Development of Expert System by using Logical Comparative Conclusion in the Function of Organizational Performance Improvement

The paper is created as the tendency of a group of authors, that with an integrative approach in the application of intelligent systems, by using analogy with some function in human body, to develop a model to improve organizational performance. The paper is based on two unique bases, of a representative number of data that reflect real business conditions and including a significant number of organizations. In order to achieve the set goals, several approaches were adopted, tools and methods, such as analytic hierarchy process (AHP) methodology, case base reasoning, artificial intelligence tools– expert systems, verification in real condition and other. As the key outcomes of the paper are obtained the fields that are critical to achieve the best organizational performance, and indicators for the development of expert systems whose functions, efficiency and effectiveness are verified in real conditions

Object Detection Based on Template Matching through Use of Best-So-Far ABC

Best-so-far ABC is a modified version of the artificial bee colony (ABC) algorithm used for optimization tasks. This algorithm is one of the swarm intelligence (SI) algorithms proposed in recent literature, in which the results demonstrated that the best-so-far ABC can produce higher quality solutions with faster convergence than either the ordinary ABC or the current state-of-the-art ABC-based algorithm. In this work, we aim to apply the best-so-far ABC-based approach for object detection based on template matching by using the difference between the RGB level histograms corresponding to the target object and the template object as the objective function. Results confirm that the proposed method was successful in both detecting objects and optimizing the time used to reach the solution

Gene flow dynamics in Baboons - The influence of social systems

Die Beziehung zwischen Genen und Verhalten ist in der Evolutionsbiologie von besonderem Interesse. Bestimmte Verhaltensweisen können die genetische Struktur natürlicher Populationen gestalten, dadurch deren genetische Diversität verändern und so ihr evolutives Schicksal beeinflussen. Abwanderung aus der Geburtsgruppe ist eine dieser Verhaltensweisen. Sie beeinflusst Genfluss, dessen Ausmaß die genetische Struktur von Populationen bestimmt. Paviane (Gattung Papio) sind ein besonders interessantes Forschungssystem um die Beziehung zwischen Verhalten und populationsgenetischer Struktur zu untersuchen. Die Evolution der Paviane wurde sowohl von historischem als auch gegenwärtigem Genfluss geprägt. Innerhalb dieser Gattung treten sowohl die überwiegende Abwanderung von Männchen als auch die überwiegende Abwanderung von Weibchen auf. Zudem wurde ihre gegenwärtige Verbreitung maßgeblich von Populationsausbreitung und –rückzug beeinflusst und es tritt häufig Genfluss zwischen verschiedenen Arten auf. In meiner Doktorarbeit untersuchte ich, wie verschiedene Abwanderungsmuster den Genfluss bei Pavianen beeinflussen. Damit hoffe ich zu einem besseren Ver-ständnis der Wechselbeziehung zwischen Verhaltensökologie und Genetik in natürlichen Populationen beizutragen. Ich fokussierte mich darauf, wie Unterschiede in den Sozialsystemen unterschiedlicher Pavianarten deren genetische Struktur beeinflussen. Die beobachteten Muster nutzte ich, um auf das geschlechtsspezifische Abwanderungsmuster bei Guineapavianen zu schließen, eine der am wenigsten untersuchten Pavianarten. Zudem untersuchte ich, wie sowohl historischer als auch gegenwärtiger Genfluss die genetische Struktur der Guineapaviane formten und ob es möglich ist von der Populationsausbreitung der Paviane Rückschlüsse auf die menschliche Evolutionsgeschichte zu ziehen. Um diese Fragen zu beantworten nutzte ich einen populationsgenetischen Ansatz, basierend auf im gesamten Verbreitungsgebiet gesammelten Kotproben, deren exakter geographischer Ursprung bekannt war. Ich analysierte sowohl autosomale Mikrosatelliten als auch Sequenzen der mitochondrialen Hypervariablen Region I. Meine Ergebnisse zeigen, dass die genetische Struktur der Guineapaviane am besten durch die überwiegende Abwanderung von Weibchen erklärt werden kann, sowohl in einem lokalen als auch im globalen Kontext. Weiblicher Genfluss führt zu einer hohen Diversität innerhalb von Populationen sowie einem Fehlen von genetisch-geographischer Struktur in mitochondrialer DNA. Nukleäre DNA hingegen zeigt eine starke globale geographische Struktur und Männchen sind im Vergleich zu Weibchen durch eine stärkere lokale Struktur gekennzeichnet. Dies entspricht den Vorhersagen für ein System, in welchem hauptsächlich Weibchen abwandern und Männchen in ihrer Geburtsgruppe verbleiben. Insgesamt scheint lokal begrenzte Abwanderung den wirksamen Genfluss auf eine Distanz unter 200 km zu beschränken, was zu einem starken Isolation-durch-Distanz Effekt und genetisch differenzierten Populationen führt. Anzeichen für Populationsausbreitung, die graduelle Struktur genetischer Variation, und mögliche Hinweise auf das “Allele-surfing” Phänomen, deuten auf eine historische westwärts gerichtete Ausbreitung von Guineapavianen hin. Introgressive Hybridisierung mit benachbarten Anubispavianen könnte genetische Muster im Bereich der Kontaktzone erklären, muss aber im Detail noch untersucht werden. Zusätzlich konnte ich zeigen, dass Mantelpaviane vermutlich im gleichen Zeitraum des Späten Pleistozäns von Afrika nach Arabien wanderten, wie Hypothesen für den modernen Menschen vorschlagen. Meine Studie ist die erste umfassende Analyse der genetischen Populationsstruktur der Guineapaviane und liefert Belege für die überwiegende Abwanderung von Weibchen in dieser Art. Dies untersützt die Ansicht, dass das Sozialsystem der Guineapaviane einige vergleichbare Merkmale zum System der Mantelpaviane aufweist und deutet somit darauf hin, dass während der Evolution dieser beiden Arten besondere evolutionäre Drücke gewirkt haben, die sie von allen anderen Pavianarten abgrenzen. In Kombination mit dem starken Einfluss von Populationsausbreitungen auf ihre Verbreitung und genetische Diversität, bekräftigt meine Arbeit Paviane als interssanten analogen Modellorganismus, der helfen kann, die Prozesse die während der Evolution des Menschen maßgeblich waren, aufzuklären

Molecular polymorphisms for phylogeny, pedigree and population structure studies

A number of types of molecular polymorphisms can be used for studying genetic relationship and evolutionary history. Microsatellites are hypervariable and can be very useful tools to determine population structure, distinguish sibling species, as well as verifying parental relationships and pedigrees. However, while microsatellite polymorphisms are useful for solving relationships between populations within a species, relations among species or genera will probably be obscured due to a high degree of homoplasy —identity arising from evolutionary convergence not by descent. For long range evolutionary history, such as phylogeny from old world monkey to human, mtDNA markers may be better candidates. The aim of this thesis is to assess molecular polymorphisms of different types and their optimal use in different situations. Two widely separated taxa were used for testing –the green monkey Chlorocebus sabaeus, and the sibling dipteran flies Bactrocera tryoni and B. neohumeralis, known collectively as the Queensland fruit fly. In the present study a complete 16,550 bp mtDNA sequence of the green monkey Chlorocebus sabaeus is reported for the fist time and has been annotated (Chapter 2). Knowledge of the mtDNA genome contributes not only to identification of large scale single nucleotide polymorphisms (SNPs) (Chapter 4) or other mtDNA polymorphisms development, but also to primate phylogenetic and evolutionary study (Chapter 3). Microsatellites used for the green monkey paternity and pedigree studies were developed by cross-amplification using human primers (Chapter 5). For studies of population structure and species discrimination in Queensland fruit fly (Chapter 7), microsatellites were isolated from a genomic library of Bactrocera tryoni (Chapter 6) The total length of 16550 bp of complete mtDNA of the green monkey C. sabaeus, which has been sequenced and annotated here, adds a new node to the primate phylogenetic tree, and creates great opportunity for SNP marker development. The heteroplasmic region was cloned and five different sequences from a single individual were obtained; the implication of this are discussed. The phylogenetic tree reconstructed using the complete mtDNA sequence of C. sabaeus and other primates was used to solve controversial taxonomic status of C. sabaeus. Phylogenies of primate evolution using different genes from mtDNA are discussed. Primate evolutionary trees using different substitution types are compared and the phylogenetic trees constructed using transversions for the complete mtDNA were found close to preconceived expectations than those with transversions + transitions. The sequence of C. sabaeus 12SrRNA reported here agrees with the one published by ven der Kuyl et al. (1996), but additional SNPs were identified. SNPs for other regions of mtDNA were explored using dHPLC. Twenty two PCR segments for 96 individuals were tested by dHPLC. Fifty five SNPs were found and 10 haplogroups were established. Microsatellite markers were used to construct a genealogy for a colony of green monkeys (C. sabaeus) in the UCLA Vervet Monkey Research Colony. Sixteen microsatellites cross-amplified from human primers were used to conduct paternity analysis and pedigree construction. Seventy-eight out of 417 offspring were assigned paternity successfully. The low success rate is attributed to a certain proportion of mismatches between mothers and offspring; the fact that not all candidate fathers were sampled, the limitations of microsatellite polymorphisms; and weakness of the exclusion method for paternity assessment. Due to the low success rate, the pedigree is split into a few small ones. In a complicated pedigree composed of 75 animals and up to four generations with multiple links a power male mated with 8 females and contributed 10 offspring to the pedigree. Close inbreeding was avoided. Population structure within two species of Queensland fruit fly Bactrocera tryoni and Bactrocera neohumeralis (Tephritidae: Diptera) is examined using microsatellite polymorphisms. Queensland fruit flies B. tryoni and B. neohumeralis are sympatric sibling species that have similar morphological and ecological features. They even share polymorphism at the molecular level. Mating time difference is the main mechanism by which they maintain separate species. In the present study, 22 polymorphic and scorable microsatellites were isolated from B. tryoni and tested in the two species sampled from sympatric distribution areas. Pairwise genetic distance analysis showed explicit differentiation in allele frequencies between the two species, but very weak differences between conspecific populations. Gene flow is higher within B. tryoni than within B. neohumeralis, and gene exchange between the two species exists. An averaging linkage clustering tree constructed by UPGMA showed two major clusters distinguishing the two species, and it appears that population structure is highly correlated with geographic distance. The relationship between molecular markers, evolution, and selection are discussed using comparative studies within two large taxa: primate and insect. The degree of conservation and polymorphism in microsatellites varies between taxa, over evolutionary time

Molecular polymorphisms for phylogeny, pedigree and population structure studies

A number of types of molecular polymorphisms can be used for studying genetic relationship and evolutionary history. Microsatellites are hypervariable and can be very useful tools to determine population structure, distinguish sibling species, as well as verifying parental relationships and pedigrees. However, while microsatellite polymorphisms are useful for solving relationships between populations within a species, relations among species or genera will probably be obscured due to a high degree of homoplasy —identity arising from evolutionary convergence not by descent. For long range evolutionary history, such as phylogeny from old world monkey to human, mtDNA markers may be better candidates. The aim of this thesis is to assess molecular polymorphisms of different types and their optimal use in different situations. Two widely separated taxa were used for testing –the green monkey Chlorocebus sabaeus, and the sibling dipteran flies Bactrocera tryoni and B. neohumeralis, known collectively as the Queensland fruit fly. In the present study a complete 16,550 bp mtDNA sequence of the green monkey Chlorocebus sabaeus is reported for the fist time and has been annotated (Chapter 2). Knowledge of the mtDNA genome contributes not only to identification of large scale single nucleotide polymorphisms (SNPs) (Chapter 4) or other mtDNA polymorphisms development, but also to primate phylogenetic and evolutionary study (Chapter 3). Microsatellites used for the green monkey paternity and pedigree studies were developed by cross-amplification using human primers (Chapter 5). For studies of population structure and species discrimination in Queensland fruit fly (Chapter 7), microsatellites were isolated from a genomic library of Bactrocera tryoni (Chapter 6) The total length of 16550 bp of complete mtDNA of the green monkey C. sabaeus, which has been sequenced and annotated here, adds a new node to the primate phylogenetic tree, and creates great opportunity for SNP marker development. The heteroplasmic region was cloned and five different sequences from a single individual were obtained; the implication of this are discussed. The phylogenetic tree reconstructed using the complete mtDNA sequence of C. sabaeus and other primates was used to solve controversial taxonomic status of C. sabaeus. Phylogenies of primate evolution using different genes from mtDNA are discussed. Primate evolutionary trees using different substitution types are compared and the phylogenetic trees constructed using transversions for the complete mtDNA were found close to preconceived expectations than those with transversions + transitions. The sequence of C. sabaeus 12SrRNA reported here agrees with the one published by ven der Kuyl et al. (1996), but additional SNPs were identified. SNPs for other regions of mtDNA were explored using dHPLC. Twenty two PCR segments for 96 individuals were tested by dHPLC. Fifty five SNPs were found and 10 haplogroups were established. Microsatellite markers were used to construct a genealogy for a colony of green monkeys (C. sabaeus) in the UCLA Vervet Monkey Research Colony. Sixteen microsatellites cross-amplified from human primers were used to conduct paternity analysis and pedigree construction. Seventy-eight out of 417 offspring were assigned paternity successfully. The low success rate is attributed to a certain proportion of mismatches between mothers and offspring; the fact that not all candidate fathers were sampled, the limitations of microsatellite polymorphisms; and weakness of the exclusion method for paternity assessment. Due to the low success rate, the pedigree is split into a few small ones. In a complicated pedigree composed of 75 animals and up to four generations with multiple links a power male mated with 8 females and contributed 10 offspring to the pedigree. Close inbreeding was avoided. Population structure within two species of Queensland fruit fly Bactrocera tryoni and Bactrocera neohumeralis (Tephritidae: Diptera) is examined using microsatellite polymorphisms. Queensland fruit flies B. tryoni and B. neohumeralis are sympatric sibling species that have similar morphological and ecological features. They even share polymorphism at the molecular level. Mating time difference is the main mechanism by which they maintain separate species. In the present study, 22 polymorphic and scorable microsatellites were isolated from B. tryoni and tested in the two species sampled from sympatric distribution areas. Pairwise genetic distance analysis showed explicit differentiation in allele frequencies between the two species, but very weak differences between conspecific populations. Gene flow is higher within B. tryoni than within B. neohumeralis, and gene exchange between the two species exists. An averaging linkage clustering tree constructed by UPGMA showed two major clusters distinguishing the two species, and it appears that population structure is highly correlated with geographic distance. The relationship between molecular markers, evolution, and selection are discussed using comparative studies within two large taxa: primate and insect. The degree of conservation and polymorphism in microsatellites varies between taxa, over evolutionary time

Co-evolution of Rabbits and the Rabbit Haemorrhagic Disease Virus (RHDV) in Australia

The European rabbit is a keystone prey species in its native range on the Iberian Peninsula, where it is under threat from two viral diseases - myxomatosis and the rabbit haemorrhagic disease virus (RHDV). However, in its alien range the rabbit is considered one of the most damaging pest species, due to overgrazing of pastures and native vegetation. In these areas myxomatosis and RHDV have been deployed as biocontrols for landscape-scale rabbit management. Despite the initial success of viral biocontrols, increases in rabbit abundance were observed between 2003 and 2015, and evolving rabbit genetic resistance to RHDV was proposed as a key cause. Although substantial investment has been made in offsetting such resistance, through the development and introduction of new RHDV strains, the existing co-evolutionary dynamic between rabbits and RHDV in Australia is poorly understood. My thesis uses next-generation sequencing technology to explore the co-evolution of rabbits and RHDV through three approaches, presented as three publication-style manuscripts. In Chapter 2, I pilot the use of blowfly vectors to monitor spatial and temporal variation in RHDV strains. I find that wind-oriented fly traps provide improved efficiency and viral detection rates that exceed previously used rabbit carcass searches. Shotgun sequencing of RHDV capsid amplicons indicated multiple co-circulating local RHDV variants with evidence of recombination between them. This implies that intraspecific competition may play a substantial role in the direction of RHDV evolution, in addition to host resistance. In Chapter 3, I examine the underlying genetic structure of Australia’s rabbit population through a genome-wide selection of SNP loci produced through reduced representation sequencing. I find strong support for three geographically widespread rabbit lineages, as well as three individual sites with strong local differentiation. This genetic structuring is consistent with an invasion history of multiple introductions, rather than the previously assumed single primary invasion front, and may contribute to geographic variance in RHDV resistance. In Chapter 4, I combine long-term capture-mark-recapture data from a single rabbit population with a SNP-based pedigree using reduced representation sequencing. I find evidence of socially structured polygynandry with male-biased dispersal and an unexpectedly high rate of breeding outside warren-based social groups. I also examine the influence on offspring survival of warren size, birth dates and maternal antibodies to RHDV and myxomatosis. This thesis contributes to our understanding of rabbit and RHDV co-evolution by validating a more effective RHDV monitoring tool, characterising the underlying genetic variation in both host and pathogen, and analysing the pressures that drive evolution of this host-pathogen system. These insights provide the building blocks for further research to understand the mechanisms of genetic resistance to RHDV in rabbits, the extent of influence of resistance on rabbit fitness and abundance, and the impacts of current and future biocontrol activities.Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 201

Analysis and standardization of marker genotype data for DNA fingerprinting applications

Genetic polymorphisms can be seen as the occurrence of more than one form of a DNA- or protein sequence at a single locus in a group of organisms, where these different forms occur more frequently than can be attributed to mutation alone. The combination of genetic polymorphisms present in the genome of a particular individual is referred to as its genotype. A wide range of genotyping techniques have been developed to detect and visualize genetic polymorphisms. One such technique examines highly polymorphic repetitive DNA regions called microsatellites, also called “short tandem repeats” (STRs) and sometimes “simple sequence repeats” (SSRs) or “simple-sequence length polymorphisms” (SSLPs). A microsatellite region consists of a DNA sequence of identical units of usually 2-6 base pairs strung together to produce highly variable numbers of tandem repeats among individuals of a population. Microsatellite genotyping is a popular choice for many types of studies including individual identification, paternity testing, germplasm evaluation, genome mapping and diversity studies and can be used in many commercial, academic, social, and agricultural applications. There are, however, many obstacles in effectively managing and analysing microsatellite genotype data. Currently, researchers are struggling to effectively manage and analyse rapidly growing volumes of genotyping data. Management problems range from simply the lack of a secure, easily accessible central data repository to more complex issues like the merging and standardization of data from multiple sources into combined datasets. Due to these issues, genetic fingerprinting applications such as identity matching and relatedness studies can be challenging when data from different experiments or laboratories have to be combined into a central database. The main aim of this M.Sc study in Bioinformatics was to develop a bioinformatics resource for the management and analysis of genetic fingerprinting data from microsatellite marker genotyping studies, and to apply the software to the analysis of microsatellite marker data from ramets of Pinus patula clones with the purpose of analysing clonal identity in pine breeding programmes. The software resource developed here is called GenoSonic. It is a web application that provides users with a secure, easily accessible space where genotyping project data can be managed and analysed as a team. Users can upload and download large amounts of marker genotype data. Once uploaded to the system, DNA fingerprint data needs to be standardised before it can be used in further analyses. To do this, a two-step approach was implemented in GenoSonic. The first step is to assign standardized allele sizes to all of the input allele sizes of the microsatellite fingerprints automatically using a novel automated binning algorithm called CSMerge-1, which was designed specifically to bin data from multiple experiments. The second step is to manually verify the results from the automated binning function and add the verified data to a standardized dataset. Once the genetic fingerprints have been standardized, allele- and genotype frequencies can be viewed for any given marker. GenoSonic also provides functionalities for identity matching. One or more DNA fingerprints from unknown samples can be matched against a standardized dataset to establish identities or infer relatedness. Finally, GenoSonic implements a genetic distance tree construction function, which can be used to visualize relatedness among samples in a selected dataset. The bioinformatics resource developed in this study was applied to a microsatellite DNA fingerprinting project aimed at the re-establishment or confirmation of clonal identity of Pinus patula ramets from pine clonal seed orchards developed by a South African forestry company at one of their new agricultural estates in South Africa. The results from GenoSonic‟s automated binning function (CSMerge-1) and the results from the identity matching and tree construction exercise were compared to results obtained by human experts who have analysed the data manually. It was demonstrated that the results from GenoSonic equalled or surpassed the manual results in terms of accuracy and consistency, and far surpasses the manual effort in terms of the speed at which analyses could be completed. GenoSonic was developed with specific focus on reusability, and the ability to be modified or extended to solve future genotyping-related problems. This study not only provides a solution to current genotype data management and analysis needs of researchers, but is aimed at serving as a basic framework, or component library for future software development projects that may be required to address specific needs of researchers dealing with high-throughput genotyping data.Dissertation (MSc)--University of Pretoria, 2011.Biochemistryunrestricte

Tetragonula carbonaria and disease : behavioural and antimicrobial defences used by colonies to limit brood pathogens

The honey bee, Apis mellifera, is suffering heavily from the impacts from intensive management. Pests and diseases contribute to the population losses experienced globally. Brood disease is of concern for the apiculture industry because of the direct effects it has on population numbers and despite control measures; resistance to antibiotics and pesticides are common. Alternative pollinators such as stingless bees, including Tetragonula carbonaria, appear to be less impacted by brood diseases. However, there is very little information regarding why this is so. Prior to this study, there are only a few indications about a possible bacterial brood disease in Brazilian stingless bees (Kerr 1948, Nogueira-Neto 1997), with no follow up investigations, and no cases of brood disease losses in Australian stingless bees. As a result, this study presents information on the behavioural and antimicrobial defences of T. carbonaria colonies as mechanisms to limit the development of brood pathogens. In addition to these aims and objectives, this study also introduces and documents the first disease causing brood pathogen in Australian stingless bees. Therefore, the interaction of the defence mechanisms and the identified brood pathogen was also explored. Suitable nest conditions need to exist to sustain pathogen growth and development. Apis mellifera pathogens such as Paenibacillus larvae and Ascosphaera apis utilise nest conditions, especially in the brood area for growth. The limited number of stingless bee pathogens may be related to brood temperature. Thermoregulation behaviour has been investigated in a number of stingless bee species; however, Australian studies are limited to Austroplebeia australis (Halcroft et al. 2013b) and greenhouse maintained T. carbonaria colonies (Amano et al. 2000, Amano 2004, A. Tse, pers. comm., 2011), with outcomes applied to their pollination servicing. This study (Chapter 2) investigated T. carbonaria thermoregulation behaviours during fluctuating ambient temperatures and the influence these have on brood production. Over the 13-month study, T. carbonaria was able to maintain brood temperatures between 15–31ºC, despite ambient temperatures ranging from 0–37°C. The recorded brood temperatures resulted in colonies maintaining yearlong brood development, which would suggest that this could provide a suitable resource for pathogen development year-round. However, pathogen occurrences are rare, it is speculated that the greater brood temperature range which is tolerated by colonies, is ultimately unsuitable for brood pathogen development, especially the lower winter temperatures

Honey Bee Health

Over the past decade, the worldwide decline in honey bee populations has been an important issue due to its implications for beekeeping and honey production. Honey bee pathologies are continuously studied by researchers, in order to investigate the host–parasite relationship and its effect on honey bee colonies. For these reasons, the interest of the veterinary community towards this issue has increased recently, and honey bee health has also become a subject of public interest. Bacteria, such as Melissococcus plutonius and Paenibacillus larvae, microsporidia, such as Nosema apis and Nosema ceranae, fungi, such as Ascosphaera apis, mites, such as Varroa destructor, predatory wasps, including Vespa velutina, and invasive beetles, such as Aethina tumida, are “old” and “new” subjects of important veterinary interest. Recently, the role of host–pathogen interactions in bee health has been included in a multifactorial approach to the study of these insects’ health, which involves a dynamic balance among a range of threats and resources interacting at multiple levels. The aim of this Special Issue is to explore honey bee health through a series of research articles that are focused on different aspects of honey bee health at different levels, including molecular health, microbial health, population genetic health, and the interaction between invasive species that live in strict contact with honey bee populations

Comparative genomics and epidemiology of the amphibian-killing fungus Batrachochytrium dendrobatidis

The primary aim of this thesis was to study the population structure and epidemiology of the fungal pathogen of amphibians, Batrachochytrium dendrobatidis (Bd). I have addressed these questions by collecting and isolating Bd from multiple infected host species. I have then extracted and sequenced whole nuclear and mitochondrial genomes for 50 isolates of Bd using the ABI SOLiD 3 and Illumina HiSeq 2000 platforms. The first aspect of the analysis was to tailor a new method for identifying variant sites amongst the isolates, as well as verifying the accuracy of the alignment and SNP-calling methods. Next, using a number of phylogenetic methods, I identified a population split into at least three deeply divergent lineages. Two of these lineages were found in multiple continents and are associated with known introductions by anthropogenic means. Isolates belonging to one clade, which we named the Global Panzootic Lineage (BdGPL), have emerged across at least five continents and are associated with the onset of epizootics in all five continents we tested. Dating the divergence between BdGPL isolates suggested a recent common ancestor in the 20th Century, and that the widespread trade of amphibians is an important mechanism of transmission. In contrast, BdGPL diverged from the other two lineages approximately 1000 years ago, clearly refuting a single emergence hypothesis. The two newly identified divergent lineages were the Cape lineage (BdCAPE) that appeared to have originated from the Cape Province in South Africa and a Swiss lineage (BdCH) comprised of a single isolate from a pond in Gamlikon, Switzerland. The secondary aim of this thesis was to identify and compare virulence determinants and other genomic features responsible for known differences in phenotypes. Using a variety of statistical and computational methods, I identified compelling evidence for genetic recombination targeting virulence factors, selection of those and other virulence factors, and rapid changes in ploidy and aneuploidy amongst the isolates of all three lineages. These genomic features shed light on the emergence, patterns of global spread, and modes of evolution in the pathogen(s) responsible for contemporary disease-driven losses in amphibian biodiversity. Finally, I discuss how these findings update our understanding of Bd and the importance for tracking and understanding the dynamics of other current emerging pathogens in an increasingly globalised habitat.Open Acces