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21.
José Alexandre Felizola Diniz Filho Fabricio Villalobos Luis Mauricio Bini 《Genetics and molecular biology》2015,38(3):396-400
Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998) proposed what they called Phylogenetic Eigenvector Regression (PVR), in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in regression, correlation or ANOVAs. More recently, a new approach called Phylogenetic Eigenvector Mapping (PEM) was proposed, with the main advantage of explicitly incorporating a model-based warping in phylogenetic distance in which an Ornstein-Uhlenbeck (O-U) process is fitted to data before eigenvector extraction. Here we compared PVR and PEM in respect to estimated phylogenetic signal, correlated evolution under alternative evolutionary models and phylogenetic imputation, using simulated data. Despite similarity between the two approaches, PEM has a slightly higher prediction ability and is more general than the original PVR. Even so, in a conceptual sense, PEM may provide a technique in the best of both worlds, combining the flexibility of data-driven and empirical eigenfunction analyses and the sounding insights provided by evolutionary models well known in comparative analyses. 相似文献
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Structural bias in aggregated species‐level variables driven by repeated species co‐occurrences: a pervasive problem in community and assemblage data 下载免费PDF全文
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Jan AM van Laar Jasper H Kappen Paul LA van Daele P Martin van Hagen 《Arthritis research & therapy》2009,11(2):109-3
Behçet's disease is a complex vasculitis of unknown etiology. Abundant neutrophils suggest the involvement of innate immunity. Cytokines are skewed to the T-helper-1 pattern. Few sterile organs are easily accessible for analysis in Behçet's disease. Cañete and coworkers identify inflamed joints as a feasible model and suggest the involvement of innate immunity in Behçet's disease. 相似文献
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Luca Testi Francisco Orgaz Francisco Villalobos 《Environmental and Experimental Botany》2008,63(1-3):168-177
We measured eddy covariance fluxes of CO2 and H2O over a flat irrigated olive orchard during growth, in different periods from Leaf Area Index (LAI) of 0.3–1.9; measurements of soil respiration were also collected. The daily net ecosystem exchange flux (FNEE) was practically zero at LAI around 0.4 or when the orchard intercepted 11% of the incoming daily radiation; at the end of the experiment, with LAI of 1.9 (and the fraction of intercepted daily radiation close to 0.5), FNEE was around 10 g CO2 m−2 day−1. The night-time ecosystem respiration (Reco), calculated from eddy fluxes in well-mixed night conditions, show a clear but non-linear dependence with LAI; it ranged from 0.05 to 0.15 mg CO2 m−2 s−1 (in average), being the lower limit ideally close to the heterotrophic soil respiration at the site. The gross primary production flux (FGPP) was linearly related to LAI within the LAI range of this experiment (with 11 g CO2 m−2 day−1 increments per unit of LAI) and to the fraction of intercepted radiation. The maximum rates of FGPP (0.75 mg CO2 m−2 s−1) were obtained in the summer mornings of 2002, at LAI close to 1.9. FGPP was strongly modulated by vapour pressure deficit (VPD) through the canopy conductance, even in absence of water stress. Hence, especially in the summer, the maximum rates of carbon assimilation are reached always before noon. The daily course of FGPP shows a two-phase pattern, first related to irradiance and then to canopy conductance. The water use efficiency (WUE) was, in average, 3.8, 6.3 and 7 g CO2 L−1 in 1999, 2001 and 2002, respectively, with maxima always in the early morning. Hourly WUE was strongly related to VPD (WUE = −10.25 + 22.52 × VPD−0.34). Our results suggest that drip irrigated orchards in general, and olive in particular, deserve specific carbon exchange and carbon budget studies and cannot be easily included in other biomes. 相似文献
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Phylogenetic eigenvectors and nonstationarity in the evolution of theropod dinosaur skulls 下载免费PDF全文
J. A. F. Diniz‐Filho D. M. C. C. Alves F. Villalobos M. Sakamoto S. L. Brusatte L. M. Bini 《Journal of evolutionary biology》2015,28(7):1410-1416
Despite the long‐standing interest in nonstationarity of both phenotypic evolution and diversification rates, only recently have methods been developed to study this property. Here, we propose a methodological expansion of the phylogenetic signal‐representation (PSR) curve based on phylogenetic eigenvectors to test for nonstationarity. The PSR curve is built by plotting the coefficients of determination R2 from phylogenetic eigenvector regression (PVR) models increasing the number of phylogenetic eigenvectors against the accumulated eigenvalues. The PSR curve is linear under a stationary model of trait evolution (i.e. the Brownian motion model). Here we describe the distribution of shifts in the models R2 and used a randomization procedure to compare observed and simulated shifts along the PSR curve, which allowed detecting nonstationarity in trait evolution. As an applied example, we show that the main evolutionary pattern of variation in the theropod dinosaur skull was nonstationary, with a significant shift in evolutionary rates in derived oviraptorosaurs, an aberrant group of mostly toothless, crested, birdlike theropods. This result is also supported by a recently proposed Bayesian‐based method (AUTEUR). A significant deviation between Ceratosaurus and Limusaurus terminal branches was also detected. We purport that our new approach is a valuable tool for evolutionary biologists, owing to its simplicity, flexibility and comprehensiveness. 相似文献
28.
J. De La Cruz‐Agüero R. Moncayo‐Estrada V. M. Cota‐Gómez H. Villalobos‐Ortiz A. Valdez‐Pelayo 《Journal of fish biology》2016,89(3):1889-1896
The first records of three midwater species for the Mexican ichthyofauna (Holtbyrnia laticauda, Brama dussumieri and Cubiceps baxteri), caught off the coast of Baja California, Mexico, in mid 2014, are reported. As far as is known, they are the first verified specimens, geo‐referenced and catalogued in a reference fish collection for the west coast of Mexico. The species' known distributions were extended northward in the eastern Pacific Ocean, ranging from 3495 to 8300 km. 相似文献
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