Understanding complex population dynamics is critical for both basic and applied ecology. Analysis of genetic data has been promoted as a way to reconstruct recent non-equilibrium processes that influence the apportioning of genetic diversity among populations of organisms. In a structured-deme context, where individual populations exist as geographically distinct units, island biogeography theory and metapopulation genetics predict that the demographic processes of extinction, colonization, and migration will affect the magnitude and rate of genetic divergence between demes. New methods have been developed to attempt to detect the influence of non-equilibrium dynamics in structured populations. I challenged two of these methods: decomposed pairwise regression and allele frequency analyses, using simulations of genetic data from structured demes. I found that these methods suffer from a high type II error rate, or failure to reject the null hypothesis of mutation-migration-drift equilibrium for demes experiencing historical demographic events. In addition, island biogeography and metapopulation ecology predict that at equilibrium, some species in a patch will be recent colonists, as equilibrium indicates a balance between colonization of the patch and extinction from the patch. Recent colonists are unlikely to have reached population mutation-migration-drift equilibrium; hence a paradox exists between population and community level equilibrium. I used nuclear and mitochondrial genetic data from populations of two species of reptiles from the Turks and Caicos Islands, British West Indies to test for patterns of equilibrium vs. non-equilibrium. I found unexpected shallow genetic divergence in the Turks Island boa (Epicrates chrysogaster), indicating that this species likely existed as a panmictic population prior to the inundation of the Turks and Caicos Banks during the last glaciation. As the initial methods I tested using simulations proved unreliable, I used methods from phylogeography, landscape genetics, and island biogeography to detect significant non-equilibrium dynamics in the Turks and Caicos curly-tailed lizard (Leiocephalus psammodromus), finding evidence for high levels of biased gene flow. I propose that studies of genetic diversity on island archipelagos use tools from all three of these methods to evaluate empirical data in the context of equilibrium and the null hypotheses offered by island biogeography and population genetics theory. I frame the results both in the context of conservation and an understanding of equilibrium and non-equilibrium dynamics.

This study reexamines the nuclear microsatellite analysis by Rooney et al. (1999a) of Bering-Chukchi-Beaufort Seas bowhead whales (Balaena mysticetus) to determine if this population underwent a genetic bottleneck as a result of 19th and early 20th Century commercial whaling. This investigation used more accurate laboratory techniques to score alleles, had a larger sample size that was divided into two groups (mainland Alaska and St. Lawrence Island (SLI)), and used a moderately different set of microsatellite loci which are more variable and thus, more informative. The results corroborate the findings of Rooney et al. (1999a) for mainland Alaska showing no evidence of a genetic bottleneck. However, the SLI data analyses provide conflicting conclusions. The Wilcoxon test is significant for a heterozygote excess (p = 0.042) suggesting that a genetic bottleneck has occurred. This is not substantiated by the exact tests of each locus or the table-wide sign test. There is a possibility that a bottleneck has occurred, but due to the small sample size this is not a definitive conclusion and warrants reanalysis with a larger sample size.

The white-tailed eagle is a formerly threatened raptor that is commonly used as a flagship and indicator species in conservation work. This thesis uses molecular genetic methods to study sex determination of nestlings, genetic variability, population structure and phylogeography of the white-tailed eagle. Fourteen microsatellite markers were developed and tested for the white-tailed eagle. A method to sex white-tailed eagle nestlings in the field is presented. The method is based on just one tarsus measure, and is suitable for situations where a single person is handling the nestlings alone in a treetop. Most European white-tailed eagle populations underwent extreme declines during the 20th century. The results presented here show that bottlenecked populations have maintained significant levels of genetic diversity. Gene flow between regions is not a main explanation for this, as indicated by both genetic and ringing data. Instead, the long generation time of white-tailed eagles has acted as an intrinsic buffer against rapid loss of genetic diversity. Additionally, local conservation led to protection of more genetic diversity than if conservation had focused on the large remnant population in Norway. Mitochondrial DNA of white-tailed eagles is structured in two main clades with a predominantly eastern and western Eurasian distribution. The clades likely correspond to separate Ice Age refugia but do not grant classification as evolutionary significant units given their current extensive overlap across large parts of Eurasia. Microsatellite variation was studied in populations across Eurasia. Variability was rather constant across the continent, but clearly lower on Iceland and Greenland. This is best explained by founder effects during their colonisation, but only weak bottlenecks during colonisation of and persistence on the continent. Current population differentiation between Europe and eastern Eurasia is not compatible with a zero gene flow model but requires some amount of gene flow over evolutionary time scales.

The thesis study reveals that the position of bottleneck is a significant importance in supplychain process. The modern supply chain is characterized as having diverse products due tomass customization, dynamic production technology and ever changing customer demand.Usually customized supply chain process consists of an assemble to order (ATO) or make-to-order (MTO) type of operation. By controlling the supply constraints at upstream, a smoothmaterial flow achieved at downstream. Effective management on operational constraint willresults in speed up customer delivery. A throughout evaluation of demand constraints isnecessary to gain the competitive benefits over the entire market. The study is based on a conceptual model, comprises of engineer to order (ETO), MTO, ATOand make to stock (MTS) separated by decoupling point. All these represent the particularprocess in supply chain. The important perspective of this study is that the constraints areallocated in particular part of supply chain, which will become the supply chain moreversatile. This thesis study explains the use of detail capacity and material planningtechniques in upstream, midstream and downstream of the customer order decoupling supplychain. A shifting bottleneck concept has been studied in a better way, in order to keep relativestability and reduce the complexity in production management. This thesis study tries to findout some possible factors that reduce the bottleneck shifting in supply chain. This research provides the guideline about the implementation of lean, leagile and agility incustomized supply chain. Also key factors are discussed which are necessary to achieve theseparadigms. Basically leagile is the mixture of both lean & agile strategies. Leagile is inclinedtowards sustaining the flow for mixed-model production. Its intent is to achieve theefficiencies in mass production, while producing a medium variety of products. The focus inleagile strategy is to gain effective control at shop floor planning, including capacity andmaterial planning systems.Different relevant aspects of standardization and customization are considered through theproduction processes. In addition to this rate base, hybrid and time phase material planningtechniques are sorted in different supply chain parts through multiple level of bill of material.

Pinus taeda L. dynamics, migration patterns and genetic structure were investigated over geological time scale (the past 21,000 years), historical time scale (the past 500 years) and recent time scale (the past 50 years ago) using multi-source data and an interdisciplinary approach. Population genetics, microsatellite markers, DNA fingerprinting, fossil records, geological history, historical records, aerial photographs, soil maps, weather data, remote sensing and geographic information systems (GIS) were used to assess the dynamics of P. taeda populations especially for the Lost Pines (LP), a disjunct population at the westernmost edge of the species range. Pinus taeda populations east and west of the Mississippi River Valley are genetically differentiated. Eastern populations had higher allelic diversity and diagnostic alleles than western populations. Gene flow estimates are high. Allelic diversity and diagnostic alleles patterns are attributed to the prevailing wind direction. Differentiation east and west of the MRV was attributed to separation to two refugia during the Pleistocene. The Lost Pines population is believed to have undergone one or more bottleneck events with loss of rare alleles. Despite the bottleneck, allelic richness was similar for the LP and the control population from the Western Gulf (WG) population. Population size contraction of the LP was attributed to climate change in central Texas over geological time scale. The natural origin of the Lost Pines was investigated. Multivariate and clustering techniques and assignment and exclusion methods using DNA markers show that the LP population shared ancestry with the WG populations with no evidence for admixture from other sources. Historical records parallel this conclusion. With the absence of logging within Bastrop and Buescher State Parks, P. taeda area and patch size increased from 1949 to 1995. Thirty six percent of the pine patches observed in 1949 had disappeared by 1995 by merging. Landscape pattern analysis shows significant dynamics. The distribution of P. taeda in Bastrop County was associated with sandy light topsoils, clayey heavy sub-soils and high permeable soils. Pinus taeda grow on various soil types as well. Growing on these soils under current climatic conditions may compensate for the precipitation regime in this area.

This study reexamines the nuclear microsatellite analysis by Rooney et al. (1999a) of Bering-Chukchi-Beaufort Seas bowhead whales (Balaena mysticetus) to determine if this population underwent a genetic bottleneck as a result of 19th and early 20th Century commercial whaling. This investigation used more accurate laboratory techniques to score alleles, had a larger sample size that was divided into two groups (mainland Alaska and St. Lawrence Island (SLI)), and used a moderately different set of microsatellite loci which are more variable and thus, more informative. The results corroborate the findings of Rooney et al. (1999a) for mainland Alaska showing no evidence of a genetic bottleneck. However, the SLI data analyses provide conflicting conclusions. The Wilcoxon test is significant for a heterozygote excess (p = 0.042) suggesting that a genetic bottleneck has occurred. This is not substantiated by the exact tests of each locus or the table-wide sign test. There is a possibility that a bottleneck has occurred, but due to the small sample size this is not a definitive conclusion and warrants reanalysis with a larger sample size.

Computer networks are becoming increasingly large and complex; more so with the recent penetration of the internet into all walks of life. It is essential to be able to monitor and to analyse networks in a timely and efficient manner; to extract important metrics and measurements and to do so in a way which does not unduly disturb or affect the performance of the network under test. Network tomography is one possible method to accomplish these aims. Drawing upon the principles of statistical inference, it is often possible to determine the statistical properties of either the links or the paths of the network, whichever is desired, by measuring at the most convenient points thus reducing the effort required. In particular, bottleneck-link detection methods in which estimates of the delay distributions on network links are inferred from measurements made at end-points on network paths, are examined as a means to determine which links of the network are experiencing the highest delay. Initially two published methods, one based upon a single Gaussian distribution and the other based upon the method-of-moments, are examined by comparing their performance using three metrics: robustness to scaling, bottleneck detection accuracy and computational complexity. Whilst there are many published algorithms, there is little literature in which said algorithms are objectively compared. In this thesis, two network topologies are considered, each with three configurations in order to determine performance in six scenarios. Two new estimation methods are then introduced, both based on Gaussian mixture models which are believed to offer an advantage over existing methods in certain scenarios. Computationally, a mixture model algorithm is much more complex than a simple parametric algorithm but the flexibility in modelling an arbitrary distribution is vastly increased. Better model accuracy potentially leads to more accurate estimation and detection of the bottleneck. The concept of increasing flexibility is again considered by using a Pearson type-1 distribution as an alternative to the single Gaussian distribution. This increases the flexibility but with a reduced complexity when compared with mixture model approaches which necessitate the use of iterative approximation methods. A hybrid approach is also considered where the method-of-moments is combined with the Pearson type-1 method in order to circumvent problems with the output stage of the former. This algorithm has a higher variance than the method-of-moments but the output stage is more convenient for manipulation. Also considered is a new approach to detection algorithms which is not dependant on any a-priori parameter selection and makes use of the Kullback-Leibler divergence. The results show that it accomplishes its aim but is not robust enough to replace the current algorithms. Delay estimation is then cast in a different role, as an integral part of an algorithm to correlate input and output streams in an anonymising network such as the onion router (TOR). TOR is used by users in an attempt to conceal network traffic from observation. Breaking the encryption protocols used is not possible without significant effort but by correlating the un-encrypted input and output streams from the TOR network, it is possible to provide a degree of certainty about the ownership of traffic streams. The delay model is essential as the network is treated as providing a pseudo-random delay to each packet; having an accurate model allows the algorithm to better correlate the streams.

Every production system has its constraints. Ever since Goldratt presented the theory of constraints in the mid 80’s a lot of effort has been made to find the best methods for constraint identification and ways to minimize the constraints in order to gain higher capacity in production. A novel method presented is Simulation-based COnstraint Removal (SCORE). The SCORE method has been proved to be more effective and detailed in the identification and sorting of the constraints when compared with other bottleneck detection methods (Pehrsson 2013). The work in this bachelor’s project has been focused on applying the method to a complex production system in order to further explore the SCORE method’s ability to identify bottlenecks and reveal opportunities to increase the throughput of a production system. NorthStar Battery Company (NSB) wishes to perform a bottleneck analysis and optimization in order to find improvements to increase the throughput with 10%. By using the SCORE method, improvement options with a potential to meet the goals of NSB was identified. It also facilitated for the author to further exploit the possibilities of simulation-based optimization and knowledge extraction through the SCORE method. By building a valid discrete event simulation model of the production line and use it for optimization, followed by a knowledge extraction, it was possible to identify the top three constraints and the level of improvement needed in the constraining operations. The identified improvements could potentially increase the throughput of the production line by 10-15 percent. The project was delimited to exclude the finishing part of the production line and only one battery variant has been included. Through continued work and analysis of the line using the SCORE method it will most likely be possible to even further increase the throughput of the production system and to provide NSB with more knowledge and opportunities to enhance their production effectiveness.

Black grouse Tetrao tetrix is a bird species composed of large, continuous as well as severely reduced and fragmented populations, making it an optimal species to investigate how genetic diversity is affected by habitat fragmentation. I have focused on genetic diversity in the Major Histocompatibility Complex (MHC) to measure the ability of the black grouse to respond to environmental changes. I partly characterized MHC class II in black grouse and found striking similarities with chicken MHC class II. I demonstrated that black grouse possess a similar compact MHC as chicken with few MHC class II B (BLB) and Y (YLB) loci. I did not find evidence of balancing selection in YLB so I concentrated further studies on BLB. I developed a PCR-based screening method for amplifying and separating expressed BLB alleles in European black grouse populations. Small fragmented populations had lost neutral genetic diversity (based on microsatellites and SNPs) compared to samples from the historical distribution and contemporary large populations. There was also a trend, albeit less pronounced, for reduced MHC diversity in these populations. Neutral markers in small isolated populations were affected by increased levels of genetic drift and were therefore genetically differentiated compared to other populations. MHC markers on the other hand, were not subjected to genetic drift to the same extent probably due a long historic process of balancing selection. Inferences of heterozygosity and evolutionary patterns as well as detailed correlations to reproductive success and diseases cannot be performed until MHC can be amplified in a locus-specific manner. Therefore, I developed a single locus sequence-based typing method for independently amplifying MHC class II B loci (BLB1 and BLB2). I found that BLB1 and BLB2 were duplicated in a common ancestor to chickens and black grouse and that these loci are subjected to homogenizing concerted evolution due to inter-genetic exchange between loci after species divergence.  I could also verify that both BLB1 and BLB2 were transcribed in black grouse and under balancing selection. This collection of work has significance for future conservation of black grouse as well as research and management of zoonotic diseases.

The European rabbit, Oryctolagus cuniculus, was introduced to Australia in 1859 and quickly became a significant vertebrate pest species in the country across a wide distribution. In arid and semi-arid environments, rabbit populations exist as metapopulations - undergoing frequent extinction recolonisation cycles. Previous studies identified population genetic structuring at the regional level between arid and semi-arid environments, and habitat heterogeneity was suggested as a possible causal factor. For the most part, rabbit behaviour has been overlooked as a factor that could contribute to explaining population genetic structure in arid and semi-arid environments. This study utilised a combination of genetic sampling techniques and a simulated territorial intrusion approach to observing wild rabbit behaviour in arid and semi-arid environments. The genetic component of the study compared population samples from each region using four polymorphic microsatellite loci. The behavioural component examined variation in the level of territoriality exhibited by three study populations in the arid region towards rabbits of known versus unknown origins (resident vs transgressor (simulating dispersal)). A difference was observed in population genetic structure determined from nuclear markers between arid and semi-arid regions, which supports findings of previous research using mitochondrial DNA data in the same area. Additionally, differences in aggressive response to known vs unknown rabbits were identified in parts of the arid region, which together with the effects of habitat heterogeneity and connectivity may explain the observed differences in population genetic structure. Knowledge of behavioural plasticity and its effect on relative dispersal success and population genetic structure may contribute to improved management and control of feral rabbit populations at the regional level within Australia; and may assist with conservation efforts in the species' natural range in Europe.