Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data

Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species. Our aims were to explore the impact of tree topology and missing data on the results, and to test which data summarising and analyses approaches would best approximate the results obtained from SNAPP for empirical data. SVD quartets retrieved the correct topology from simulated data, as did SNAPP except in the case of a very unbalanced phylogeny. Both methods failed to retrieve the correct topology when large amounts of data were missing. Bayesian analysis of species level summary data scoring the two alleles of each SNP as independent characters and parsimony analysis of data scoring each SNP as one character produced trees with branch length distributions closest to the true trees on which SNPs were simulated. For empirical data, Bayesian inference and Dollo parsimony analysis of data scored allele-wise produced phylogenies most congruent with the results of SNAPP. In the case of study groups divergent enough for missing data to be phylogenetically informative (because of additional mutations preventing amplification of genomic fragments or bioinformatic establishment of homology), scoring of SNP data as a presence/absence matrix irrespective of allele content might be an additional option. As this depends on sampling across species being reasonably even and a random distribution of non-informative instances of missing data, however, further exploration of this approach is needed. Properly chosen data summary approaches to inferring species trees from SNP data may represent a potential alternative to currently available individual-level coalescent analyses especially for quick data exploration and when dealing with computationally demanding or patchy datasets.This study was partly supported by a Centre of Biodiversity Analysis Ignition Grant to A.N.S.-L. and Justin Borevitz in 2013/14

Childhood and the politics of scale: Descaling children's geographies?

This is the post-print version of the final published paper that is available from the link below. Copyright @ 2008 SAGE Publications.The past decade has witnessed a resurgence of interest in the geographies of children's lives, and particularly in engaging the voices and activities of young people in geographical research. Much of this growing body of scholarship is characterized by a very parochial locus of interest — the neighbourhood, playground, shopping mall or journey to school. In this paper I explore some of the roots of children's geographies' preoccupation with the micro-scale and argue that it limits the relevance of research, both politically and to other areas of geography. In order to widen the scope of children's geographies, some scholars have engaged with developments in the theorization of scale. I present these arguments but also point to their limitations. As an alternative, I propose that the notion of a flat ontology might help overcome some difficulties around scalar thinking, and provide a useful means of conceptualizing sociospatiality in material and non-hierarchical terms. Bringing together flat ontology and work in children's geographies on embodied subjectivity, I argue that it is important to examine the nature and limits of children's spaces of perception and action. While these spaces are not simply `local', they seldom afford children opportunities to comment on, or intervene in, the events, processes and decisions that shape their own lives. The implications for the substance and method of children's geographies and for geographical work on scale are considered

A comfort assessment of existing cervical orthoses

Purpose: identify location and intensity of discomfort experienced by healthy participants wearing cervical orthoses. Method: convenience sample of 34 healthy participants wore Stro II, Philadelphia, Headmaster, and AspenVista® cervical orthoses for four-hour periods. Participants reported discomfort level (scale 0-6) and location. Results: participants reported mean discomfort for all orthoses over the four-hour test between ‘a little discomfort’ and ‘very uncomfortable’ (mean discomfort score=1.64, SD=1.50). Seven participants prematurely stopped tests due to pain and six reported maximum discomfort scores. Significant linear increase in discomfort with duration of wear was found for all orthoses. Significantly less discomfort was reported with Stro II than Headmaster and Philadelphia. Age correlated with greater perceived discomfort. Orthoses differed in the location discomfort was experienced. Conclusion: existing cervical orthoses cause discomfort influenced by design and duration of wear with orthoses' design the more significant factor. This work informed the design of a new orthosis and future orthoses developments

Global diversity of the Brachypodium species complex as a resource for genome-wide association studies demonstrated for agronomic traits in response to climate

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.We are grateful for funding and support from the Australian Research Council Centre of Excellence in Plant Energy Biology (CE140100008). Australian Plant Phenomics Facility is supported under the National Collaborative Research Infrastructure Strategy of the Australian Government. The research was undertaken with the assistance of resources from the National Computational Infrastructure (NCI), which is supported by the Australian Government

Landscape genomic prediction for restoration of a Eucalyptus foundation species under climate change

As species face rapid environmental change, we can build resilient populations through restoration projects that incorporate predicted future climates into seed sourcing decisions. Eucalyptus melliodora is a foundation species of a critically endangered community in Australia that is a target for restoration. We examined genomic and phenotypic variation to make empirical based recommendations for seed sourcing. We examined isolation by distance and isolation by environment, determining high levels of gene flow extending for 500 km and correlations with climate and soil variables. Growth experiments revealed extensive phenotypic variation both within and among sampling sites, but no site-specific differentiation in phenotypic plasticity. Model predictions suggest that seed can be sourced broadly across the landscape, providing ample diversity for adaptation to environmental change. Application of our landscape genomic model to E. melliodora restoration projects can identify genomic variation suitable for predicted future climates, thereby increasing the long term probability of successful restoration

‘Where we stayed was very bad …’: migrant children’s perspectives on life in informal rented accommodation in two southern African cities

Most research and initiatives relating to children's experiences of urban space have focused on the physical environment. Housing policies in Third World countries have also emphas- ised the provision of physical infrastructure and buildings, and urban aesthetics. In this paper the authors draw on the voices of young informants from Maseru (Lesotho), and Blantyre (Malawi), who, in discussions concerning moving house, chose to talk about social and economic aspects of life in the informal sector rented accommodation that is increasingly characteristic of these and many other African cities. The children offer insight into the peopling of urban space, mapping unruly environments characterised by disorder, gossip, and social contestation, far removed from the hard technocratic spaces imagined by planners. Their observations are important not only because children represent a very large and relatively neglected proportion of African urban dwellers but also because they offer a unique insight into the dynamic character of urban environments. As close observers of adult decisionmaking processes, children are informed commentators on motivations for moving house as well as the impacts of urban environments on their own lives. Not only do the children highlight the inadequacies of the informal private rental sector but they also offer a window onto why it is inadequate

IL28B, HLA-C, and KIR Variants Additively Predict Response to Therapy in Chronic Hepatitis C Virus Infection in a European Cohort: A Cross-Sectional Study

Vijayaprakash Suppiah and colleagues show that genotyping hepatitis C patients for the IL28B, HLA-C, and KIR genes improves the ability to predict whether or not patients will respond to antiviral treatment

Virological failure and development of new resistance mutations according to CD4 count at combination antiretroviral therapy initiation

Objectives: No randomized controlled trials have yet reported an individual patient benefit of initiating combination antiretroviral therapy (cART) at CD4 counts > 350 cells/μL. It is hypothesized that earlier initiation of cART in asymptomatic and otherwise healthy individuals may lead to poorer adherence and subsequently higher rates of resistance development. Methods: In a large cohort of HIV-positive individuals, we investigated the emergence of new resistance mutations upon virological treatment failure according to the CD4 count at the initiation of cART. Results: Of 7918 included individuals, 6514 (82.3%), 996 (12.6%) and 408 (5.2%) started cART with a CD4 count ≤ 350, 351-499 and ≥ 500 cells/μL, respectively. Virological rebound occurred while on cART in 488 (7.5%), 46 (4.6%) and 30 (7.4%) with a baseline CD4 count ≤ 350, 351-499 and ≥ 500 cells/μL, respectively. Only four (13.0%) individuals with a baseline CD4 count > 350 cells/μL in receipt of a resistance test at viral load rebound were found to have developed new resistance mutations. This compared to 107 (41.2%) of those with virological failure who had initiated cART with a CD4 count < 350 cells/μL. Conclusions: We found no evidence of increased rates of resistance development when cART was initiated at CD4 counts above 350 cells/μL. HIV Medicin