Model-based control of observer bias for the analysis of presence-only data in ecology

Presence-only data, where information is available concerning species presence but not species absence, are subject to bias due to observers being more likely to visit and record sightings at some locations than others (hereafter "observer bias"). In this paper, we describe and evaluate a model-based approach to accounting for observer bias directly - by modelling presence locations as a function of known observer bias variables (such as accessibility variables) in addition to environmental variables, then conditioning on a common level of bias to make predictions of species occurrence free of such observer bias. We implement this idea using point process models with a LASSO penalty, a new presence-only method related to maximum entropy modelling, that implicitly addresses the "pseudo-absence problem" of where to locate pseudo-absences (and how many). The proposed method of bias-correction is evaluated using systematically collected presence/absence data for 62 plant species endemic to the Blue Mountains near Sydney, Australia. It is shown that modelling and controlling for observer bias significantly improves the accuracy of predictions made using presence-only data, and usually improves predictions as compared to pseudo-absence or "inventory" methods of bias correction based on absences from non-target species. Future research will consider the potential for improving the proposed bias-correction approach by estimating the observer bias simultaneously across multiple species. © 2013 Warton et al

Robust dynamic classes revealed by measuring the response function of a social system

We study the relaxation response of a social system after endogenous and exogenous bursts of activity using the time-series of daily views for nearly 5 million videos on YouTube. We find that most activity can be described accurately as a Poisson process. However, we also find hundreds of thousands of examples in which a burst of activity is followed by an ubiquitous power-law relaxation governing the timing of views. We find that these relaxation exponents cluster into three distinct classes, and allow for the classification of collective human dynamics. This is consistent with an epidemic model on a social network containing two ingredients: A power law distribution of waiting times between cause and action and an epidemic cascade of actions becoming the cause of future actions. This model is a conceptual extension of the fluctuation-dissipation theorem to social systems, and provides a unique framework for the investigation of timing in complex systems.Comment: 5 pages, 5 figures, submitted to PNA

A Heuristic Image Search Algorithm for Active Shape Model Segmentation of the Caudate Nucleus and Hippocampus in Brain MR Images of Children with FASD

Magnetic Resonance Imaging provides a non-invasive means to study the neural correlates of Fetal Alcohol Spectrum Disorder (FASD) - the most common form of preventable mental retardation worldwide. One approach aims to detect brain abnormalities through an assessment of volume and shape of two sub-cortical structures, the caudate nucleus and hippocampus. We present a method for automatically segmenting these structures from high-resolution MR images captured as part of an ongoing study into the neural correlates of FASD. Our method incorporates an Active Shape Model, which is used to learn shape variation from manually segmented training data. A modified discrete Geometrically Deformable Model is used to generate point correspondence between training models. An ASM is then created from the landmark points. Experiments were conducted on the image search phase of ASM segmentation, in order to find the technique best suited to segmentation of the hippocampus and caudate nucleus. Various popular image search techniques were tested, including an edge detection method and a method based on grey profile Mahalanobis distance measurement. A novel heuristic image search method was also developed and tested. This heuristic method improves image segmentation by taking advantage of characteristics specific to the target data, such as a relatively homogeneous tissue colour in target structures. Results show that ASMs that use the heuristic image search technique produce the most accurate segmentations. An ASM constructed using this technique will enable researchers to quickly, reliably, and automatically segment test data for use in the FASD study

A climate of uncertainty: accounting for error in climate variables for species distribution models

1. Spatial climate variables are routinely used in species distribution models (SDMs) without accounting for the fact that they have been predicted with uncertainty, which can lead to biased estimates, erroneous inference and poor performances when predicting to new settings – for example under climate change scenarios. 2. We show how information on uncertainty associated with spatial climate variables can be obtained from climate data models. We then explain different types of uncertainty (i.e. classical and Berkson error) and use two statistical methods that incorporate uncertainty in climate variables into SDMs by means of (i) hierarchical modelling and (ii) simulation–extrapolation. 3. We used simulation to study the consequences of failure to account for measurement error. When uncertainty in explanatory variables was not accounted for, we found that coefficient estimates were biased and the SDM had a loss of statistical power. Further, this bias led to biased predictions when projecting change in distribution under climate change scenarios. The proposed errors-in-variables methods were less sensitive to these issues. 4. We also fit the proposed models to real data (presence/absence data on the Carolina wren, Thryothorus ludovicianus), as a function of temperature variables. 5. The proposed framework allows for many possible extensions and improvements to SDMs. If information on the uncertainty of spatial climate variables is available to researchers, we recommend the following: (i) first identify the type of uncertainty; (ii) consider whether any spatial autocorrelation or independence assumptions are required; and (iii) attempt to incorporate the uncertainty into the SDM through established statistical methods and their extensions.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd on behalf of the British Ecological Society. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%292041-210X.Keywords: Measurement error, Errors-in-variables, Hierarchical statistical models, Climate maps, SIMEX, Prediction error, PRIS

Putting plant resistance traits on the map: a test of the idea that plants are better defended at lower latitudes

It has long been believed that plant species from the tropics have higher levels of traits associated with resistance to herbivores than do species from higher latitudes. A meta-analysis recently showed that the published literature does not support this theory. However, the idea has never been tested using data gathered with consistent methods from a wide range of latitudes. We quantified the relationship between latitude and a broad range of chemical and physical traits across 301 species from 75 sites world-wide. Six putative resistance traits, including tannins, the concentration of lipids (an indicator of oils, waxes and resins), and leaf toughness were greater in highlatitude species. Six traits, including cyanide production and the presence of spines, were unrelated to latitude. Only ash content (an indicator of inorganic substances such as calcium oxalates and phytoliths) and the properties of species with delayed greening were higher in the tropics. Our results do not support the hypothesis that tropical plants have higher levels of resistance traits than do plants from higher latitudes. If anything, plants have higher resistance toward the poles. The greater resistance traits of high-latitude species might be explained by the greater cost of losing a given amount of leaf tissue in low-productivity environments.EEA Santa CruzFil: Moles, Angela T. The University of New South Wales. School of Biological, Earth and Environmental Sciences. Evolution & Ecology Research Centre; Australia.Fil: Moles, Angela T. Victoria University of Wellington. School of Biological Sciences; Nueva ZelandiaFil: Moles, Angela T. Australian National University. Research School of Biology; Australia.Fil: Moles, Angela T. Macquarie University. Department of Biological Sciences; Australia.Fil: Wallis, Ian R. Australian National University. Research School of Biology; Australia.Fil: Foley, William J. Australian National University. Research School of Biology; Australia.Fil: Warton, David I. The University of New South Wales. School of Mathematics and Statistics and Evolution & Ecology Research Centre; Australia.Fil: Stegen, James C. University of North Carolina. Department of Biology; Estados UnidosFil: Bisigato, Alejandro J. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina.Fil: Cella-Pizarro, Lucrecia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina.Fil: Clark, Connie J. Woods Hole Research Center; Estados UnidosFil: Cohen, Philippe S. Stanford University. Jasper Ridge Biological Preserve; Estados UnidosFil: Cornwell, William K. University of British Columbia. Biodiversity Research Centre; Canadá.Fil: Peri, Pablo Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina.Fil: Peri, Pablo Luis. Universidad Nacional de la Patagonia Austral; Argentina.Fil: Peri, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Prior, Lynda D. University of Tasmania. School of Plant Science; Australia

Sexual dimorphism in the size and shape of the raptorial pedipalps of Giant Whip Spiders (Arachnida: Amblypygi)

Sexual dimorphism in the form of elaborate crests, horns and swellings can be a clear indicator of the differing evolutionary pressures to which males and females are subject. However, dimorphism can also be expressed in more subtle shape differences not outwardly obvious to the observer. Whip spiders (Amblypygi) possess a unique pair of spined pedipalps hypothesized to primarily function in prey capture, but also serving multiple other functions. Little is known regarding the intraspecific shape variation of these limbs and its potential causes. Because a role during courtship and male contest has also been hypothesized, sexual selection may contribute to shape differences. As such, we hypothesize that sexual dimorphism will be present in the size and shape of amblypygid pedipalps, with male contest selecting for longer and thicker pedipalps, and larger spines in males. This study aims to test this hypothesis, by quantifying the contribution of ontogeny and sexual dimorphism to shape within the raptorial pedipalps of Damon variegatus. Discriminant function analysis using GMM landmark data reveals statistically significant sexual shape dimorphism in both the tibia and femur of the pedipalp. Contrary to our hypothesis, males display a more gracile pedipalp morphology with reduced spination. Sex differences in the allometric slope and overall size were also found in a number of linear appendicular metrics using Type-II regression. Males have statistically longer pedipalp tibiae, whip femora, and leg two femora. We propose that males have evolved a longer pedipalps in the context of display contest rather than physical aggression. The elongation of structures used in display-based contest and courtship found herein further emphasizes the contribution of visual cues to the evolution of morphology more broadly