Evaluating genetic drift in time-series evolutionary analysis

The Wright-Fisher model is the most popular population model for describing the behaviour of evolutionary systems with a finite population size. Approximations have commonly been used but the model itself has rarely been tested against time-resolved genomic data. Here, we evaluate the extent to which it can be inferred as the correct model under a likelihood framework. Given genome-wide data from an evolutionary experiment, we validate the Wright-Fisher drift model as the better option for describing evolutionary trajectories in a finite population. This was found by evaluating its performance against a Gaussian model of allele frequency propagation. However, we note a range of circumstances under which standard Wright-Fisher drift cannot be correctly identified. (C) 2017 The Author(s). Published by Elsevier Ltd.Peer reviewe

Enhanced Tunnelling in a Hybrid of Single-Walled Carbon Nanotubes and Graphene

Transparent and conductive films (TCFs) are of great technological importance. The high transmittance, electrical conductivity and mechanical strength make single-walled carbon nanotubes (SWCNTs) a good candidate for their raw material. Despite the ballistic transport in individual SWCNTs, however, the electrical conductivity of their networks is limited by low efficiency of charge tunneling between the tube elements. Here, we demonstrate that the nanotube network sheet resistance at high optical transmittance is decreased by more than 50% when fabricated on graphene and thus provides a comparable improvement as widely adopted gold chloride ($\mathrm{AuCl_3}$) doping. However, while Raman spectroscopy reveals substantial changes in spectral features of doped nanotubes, no similar effect is observed in presence of graphene. Instead, temperature dependent transport measurements indicate that graphene substrate reduces the tunneling barrier heights while its parallel conductivity contribution is almost negligible. Finally, we show that combining the graphene substrate and $\mathrm{AuCl_3}$ doping, the SWCNT thin films can exhibit sheet resistance as low as 36 $\Omega$/sq. at 90% transmittance.Comment: 21 pages, 6 figure

Numerical Estimation of the Asymptotic Behaviour of Solid Partitions of an Integer

The number of solid partitions of a positive integer is an unsolved problem in combinatorial number theory. In this paper, solid partitions are studied numerically by the method of exact enumeration for integers up to 50 and by Monte Carlo simulations using Wang-Landau sampling method for integers up to 8000. It is shown that, for large n, ln[p(n)]/n^(3/4) = 1.79 \pm 0.01, where p(n) is the number of solid partitions of the integer n. This result strongly suggests that the MacMahon conjecture for solid partitions, though not exact, could still give the correct leading asymptotic behaviour.Comment: 6 pages, 4 figures, revtex

Monotonicity of Fitness Landscapes and Mutation Rate Control

A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the performance of evolutionary algorithms. Much biological theory in this area is based on Ronald Fisher's work, who used Euclidean geometry to study the relation between mutation size and expected fitness of the offspring in infinite phenotypic spaces. Here we reconsider this theory based on the alternative geometry of discrete and finite spaces of DNA sequences. First, we consider the geometric case of fitness being isomorphic to distance from an optimum, and show how problems of optimal mutation rate control can be solved exactly or approximately depending on additional constraints of the problem. Then we consider the general case of fitness communicating only partial information about the distance. We define weak monotonicity of fitness landscapes and prove that this property holds in all landscapes that are continuous and open at the optimum. This theoretical result motivates our hypothesis that optimal mutation rate functions in such landscapes will increase when fitness decreases in some neighbourhood of an optimum, resembling the control functions derived in the geometric case. We test this hypothesis experimentally by analysing approximately optimal mutation rate control functions in 115 complete landscapes of binding scores between DNA sequences and transcription factors. Our findings support the hypothesis and find that the increase of mutation rate is more rapid in landscapes that are less monotonic (more rugged). We discuss the relevance of these findings to living organisms

Formation of regulatory modules by local sequence duplication

Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of neighboring transcription factor binding sites in the fly genome have formed from a common sequence origin by local duplications. This mode of evolution is found to produce regulatory information: duplications can seed new sites in the neighborhood of existing sites. Duplicate seeds evolve subsequently by point mutations, often towards binding a different factor than their ancestral neighbor sites. These results are based on a statistical analysis of 346 cis-regulatory modules in the Drosophila melanogaster genome, and a comparison set of intergenic regulatory sequence in Saccharomyces cerevisiae. In fly regulatory modules, pairs of binding sites show significantly enhanced sequence similarity up to distances of about 50 bp. We analyze these data in terms of an evolutionary model with two distinct modes of site formation: (i) evolution from independent sequence origin and (ii) divergent evolution following duplication of a common ancestor sequence. Our results suggest that pervasive formation of binding sites by local sequence duplications distinguishes the complex regulatory architecture of higher eukaryotes from the simpler architecture of unicellular organisms

A driving simulator study to explore the effects of text size on the visual demand of in-vehicle displays

Modern vehicles increasingly utilise a large display within the centre console, often with touchscreen capability, to enable access to a wide range of driving and non-driving-related functionality. The text provided on such displays can vary considerably in size, yet little is known about the effects of different text dimensions on how drivers visually sample the interface while driving and the potential implications for driving performance and user acceptance. A study is described in which sixteen people drove motorway routes in a medium-fidelity simulator and were asked to read text of varying sizes (9 mm, 8 mm, 6.5 mm, 5 mm, or 4 mm) from a central in-vehicle display. Pseudo-text was used as a stimulus to ensure that participants scanned the text in a consistent fashion that was unaffected by comprehension. There was no evidence of an effect of text size on the total time spent glancing at the display, but significant differences arose regarding how glances were distributed. Specifically, larger text sizes were associated with a high number of relatively short glances, whereas smaller text led to a smaller number of long glances. No differences were found in driving performance measures (speed, lateral lane position). Drivers overwhelmingly preferred the ‘compromise’ text sizes (6.5 mm and 8 mm). Results are discussed in relation to the development of large touchscreens within vehicles

Artificial drainage of peatlands: hydrological and hydrochemical process and wetland restoration

Peatlands have been subject to artificial drainage for centuries. This drainage has been in response to agricultural demand, forestry, horticultural and energy properties of peat and alleviation of flood risk. However, the are several environmental problems associated with drainage of peatlands. This paper describes the nature of these problems and examines the evidence for changes in hydrological and hydrochemical processes associated with these changes. Traditional black-box water balance approaches demonstrate little about wetland dynamics and therefore the science of catchment response to peat drainage is poorly understood. It is crucial that a more process-based approach be adopted within peatland ecosystems. The environmental problems associated with peat drainage have led, in part, to a recent reversal in attitudes to peatlands and we have seen a move towards wetland restoration. However, a detailed understanding of hydrological, hydrochemical and ecological process-interactions will be fundamental if we are to adequately restore degraded peatlands, preserve those that are still intact and understand the impacts of such management actions at the catchment scale

Nunalleq, Stories from the Village of Our Ancestors:Co-designing a multivocal educational resource based on an archaeological excavation

This work was funded by the UK-based Arts and Humanities Research Council through grants (AH/K006029/1) and (AH/R014523/1), a University of Aberdeen IKEC Award with additional support for travel and subsistence from the University of Dundee, DJCAD Research Committee RS2 project funding. Thank you to the many people who contributed their support, knowledge, feedback, voices and faces throughout the project, this list includes members of the local community, colleagues, specialists, students, and volunteers. If we have missed out any names we apologize but know that your help was appreciated. Jimmy Anaver, John Anderson, Alice Bailey, Kieran Baxter, Pauline Beebe, Ellinor Berggren, Dawn Biddison, Joshua Branstetter, Brendan Body, Lise Bos, Michael Broderick, Sarah Brown, Crystal Carter, Joseph Carter, Lucy Carter, Sally Carter, Ben Charles, Mary Church, Willard Church, Daniele Clementi, Annie Cleveland, Emily Cleveland, Joshua Cleveland, Aron Crowell, Neil Curtis, Angie Demma, Annie Don, Julia Farley, Veronique Forbes, Patti Fredericks, Tricia Gillam, Sean Gleason, Sven Haakanson, Cheryl Heitman, Grace Hill, Diana Hunter, Joel Isaak, Warren Jones, Stephan Jones, Ana Jorge, Solveig Junglas, Melia Knecht, Rick Knecht, Erika Larsen, Paul Ledger, Jonathan Lim Soon, Amber Lincoln, Steve Luke, Francis Lukezic, Eva Malvich, Pauline Matthews, Roy Mark, Edouard Masson-MacLean, Julie Masson-MacLean, Mhairi Maxwell, Chuna Mcintyre, Drew Michael, Amanda Mina, Anna Mossolova, Carl Nicolai Jr, Chris Niskanen, Molly Odell, Tom Paxton, Lauren Phillips, Lucy Qin, Charlie Roberts, Chris Rowe, Rufus Rowe,Chris Rowland, John Rundall, Melissa Shaginoff, Monica Shah, Anna Sloan, Darryl Small Jr, John Smith, Mike Smith, Joey Sparaga, Hannah Strehlau, Dora Strunk, Larissa Strunk, Lonny Strunk, Larry Strunk, Robbie Strunk, Sandra Toloczko, Richard Vanderhoek, the Qanirtuuq Incorporated Board, the Quinhagak Dance Group and the staff at Kuinerrarmiut Elitnaurviat. We also extend our thanks to three anonymous reviewers for their valuable comments on our paper.Peer reviewedPublisher PD

Adenoma development in familial adenomatous polyposis andMUTYH-associated polyposis: somatic landscape and driver genes

Familial adenomatous polyposis (FAP) and MUTYH‐associated polyposis (MAP) are inherited disorders associated with multiple colorectal adenomas that lead to a very high risk of colorectal cancer. The somatic mutations that drive adenoma development in these conditions have not been investigated comprehensively. In this study we performed analysis of paired colorectal adenoma and normal tissue DNA from individuals with FAP or MAP, sequencing 14 adenoma whole exomes (eight MAP, six FAP), 55 adenoma targeted exomes (33 MAP, 22 FAP) and germline DNA from each patient, and a further 63 adenomas by capillary sequencing (41 FAP, 22 MAP). With these data we examined the profile of mutated genes, the mutational signatures and the somatic mutation rates, observing significant diversity in the constellations of mutated driver genes in different adenomas, and loss‐of‐function mutations in WTX (9%; p < 9.99e‐06), a gene implicated in regulation of the WNT pathway and p53 acetylation. These data extend our understanding of the early events in colorectal tumourigenesis in the polyposis syndromes. © 2015 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland

Bioenergy consumption and biogas potential in Cambodian households

&nbsp; Residential bioenergy consumption and bioenergy resources based on by-products of residential agricultural production and animal husbandry have been analyzed statistically, based on a nationwide residential livelihood and energy survey conducted in Cambodia in 2009. Furthermore, the potential for biomethanation, residential biogas consumption and small-scale power generation for non-electrified rural areas has been assessed. Household potential of biogas substrates in Cambodia, based on nationally representative data has not been presented earlier. This paper proposes mixtures of substrates for biogas production for various livelihood zones of Cambodia. The occurrence of biomass suitable for biomethanation is most favorable in unelectrified rural areas, except for fishing villages. The theoretical daily biogas potential from animal dung and rice husk appears to be promising for households in unelectrified rural villages, both for household digesters and units designed for small-scale electricity generation. Theoretical CH4 content of biogas was 63.9% and specific biogas yield 0.41 Nm3/kg for households in unelectrified villages. Based on the survey, the energy content of biogas potential is 25.5 PJ per year. This study shows that biogas has nationally significant technical potential in Cambodia. </p