Richard Anderson-Sprecher

Model Comparisons and R 2

Abstract Much of the confusion surrounding interpretation and application of the coefficient of determination, R 2, can be alleviated if it is defined explicitly as a comparison of a given model to the null model EY = β0. The model-comparison definition allows R 2 to be easily generalized, and standard extensions such as coefficients of partial determination are seen to be special cases of this generalization. Formulas become simpler, more unified, and more easily understood. Commonly cited problem areas such as R 2 for the no-intercept model and model comparisons using different values of R 2 are also clarified by this perspective.

Beyond the reaction progress variable : the meaning and significance of isotopic incorporation data

Ecologists conduct isotopic incorporation experiments to determine the residence time of various stable isotopes in animal tissues. These experiments permit determining the time window through which isotopic ecologists perceive the course of diet changes, and therefore the scale of the inferences that we can make from isotopic data. Until recently, the results of these experiments were analyzed using first-order, one-compartment models. Cerling et al. (Oecologia 151:175–189, 2007) proposed an approach they named the reaction progress variable to: (1) determine how many compartments are needed to describe a pattern of istopic incorporation, and (2) to estimate the size and rate constant of each pool. We elaborate on the approach described by Cerling et al. (Oecologia 151:175–189, 2007) by providing a way to estimate average retention times for an isotope in a tissue (and its associate error) for multi-compartment models. We also qualify the interpretation of the parameters in multi-compartment models by showing that many possible mechanisms yield models with the same functional form. Multi-compartment models are phenomenological, rather than mechanistic descriptions, of incorporation data. Finally, we propose the use of information theoretic criteria to assess the number of compartments that must be included in models of isotopic incorporation.

TRANSPLACENTAL TRANSMISSION AND ABORTION IN COWS ADMINISTERED NEOSPORA CANINUM OOCYSTS

Neospora caninum infection is a common cause of bovine abortion. One method by which cattle can acquire infection is through ingestion of oocysts; however, this has not yet been proved to cause transplacental infection or abortion. In this study, 19 cows, pregnant between 70 and 176 days, were administered 1,500 to 115,000 oocysts through an esophageal tube. Seventeen of the cows became seropositive, indicating acquisition of infection, whereas 8 negative control cows remained seronegative (P < 0.001). Offspring were examined using serology, histology, immunohistochemistry, parasite isolation, and polymerase chain reaction (PCR). Six offspring were infected and 1 of them was aborted. The aborted fetus had typical lesions and positive immunohistochemistry and PCR for N. caninum. All 6 cows with infected offspring had continuously rising antibody titers, whereas 10 of 11 infected cows with uninfected offspring had falling titers after an early apex. The risk of transplacental transmission was increased by later exposure times during gestation and by the dose of oocysts (P < 0.01 for the 2 combined variables). The lowest dose of oocysts, when administered after the 160th day of gestation, caused transplacental infection in 1 of 2 animals. This study demonstrates that infection with N. caninum oocysts can cause transplacental transmission and abortion in cattle.

Should we use one‐, or multi‐compartment models to describe 13C incorporation into animal tissues?

Understanding rates of isotopic incorporation and discrimination factors between tissues and diet is an important focus of ecologists seeking to use stable isotopes to track temporal changes in diet. We used a diet-shift experiment to measure differences among tissues in (13)C incorporation rates in house sparrows (Passer domesticus). We predicted faster incorporation rates in splanchnic than in structural tissues. We also assessed whether isotopic incorporation data were better supported by the one-compartment models most commonly used by ecologists or by multi-compartment models. We found large differences in the residence time of (13)C among tissues and, as predicted, splanchnic tissues had faster rates of isotopic incorporation and thus shorter retention times than structural tissues. We found that one-compartment models supported isotopic incorporation data better in breath, excreta, red blood cells, bone collagen, and claw tissues. However, data in plasma, intestine, liver, pectoralis muscle, gizzard, and intestine tissues supported two-compartment models. More importantly, the inferences that we derived from the two types of models differed. Two-compartment models estimated longer (13)C residence times, and smaller tissue to diet differences in isotopic composition, than one-compartment models. Our study highlights the importance of considering both one- and multi-compartment models when interpreting laboratory and field isotopic incorporation studies. It also emphasizes the opportunities that measuring several tissues with contrasting isotopic residence times offer to elucidate animal diets at different time scales.

Dietary and isotopic specialization: the isotopic niche of three Cinclodes ovenbirds.

By comparing the isotopic composition of tissues deposited at different times, we can identify individuals that shift diets over time and individuals with constant diets. We define an individual as an isotopic specialist if tissues deposited at different times have similar isotopic composition. If tissues deposited at different times differ in isotopic composition we define an individual as an isotopic generalist. Individuals can be dietary generalists but isotopic specialists if they feed on the same resource mixture at all times. We assessed the degree of isotopic and dietary specialization in three related Chilean bird species that occupy coastal and/or freshwater environments: Cinclodes oustaleti, Cinclodes patagonicus, and Cinclodes nigrofumosus. C. oustaleti individuals were both isotopic and dietary generalists. Tissues deposited in winter (liver and muscle) had distinct stable C (δ13C) and stable N isotope ratio (δ15N) values from tissues deposited in the summer (wing feathers) suggesting that birds changed the resources that they used seasonally from freshwater habitats in the summer to coastal habitats in the winter. Although the magnitude of seasonal isotopic change was high, the direction of isotopic change varied little among individuals. C. patagonicus included both isotopic specialists and generalists, as well as dietary specialists and generalists. The isotopic composition of the feathers and liver of some C. patagonicus individuals was similar, whereas that of others differed. In C. patagonicus, there were large inter-individual differences in the magnitude and the direction of seasonal isotopic change. All individuals of C. nigrofumosus were both isotopic and dietary specialists. The distribution of δ13C and δ15N values overlapped broadly among tissues and clustered in a small, and distinctly intertidal, region of δ space. Assessing individual specialization and unraveling the factors that influence it, have been key questions in animal ecology for decades. Stable isotope analyses of several tissues in appropriate study systems provide an unparalleled opportunity to answer them.

Quadrature receiver mismatch calibration

This article introduces nonlinear regression techniques to estimate gain and phase mismatches between the in-phase (I) and quadrature (Q) branches of a quadrature receiver. Under modest assumptions, the system intrinsically follows a nonlinear regression model. The algorithm is effective, easily implemented, customizable, and requires few assumptions. Large-sample, jackknife, and bootstrap techniques provide on-line error assessment and parameter inference.

State-Space Analysis of Wildlife Telemetry Data

Abstract The location of wildlife is frequently determined from telemetry data. Current procedures may inadequately account for time-dependencies in the data and errors in the observations. We propose a nonlinear state-space model that addresses these two shortcomings. Let y t be a vector of angles measured between known antenna locations and unknown animal positions, and let states x t be the rectangular coordinates of animal position at time t. If x t follows a two-dimensional stochastic process and observation errors are additive, independent, and normal, then location estimates and their precisions may be determined recursively using extensions of the Kalman filter-smoother. We outline the application of the iterated extended Kalman filter-smoother to this situation and consider problems of initial conditions, the identification of filter parameters based on maximum likelihood principles, and the treatment of missing data. Using simulated data, we compare state-space and current procedures according t...

A New Method to Compute Standard-Weight Equations That Reduces Length-Related Bias

Abstract We propose a new method for developing standard-weight (W s) equations for use in the computation of relative weight (W r) because the regression line–percentile (RLP) method often leads to length-related biases in W s equations. We studied the structural properties of W s equations developed by the RLP method through simulations, identified reasons for biases, and compared W s equations computed by the RLP method and the new method. The new method is similar to the RLP method but is based on means of measured weights rather than on means of weights predicted from regression models. The new method also models curvilinear W s relationships not accounted for by the RLP method. For some length-classes in some species, the relative weights computed from W s equations developed by the new method were more than 20 W r units different from those using W s equations developed by the RLP method. We recommend assessment of published W s equations developed by the RLP method for length-related bias and use ...

An alternative approach to detection of length-related biases in standard weight equations

Abstract We propose a new method for assessing length-related biases in standard weight (W s) equations computed by the regression-line−percentile method. We evaluated the performance of the new method relative to two previous methods for assessing length-related biases using 15 data sets from which W s equations have been computed. The new method detected potentially serious length-related biases in 10 W s equations, whereas one of the previously used methods failed to detect any biologically significant biases and the other method detected biases in only one equation. The new method can detect curvilinear relationships between W s and length, so it provides insight that is not available from previous methods.

Test of Martin’s overkill hypothesis using radiocarbon dates on extinct megafauna

Significance Coincident with the human colonization of the Western Hemisphere, dozens of genera of Pleistocene megafauna were lost to extinction. Following Martin, we argue that declines in the record of radiocarbon dates of extinct genera may be used as an independent means of detecting the first presence of humans in the New World. Our results, based on analyses of radiocarbon dates from Eastern Beringia, the contiguous United States, and South America, suggest north to south, time, and space transgressive declines in megafaunal populations as predicted by the overkill hypothesis. This finding is difficult to reconcile with other extinction hypotheses. However, it remains to be determined whether these findings will hold with larger samples of radiocarbon dates from all regions. Following Martin [Martin PS (1973) Science 179:969–974], we propose the hypothesis that the timing of human arrival to the New World can be assessed by examining the ecological impacts of a small population of people on extinct Pleistocene megafauna. To that end, we compiled lists of direct radiocarbon dates on paleontological specimens of extinct genera from North and South America with the expectation that the initial decline of extinct megafauna should correspond in time with the initial evidence for human colonization and that those declines should occur first in eastern Beringia, next in the contiguous United States, and last in South America. Analyses of spacings and frequency distributions of radiocarbon dates for each region support the idea that the extinction event first commenced in Beringia, roughly 13,300–15,000 BP. For the United States and South America, extinctions commenced considerably later but were closely spaced in time. For the contiguous United States, extinction began at ca. 12,900–13,200 BP, and at ca. 12,600–13,900 BP in South America. For areas south of Beringia, these estimates correspond well with the first significant evidence for human presence and are consistent with the predictions of the overkill hypothesis.