Analysis of the impact on phylogenetic inference of non-reversible nucleotide substitution models

Most phylogenetic trees are inferred using time-reversible evolutionary models that assume that the relative rates of substitution for any given pair of nucleotides are the same regardless of the direction of the substitutions. However, there is no reason to assume that the underlying biochemical mutational processes that cause substitutions are similarly symmetrical. Here, we evaluate the effect on phylogenetic inference in empirical viral and simulated data of incorporating non-reversibility into models of nucleotide substitution processes. I consider two non-reversible nucleotide substitution models: (1) a 6-rate nonreversible model (NREV6) that is applicable to analyzing mutational processes in double-stranded genomes in that complementary substitutions occur at identical rates; and (2) a 12-rate non-reversible model (NREV12) that is applicable to analyzing mutational processes in single-stranded (ss) genomes in that all substitution types are free to occur at different rates. Using likelihood ratio and Akaike Information Criterion-based model tests, we show that, surprisingly, NREV12 provided a significantly better fit than the General Time Reversible (GTR) and NREV6 models to 21/31 dsRNA and 20/30 dsDNA datasets. As expected, however, NREV12 provided a significantly better fit to 24/33 ssDNA and 40/47 ssRNA datasets. I tested how non-reversibility impacts the accuracy with which phylogenetic trees are inferred. As simulated degrees of non-reversibility (DNR) increased, the tree topology inferences using both NREV12 and GTR became more accurate, whereas inferred tree branch lengths became less accurate. I conclude that while non-reversible models should be helpful in the analysis of mutational processes in most virus species, there is no pressing need to use these models for routine phylogenetic inference. Finally, I introduce a web application, RpNRM, that roots phylogenetic trees using a non-reversible nucleotide substitution model. The phylogenetic tree is rooted on every branch and the likelihoods of each rooting are determined and compared with the highest likelihood tree being identified as that with the most plausible rooting. The rooting accuracy of RpNRM was compared to that of the outgroup rooting method, the midpoint rooting method and another non-reversible model-based rooting method implemented in the program IQTREE. I find that although the RpNRM and IQTREE reversible model-based methods are not as accurate on their own as outgroup or midpoint rooting methods, they nevertheless provide an independent means of verifying the root locations that are inferred by these other methods

Development of Social Studies Learners’ Textbooks for Secondary Schools in Zambia

Learner’s text books are one of the most important teaching and learning resources in most schools in developing countries, Zambia inclusive. This study was triggered as a result of concerns by various stakeholders and scholars regarding the quality of Social Studies learners’ textbooks for the junior secondary school which were developed following the 2013 revised Zambian school curriculum. The embedded research design of the mixed methods research approach was employed for this study. Using interview guides and questionnaires for data collection, information was collected from book publishers and 91 teachers of social studies. The findings of this study revealed that privatization of textbook development resulted in the development of poor quality textbooks. Furthermore, failure to adhere to a specific national textbook policy to guide the development of learners’ textbooks also contributed to the development of poor textbooks. It was further revealed that there was lack of coordination between the Curriculum Development Center and textbook publishing companies. Additionally, findings pointed to the fact that secondary school teachers of Social Studies were not fully involved in developing learners’ textbooks and political interference in textbook development was found to have also contributed to poor quality textbook development. Researchers in this study recommended that the Ministry of General Education (MoGE) through the Curriculum Development Centre should thoroughly revise the textbooks in question, broaden the scope of teacher involvement and stop the privatization of textbook development in Zambia. Keywords: Textbook development, Quality, Social Studies DOI: 10.7176/JEP/10-6-1

An analysis of the development of social studies learners’ textbooks for junior secondary schools in Zambia

Thesisiv ABSTRACT The revision of the Zambian school curriculum in 2013 brought about the integration of the three learning areas namely; Civics, Geography and History at Junior Secondary School resulting in one subject, Social Studies. Hence, there was a need to develop Social Studies learners’ textbooks for Junior Secondary School in order to facilitate the implementation of the revised curriculum. During the Ministry of General Education (MoGE) meetings and subject associations, teachers and other education stakeholders such as NGOs complained that the quality of curriculum materials such as textbooks developed following the 2013 revised curriculum were of poor quality. However, no study seems to have been done to establish the extent to which such materials were of quality. Therefore, this study sought to assess the quality of Social Studies learners’ textbooks for junior secondary school in Zambia, analyse the procedure of developing Social Studies learners’ textbooks for Junior Secondary School in Zambia, establish the criteria applied to select who were involved in the development of the Social Studies learners’ textbooks for junior secondary school in Zambia, analyse the steps that should be followed in developing and evaluating Social Studies learners’ textbooks in Zambia. The researcher employed a mixed methods approach to conduct this study. An embedded research design used in this study was more based on qualitative than quantitative methods because the study was descriptive in nature. Questionnaires were administered to teachers of junior secondary school of Social Studies. Additionally, interviews were conducted with the Curriculum Specialist, Chief Curriculum Specialist, Senior Education Standards Officer and textbook publishers. Data that was collected from interviews and questionnaires for Social Sciences were analysed using themes and descriptive statistics. The findings of the study showed that the Social Studies learners’ textbooks were of poor quality indeed; lack of teacher involvement in textbook development; lack of coordination in textbook development; failure to adhere to a national textbook policy; political interference in textbook development were found to be the main contributing factors to this situation. Based on these findings, it is recommended that MoGE through CDC should broaden the scope of teacher involvement in textbook development, revise the Social Studies learners’ textbooks for junior secondary school, adhere to a national textbook policy that should guide textbook development and privatization of textbook development should not be continued. Key words: textbook development, quality, Social Studies

Integration of Faith-Based Modules in Undergraduate Nursing Curricula: Implications on Graduate Work Ethic and Health Care Delivery

Nursing education programs provide commendable training in keeping pace with the rapid advances in disease management. The tradition of incorporating faith within nursing curricula has existed for centuries. However, consensus on faith-based/spirituality has received far less attention in nursing curricula, and nursing students often do not have a strong foundation in this area. This study aimed to explore the implications of faith-based/ spirituality on the work ethic and health care delivery disposition of nursing students/graduates in the Southern District, Botswana

An approach to sustainable, energy efficient design for low-cost housing in Botswana

The study was premised by the apparent lack of sustainability and poor quality of low cost housing of Botswana. The overall aim of the study was to investigate the possibility of integration of sustainability and resource efficiency into housing practice. The research first conducted a desk study into the low cost housing industry of Botswana which was followed by a survey in a representative area of Gaborone, the capital city of Botswana. The survey was in the form of a situational analysis which was conducted through user questionnaires. This was followed by structured interviews that were administered to stakeholders to gain insight into housing and design practice. In order to investigate the performance of different types of existing low cost housing, the following parameters were identified; planning and implementation, housing design, the building envelope and its response to its environment, materials and resources used in low cost housing, their application and consumption pattern. The study found that sustainable, energy conscious design of housing makes a considerable difference to the building’s thermal performance, user comfort, health, appropriate use of resources and the environment. It results in cost savings for services by the occupants, reduces institutional expenditure on programmes and maintenance costs, and reduces the negative impact on the environment by the building sector. Following the research, the study found that for successful integration of sustainability and energy efficiency in low cost housing for Botswana, there must be a balance in the integration of three primary elements; energy efficient housing, culture and regional identity and the environment. Institutional low cost housing was targeted as the first point of intervention for better impact. The study recommended a phased implementation approach. The output of the study was a framework for the integration of these strategies into new and existing housing for the institutional low cost housing sector.Dissertation (MArch)--University of Pretoria, 2008.Architectureunrestricte

Establishment and early growth of jack pine (Pinus banksiana Lamb.) in Acton Township Ontario

The objective of this study was to investigate the effect of different site preparation methods on the establishment and growth of jack pine (Pinus banksiana Lamb.) on two different soil types. These sites were either site prepared using TTS Disc Trencher or by prescribed burning; sites were regenerated by seeding or by containerized planting. Data were collected in 7 year old jack pine plantations near Wawa, Ontario on soils developed from glacialfluvial and moraine deposits. A total of 600 sample trees were randomly selected representing the soil types, the site preparation and the regeneration methods. The sampled trees were cut and their total volume determined. The data were analysed as a split-plot design. The analysis of variance showed no significant difference between the seeded and containerized planted trees except with growth of basal area per hectare. There was also no significant difference in growth between soil type or between areas site prepared by the TTS Disc Trencher, prescribed burn or without site preparation. Both the seeded and containerized planted areas met the jack pine growth standards set by the Ontario Ministry of Natural Resources. Although planted trees are larger than those obtained by seeding, the present net value for seeded stock is greater than that for planted stock. A complete factorial analysis of the data showed a significant difference in stems per hectare and total tree volume for the soil types and site preparation methods. Further investigation of these differences may be important to the forest manager