog, Agalychnis callidryas, is one species in which pairs of males appear to simultaneously fertilize the clutch of a Single female. DNA fingerprinting revealed the presence of multiple paternity in two egg clutches examined from two matings involving a female with two males. The breeding biology of females and the potential costs and benefits of mating with multiple males were examined. Females were found to decrease the number of eggs in matings with multiple males. In addition, amplexed females moving toward Oviposition sites avoided secondary males by moving when approached by secondary males. Mortality to the eggs as a result of multiple males attempting to amplex females is suggested as the reason females avoid multiple males. Males were found to exhibit calling site defense from other males. Males used a combination of auditory and a visual behavior in defending calling sites. The call types are described and the contexts within which calls occur is discussed. Density of frogs was found to be a better indicator of the occurrence of matings involving multiple males than the operational sex ratio (number of males/number of females). / Ph. D.

Escherichia coli is part of the normal gastrointestinal microbiota of many animals, especially cattle. While most strains are commensal, Shiga toxin-producing E. coli (STEC) can cause severe human illness. Pathogenicity of STEC is associated with genes such as those encoding Shiga toxins, enterohemolysin, and intimin. By targeting these genes, highly sensitive molecular-based techniques help detect potentially harmful STEC. Persistent carriers and environmental contamination may be responsible for maintenance of STEC in cattle farms. Prevalence may be further influenced by diet, distance to contaminated water-sources, wildlife contact, slurry application to pasture, and population density. Relevance in environmental contamination is expected proportional to the amount of STEC shed in feces, but there is no consensus as to which production stage/age is most important. Distribution and transmission of STEC O157 are widely studied, but risk factors for non-O157 STEC are not as well defined. Understanding what contributes for contamination of animals prior to concentration in high-density feedlots may reveal opportunities for upstream control of shedding and transmission. Our purpose was to: (a) determine prevalence of STEC in fecal samples from animals in a cow-calf pasture-based production system; (b) describe effects of age class (dam, calf), spatial distribution of cattle, and time-point of sampling on distribution of strains positive for virulence genes stx1, stx2, eaeA, and hlyA; (c) isolate and identify serotypes present in stx-positive samples; and (d) assess genetic similarity of isolates. Understanding factors that influence distribution of STEC strains may help support on-farm management strategies with potential to yield safer beef products. / Master of Science

The hermaphroditic fish, Rivulus marmoratus, is the only vertebrate known to reproduce by internal self-fertilization; this process results in populations of homozygous clones. Most natural populations consist entirely of hermaphrodites, but phenotypically distinct, fertile males occur at frequencies up to 24% on some islands off the coast of Belize. The presence of large numbers of males in natural populations prompted this study to determine if males are involved in the mating system. The occurrence of cross-fertilization between males and hermaphrodites was determined by surveying progeny of field-caught hermaphrodites for non-segregation or segregation of DNA fingerprint markers as an indication of the homozygosity or heterozygosity of the parent. DNA fingerprinting revealed no segregation of markers among the offspring in 12 of 12 Florida and Brazil laboratory lines and in 5 of 30 Belize Cay broods. These data indicate that the hermaphrodite parents were homozygous; thus, no detectable outcrossing has occurred in these populations. However, DNA fingerprinting revealed segregation of markers among the offspring in 25 of 30 Belize Cay broods. Twenty-four of these broods were from the island of Twin Cays. An average of 30% of the parental bands were segregating among the offspring; values ranged from 0.09 to 0.50. Offspring were, on average, 8% dissimilar to one another; values ranged from 2.08% to 15.09%. These data suggest that the 25 hermaphrodite parents were heterozygous; thus, males are involved in the mating system in some Belize Cay populations. These data are the first evidence of outcrossing in this species. / Master of Science