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4 results on '"Braak, Cajo J.F. ter"'

2. Functional biogeography of Neotropical moist forests : Trait–climate relationships and assembly patterns of tree communities

Author

Pinho, Bruno X., Tabarelli, Marcelo, Braak, Cajo J.F., ter, Wright, S.J., Arroyo-Rodríguez, Víctor, Benchimol, Maíra, Engelbrecht, Bettina M.J., Pierce, Simon, Hietz, Peter, Santos, Bráulio A., Peres, Carlos A., Müller, Sandra C., Wright, Ian J., Bongers, Frans, Lohbeck, Madelon, Niinemets, Ülo, Slot, Martijn, Jansen, Steven, Jamelli, Davi, Lima, Renato A.F., de, Swenson, Nathan, Condit, Richard, Barlow, Jos, Slik, Ferry, Hernández-Ruedas, Manuel A., Mendes, Gabriel, Martínez-Ramos, Miguel, Pitman, Nigel, Kraft, Nathan, Garwood, Nancy, Guevara Andino, Juan Ernesto, Faria, Deborah, Chacón-Madrigal, Eduardo, Mariano-Neto, Eduardo, Júnior, Valdecir, Kattge, Jens, Melo, Felipe P.L., Pinho, Bruno X., Tabarelli, Marcelo, Braak, Cajo J.F., ter, Wright, S.J., Arroyo-Rodríguez, Víctor, Benchimol, Maíra, Engelbrecht, Bettina M.J., Pierce, Simon, Hietz, Peter, Santos, Bráulio A., Peres, Carlos A., Müller, Sandra C., Wright, Ian J., Bongers, Frans, Lohbeck, Madelon, Niinemets, Ülo, Slot, Martijn, Jansen, Steven, Jamelli, Davi, Lima, Renato A.F., de, Swenson, Nathan, Condit, Richard, Barlow, Jos, Slik, Ferry, Hernández-Ruedas, Manuel A., Mendes, Gabriel, Martínez-Ramos, Miguel, Pitman, Nigel, Kraft, Nathan, Garwood, Nancy, Guevara Andino, Juan Ernesto, Faria, Deborah, Chacón-Madrigal, Eduardo, Mariano-Neto, Eduardo, Júnior, Valdecir, Kattge, Jens, and Melo, Felipe P.L.

Abstract

Aim: Here we examine the functional profile of regional tree species pools across the latitudinal distribution of Neotropical moist forests, and test trait–climate relationships among local communities. We expected opportunistic strategies (acquisitive traits, small seeds) to be overrepresented in species pools further from the equator, but also in terms of abundance in local communities in currently wetter, warmer and more seasonal climates. Location: Neotropics. Time period: Recent. Major taxa studied: Trees. Methods: We obtained abundance data from 471 plots across nine Neotropical regions, including c. 100,000 trees of 3,417 species, in addition to six functional traits. We compared occurrence-based trait distributions among regional species pools, and evaluated single trait–climate relationships across local communities using community abundance-weighted means (CWMs). Multivariate trait–climate relationships were assessed by a double-constrained correspondence analysis that tests both how CWMs relate to climate and how species distributions, parameterized by niche centroids in climate space, relate to their traits. Results: Regional species pools were undistinguished in functional terms, but opportunistic strategies dominated local communities further from the equator, particularly in the Northern Hemisphere. Climate explained up to 57% of the variation in CWM traits, with increasing prevalence of lower-statured, light-wooded and softer-leaved species bearing smaller seeds in more seasonal, wetter and warmer climates. Species distributions were significantly but weakly related to functional traits. Main conclusions: Neotropical moist forest regions share similar sets of functional strategies, from which local assembly processes, driven by current climatic conditions, select for species with different functional strategies. We can thus expect functional responses to climate change driven by changes in relative abundances of species already present regionally.

Published
2021

3. A Penalized Likelihood Method for Mapping Epistatic Quantitative Trait Loci With One-Dimensional Genome Searches.

Author

Boer, Martin P., Braak, Cajo J.F. ter, and Jansen, Ritsert C.

Subjects
*EPISTASIS (Genetics), *GENOMES
Abstract

Epistasis is a common and important phenomenon, as indicated by results from a number of recent experiments. Unfortunately, the discovery of epistatic quantitative trait loci (QTL) is difficult since one must search for multiple QTL simultaneously in two or more dimensions. Such a multidimensional search necessitates many statistical tests, and a high statistical threshold must be adopted to avoid false positives. Furthermore, the large number of (interaction) parameters in comparison with the number of observations results in a serious danger of overfitting and overinterpretation of the data. In this article we present a new statistical framework for mapping epistasis in inbred line crosses. It is based on reducing the high dimensionality of the problem in two ways. First, epistatic QTL are mapped in a one-dimensional genome scan for high interactions between QTL and the genetic background. Second, the dimension of the search is bounded by penalized likelihood methods. We use simulated backcross data to illustrate the new approach. [ABSTRACT FROM AUTHOR]

Published
2002
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4. Non-linear methods for multivariate statistical calibration and their use in palaeoecology: a comparison of inverse ( k -nearest neighbours, partial least squares and weighted averaging partial least squares) and classical approaches

Author

Braak, Cajo J.F. ter

Abstract

Current environmental problems, such as acid rain and global warming, have greatly increased interest in fossil species assemblages as indicators of the palaeoenvironment and thus in quantitative methods for reconstructing environmental variables from species assemblage data. The ensuing multivariate calibration problem appears to be even harder than that of spectroscopic calibration, primarily because the basic model is unimodal (Shelford's law of tolerance) instead of being linear (Beer's law). The strong non-linearity has led to the use of non-parametric calibration methods, in particular the smooth response surface method (SRS) and the method of best modern analogues, alias k -nearest neighbours ( k -NN), and to a form of non-linear partial least squares (PLS), called weighted averaging partial least squares (WA-PLS), specially designed to analyze unimodal data. SRS and k -NN are recognized as non-parametric smoothing versions of the classical and inverse approach to linear calibration, respectively, whereas PLS and WA-PLS are inverse methods that bring in the aspect of dimension reduction. In a comparison on 'realistically looking' simulated compositional data with 100 training samples and 500 independent evaluation samples, WA-PLS and k -NN outperformed PLS when the species response functions were unimodal. For such data, k -NN resisted the curse of dimensionality. However, when the response functions were near-linear, WA-PLS and PLS performed about equally and clearly outperformed k -NN. On other simulated data, simultaneous calibration of two climate variables via a parametric non-linear classical method was compared with individual calibrations via inverse methods. The simultaneous calibration method was better at the border of the sampled space than the best inverse method (WA-PLS) and much better than k -NN. The simulations demonstrated the limitations of the leave-one-out estimate of prediction error: it showed severe method-dependent bias.

Published
1995
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