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Osawa T.,Japan National Institute for Agro - Environmental Sciences | Mitsuhashi H.,The Museum of Nature and Human Activities Hyogo | Uematsu Y.,Kobe University | Ushimaru A.,Kobe University
Ecological Informatics | Year: 2011

Species-occurrence data sets tend to contain a large proportion of zero values, i.e., absence values (zero-inflated). Statistical inference using such data sets is likely to be inefficient or lead to incorrect conclusions unless the data are treated carefully. In this study, we propose a new modeling method to overcome the problems caused by zero-inflated data sets that involves a regression model and a machine-learning technique. We combined a generalized liner model (GLM), which is widely used in ecology, and bootstrap aggregation (bagging), a machine-learning technique. We established distribution models of Vincetoxicum pycnostelma (a vascular plant) and Ninox scutulata (an owl), both of which are endangered and have zero-inflated distribution patterns, using our new method and traditional GLM and compared model performances. At the same time we modeled four theoretical data sets that contained different ratios of presence/absence values using new and traditional methods and also compared model performances. For distribution models, our new method showed good performance compared to traditional GLMs. After bagging, area under the curve (AUC) values were almost the same as with traditional methods, but sensitivity values were higher. Additionally, our new method showed high sensitivity values compared to the traditional GLM when modeling a theoretical data set containing a large proportion of zero values. These results indicate that our new method has high predictive ability with presence data when analyzing zero-inflated data sets. Generally, predicting presence data is more difficult than predicting absence data. Our new modeling method has potential for advancing species distribution modeling. © 2011 Elsevier B.V. Source


Osawa T.,Kobe University | Osawa T.,Japan National Institute for Agro - Environmental Sciences | Mitsuhashi H.,The Museum of Nature and Human Activities Hyogo | Niwa H.,Kyoto University | Ushimaru A.,Kobe University
Open Ecology Journal | Year: 2010

Although dendritic networks within ecosystems have typically been considered a special case of network topology, they have attracted a great deal of attention in recent years. These systems exhibit unique features in that both the nodes and branches provide distinct habitats. Within a river discontinuum context, river confluences, which are nodes of dendritic river networks, are hypothesised to have particular hydrodynamic traits that create heterogeneous habitats through a unique disturbance regime, although this hypothesis has not yet been tested. We tested this hypothesis using a vegetation data set collected from 14 river basin systems in Hyogo Prefecture, Japan. We compared vegetation-patch diversity between confluence and single-flow areas using hierarchical Bayesian models. Our results demonstrated greater vegetation-patch diversity in confluence areas compared to single-flow areas. Our findings support the hypothesis that confluences result in highly heterogeneous habitats. To the best of our knowledge, this is the first empirical report to demonstrate that river confluences have high vegetation-patch diversity. We conclude that network nodes play an important role in maintaining the biodiversity of river networks. © Osawa et al. Source


Osawa T.,Kobe University | Mitsuhashi H.,The Museum of Nature and Human Activities Hyogo | Ushimaru A.,Kobe University
Plant Ecology | Year: 2010

In riparian zones along the banks of streams and rivers, flooding often causes large changes in environmental conditions immediately downstream of confluences. In turn, spatial heterogeneity in flooding along rivers and streams likely affects local species diversity. Furthermore, flooding during the plant growing season can strongly affect plant survival. In this study, we hypothesized that confluences have impacts on plant species diversity, and that these impacts are larger during the plant growing season. To test this hypothesis, we measured plant species diversity and the extent of natural bare ground at 11 river confluences during two different seasons (summer and spring) within the Mukogawa River basin system, Japan. Species diversity was highest at down-confluence areas in the summer. We linked the pattern of species diversity to that of bare ground creation by floods around the confluences and to the seasonality of annual plant recruitment. The extent of bare ground was significantly greater at down-confluence areas than at up-confluence areas. The recruitment of annual species was higher in the summer than in the spring and included rapid occupancy of bare ground in the summer. We suggest that within river systems, spatial and seasonal differences in patterns of flooding function together to regulate plant species diversity. © 2010 Springer Science+Business Media B.V. Source


Osawa T.,Japan National Institute for Agro - Environmental Sciences | Mitsuhashi H.,The Museum of Nature and Human Activities Hyogo | Ushimaru A.,Kobe University
Plant Ecology | Year: 2014

Although several studies have demonstrated that disturbance contributes to species' diversity, little emphasis has been placed on the identification of species' coexistence mechanisms related to life history traits. In this study, we compared species' richness and components of plant communities around river confluences to explore how disturbance promotes the coexistence of species with different life history traits. Sites upstream and downstream of confluences are ideal for such comparisons because they draw on the same species' pools and have similar ambient conditions, but differ markedly in the extents of flooding disturbance. We compared sites upstream and downstream of confluences by calculating species' richness and community similarity indices for several life history traits in both summer and spring. In summer, the combined richness of all the species, of annual- and summer-flowering species, was higher downstream from confluences than upstream, but this was not the case for perennials. Similarity analyses suggested that plant communities are constructed according to a neutral process, whereby interactions between the coexisting species are neutral. However, in spring, species' richness was similar upstream and downstream of confluences for all life history traits. Similarity analyses suggested that under these circumstances, the communities were constructed through a species-sorting process; i.e., each life history trait had a distinct habitat preference. Thus, the relative strengths of different community assembly processes may change seasonally. We concluded that species groups differing in their responses to disturbance may coexist in a single community. Thus, community structuring following disturbance may involve two processes: a neutral and a species-sorting process. The relative importance of each may vary between species' life history traits and between seasons, and the interaction may account for current community structures. © 2014 Springer Science+Business Media Dordrecht. Source


Osawa T.,Kobe University | Osawa T.,Japan National Institute for Agro - Environmental Sciences | Mitsuhashi H.,The Museum of Nature and Human Activities Hyogo | Niwa H.,Kyoto University | Ushimaru A.,Kobe University
Ecological Research | Year: 2010

In riparian areas, the distribution patterns of plant species are generally considered to depend on their flooding tolerance. Areas around river confluences are known to experience frequent and/or strong flooding events and provide diverse habitats for plants in riparian areas. However, the degree to which hydrophilic vegetation types increase their distribution around confluences may depend on their flooding tolerance. To test this hypothesis, we compared patch numbers and total areas of ten vegetation groups between confluences and single-flow areas. The vegetation groups were classified on the basis of life form and morphology of dominant species. Additionally, we compared total area of natural bare ground (an index of flooding disturbance) between confluences and single-flow areas. We found that patch numbers of annual grass, forb, and vine, perennial grass and forb, and riparian forest vegetation, as well as total areas of annual forb and vine, perennial grass and forb, bamboo and riparian forest vegetation, and natural bare ground, were greater around river confluences than in single-flow areas. On the other hand, patch numbers of shrub vegetation and total areas of annual grass, perennial vine, willow, and shrub vegetation decreased around confluences. These results suggest that confluences enhance diverse, but not all, types of habitat for hydrophilic vegetation. Thus, river confluences are a key element in maintaining diverse riparian vegetation. © 2010 The Ecological Society of Japan. Source

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