The evolutionary relationships and age of Homo naledi : an assessment using dated Bayesian phylogenetic methods

Acknowledgements We wish to express our gratitude to the National Geographic Society and the National Research Foundation of South Africa for funding the discovery, recovery, and analysis of the H. naledi material. The study reported here was also made possible by grants from the Social Sciences and Humanities Research Council of Canada, the Canada Foundation for Innovation, the British Columbia Knowledge Development Fund, the Canada Research Chairs Program, Simon Fraser University, the DST/NRF Centre of Excellence in Palaeosciences (COE-Pal), as well as by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada, a Young Scientist Development Grant from the Paleontological Scientific Trust (PAST), a Baldwin Fellowship from the L.S.B. Leakey Foundation, and a Seed Grant and a Cornerstone Faculty Fellowship from the Texas A&M University College of Liberal Arts. We would like to thank the South African Heritage Resource Agency for the permits necessary to work on the Rising Star site; the Jacobs family for granting access; Wilma Lawrence, Bonita De Klerk, Merrill Van der Walt, and Justin Mukanku for their assistance during all phases of the project; Lucas Delezene for valuable discussion on the dental characters of H. naledi. We would also like to thank Peter Schmid for the preparation of the Dinaledi fossil material; Yoel Rak for explaining in detail some of the characters used in previous studies; William Kimbel for drawing our attention to the possibility that there might be a problem with Dembo et al.’s (2015) codes for the two characters related to the articular eminence; Will Stein for helpful discussion about the Bayesian analyses; Mike Lee for his comments on this manuscript; John Hawks for his support in organizing the Rising Star workshop; and the associate editor and three anonymous reviewers for their valuable comments. We are grateful to S. Potze and the Ditsong Museum, B. Billings and the School of Anatomical Sciences at the University of the Witwatersrand, and B. Zipfel and the Evolutionary Studies Institute at the University of the Witwatersrand for providing access to the specimens in their care; the University of the Witwatersrand, the Evolutionary Studies Institute, and the South African National Centre of Excellence in PalaeoSciences for hosting a number of the authors while studying the material; and the Western Canada Research Grid for providing access to the high-performance computing facilities for the Bayesian analyses. Last but definitely not least, we thank the head of the Rising Star project, Lee Berger, for his leadership and support, and for encouraging us to pursue the study reported here.

Mutations as molecular tools : The metabolic-rate dependent molecular clock and DNA barcoding of allied species

Mutation and recombination are the fundamental processes leading to genetic variation in natural populations. This variation forms the raw material for evolution through natural selection and drift. Therefore, studying mutation rates may reveal information about evolutionary histories as well as phylogenetic interrelationships of organisms. In this thesis two molecular tools, DNA barcoding and the molecular clock were examined. In the first part, the efficiency of mutations to delineate closely related species was tested and the implications for conservation practices were assessed. The second part investigated the proposition that a constant mutation rate exists within invertebrates, in form of a metabolic-rate dependent molecular clock, which can be applied to accurately date speciation events. DNA barcoding aspires to be an efficient technique to not only distinguish between species but also reveal population-level variation solely relying on mutations found on a short stretch of a single gene. In this thesis barcoding was applied to discriminate between Hylochares populations from Russian Karelia and new Hylochares findings from the greater Helsinki region in Finland. Although barcoding failed to delineate the two reproductively isolated groups, their distinct morphological features and differing life-history traits led to their classification as two closely related, although separate species. The lack of genetic differentiation appears to be due to a recent divergence event not yet reflected in the beetles molecular make-up. Thus, the Russian Hylochares was described as a new species. The Finnish species, previously considered as locally extinct, was recognized as endangered. Even if, due to their identical genetic make-up, the populations had been regarded as conspecific, conservation strategies based on prior knowledge from Russia would not have guaranteed the survival of the Finnish beetle. Therefore, new conservation actions based on detailed studies of the biology and life-history of the Finnish Hylochares were conducted to protect this endemic rarity in Finland. The idea behind the strict molecular clock is that mutation rates are constant over evolutionary time and may thus be used to infer species divergence dates. However, one of the most recent theories argues that a strict clock does not tick per unit of time but that it has a constant substitution rate per unit of mass-specific metabolic energy. Therefore, according to this hypothesis, molecular clocks have to be recalibrated taking body size and temperature into account. This thesis tested the temperature effect on mutation rates in equally sized invertebrates. For the first dataset (family Eucnemidae, Coleoptera) the phylogenetic interrelationships and evolutionary history of the genus Arrhipis had to be inferred before the influence of temperature on substitution rates could be studied. Further, a second, larger invertebrate dataset (family Syrphidae, Diptera) was employed. Several methodological approaches, a number of genes and multiple molecular clock models revealed that there was no consistent relationship between temperature and mutation rate for the taxa under study. Thus, the body size effect, observed in vertebrates but controversial for invertebrates, rather than temperature may be the underlying driving force behind the metabolic-rate dependent molecular clock. Therefore, the metabolic-rate dependent molecular clock does not hold for the here studied invertebrate groups. This thesis emphasizes that molecular techniques relying on mutation rates have to be applied with caution. Whereas they may work satisfactorily under certain conditions for specific taxa, they may fail for others. The molecular clock as well as DNA barcoding should incorporate all the information and data available to obtain comprehensive estimations of the existing biodiversity and its evolutionary history.

Discordances between phylogenetic and morphological patterns in alpine leaf beetles attest to an intricate biogeographic history of lineages in postglacial Europe.

Pleistocene glacial and interglacial periods have moulded the evolutionary history of European cold-adapted organisms. The role of the different mountain massifs has, however, not been accurately investigated in the case of high-altitude insect species. Here, we focus on three closely related species of non-flying leaf beetles of the genus Oreina (Coleoptera, Chrysomelidae), which are often found in sympatry within the mountain ranges of Europe. After showing that the species concept as currently applied does not match barcoding results, we show, based on more than 700 sequences from one nuclear and three mitochondrial genes, the role of biogeography in shaping the phylogenetic hypothesis. Dating the phylogeny using an insect molecular clock, we show that the earliest lineages diverged more than 1 Mya and that the main shift in diversification rate occurred between 0.36 and 0.18 Mya. By using a probabilistic approach on the parsimony-based dispersal/vicariance framework (MP-DIVA) as well as a direct likelihood method of state change optimization, we show that the Alps acted as a cross-roads with multiple events of dispersal to and reinvasion from neighbouring mountains. However, the relative importance of vicariance vs. dispersal events on the process of rapid diversification remains difficult to evaluate because of a bias towards overestimation of vicariance in the DIVA algorithm. Parallels are drawn with recent studies of cold-adapted species, although our study reveals novel patterns in diversity and genetic links between European mountains, and highlights the importance of neglected regions, such as the Jura and the Balkanic range.

Through the clock's workings

Through the Clock’s Workings is a world first: a remixed and remixable anthology of literature.----- Prominent Australian authors have written new short stories and released them under a Creative Commons Attribution Non-Commercial ShareAlike licence. What that means is you can remix the stories, but only if you acknowledge the author, the remix is not for commercial use, and your new work is available for others to remix. The authors’ stories were made available on our website and new and emerging writers were invited to create their own remixes to be posted on the website and considered for publication in the print anthology alongside the original stories.----- The result is a world first: a remixed and remixable anthology of literature. Buy your copy now from the Sydney University Press eStore or download the electronic version.----- So how do you use a remixable anthology? Simple.----- Step 1 - Read. Thumb your way through the pages at will. Find the stories you love, the ones you hate, the ones that could be better.----- Step 2 - Re/create. Each story is yours to share and to remix. Use only one paragraph or character or just make subtle changes. Change the genre, alter its formal or stylistic characteristics, or revise its message. Use as little or as much as you like - as long as it works.----- Step 3 - Share. Be part of a growing community of literature remixing. Email your remix to us and start sharing. The entire anthology can be remixed - the original stories, the remixes, and even the fonts.----- Through the Clock’s Workings is Read&Write!

Towards automatic tree crown detection and delineation in spectral feature space using PCNN and morphological reconstruction

The application of object-based approaches to the problem of extracting vegetation information from images requires accurate delineation of individual tree crowns. This paper presents an automated method for individual tree crown detection and delineation by applying a simplified PCNN model in spectral feature space followed by post-processing using morphological reconstruction. The algorithm was tested on high resolution multi-spectral aerial images and the results are compared with two existing image segmentation algorithms. The results demonstrate that our algorithm outperforms the other two solutions with the average accuracy of 81.8%.

PDMS spreading morphological patterns on substrates of different hydrophilicity in air vacuum and water

In paper has been to investigate the morphological patterns and kinetics of PDMS spreading on silicon wafer using combination of techniques like ellipsometry, atomic force microscope (AFM), scanning electron microscope (SEM) and optical microscopy. A macroscopic silicone oil drops as well as PDMS water based emulsions were studied after deposition on a flat surface of silicon wafer in air, water and vacuum. our own measurements using an imaging ellipsometer, which also clearly shows the presence of a precursor film. The diffusion constant of this film, measured with a 60 000 cS PDMS sample spreading on a hydrophilic silicon wafer, is Df = 1.4  10-11 m2/s. Regardless of their size, density and method of deposition, droplets on both types of wafer (hydrophilic and hydrophobic) flatten out over a period of many hours, up to 3 days. During this process neighbouring droplets may coalesce, but there is strong evidence that some of the PDMS from the droplets migrates into a thin, continuous film that covers the surface in between droplets. The thin film appears to be ubiquitous if there has been any deposition of PDMS. However, this statement needs further verification. One question is whether the film forms immediately after forced drying, or whether in some or all cases it only forms by spreading from isolated droplets as they slowly flatten out.

Algebraic attacks on clock-controlled stream ciphers

Stream ciphers are encryption algorithms used for ensuring the privacy of digital telecommunications. They have been widely used for encrypting military communications, satellite communications, pay TV encryption and for voice encryption of both fixed lined and wireless networks. The current multi year European project eSTREAM, which aims to select stream ciphers suitable for widespread adoptation, reflects the importance of this area of research. Stream ciphers consist of a keystream generator and an output function. Keystream generators produce a sequence that appears to be random, which is combined with the plaintext message using the output function. Most commonly, the output function is binary addition modulo two. Cryptanalysis of these ciphers focuses largely on analysis of the keystream generators and of relationships between the generator and the keystream it produces. Linear feedback shift registers are widely used components in building keystream generators, as the sequences they produce are well understood. Many types of attack have been proposed for breaking various LFSR based stream ciphers. A recent attack type is known as an algebraic attack. Algebraic attacks transform the problem of recovering the key into a problem of solving multivariate system of equations, which eventually recover the internal state bits or the key bits. This type of attack has been shown to be effective on a number of regularly clocked LFSR based stream ciphers. In this thesis, algebraic attacks are extended to a number of well known stream ciphers where at least one LFSR in the system is irregularly clocked. Applying algebriac attacks to these ciphers has only been discussed previously in the open literature for LILI-128. In this thesis, algebraic attacks are first applied to keystream generators using stop-and go clocking. Four ciphers belonging to this group are investigated: the Beth-Piper stop-and-go generator, the alternating step generator, the Gollmann cascade generator and the eSTREAM candidate: the Pomaranch cipher. It is shown that algebraic attacks are very effective on the first three of these ciphers. Although no effective algebraic attack was found for Pomaranch, the algebraic analysis lead to some interesting findings including weaknesses that may be exploited in future attacks. Algebraic attacks are then applied to keystream generators using (p; q) clocking. Two well known examples of such ciphers, the step1/step2 generator and the self decimated generator are investigated. Algebraic attacks are shown to be very powerful attack in recovering the internal state of these generators. A more complex clocking mechanism than either stop-and-go or the (p; q) clocking keystream generators is known as mutual clock control. In mutual clock control generators, the LFSRs control the clocking of each other. Four well known stream ciphers belonging to this group are investigated with respect to algebraic attacks: the Bilateral-stop-and-go generator, A5/1 stream cipher, Alpha 1 stream cipher, and the more recent eSTREAM proposal, the MICKEY stream ciphers. Some theoretical results with regards to the complexity of algebraic attacks on these ciphers are presented. The algebraic analysis of these ciphers showed that generally, it is hard to generate the system of equations required for an algebraic attack on these ciphers. As the algebraic attack could not be applied directly on these ciphers, a different approach was used, namely guessing some bits of the internal state, in order to reduce the degree of the equations. Finally, an algebraic attack on Alpha 1 that requires only 128 bits of keystream to recover the 128 internal state bits is presented. An essential process associated with stream cipher proposals is key initialization. Many recently proposed stream ciphers use an algorithm to initialize the large internal state with a smaller key and possibly publicly known initialization vectors. The effect of key initialization on the performance of algebraic attacks is also investigated in this thesis. The relationships between the two have not been investigated before in the open literature. The investigation is conducted on Trivium and Grain-128, two eSTREAM ciphers. It is shown that the key initialization process has an effect on the success of algebraic attacks, unlike other conventional attacks. In particular, the key initialization process allows an attacker to firstly generate a small number of equations of low degree and then perform an algebraic attack using multiple keystreams. The effect of the number of iterations performed during key initialization is investigated. It is shown that both the number of iterations and the maximum number of initialization vectors to be used with one key should be carefully chosen. Some experimental results on Trivium and Grain-128 are then presented. Finally, the security with respect to algebraic attacks of the well known LILI family of stream ciphers, including the unbroken LILI-II, is investigated. These are irregularly clock- controlled nonlinear filtered generators. While the structure is defined for the LILI family, a particular paramater choice defines a specific instance. Two well known such instances are LILI-128 and LILI-II. The security of these and other instances is investigated to identify which instances are vulnerable to algebraic attacks. The feasibility of recovering the key bits using algebraic attacks is then investigated for both LILI- 128 and LILI-II. Algebraic attacks which recover the internal state with less effort than exhaustive key search are possible for LILI-128 but not for LILI-II. Given the internal state at some point in time, the feasibility of recovering the key bits is also investigated, showing that the parameters used in the key initialization process, if poorly chosen, can lead to a key recovery using algebraic attacks.

Morphological investigations of supported titania photocatalysts

Due in no small part to an increasing need to augment existing water purification strategies, the synthesis of titania photocatalysts has been under considerable examination. However, in order to make the use of titania photocatalysts commercially viable there needs to be an increase in the efficiency of the catalysts while decreasing the potential toxicity. Due to its high porosity and novel optical properties, inverse opal titania derived from colloidal crystal templating offers one of the most efficient solutions. While a number of synthesis methods for inverse opal titania have been presented in the literature, the co�]deposition method offers the most effective method of generating the relative large areas of inverse opal material. The factors which affect the codeposition method and the mechanism by which titania inverse opals form in general remain relatively unstudied. This manuscript presents an examination of the morphology of inverse opals generated by the co�]deposition method while proposing a mechanism by which the inverse structures form.

Morphological classification of bovine ovarian follicles

Follicle classification is an important aid to the understanding of follicular development and atresia. Some bovine primordial follicles have the classical primordial shape, but ellipsoidal shaped follicles with some cuboidal granulosa cells at the poles are far more common. Preantral follicles have one of two basal lamina phenotypes, either a single aligned layer or one with additional layers. In antral follicles <5 mm diameter, half of the healthy follicles have columnar shaped basal granulosa cells and additional layers of basal lamina, which appear as loops in cross section (‘loopy’). The remainder have aligned single-layered follicular basal laminas with rounded basal cells, and contain better quality oocytes than the loopy/columnar follicles. In sizes >5 mm, only aligned/rounded phenotypes are present. Dominant and subordinate follicles can be identified by ultrasound and/or histological examination of pairs of ovaries. Atretic follicles <5 mm are either basal atretic or antral atretic, named on the basis of the location in the membrana granulosa where cells die first. Basal atretic follicles have considerable biological differences to antral atretic follicles. In follicles >5 mm, only antral atresia is observed. The concentrations of follicular fluid steroid hormones can be used to classify atresia and distinguish some of the different types of atresia; however, this method is unlikely to identify follicles early in atresia, and hence misclassify them as healthy. Other biochemical and histological methods can be used, but since cell death is a part of normal homoeostatis, deciding when a follicle has entered atresia remains somewhat subjective.

Morphological design control for large-scale city development : a new proposal

Whereas many good examples can be found of the study of urban morphology informing the design of new residential areas in Europe, it is much more difficult to find examples relating to other land uses and outside of Europe. This paper addresses a particular issue, the control and coordination of large and complex development schemes within cities, and, in doing so, considers commercial and mixed-use schemes outside of Europe. It is argued that urban morphology has much to offer for both the design of such development and its implementation over time. Firstly, lessons are drawn from the work of Krier and Rossi in Berlin, the form-based guidance developed in Chelmsford, UK, and the redesign and coordination of the Melrose Arch project in Johannesburg, SA. A recent development at Boggo Road in Brisbane, Australia, is then subjected to a more detailed examination. It is argued that the scheme has been unsatisfactory in terms of both design and implementation. An alternative framework based on historical morphological studies is proposed that would overcome these deficiencies. It is proposed that this points the way to a general approach that could be incorporated within the planning process internationally.