Dissertations / Theses on the topic 'Simpson’s index'

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
Diversity as a concept was first introduced by Williams in Fisher et al. (1943). Later, Good (1953, 1982) proposed a generalized index that included as special cases both Shannon’s and Simpson’s indices. Baczkowski et al. (1997, 1998) generalized the proposed generalization deriving the first four moments and then obtaining a distribution prior to the general index for Good (BACZKOWSKI et al., 2000). Therefore, is proposed a new generalization that, in addition to the indices the Shannon and Simpson as special cases, includes more general indices such as the unfamiliar (PATIL & TAILIIE, 1982). The moments of h(a,b,d) presented here extend the results presented in Baczkowski et al. and Bowman et al. for a class of diversity indices of more general and it is concluded then that while the distribution of index Shannon can be approximated by a Gaussian distribution, if any difference between abundance of species, to more general values of (a,b,d), it is suggested a distribution of type I as the most appropriated. The results are also consistent with those presented for real populations, as in Heip & Engels (1974), especially when it examines the index of Shannon.
A diversidade como um conceito foi inicialmente introduzida por Williams em Fisher et al. (1943). Mais tarde, Good (1953, 1982) propôs um índice generalizado que incluía como casos especiais os índices de Shannon e o de Simpson. Baczkowski et al. (1997, 1998) propuseram generalizar essa generalização derivando os quatro primeiros momentos e obtendo assim uma distribuição para o índice antes generalizado por Good (BACZKOWSKI et al., 2000). Sendo assim, apresenta-se uma nova generalização que, além de ter os índices de Shannon e Simpson como casos especiais, engloba índices mais gerais como o não familiar (PATIL & TAILIIE, 1982). Os momentos de h(a,b,d) aqui apresentados estendem os resultados apresentados em Baczkowski et al. e Bowman et al. para uma classe de índices de diversidade mais geral, concluindo-se então que enquanto a distribuição do índice de Shannon pode ser aproximado por uma distribuição Gaussiana, caso haja diferença entre abundância de espécies, para valores mais gerais de (a,b,d), sugere-se uma distribuição do tipo I como sendo a mais apropriada. Os resultados obtidos são tão consistentes quanto os de trabalhos que lidam com populações reais como em Heip & Engels (1974), principalmente quando examina-se o índice de Shannon.

This study examines the relationship between land fragmentation and agricultural productivity in Vietnam, as well as the outcomes of land consolidation programs on productivity. Data from the Vietnam Household Living Standard Survey 2004 and data on the land consolidation process was used for the regression analysis. The results show weak correlations between fragmentation and productivity. Land fragmentation seems to be positively correlated to productivity due to more use of fertilizers and labour input. The communes that have consolidated their land are more productive, but this seems to be explained by initial differences in productivity. Our results suggest that there are no immidiate gains in land consolidation.

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The diagnosis of lung nodules has been constantly looked for by researchers as a way to minimize the high global mortality indices related to lung cancer. The usage of medical images, such as Computerized Tomography, has made possible the deepening and the improvement of techniques used to evaluate exams and provide diagnosis. This work presents a methodology for diagnosing single lung nodules that can be an aid for studies performed on similar areas and for specialists. This methodology was applied to two different image databases. The representation of the nodules was done with extraction of geometry and texture features, being the last one described through Simpson’s Index, a statistic used in Spatial Analysis and in Ecology. These features were submitted to the Support Vector Machine classifier (SVM) in two approaches: the traditional approach and the approach by using One Class. With the traditional SVM approach, we have obtained sensibility rates of 90%, specificity of 96.67% and accuracy of 95%. Using One Class SVM, the obtained rates were: sensibility of 89.7%, specificity of 89.7% and accuracy of 89.7%.
O diagnóstico de nódulos pulmonares tem sido buscado constantemente por pesquisadores como forma de amenizar os altos índices de mortalidade mundial relacionado ao câncer de pulmão. O uso de imagens médicas, como a Tomografia Computadorizada, tem possibilitado um aprofundamento e melhoramento de técnicas para avaliar exames e prover diagnósticos. Este trabalho apresenta uma metodologia para diagnóstico de nódulos pulmonares solitários que possa servir como um auxílio para estudos realizados em áreas afins e para especialistas. Esta metodologia foi aplicada a duas diferentes bases de dados de imagens. A representação dos nódulos foi feita com a extração de medidas de geometria e de textura sendo esta última descrita através do Índice de Simpson, uma estatística utilizada na Análise Espacial e na Ecologia. Essas medidas foram submetidas ao classificador Máquina de Vetores de Suporte - MVS em duas abordagens: a abordagem tradicional e abordagem usando uma classe. Com abordagem MVS tradicional, obtiveramse taxas de sensibilidade de 90%, especificidade de 96,67% e acurácia de 95%. Usando MVS de uma classe, as taxas obtidas foram: sensibilidade igual a 89,7%, especificidade igual a 89,7% e acurácia igual a 89,7%.

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Breast cancer is one of the major causes of mortality among women throughout the world. Presently, the analysis of breast radiography is the most used method to early detection of this kind of cancer. It enables the identification of anomalies at their initial stage, which is a fundamental factor for success in the treatment. The sensitivity of this kind of exam, although, depends on several factors, such as the size and the location of the abnormalities, density of the breast tissue, quality of the technical resources and radiologist's ability. This work presents a methodology that uses the K-Means clustering algorithm and the Template Matching technique for segmentation of suspicious regions. Next, geometry and texture features are extracted from each of these regions, being the texture described by the Simpson's Diversity Index, a statistic used in Ecology to measure the biodiversity of an ecosystem. Finally, this information is submitted to a Support Vector Machine so that the suspicious regions are classified into masses and non-masses. The methodology was tested with 650 mammographic images from the DDSM database, achieving 83.94% of accuracy, 83.24% of sensibility and 84.14% of specificity in average.
O câncer de mama é uma das maiores causas de mortalidade entre as mulheres no mundo todo. Atualmente, a análise da radiografia da mama é o recurso mais utilizado na detecção precoce desse tipo de câncer, pois possibilita a identificação de anomalias em sua fase inicial, fator fundamental para o sucesso do tratamento. A sensibilidade desse tipo de exame, no entanto, depende de diversos fatores, tais como tamanho e localização das anomalias, densidade do tecido mamário, qualidade dos recursos técnicos e habilidade do radiologista. Este trabalho apresenta uma metodologia para detecção de massas em imagens digitais de mamografias que poderá auxiliar o especialista em sua análise. O método proposto utiliza o algoritmo de agrupamento K-Means e a técnica de Template Matching para segmentar as regiões suspeitas de conterem massas. Em seguida, medidas de geometria e textura são extraídas de cada uma dessas regiões, sendo a textura descrita através do Índice de Diversidade de Simpson, uma estatística usada na Ecologia para mensurar a biodiversidade de um ecossistema. Finalmente, essas informações são submetidas a uma Máquina de Vetores de Suporte para que as regiões suspeitas sejam classificadas em massas ou não massas. A metodologia foi testada com 650 imagens mamográficas obtidas da base de dados DDSM, atingindo 83,94% de acurácia, 83,24% de sensibilidade, e 84,14% de especificidade em média.

Šio darbo tikslas – įvertinti Dubysos upės vidurupio vandens kokybę, taikant bioindikacinius vandens telkinių vertinimo metodus. Naudojant Saprobiškumo (S) ir Simpsono įvairovės indeksų (D) metodus buvo identifikuoti zooplanktoniniai organizmai bei įvertinti rūšių skaičiaus, gausumo ir įvairovės pasiskirstymo dėsningumai. Pagal J. Brown-Blanquet skalę atliktas atskirų augalų rūšių gausumo (projekcinis padengimo) barelyje vertinamas. Apie 50 km atkarpoje buvo išdėstytos 15 tyrimų vietų, kurias pasirenkant buvo atsižvelgiama į netoliese esančius žemės ūkio, pramonės, transporto objektus bei gamtinę aplinką. Tiriant zooplanktoniną paimti 270 vandens ir vandens – dumblo mėginiai. Šie tyrimai atlikti tris kartus metuose, bandymą pakartojant tris kartus. Naudojant J. Brown-Blanquet skalę augalų projekcinio padengimo vertinimas atliktas liepos mėn. Taigi vandens kokybės vertinimui buvo skaičiuoti tokie rodikliai: zooplanktoninių organizmų rūšių skaičius, gausumas, Simpsono įvairovės (D), Saprobiškumo (S) indeksai bei augalų projekcinis padengimas. Tirtoje teritorijoje buvo aptikta 33 zooplanktono rūšys: 8 infuzorijos, 8 dumbliai, 2 bakterijos, 2 vabzdžių lervos, 3 verpetės, 4 pirmuonys, 2 šakotaūsiai ir 3 irklakojai vėžiagyviai. Taikyta vienfaktorinė dispersinė analizė (One–way ANOVA) parodė, kad tyrimų vietos vandens kokybė (vandens užterštumas arba švarumas) turi įtakos vandens kokybę indikuojantiems rodikliams (rūšių skaičiui, gausumui, D bei S indeksams). Rūšių sudėtis ir... [toliau žr. visą tekstą]
The aim – to assess middle of the river Dubysa water quality, using valuation techniques by bioindicationous water mines. Using saprobic index (S) and Simpson's diversity index (D) methods have been identified zooplanktons organisms and the number of species, abundance and diversity of distribution patterns. According to J. Brown-Blanquet scale of an individual plant species richness (covering projection) rating in the barrel. About 50 km stretch was down 15 test sites, the choice was taken to the nearby agricultural, industrial, transport facilities and the environment. Studying zooplankton, it was taken of 270 water mines, and water - sludge ("hanging drop") samples. These studies were conducted three times a year, repeating the test three times. Using J. Brown-Blanquet scale projection covering the plant assessment was carried out in July. Thus, the assessment of water quality indicators have been calculated as follows: organisms zooplankton number of species, abundance, Simpson's diversity index (D), saprobic index (S) and the projection coating plant. There was found 33 species of investigated zooplankton area: 8 infusoria, 8 algae, 2 bacteria, 2 insect larvae, 3 vortex, 4 protozoa, crustaceans 2 and 3 copepods. Applied to one factor analysis of variance (one-way ANOVA) revealed that research on local water quality (water pollution or purity) affect water quality for indication indicators (number of species, abundance, D index). Species composition and quantitative... [to full text]

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The purpose of this work is to evaluate the quality of water evironment of the hydrographic basin of river Piracanjuba, river Meia Ponte stream Santa Maria. Appendages of alto Paraná river basin, making used index based in fishes developed by Fialho (2009). For that then it was considered 14 describes: Globals ( Diversity simpson s rate e equitability), taxonomic (abundance and rich resourse of the species of those families Callichthyidae, Genere Incertae Sedis in Characidae (GISC), Curimatidae and Gymnotidae and trofic group of detritivory and abundance of Sternopygidae family and the rich specie of the Heptapteridae family. In this work the sampling was maden on the dry weater (from may to September of 2009). In 27 sampling sites 14 afluents streams of river Piracanjuba, 7 afluentes of river Meia Ponte and 6 of stream Santa Maria the collect icthyofauna it was maden by the electrofishing method. Witch in on single passing in on part of 100 m located amount and others low waters. The results show that 27 stream reaches only the sampling sites P03, P11, and P21 had a bigger escores value but it was not considered as preserved as IBP protocol prosposed by Fialho (2009). For other wise 10 sampling sites (P01,P07,P08,P09,P12,P16,P18,P19,P22 and P25) showed values igual 0, then it is considered with higher degree of anthropogenic desarrengement. With tthis comes with the conclusion all the sampling site are anthropogenic that can be explained by the intense cattle raising activity in that place.
Este trabalho tem como objetivo, avaliar a qualidade do meio aquático das bacias hidrográficas dos rios Piracanjuba, Meia Ponte e ribeirão Santa Maria, pertencentes à bacia do alto rio Paraná, utilizando um índice baseado em peixes, desenvolvido por Fialho (2009). Para isso, foram considerados 14 descritores, assim distribuídos: globais (Índice de diversidade de Simpson, Equitabilidade), taxonômicos (abundâncias e riqueza de espécies das famílias Callichthyidae, Genere Incertae Sedis in Characidae (GISC), Curimatidae e Gymnotidae e do grupo trófico dos detritívoros; abundância da família Sternopygidae e a riqueza de espécies da família Heptapteridae). Neste trabalho, as coletas foram realizadas no período de estiagem (maio a setembro de 2009), em 27 pontos amostrais, sendo 14 riachos afluentes do rio Piracanjuba, sete afluentes do rio Meia Ponte e seis do ribeirão Santa Maria. A coleta da ictiofauna foi realizada pelo método da pesca elétrica com uma única passada em um trecho de 100 m, localizados a montante e outro na jusante. Os resultados mostraram que dos 27 pontos amostrais, apenas os pontos P03, P11 e P21 tiveram maiores valores dos escores, mas não foram classificados como preservados, conforme protocolo do IBP, proposto por Fialho (2009). Por outro lado, dez pontos (P01, P07, P08, P09, P12, P16, P18, P19, P22, P25) apresentaram valores iguais a zero, sendo assim considerados com maior grau de perturbação antrópica. Com isso, conclui-se que todos os pontos amostrais são antropizados, o que pode ser explicado pela intensa atividade agropecuária da região.

Dynamics of species, families and plant functional types (PFTs), and diversity of a natural grassland submitted or not to burning and grazing, in different relief positions (concave a convex slope) were evaluated. Treatments consisted of the associations of those three factors, in a completely randomized design, with variable number of replicates, from two to five. Rotational grazing were used, with an average occupation period of six days. Grazing animals were from Nelore, Charolais and its crosses. Stocking rate was calculated to obtain between 20 to 35 % of disappearing of forage mass. Diversity was evaluated using Shannon and Simpson index and frequency of species. The analysis of dry matter availability, on the relative participation of main species and the relative frequency of the other species were performed by double sampling. Data were submitted to cluster and ordination analysis and an analysis of variance via randomization tests. With respect to diversity, burned and grazed areas had lower index than those only grazed. Considering relief and grazing interaction, higher diversity occurred in convex slope. Including burning interaction, diversity was higher in concave slope. In grazing excluded areas, higher index were observed under burning effect, and considering this factor, higher diversity were registered in convex slope. Analyzing frequency of families, Poaceae, Cyperaceae and Asteraceae were present in all plots. The most versatile species were A. lateralis, Frimbristylis diphylla and Dichanthelium sabulorum, occurring in all treatments. Burning and grazing had a positive influence in vegetation diversity, however when interacting or in its absence, they turned dynamics to a dominance of a few species. The evaluation of dynamics showed that interpretation of the results through PFTs were more efficient to explore the differences between treatments, when compared to analysis by families or by species. The seasonal dynamics of the vegetation was affected both by grazing, burning and relief position, independently if evaluated through species or functional types of plants.
Foi avaliada a dinâmica por meio de espécies, famílias e tipos funcionais de plantas (TFs), e a diversidade de uma pastagem natural submetida aos fatores queima (presença ou ausência) e pastejo (ausência ou presença), em diferentes posições topográficas (encosta ou baixada). Os tratamentos foram constituídos pela associação dos três fatores, em um delineamento completamente casualizado com número variável de repetições, entre duas e cinco. O pastejo foi rotacionado, com um período de ocupação médio de seis dias, sendo utilizados animais das raças Nelore, Charolês e suas cruzas. A carga foi calculada adotando-se uma taxa de desaparecimento entre 20-35% da massa de forragem existente. A diversidade foi avaliada através dos índices de Shannon, Simpson e da freqüência de ocorrência de espécies. As avaliações da disponibilidade total de matéria seca, da participação relativa das principais espécies e da freqüência relativa das demais espécies foram realizadas por meio de dupla amostragem. Os dados obtidos foram submetidos às análises de agrupamento, ordenação e de variância via teste de aleatorização. Com relação à diversidade, as áreas queimadas com pastejo possuíram índices menores do que apenas com pastejo. Considerando a interação relevo e pastejo, a maior diversidade se deu na encosta. Incluindo-se a interação com o efeito de queima, essa foi superior nas áreas de baixada. Na exclusão de pastejo, os índices mais elevados foram encontrados com queima, e dentro desse distúrbio, maiores índices na posição de relevo de encosta. Já na ausência da queima, o maior índice foi observado na baixada. Na análise da freqüência de ocorrência por família, destacaram-se Poaceae, Cyperaceae e Asteraceae, com presença em todos os ambientes estudados. Já as espécies com maior versatilidade foram A. lateralis, Frimbristylis diphylla e Dichanthelium sabulorum, encontrados em todos os tratamentos avaliados. O emprego da queima ou pastejo tiveram uma influência positiva na diversidade da vegetação, porém quando em conjunto ou totalmente ausentes direcionaram a dinâmica a uma dominância de poucas espécies. O estudo da dinâmica mostrou que a interpretação dos resultados através dos TFs foi mais eficiente para explorar as diferenças entre os tratamentos, quando comparado às análises por famílias botânicas ou por espécies. A dinâmica estacional da vegetação foi afetada pelos fatores pastejo, queima e posição de relevo, independentemente se avaliados através de espécies ou tipos funcionais de plantas.

The availability of several methods to unambiguously mark individual cells has strongly fostered the understanding of clonal developments in hematopoiesis and other stem cell driven regenerative tissues. While cellular barcoding is the method of choice for experimental studies, patients that underwent gene therapy carry a unique insertional mark within the transplanted cells originating from the integration of the retroviral vector. Close monitoring of such patients allows accessing their clonal dynamics, however, the early detection of events that predict monoclonal conversion and potentially the onset of leukemia are beneficial for treatment. We developed a simple mathematical model of a self-stabilizing hematopoietic stem cell population to generate a wide range of possible clonal developments, reproducing typical, experimentally and clinically observed scenarios. We use the resulting model scenarios to suggest and test a set of statistical measures that should allow for an interpretation and classification of relevant clonal dynamics. Apart from the assessment of several established diversity indices we suggest a measure that quantifies the extension to which the increase in the size of one clone is attributed to the total loss in the size of all other clones. By evaluating the change in relative clone sizes between consecutive measurements, the suggested measure, referred to as maximum relative clonal expansion (mRCE), proves to be highly sensitive in the detection of rapidly expanding cell clones prior to their dominant manifestation. This predictive potential places the mRCE as a suitable means for the early recognition of leukemogenesis especially in gene therapy patients that are closely monitored. Our model based approach illustrates how simulation studies can actively support the design and evaluation of preclinical strategies for the analysis and risk evaluation of clonal developments.

The availability of several methods to unambiguously mark individual cells has strongly fostered the understanding of clonal developments in hematopoiesis and other stem cell driven regenerative tissues. While cellular barcoding is the method of choice for experimental studies, patients that underwent gene therapy carry a unique insertional mark within the transplanted cells originating from the integration of the retroviral vector. Close monitoring of such patients allows accessing their clonal dynamics, however, the early detection of events that predict monoclonal conversion and potentially the onset of leukemia are beneficial for treatment. We developed a simple mathematical model of a self-stabilizing hematopoietic stem cell population to generate a wide range of possible clonal developments, reproducing typical, experimentally and clinically observed scenarios. We use the resulting model scenarios to suggest and test a set of statistical measures that should allow for an interpretation and classification of relevant clonal dynamics. Apart from the assessment of several established diversity indices we suggest a measure that quantifies the extension to which the increase in the size of one clone is attributed to the total loss in the size of all other clones. By evaluating the change in relative clone sizes between consecutive measurements, the suggested measure, referred to as maximum relative clonal expansion (mRCE), proves to be highly sensitive in the detection of rapidly expanding cell clones prior to their dominant manifestation. This predictive potential places the mRCE as a suitable means for the early recognition of leukemogenesis especially in gene therapy patients that are closely monitored. Our model based approach illustrates how simulation studies can actively support the design and evaluation of preclinical strategies for the analysis and risk evaluation of clonal developments.

Malaise traps are a common tool for collecting insects used by many researchers. Although there have been variations in the models and materials used for Malaise traps, the potential for sampling bias due to mesh gague has been explored inadequately. This study compared coarse and fine mesh Townes model Malaise traps in two habitats on the Grand Staircase-Escalante National Monument. The two habitats next to the Lick Wash trailhead were defined by dominant vegetation type – sagebrush and grasses or Piñon-Juniper. We collected from three sites per habitat type, over three consecutive days in June in both 2006 and 2007. A pair of Malaise traps consisting of one coarse mesh and one fine mesh trap were used at each site in order to compare differences in the diversity and in the average size of individuals collected by each type of Malaise trap. We measured diversity using both presence-absence data such as richness scores and Jaccard's Index of Similarity, and abundance-based measures of comparison, including Simpson's Index of Diversity and non-metric multidimensional scaling. We identified all individuals according to Order, and because of our interest in flies and their abundance, we further identified the Dipter ta to the Family level. Average insect size was determined by categorizing individuals according to one of 14 distinct size-classes. In sum, 71 samples totaling approximately 62,500 insects were identified and sized. Because we sampled from two adjacent habitats, we also discuss beta diversity across the sample sites. Although mesh-size appears to have a significant effect on the diversity of the catch according to some tests, not all of our analysis agrees. In addition, the gain in the amount of diversity collected by incorporating both mesh-sizes may not be worth the costs of that kind of sampling. Other means of collection may adequately make up that difference. Habitat on the other hand was a clear marker for difference in diversity. Size was not found to be significant overall, but there still may be reasons to examine the effect of mesh-size with respect to the Hymenoptera.

It is well established that national retail chains impact small, single location retail businesses in terms of revenue generation, retail structure, retail type diversity, and location. This study examines the retail structure and diversity of five retail districts in the City of Denton, Texas. The analysis focuses on one central business district (CBD), one traditional retail strip center (University Drive, also known as US HWY 380), one special retail district (Fry Street District), one traditional enclosed shopping mall and associated development (Golden Triangle Mall), and one power retail center (Denton Crossing). The empirical foundation for the investigation is a historical business database covering years 1997 to 2010, obtained from Info Group's Reference USA. This Reference USA database includes location, industry, and status (single versus chain location) information for each business. Retail diversity and evenness were measured for each of the five retail districts using the Simpson's Diversity Index and the Simpsons Measure of Evenness, leading to specification of the differences that exist in retail structure and diversity among the districts. Golden Triangle Mall and Denton Crossing were primarily chain location in composition while Fry Street District, the CBD, and University Drive were primarily single location in composition. Across all years, the single versus chain status of the local business communities did not substantially change within any of the districts. The Fry Street District exhibited the most change in diversity as well as the lowest overall diversity among the retail districts, followed by University Drive and Golden Triangle Mall. The CBD did not experience any major change in retail type diversity. However, all retail districts experienced major changes in retail evenness. Overall for the city, single location retail businesses accounted for the majority of all the retail businesses, however, chain locations employed more people. In total, these findings indicate that the development of retail districts composed primarily of chain location retailer's affects retail district diversity and evenness but not retail structure.

The possibility of identifying single nucleotide polymorphisms (SNPs) that would be useful for rapid bacterial typing was investigated. Neisseria meningitidis was the organism chosen for modelling the approach since informative SNPs could be found amongst the sequence data available for multi-locus sequence typing (MLST) at http://www.mlst.net. The hypothesis tested was that a small number of SNPs located within the seven gene fragments sequenced for MLST provide information equivalent to MLST. Preliminary investigations revealed that a small number of SNPs could be utilised to highly discriminate sequence types (STs) of clinical interest. Laboratory procedures demonstrated that SNP fingerprinting of N. meningitidis isolates is achievable. Further tests showed that laboratory identification of a defining SNP in the genome of isolates was to be a practical method of obtaining relevant typing information. Identification of the most discriminating SNPs amongst the ever-increasing amount of MLST sequence data summoned the need for computer-based assistance. Two methods of SNP selection devised by the author of this thesis were translated into computer-based algorithms by contributing team members. Software for two computer programs was produced. The algorithms facilitate the optimal selection of SNPs useful for (1) distinguishing specific STs and (2) differentiating non-specific STs. Current input information can be obtained from the MLST database and consequently the programs can be applied to any bacterial species for which MLST data have been entered. The two algorithms for the selection of SNPs were designed to serve contrasting purposes. The first of these was to determine the ST identity of isolates from an outbreak of disease. In this case, isolates would be tested for their membership to any of the STs known to be associated with disease. It was shown that one SNP per ST could distinguish each of four hyperinvasive STs of N. meningitidis from between 92.5% and 97.5% of all other STs. With two SNPs per ST, between 96.7% and 99.0% discrimination is achieved. The SNPs were selected from MLST loci with the assistance of the first algorithm which scores SNPs according to the number of base mismatches in a sequence alignment between an allele of an ST of interest and alleles belonging to all other STs at a specified locus. The second purpose was to determine whether or not isolates from different sources belong to the same ST, regardless of their actual ST identity. It was shown that with seven SNPs, four sample STs of N. meningitidis could, on average, be discriminated from 97.1% of all other STs. The SNPs were selected with the aid of the second algorithm which scores SNPs at MLST loci for the relative frequency of each nucleotide base in a sequence alignment as a measure of the extent of their polymorphism. A third algorithm for selecting SNPs has been discussed. By altering the method of scoring SNPs, it is possible to overcome the limitations inherent in the two algorithms that were utilised for finding SNPs. In addition, the third approach caters for finding SNPs that distinguish members of a complex from non-members.

The global loss of biodiversity calls for robust large-scale diversity assessment. Biological diversity is a multi-faceted concept; defined as the “variety of life”, answering questions such as “How much is there?” or more precisely “Have we succeeded in reducing the rate of its decline?” is not straightforward. While various aspects of biodiversity give rise to numerous ways of quantification, we focus on temporal (and spatial) trends and their changes in species diversity. Traditional diversity indices summarise information contained in the species abundance distribution, i.e. each species' proportional contribution to total abundance. Estimated from data, these indices can be biased if variation in detection probability is ignored. We discuss differences between diversity indices and demonstrate possible adjustments for detectability. Additionally, most indices focus on the most abundant species in ecological communities. We introduce a new set of diversity measures, based on a family of goodness-of-fit statistics. A function of a free parameter, this family allows us to vary the sensitivity of these measures to dominance and rarity of species. Their performance is studied by assessing temporal trends in diversity for five communities of British breeding birds based on 14 years of survey data, where they are applied alongside the current headline index, a geometric mean of relative abundances. Revealing the contributions of both rare and common species to biodiversity trends, these "goodness-of-fit" measures provide novel insights into how ecological communities change over time. Biodiversity is not only subject to temporal changes, but it also varies across space. We take first steps towards estimating spatial diversity trends. Finally, processes maintaining biodiversity act locally, at specific spatial scales. Contrary to abundance-based summary statistics, spatial characteristics of ecological communities may distinguish these processes. We suggest a generalisation to a spatial summary, the cross-pair overlap distribution, to render it more flexible to spatial scale.

This thesis studies the relationships between newcomers employed by the Hudson’s Bay Company at Fort Simpson and the Ts’msyen people who came to live outside the fort from its establishment in Ts’msyen territory in 1834 until the founding of a Christian Ts’msyen village at Metlakatla in 1862. I argue that a mutually intelligible – if not equally understood – world was developed at this site in which the lives of these newcomers and local Ts’msyen people became intertwined and somewhat interdependent. While this world was not characterized by universal conditions of fellowship and trust it did involve shared Ts’msyen-newcomer participation in significant cultural activities, the repurposing or remaking of each other’s customs, and jointly developed practices in which customs from both groups were intermingled. I propose that some of these practices, particularly those of law and marriage, can be considered as culturally hybrid. This study suggests the compromised position of the HBC on the northern Northwest Coast, Ts’msyen cultural disposition, and dynamics of power within and between these groups fostered the development a mutually intelligible world and hybrid Ts’msyen-newcomer practices. Far from any centre of British power, greatly outnumbered by the Ts’msyen, and soon out-armed, the newcomers of Fort Simpson were particularly vulnerable. Ts’msyen people, it is claimed, generally valued innovation and had a long-established system for acquiring ownership of changes brought from outside into their communities. Ts’msyen women had a special role in this process. Moreover, both the Ts’msyen and the newcomers had hierarchically structured societies in which displays of power and authority were important. These local circumstances were fundamental to the formation of the hybrid institutions of marriage and law at Fort Simpson/Laxłgu’alaams and to the other complex social and cultural interactions of the two groups documented here. While this study acknowledges that Ts’msyen and newcomer people had distinct motivations for entering relationships with each other, for sharing and cross-participating in customs of the other, and for developing new joint and hybrid practices, it argues that for both groups power and authority were crucial factors. The distinct circumstances which made a mutually intelligible world possible at Fort Simpson/Laxłgu’alaams came to an end in 1862. The return of smallpox in Ts’msyen territory, the removal of the missionary William Duncan and his followers from Fort Simpson to Metlakatla, and the increasing colonial regulation of Indigenous people brought an end to the brief period of accommodation and collaboration between HBC newcomers and Ts’msyen people.

Das Miandam-Untersuchungsgebiet (35° 1′- 5′ N, 72° 30′-37′ E) liegt in der Swat-Region der Provinz Khyber Pakhtunkhwa (ehemals North West Frontier Province) im nördlichen Pakistan. Die vorliegende Arbeit berücksichtigt sowohl ethnobotanische und pflanzensoziologische Aspekte als auch die Pflanzenartendiversität innerhalb des Gebietes. Aufgrund der hohen Habitatvielfalt weist das Miandam-Gebiet einen großen Reichtum von Medizinalpflanzen auf. Die im Rahmen der Arbeit durchgeführte ethnobotanische Studie dokumentiert das Vorkommen der Medizinalpflanzen sowie deren Nutzung in der Region. Weiterhin wurden die durch Sammlerpräferierten Lebensräume bestimmt und evaluiert inwiefern die Heilpflanzen durch Sammlung und Habitatzerstörung bedroht werden. Insgesamt wurden 106 traditionelle Heilpflanzen aus 54 Pflanzenfamilien verzeichnet. Zu den am häufigsten gefundenen Wuchsformen zählten mehrjährige (43%) und kurzlebige Kräuter (23%), Sträucher (16%) und Bäume (15%). Ein Großteil der untersuchten Heilpflanzen und ihrer Produkte wird zur Behandlung von Magen-Darm-Erkrankungen eingesetzt. Die Produkte werden vorrangig als Sud oder Pulver zubereitet und oral angewendet. Achtzig der 106 traditionellen Heilpflanzen gehören der Gruppe der einheimischen Arten an. Fast 50% der Pflanzenarten treten dabei in synanthroper Vegetation auf, während der Rest in naturnaher Umgebung (z.B. extensiv beweidete Wald- und Graslandbereiche) vorgefunden werden kann. Wälder sind der Ursprung der meisten nicht synanthropen einheimischen Medizinalpflanzen. Drei Arten (Aconitum violaceum, Colchicum luteum, Jasminum humile) können als Folge intensiven Sammelns als bedroht eingestuft werden. Um die pflanzensoziologischen und phytogeografischen Aspekte des Projektes abzudecken wurde die Vegetation des Miandam-Gebietes mit einem Fokus auf Wäldern, Gebüschen und anderen Formationen untersucht. Die Ergebnisse der Vegetationserhebungen wurden mit denen anderer Studien in der weiteren Umgebung des Hindukush-Himalayas verglichen. Weiterhin wurde untersucht inwiefern die Waldökosysteme durch anthropogene Aktivitäten im Untersuchungsgebiet bedroht sind. Die im Gebiet verzeichneten Gefäßpflanzenarten umfassen insgesamt 33 Bäume, 52 Sträucher, 305 Kräuter und 11 Lianen. Basierend auf einer multivariaten Analyse konnten 12 Pflanzengesellschaften identifiziert werden. Die Spanne dieser Gesellschaften reichte von subtropischen semiariden Wäldern mit Ailanthus altissima im Tiefland zu alpinen Rasen von Sibbaldia cuneata durchsetzt mit Juniperus. Die dominierende Vegetation des Untersuchungsgebietes besteht aus von Abies pindrow und Viburnum grandiflorum Wäldern. Eine georeferenzierte Karte der Vegetation erleichtert die Lokalisierung der ökologisch interessanten Vegetation. Artenreichtum und –diversität wurden entlang eines Höhengradienten untersucht. Dazu wurde die Alpha- sowie Beta-Diversität verschiedener Wuchsformtypen bestimmt. Der Artenreichtum aller Gefäßpflanzenarten erreichte sein Maximum zwischen 2200-2500 m. Dagegen zeigte der Artenreichtum der Sträucher einen glockenkurvenartigen Verlauf mit einem Maximum zwischen 2000 und 2200 m. Die höchste Alpha-Diversität der Gefäßpflanzenarten wurde in den tieferen Lagen des Untersuchungsgebietes verzeichnet. Die Beta-Diversität aller Wuchsformtypen zeigte entlang des gesamten Höhengradienten hohe Werte und somit einen starken Artenwechsel. Die Beta-Diversität der Straucharten fluktuiert entlang des Höhengradienten und zeigt damit ein einzigartiges Muster.

Vegetative species diversity is under threat from environmental pressures, particularly climate change. As the impacts of climate change vary from place to place, response of vegetative species diversity to a changing climate also vary depending on geographical location. The response of vegetative species diversity under dry conditions in Zimbabwe is not well known. This study assessed the impact of climate change on vegetative species diversity under semiarid conditions of Masvingo province in Zimbabwe. This was achieved by determining climate change trends over a period of forty years (1974-2014), and examining the relationship between vegetative species diversity and spatially interpolated climate data. The absence of historical diversity data prompted the use of remote sensing to enable the assessment of spatial and temporal changes. Thus, the Normalised difference vegetation index (NDVI) was used to assess vegetative species diversity changes after establishing a positive relationship between species diversity and NDVI. The mixed methods research design was used as the strategy of inquiry. The non-aligned block sampling design was used as the sampling framework from which 198 sampling points were identified. Meteorological data obtained from Zimbabwe Meteorological Services Department (ZMSD) and the National Climate Data Centre (NCDC) were used for climate change analysis. Data collected through image analysis, direct observations, questionnaire surveys and interviews were used to assess the impact of climate change on vegetative species diversity. Results indicate that all temperature and precipitation variables have significant (p<0.05) trends over the period under study. However, the trend for seasonal total precipitation was not significant but declining. The significant trends indicate that climate change occurred over the period under study. 93% of the respondents confirmed having experienced the climate change phenomenon. Results also show a significant relationship between climate elements (precipitation and temperature) and vegetative species diversity represented by Shannon Weaver Index (H). More so, there is a positive relationship between NDVI and H. Vegetative species diversity represented by NDVI decreased over the period under review. The results indicate that climate change has contributed to the decrease of vegetative species diversity in Masvingo province, thus it is a force behind many other factors contributing to biodiversity loss.
College of Agriculture and Environmental Sciences
Ph. D. (Environmental Sciences)