Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages

Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible, and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modeled accurately using the distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or underparameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10 000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42 337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these three sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modeled by a combination of eight edge-specific rate matrices (four for V1 and four for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the seven species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.

An account and analysis of the implementation of various ebook business models at QUT, Australia

QUT (Queensland University of Technology) is a leading university based in the city of Brisbane, Queensland, Australia and is a selectively research intensive university with 2,500 higher degree research students and an overall student population of 45,000 students. The transition from print to online resources is largely completed and the library now provides access to 450,000 print books, 1,000 print journals, 600,000 ebooks, 120,000 ejournals and 100,000 online videos. The ebook collection is now used three times as much as the print book collection. This paper focuses on QUT Library’s ebook strategy and the challenges of building and managing a rapidly growing collection of ebooks using a range of publishers, platforms, and business and financial models. The paper provides an account of QUT Library’s experiences in using Patron Driven Acquisition (PDA) using eBook Library (EBL); the strategic procurement of publisher and subject collections by lease and outright purchase models, the more recent transition to Evidence Based Selection (EBS) options provided by some publishers, and its piloting of etextbook models. The paper provides an in-depth analysis of each of these business models at QUT, focusing on access verses collection development, usage, cost per use, and value for money.

An account of chronological developments in control of distributed parameter systems

Control systems arising in many engineering fields are often of distributed parameter type, which are modeled by partial differential equations. Decades of research have lead to a great deal of literature on distributed parameter systems scattered in a wide spectrum.Extensions of popular finite-dimensional techniques to infinite-dimensional systems as well as innovative infinite-dimensional specific control design approaches have been proposed. A comprehensive account of all the developments would probably require several volumes and is perhaps a very difficult task. In this paper, however, an attempt has been made to give a brief yet reasonably representative account of many of these developments in a chronological order. To make it accessible to a wide audience, mathematical descriptions have been completely avoided with the assumption that an interested reader can always find the mathematical details in the relevant references.

Growing banana prawns in prawn farm settlement ponds to utilise and help remove waste nutrients.

To assess their utility for profitable wastewater bioremediation, banana prawns, Penaeus (Fenneropenaeus) merguiensis (de Man), were stocked at low densities (1 – 5 m-2) and grown without supplemental feeding in five commercial-prawn-farm settlement ponds (0.3 to 6.0 ha). The prawns free-ranged in the variously designed ponds for 160 to 212 days after stocking as PL15. Survival estimates ranged from 12% to 60% with production of 50 – 528 kg ha-1. Over 1150 kg of marketable product was produced in the study. Exceptional growth was monitored at one farm where prawns reached an average size of 17g in 80 days. Nutrients in water flowing into (8 - 40 ML d-1) and out of the settlement pond at that farm were assessed twice weekly along with routine water quality measurements. Only small differences in water qualities were detected between waters running into and out of this settlement pond. Total nitrogen levels gradually increased from 1 - 1.5 mg L-1 early in the season to over 3 mg L-1 towards the end of the season. Total phosphorus levels similarly rose from 0.1 - 0.2 mg L-1 to 0.3 - 0.4 mg L-1 in the middle of the season, but fell to 0.2 – 0.3 mg L-1 towards the end when approximately 12,000 prawns were harvested with a total weight of 175 kg. No significant differences (P > 0.05) were detected in the overall acceptability of prawns harvested from each of the 5 settlement ponds in small-scale consumer sensory analyses. The prawns from settlement ponds were rated similarly to banana prawns grown with commercial diets at two other establishments. Microbiological analyses of prawns from all farms showed bacterial levels to be well within food-grade standards and lower than prawns produced in a normal growout pond. These results demonstrate that high quality food grade banana prawns can be produced in these wastewater treatment systems.

Are high-impact species predictable? An analysis of naturalised grasses in northern Australia

Predicting which species are likely to cause serious impacts in the future is crucial for targeting management efforts, but the characteristics of such species remain largely unconfirmed. We use data and expert opinion on tropical and subtropical grasses naturalised in Australia since European settlement to identify naturalised and high-impact species and subsequently to test whether high-impact species are predictable. High-impact species for the three main affected sectors (environment, pastoral and agriculture) were determined by assessing evidence against pre-defined criteria. Twenty-one of the 155 naturalised species (14%) were classified as high-impact, including four that affected more than one sector. High-impact species were more likely to have faster spread rates (regions invaded per decade) and to be semi-aquatic. Spread rate was best explained by whether species had been actively spread (as pasture), and time since naturalisation, but may not be explanatory as it was tightly correlated with range size and incidence rate. Giving more weight to minimising the chance of overlooking high-impact species, a priority for biosecurity, meant a wider range of predictors was required to identify high-impact species, and the predictive power of the models was reduced. By-sector analysis of predictors of high impact species was limited by their relative rarity, but showed sector differences, including to the universal predictors (spread rate and habitat) and life history. Furthermore, species causing high impact to agriculture have changed in the past 10 years with changes in farming practice, highlighting the importance of context in determining impact. A rationale for invasion ecology is to improve the prediction and response to future threats. Although our study identifies some universal predictors, it suggests improved prediction will require a far greater emphasis on impact rather than invasiveness, and will need to account for the individual circumstances of affected sectors and the relative rarity of high-impact species.

100 Years of Settlement Commemorative Medal

Obverse: Shape of the State of Israel filled with flowers in blossom. Reverse: A stylized plough.

The Interplays of Histories, Economies and Cultures in Human Adaptation and Settlement Patterns : The Cases of the Faroe Islands and Greenland

The Arctic peoples are currently faced with the challenge of adapting to climate change. Adaptive strategies have been central for the survival of the Northern communities also in the past. This doctoral dissertation is a comparative study of how two Northern societies, the Faroe Islands and Greenland, have responded to challenges caused by the interplay of environmental, political and socio-economic changes. Its main objective is to describe the characteristics of respective adaptive strategies developed in the two societies and to show which connections exist between adaptation and the development of the settlement patterns. This study is based on document analysis, supported by an analysis of demographic and economic statistics. For the field work, the empirical method of landscape-reading was applied. A narrative approach was used to explain interrelations between adaptive strategies and societal developments in the Faroe Islands and Greenland. Maps illustrating development and changes in settlement patterns in different time periods are central for this study because they illustrate the impacts of adaptation on settlement development. The results of this dissertation show that people in the Faroe Islands and Greenland have consciously developed their settlements and used this as an adaptive strategy: different types of settlements were established depending on which kind of resource base was available. Strong dependency on a single resource is likely to increase the probability that settlement development was impacted by it. The interrelation of natural resource use and settlement pattern development has weakened in the Faroe Islands and Greenland from the mid-1900s. Since then, the importance of the government settlement policies has become pronounced and the existing settlement pattern, including settlements without prospects for genuine economic viability, has been preserved. Currently, the Northern communities are increasingly dependent on worldwide developments. In the light of this study, the communities can respond to challenges of globalization and climate change and develop new kind of adaptive strategies, such as diversification of their economic activities. This dissertation shows that it is important to extend studies about community adaptation in the High North to consider the overall development of the Northern settlement patterns.

Franks family papers, 1711-1821, [1965-1968].

Contains business correspondence, accounts and documents relating to Jacob Franks of New York, his two sons, Moses and David, a nephew, Isaac, and a John Franks of Halifax, possibly a member of the family.

Industrial Removal Office records undated, 1899-1922

Contains Board of Directors minutes (1903, 1907), Executive Committee minutes (1907), Removal Committee minutes (1903-1917), Annual Reports (1910, 1913), Monthly Reports (1901-1919), Monthly Bulletins (1914-1915), studies of those removed, Bressler's "The Removal Work, Including Galveston," and several papers relating to the IRO and immigration. Financial papers include a budget (1914), comparative per capita cost figures (1909-1922), audits (1915-1918), receipts and expenditures (1918-1922), investment records, bank balances (1907-1922), removal work cash book (1904-1911), office expenses cash account (1903-1906), and the financial records of other agencies working with the IRO (1906). Includes also removal case records of first the Jewish Agricultural Society (1899-1900), and then of the IRO (1901-1922) when it took over its work, family reunion case records (1901-1904), and the follow-up records of persons removed to various cities (1903-1914). Contains also the correspondence of traveling agents' contacts throughout the U.S. from 1905-1914, among them Stanley Bero, Henry P. Goldstein, Philip Seman, and Morris D. Waldman.

Map detailing growth of settlement tracts by year 1925-1929

Digital image

Account of the estate of Salmen Abt, Melsungen, Kur-Hessen 1829-1842

Bound photocopies of various documents, describing the estate of Solomon Abt in the town of Melsungen in Hesse, Germany. Included are the copies of a marriage contract between Solomon Abt and Vogel Tebler; extensive lists of all of Solomon Abt’s possession when he died in 1829; correspondence of his heirs and the guardians of his children, as well as various court documents.