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Takashina N , Kusumoto B, Kubota Y, Economo E P (2019). A geometric approach to scaling individual distributions to macroecological patterns : Journal of theoretical biology 461, 170-188
Highlights
•Developed theory scales up the individual distributions to macroecological patterns.
•We derived general forms of species abundance, species-area and endemic-area curves.
•We demonstrated how relative species abundance is unified across scales.
•Sampling shape and area affect macroecological predictions.
•As an example, the theory can help understand scaling problems of beta diversity.
•Developed theory scales up the individual distributions to macroecological patterns.
•We derived general forms of species abundance, species-area and endemic-area curves.
•We demonstrated how relative species abundance is unified across scales.
•Sampling shape and area affect macroecological predictions.
•As an example, the theory can help understand scaling problems of beta diversity.
Ulrich W, Nakadai R, Matthews T J , Kubota Y (2018) The two-parameter Weibull distribution as a universal tool to model the variation in species relative abundances : Ecological Complexity 36, 110-116
Highlights
•We identify the Weibull model as a flexible model for species abundance distributions.
•Parameters of the Weibull model define the possible abundance distribution space.
•Not realized parameter values inform about constraints on ecological community assembly.
•We identify the Weibull model as a flexible model for species abundance distributions.
•Parameters of the Weibull model define the possible abundance distribution space.
•Not realized parameter values inform about constraints on ecological community assembly.
Matthews T J , Borregaard M K , Gillespie C S , Rigal F, Ugland K , Krüger R F, Marques R, Sadler J P , Borges P AV , Kubota Y, Whittaker R J (2018) Extension of the gambin model to multimodal species abundance distributions: Methods in Ecology and Evolution
Abstract
- Species abundance distributions (SADs) are one of the most widely used tools in macroecology, and it has become increasingly apparent that many empirical SADs can best be described as multimodal. However, only a few SAD models have been extended to incorporate multiple modes and no software packages are available to fit multimodal SAD models. In this study, we present an extension of the gambin SAD model to multimodal SADs.
- We derive the maximum likelihood equations for fitting the bimodal gambin distribution and generalize this approach to fit gambin models with any number of modes. We present these new functions, along with additional functions to aid in the analysis of multimodal SADs, within an updated r package (“gambin”; version 2.4.0) that enables the fitting, plotting and evaluating of gambin models with any number of modes.
- We use a mixture of simulations and empirical datasets to test our new models, including tests of the sensitivity of the model parameters to the number of individuals and the number of species in a sample. We show that the new multimodal gambin models perform well under a variety of circumstances, and that the application of these new models to empirical SAD and other macroecological (e.g., species range size distributions) datasets can provide interesting insights. The updated software package is simple to use and provides straightforward yet flexible statistical analyses of multimodality in SAD‐type datasets.
Saihanna S, Tanaka T, Okamura Y, Kusumoto B, Shiono T, Hirao T, Kubota Y, Murakami M (2018) Correction to: A paradox of latitudinal leaf defense strategies in deciduous and evergreen broadleaved trees:Ecological research 33 (5), 1019-1019
Abstract
The classical “low latitude–high defense” hypothesis is seldom supported by empirical evidence. In this context, we tested latitudinal patterns in the leaf defense traits of deciduous broadleaved (DB) and evergreen broadleaved (EGB) tree species, which are expected to affect herbivore diversity. We examined the co‐occurrence of leaf defense traits (tannin and phenol content, leaf mechanical strength, leaf dry matter content, leaf mass per area, and leaf thickness) in 741 broadleaved tree species and their correlations with species geographical range in East Asian island flora. We discovered contrasting latitudinal defense strategy gradients in DB and EGB tree species. DB species employed chemical defenses (increasing tannin and phenol content) at higher latitudes and physical defenses (softer and thinner leaves) at lower latitudes, whereas EGB tree species exhibited opposite latitudinal defense patterns. The “low latitude high defense” hypothesis included a paradoxical aspect in chemical and physical defense traits across broadleaved tree species. To reconcile paradoxical defense strategies along the latitudinal gradient, we conclude that interactive correlations among leaf traits are controlled by leaf longevity, which differs between DB and EGB tree species.
Nagahama A , Kubota Y, Satake A (2018) Climate warming shortens flowering duration: a comprehensive assessment of plant phenological responses based on gene expression analyses and mathematical modeling : Ecological research 33 (5), 1059-1068
There is an increasing potential to incorporate recent advances in our understanding of molecular-genetic pathways of flowering-time regulation to forecast shifts in flowering phenology in response to rising temperature. Recent studies developed models that integrate temperature and photoperiod signals into the network of floral regulatory genes, and predicted the shortening of flowering duration under warming based on the expression dynamics of major flowering-time genes in the perennial herb Arabidopsis halleri subsp. gemmifera. Nevertheless, empirical testing of the model prediction is still lacking. We performed temperature manipulation experiments and common garden experiments to test the model predictions using plants from two distant populations of A. halleri. We also quantified expression levels of two major flowering-time genes and compared the observed and predicted gene expression patterns. Our experiments in the laboratory and the field demonstrated that flowering duration of A. halleri was significantly shortened under warming conditions. Our results also revealed that the end of flowering was more sensitive to the climate warming than the onset of flowering in A. halleri. The observed gene expression dynamics in the warming condition were predicted well by the gene regulatory model. The transplant experiment of plants from Hokkaido, the northernmost island, to the subtropical field site in Okinawa, Japan, showed that plants flowered without significant activation of FLOWERING LOCUS T, a floral integrator crucial for the accelerated flowering in long days. The study suggested that the redundancy of flowering gene regulatory network could be beneficial to the persistence of flowering ability under extreme climatic conditions.