Biology subjects

Nakadai, R.

Publications and source records attributed to Nakadai, R..

9 recordsLinked to original sources

bioRxiv2022

Higher-order dissimilarity in biodiversity: Identifying dissimilarities of spatial or temporal dissimilarity structures

O_LIElucidating biodiversity patterns and their background processes is critical in biodiversity science. Dissimilarity, which is calculated based on multivariate biological quantities, is a major component of biodiversity. As spatial and temporal biodiversity information availability increases, the scope of dissimilarity studies has been expanded to cover various levels and types of spatio-temporal biodiversity facets (e.g., gene, community, and ecosystem function), and diverse pairwise dissimilarity indices have been developed. However, further development of the dissimilarity concept is required in comparative studies on spatio-temporal structures of biodiversity compositional patterns, such as those exploring commonalities of biogeographical boundaries among taxa, compared to the conventional ones to consider higher dimensions of dissimilarity: dissimilarity of dissimilarity structures. C_LIO_LIThis study proposes a novel and general concept, high-order dissimilarity (HOD), for quantitatively evaluating the dissimilarities of spatial or temporal dissimilarity structures among different datasets, proposes specific implementations of HOD as operational indices, and illustrates the potential resolution of scientific and practical questions through HOD. C_LIO_LIWe further demonstrate the advantages of the HOD concept by applying it to actual patterns, such as long-term and/or large-spatial hypothetical monitoring datasets. C_LIO_LIOur conceptual framework on HOD extends the existing framework of biodiversity science and is versatile, with many potential applications in acquiring more valuable information from ever-increasing biodiversity data. C_LI

ecology↗

bioRxiv2022

Ecological succession revisited from a temporal beta-diversity perspective

O_LIEcological succession, which is the community re-assembly process after a disturbance, is a study topic receiving renewed attention in relation to anthropogenic disturbance as well as one of the most classical ones in ecology. Previous studies occasionally revealed that compositional shifts decrease toward late succession stages and discussed the potential links with species life history and longevity. However, clear empirical evidence is not available until now because of limited analytical approaches. Therefore, traditional approaches used in previous studies could not quantify the relative contribution of demographic processes to apparent compositional shifts in communities. C_LIO_LIIn the present study, we aimed to understand ecological succession processes by revealing the patterns of temporal beta diversity based on both conventional Bray-Curtis dissimilarity and recently developed individual-based dissimilarity indices using a long-term dataset. Specifically, we used published forest inventory data from permanent forest plots in cool temperate forests along a secondary successional chronosequence, with stands at 17 to 106 years post clear-cutting. C_LIO_LIWe clearly demonstrated the detailed patterns of temporal beta-diversity indices (i.e., conventional Bray-Curtis dissimilarity and individual-based dissimilarity indices) based on stem number and stem basal area along long-term chronosequences across approximately one hundred years. C_LIO_LISynthesis. Using a long-term forest inventory dataset, this study demonstrated the link between the apparent compositional shifts and the changes in each component of the demographic processes (i.e., recruitment, growth, and mortality) during secondary forest succession in the context of temporal beta diversity. As done in this study, future research on changes in community composition during ecological successions at various sites and systems will help elucidate the relationships between temporal changes in global biodiversity and the impact of anthropogenic environmental changes. C_LI

ecology↗

bioRxiv2022

Individual-based quantitative temporal beta-diversity: Novel indices for assessing community compositional shifts accounting for changes in the properties of individuals

Revealing the patterns of temporal biodiversity changes and deciphering the connection between individual life histories and large-scale ecological patterns is essential for improving the mechanistic understanding of macroecology. However, this is challenging because the relationship between individual life history and biodiversity remains unclear. In the present study, in order to link the individual life history and community-level phenomena, I developed novel indices that allow the evaluation of community compositional shifts over time by explicitly considering the contributions of the life histories of individuals (i.e. growth, mortality, and recruitment) in a community. These novel indices are quantitative extensions of the individual-based temporal beta-diversity indices which can include information on individual sizes. The indices were applied to a subset of data from the US Forest Inventory and Analysis database for the state of Rhode Island, USA, to identify changes in the contribution of individual life histories to biodiversity change. The results of this study represent methodological progress in community ecology and macroecology, as well as a conceptual advancement in bridging studies on biodiversity with those on individual life history and physiology. The individual-based diversity indices developed here pave the way for individual-based biodiversity science, which may facilitate the understanding of the effects of climate change across different hierarchies of biological organisation.

ecology↗

bioRxiv2021

Individual-based multiple-unit dissimilarity: novel indices for assessing temporal variability in community composition

Beta-diversity was originally defined spatially, i.e., as variation in community composition among sites in a region. However, the concept of beta-diversity has since been expanded to temporal contexts. This is referred to as "temporal beta-diversity", and most approaches are simply an extension of spatial beta-diversity. The persistence and turnover of individuals over time is a unique feature of temporal beta-diversity. Nakadai (2020) introduced the "individual-based beta-diversity" concept, and provided novel indices to evaluate individual turnover and compositional shift by comparing individual turnover between two periods at a given site. However, the proposed individual-based indices are applicable only to pairwise dissimilarity, not to multiple-temporal (or more generally, multiple-unit) dissimilarity. Here, individual-based beta-diversity indices are extended to multiple-unit cases. In addition, a novel type of random permutation criterion related to these multiple-unit indices for detecting patterns of individual persistence is introduced in the present study. To demonstrate the usage the properties of these indices compared to average pairwise measures, I applied them to a dataset for a permanent 50-ha forest dynamics plot on Barro Colorado Island in Panama. Information regarding "individuals" is generally missing from community ecology and biodiversity studies of temporal dynamics. In this context, the methods proposed here are expected to be useful for addressing a wide range of research questions regarding temporal changes in biodiversity, especially studies using traditional individual-tracked forest monitoring data.

ecology↗

bioRxiv2020

Degrees of compositional equilibrium in tree communities vary along a gradient of temperature change rates over one decade: Application of an individual-based temporal beta diversity concept

Temporal patterns in communities have gained widespread attention recently, to the extent that temporal changes in community composition are now termed "temporal beta-diversity". Previous studies of beta-diversity have made use of two classes of dissimilarity indices: incidence-based (e.g., Sorensen and Jaccard dissimilarity) and abundance-based (e.g., Bray-Curtis and Ru[z]i[c]ka dissimilarity). However, in the context of temporal beta-diversity, the persistence of identical individuals and turnover among other individuals within the same species over time have not been considered, despite the fact that both will affect compositional changes in communities. To address this issue, I propose new index concepts for beta-diversity and the relative speed of compositional shifts in relation to individual turnover based on individual identity information. Individual-based beta-diversity indices are novel dissimilarity indices that consider individual identity information to quantitatively evaluate temporal change in individual turnover and community composition. I applied these new indices to individually tracked tree monitoring data in deciduous and evergreen broad-leaved forests across the Japanese archipelago with the objective of quantifying the effect of climate change trends (i.e., rates of change of both annual mean temperature and annual precipitation) on individual turnover and compositional shifts at each site. A new index explored the relative contributions of mortality and recruitment processes to temporal changes in community composition. Clear patterns emerged showing that an increase in the temperature change rate facilitated the relative contribution of mortality components. The relative speed of compositional shift increased with increasing temperature change rates in deciduous forests but decreased with increasing warming rates in evergreen forests. These new concepts provide a way to identify novel and high-resolution temporal patterns in communities.

ecology↗

bioRxiv2020

Climate, species richness, and body size drive geographical variation in resource specialization of herbivorous butterflies

AimIt is generally assumed that the degree of resource specialization in herbivorous insects increases towards lower latitudes. However, latitudinal patterns in herbivore diet breadth at large spatial scales remain poorly understood. In this work, we investigated drivers of latitudinal variation in lepidopteran "fundamental" resource specialization, which we defined as the host breadth when not limited by interspecific interactions at the same trophic level. LocationThe Japanese archipelago (22{degrees}N-45{degrees}N), including hemiboreal, temperate, and subtropical zones. TaxonHerbivorous butterflies. MethodsSpecies-specific fundamental host breadth was calculated based on pooled geographical occurrence and host-use records. We investigated the latitudinal pattern and significant drivers of the degree of specialization in regional species pools at a 10-km grid level. As potential drivers, we focused on geography, current climate, and diversity and body size of butterflies. Through Bayesian structural equation modeling, we investigated the complicated relationships between these variables and community-level resource specialization represented by three different indices of host breadth. ResultsWe found that fundamental resource specialization of butterfly communities increases toward higher latitudes. This pattern is contrary to the presumed general trend found in studies based on realized resource specialization within local communities. We found that the observed pattern is driven mainly by factors related to climate, butterfly diversity, and body size in each community. Above all, annual mean temperature most strongly drove community-level fundamental host breadth of butterflies. Main conclusionsOur findings suggest that fundamental resource specialization may show different latitudinal patterns from the conventional prediction based on knowledge of realized resource specialization. Our results emphasize the importance of the current climate as a major factor regulating butterfly morphology and fundamental host breadth, regardless of whether the impact is direct or indirect.

ecology↗

bioRxiv2019

Describing macroecological patterns in microbes: Approaches for comparative analyses of operational taxonomic unit read number distribution with a case study of global oceanic bacteria

Describing the variation in commonness and rarity in a community is a fundamental method of evaluating biodiversity. Such patterns have been studied in the context of species abundance distributions (SADs) among macroscopic organisms in numerous communities. Recently, models for analyzing variation in local SAD shapes along environmental gradients have been constructed. The recent development of high-throughput sequencing enables evaluation of commonness and rarity in local communities of microbes using operational taxonomic unit (OTU) read number distributions (ORDs), which are conceptually similar to SADs. However, few studies have explored the variation in local microbial ORD shapes along environmental gradients. Therefore, the similarities and differences between SADs and ORDs are unclear, clouding any universal rules of global biodiversity patterns. We investigated the similarities and differences in ORD shapes vs. SADs, and how well environmental variables explain the variation in ORDs along latitudinal and depth gradients. Herein, we integrate ORDS into recent comparative analysis methods for SAD shape using datasets generated on the Tara Oceans expedition. About 56% of the variance in skewness of ORDs among global oceanic bacterial communities was explained with this method. Moreover, we confirmed that the parameter combination constraints of Weibull distributions were shared by ORDs of bacterial communities and SADs of tree communities, suggesting common long-term limitation processes such as adaptation and community persistence acting on current abundance variation. On the other hand, skewness was significantly greater for bacterial communities than tree communities, and many ecological predictions did not apply to bacterial communities, suggesting differences in the community assembly rules for microbes and macroscopic organisms. Approaches based on ORDs provide opportunities to quantify macroecological patterns of microbes under the same framework as macroscopic organisms.

ecology↗

bioRxiv2017

Niche filtering, not interspecific resource competition, explains the co-occurrence of butterfly species across the Japanese archipelago

The relevance of interspecific resource competition in the context of community assembly by herbivorous insects is a well-known topic in ecology. Most previous studies focused on local species assemblies, that shared host plants. Few studies evaluated species pairs within a single taxon when investigating the effects of host plant sharing at the regional scale. Herein, we explore the effect of plant sharing on the geographical co-occurrence patterns of 232 butterflies distributed across the Japanese archipelago; we use two spatial scales (10 x 10 km and 1 x 1 km grids) to this end. We considered that we might encounter one of two predictable patterns in terms of the relationship between co-occurrence and host sharing among butterflies. On the one hand, host sharing might promote distributional exclusivity attributable to interspecific resource competition. On the other hand, sharing of host plants may promote co-occurrence attributable to filtering by resource niche. At both grid scales, we found significant negative correlations between host use similarity and distributional exclusivity. Our results support the hypothesis that the butterfly co-occurrence pattern across the Japanese archipelago is better explained by filtering via resource niche rather than interspecific resource competition.

ecology↗

bioRxiv2016

Patterns of temporal and enemy niche use by a community of leaf cone moths (Caloptilia) coexisting on maples (Acer) as revealed by metabarcoding

The diversity of herbivorous insects is often considered a function of host plant diversity. However, recent research has uncovered many examples of closely related herbivores using the same host plant(s), suggesting that partitioning of host plants is not the only mechanism generating diversity. Herbivores sharing hosts may utilize different parts of the same plant, but such resource partitioning is often not apparent; hence, the factors that allow closely related herbivores to coexist are still largely undetermined. We examined whether partitioning of phenology or natural enemies may explain the coexistence of leaf cone moths (Caloptilia; Gracillariidae) associated with maples (Acer; Sapindaceae). Larval activity of 10 sympatric Caloptilia species found on nine maple species was monitored every 2-3 weeks for a total of 13 sampling events, and an exhaustive search for internal parasitoid wasps was conducted using high-throughput sequencing. Blocking primers were used to facilitate the detection of wasp larvae inside moth tissue. We found considerable phenological overlap among Caloptilia species, with two clear peaks in July and September-October. Coexisting Caloptilia species also had largely overlapping parasitoid communities; a total of 13 wasp species belonging to four families attacked Caloptilia in a non-specific fashion at an overall parasitism rate of 46.4%. Although coexistence may be facilitated by factors not accounted for in this study, it appears that niche partitioning is not necessary for closely related herbivores to stably coexist on shared hosts. Co-occurrence without resource partitioning may provide an additional axis along which herbivorous insects attain increased species richness.

ecology↗