Marginal likelihoods in phylogenetics: a review of methods and applications

By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory. Given the rapid increase in the number and complexity of phylogenetic models, methods for approximating marginal likelihoods are increasingly important. Here we try to provide an intuitive description of marginal likelihoods and why they are important in Bayesian model testing. We also categorize and review methods for estimating marginal likelihoods of phylogenetic models, highlighting several recent methods that provide well-behaved estimates. Furthermore, we review some empirical studies that demonstrate how marginal likelihoods can be used to learn about models of evolution from biological data. We discuss promising alternatives that can complement marginal likelihoods for Bayesian model choice, including posterior-predictive methods. Using simulations, we find one alternative method based on approximate-Bayesian computation (ABC) to be biased. We conclude by discussing the challenges of Bayesian model choice and future directions that promise to improve the approximation of marginal likelihoods and Bayesian phylogenetics as a whole.Comment: 33 pages, 3 figure

Spatiotemporal variability in the O-18-salinity relationship of seawater across the tropical Pacific Ocean

The relationship between salinity and the stable oxygen isotope ratio of seawater (δ18Osw) is of utmost importance to the quantitative reconstruction of past changes in salinity from δ18O values of marine carbonates. This relationship is often considered to be uniform across water masses, but the constancy of the δ18Osw-salinity relationship across space and time remains uncertain, as δ18Osw responds to varying atmospheric vapor sources and pathways, while salinity does not. Here we present new δ18Osw-salinity data from sites spanning the tropical Pacific Ocean. New data from Palau, Papua New Guinea, Kiritimati, and Galápagos show slopes ranging from 0.09 ‰/psu in the Galápagos to 0.32‰/psu in Palau. The slope of the δ18Osw-salinity relationship is higher in the western tropical Pacific versus the eastern tropical Pacific in observations and in two isotope-enabled climate model simulations. A comparison of δ18Osw-salinity relationships derived from short-term spatial surveys and multiyear time series at Papua New Guinea and Galápagos suggests spatial relationships can be substituted for temporal relationships at these sites, at least within the time period of the investigation. However, the δ18Osw-salinity relationship varied temporally at Palau, likely in response to water mass changes associated with interannual El Niño–Southern Oscillation (ENSO) variability, suggesting nonstationarity in this local δ18Osw-salinity relationship. Applying local δ18Osw-salinity relationships in a coral δ18O forward model shows that using a constant, basinwide δ18Osw-salinity slope can both overestimate and underestimate the contribution of δ18Osw to carbonate δ18O variance at individual sites in the western tropical Pacific.We are grateful for the dedicated water samplers who enabled this research: Lori J. Bell and Gerda Ucharm of the Coral Reef Research Foundation, Palau; Rosa Maritza Motoche Gonzalez and the Fuerza Aerea Ecuatoriana, Santa Cruz, Galapagos, Ecuador; Taonateiti Kabiri and the students of Tennessee Primary School, London, Kiritimati; and the Manus Weather Observers, U.S. Department of Energy ARM Climate Research Facility, Manus, Papua New Guinea. We would like to thank the Galapagos National Park, the Kiritimati Ministry of Environment Lands and Agricultural Development for sample permits, and the Charles Darwin Research Station for logistical support. Funding sources for this work includes NSF-AGS-PF 1049664 to J.L.C., NSF P2C2-1203785 to K.M.C., J.L.C., and D.N. This research was also supported by the Office of Biological and Environment Research of the U.S. Department of Energy as part of the Atmospheric Radiation Measurement Climate Research Facility. Isotope data are available as supporting information associated with the manuscript. (1049664 - NSF-AGS-PF; P2C2-1203785 - NSF; Office of Biological and Environment Research of the U.S. Department of Energy as part of the Atmospheric Radiation Measurement Climate Research Facility

Gaining approval for clinical research

Set-up and delivery of a clinical research project can be complicated and difficult. This article introduces the regulatory processes involved in gaining approval for clinical research and discusses the obstacles that may be encountered

Will Health Literacy Research and Initiatives End the Confusion?

No abstract available

The Man Who Mistook His Neuropsychologist For a Popstar: When Configural Processing Fails in Acquired Prosopagnosia

We report the case of an individual with acquired prosopagnosia who experiences extreme difficulties in recognizing familiar faces in everyday life despite excellent object recognition skills. Formal testing indicates that he is also severely impaired at remembering pre-experimentally unfamiliar faces and that he takes an extremely long time to identify famous faces and to match unfamiliar faces. Nevertheless, he performs as accurately and quickly as controls at identifying inverted familiar and unfamiliar faces and can recognize famous faces from their external features. He also performs as accurately as controls at recognizing famous faces when fracturing conceals the configural information in the face. He shows evidence of impaired global processing but normal local processing of Navon figures. This case appears to reflect the clearest example yet of an acquired prosopagnosic patient whose familiar face recognition deficit is caused by a severe configural processing deficit in the absence of any problems in featural processing. These preserved featural skills together with apparently intact visual imagery for faces allow him to identify a surprisingly large number of famous faces when unlimited time is available. The theoretical implications of this pattern of performance for understanding the nature of acquired prosopagnosia are discussed.DY, Avery Braun, Jacob Waite, and Nadine Wanke, Bruno Rossion, Thomas Busigny and the grant awarded by AJ by the Experimental Psychology Society (EPS

Enhanced hippocampal long-term potentiation and spatial learning in aged 11ß-hydroxysteroid dehydrogenase type 1 knock-out mice

Glucocorticoids are pivotal in the maintenance of memory and cognitive functions as well as other essential physiological processes including energy metabolism, stress responses, and cell proliferation. Normal aging in both rodents and humans is often characterized by elevated glucocorticoid levels that correlate with hippocampus-dependent memory impairments. 11ß-Hydroxysteroid dehydrogenase type 1 (11ß-HSD1) amplifies local intracellular ("intracrine") glucocorticoid action; in the brain it is highly expressed in the hippocampus. We investigated whether the impact of 11ß-HSD1 deficiency in knock-out mice (congenic on C57BL/6J strain) on cognitive function with aging reflects direct CNS or indirect effects of altered peripheral insulin-glucose metabolism. Spatial learning and memory was enhanced in 12 month "middle-aged" and 24 month "aged" 11ß-HSD1<sup>–/–</sup> mice compared with age-matched congenic controls. These effects were not caused by alterations in other cognitive (working memory in a spontaneous alternation task) or affective domains (anxiety-related behaviors), to changes in plasma corticosterone or glucose levels, or to altered age-related pathologies in 11ß-HSD1<sup>–/–</sup> mice. Young 11ß-HSD1<sup>–/–</sup> mice showed significantly increased newborn cell proliferation in the dentate gyrus, but this was not maintained into aging. Long-term potentiation was significantly enhanced in subfield CA1 of hippocampal slices from aged 11ß-HSD1<sup>–/–</sup> mice. These data suggest that 11ß-HSD1 deficiency enhances synaptic potentiation in the aged hippocampus and this may underlie the better maintenance of learning and memory with aging, which occurs in the absence of increased neurogenesis

Stable States of Biological Organisms

A novel model of biological organisms is advanced, treating an organism as a self-consistent system subject to a pathogen flux. The principal novelty of the model is that it describes not some parts, but a biological organism as a whole. The organism is modeled by a five-dimensional dynamical system. The organism homeostasis is described by the evolution equations for five interacting components: healthy cells, ill cells, innate immune cells, specific immune cells, and pathogens. The stability analysis demonstrates that, in a wide domain of the parameter space, the system exhibits robust structural stability. There always exist four stable stationary solutions characterizing four qualitatively differing states of the organism: alive state, boundary state, critical state, and dead state.Comment: Latex file, 12 pages, 4 figure

Structured evaluation of virtual environments for special-needs education

This paper describes the development of a structured approach to evaluate experiential and communication virtual learning environments (VLEs) designed specifically for use in the education of children with severe learning difficulties at the Shepherd special needs school in Nottingham, UK. Constructivist learning theory was used as a basis for the production of an evaluation framework, used to evaluate the design of three VLEs and how they were used by students with respect to this learning theory. From an observational field study of student-teacher pairs using the VLEs, 18 behaviour categories were identified as relevant to five of the seven constructivist principles defined by Jonassen (1994). Analysis of student-teacher behaviour was used to provide support for, or against, the constructivist principles. The results show that the three VLEs meet the constructivist principles in very different ways and recommendations for design modifications are put forward

The shapes of bird beaks are highly controlled by nondietary factors

Bird beaks are textbook examples of ecological adaptation to diet, but their shapes are also controlled by genetic and developmental histories. To test the effects of these factors on the avian craniofacial skeleton, we conducted morphometric analyses on raptors, a polyphyletic group at the base of the landbird radiation. Despite common perception, we find that the beak is not an independently targeted module for selection. Instead, the beak and skull are highly integrated structures strongly regulated by size, with axes of shape change linked to the actions of recently identified regulatory genes. Together, size and integration account for almost 80% of the shape variation seen between different species to the exclusion of morphological dietary adaptation. Instead, birds of prey use size as a mechanism to modify their feeding ecology. The extent to which shape variation is confined to a few major axes may provide an advantage in that it facilitates rapid morphological evolution via changes in body size, but may also make raptors especially vulnerable when selection pressures act against these axes. The phylogenetic position of raptors suggests that this constraint is prevalent in all landbirds and that breaking the developmental correspondence between beak and braincase may be the key novelty in classic passerine adaptive radiations