Biology subjects

Fukaya, K.

Publications and source records attributed to Fukaya, K..

6 recordsLinked to original sources

bioRxiv2025

occumb: An R package for site occupancy modeling of eDNA metabarcoding data

Environmental DNA (eDNA) metabarcoding has become an increasingly popular method for the rapid assessment of species distribution and diversity. However, the detection of DNA sequences of species in eDNA metabarcoding is not flawless; thus, accounting for potential false negatives (nondetection of DNA sequences of existing species) is crucial for the effective implementation of eDNA-based monitoring and research. This study introduces the occumb R package, which was developed to facilitate the easy and flexible application of community site occupancy modeling for eDNA metabarcoding that accounts for the imperfect detection of DNA sequences of species. The package provides functions for specifying models using the formula syntax, Bayesian model fitting using Markov chain Monte Carlo (MCMC), posterior inferences, and model assessments and exploring optimal study settings based on the fitted model. A case study of eDNA metabarcoding on riverine aquatic insects is illustrated using the occumb package, emphasizing the importance of ensuring biological replicates in achieving reliable species detection in eDNA metabarcoding. By making complex community site occupancy models easily accessible to users, we hope that the development of the occumb package will promote eDNA metabarcoding applications for the accurate assessment of species distribution and diversity.

ecology↗

bioRxiv2023

Interstage flow matrices: population statistic derived from matrix population models

O_LIMany population statistics describe the characteristics of populations within and among species. These are useful for describing population dynamics, understanding how environmental factors alter demographic patterns, testing hypotheses related to the evolution of life history characteristics, and informing the effective management of populations. C_LIO_LIIn this study, we propose a population statistic: the interstage flow. The interstage flow is defined as the product of the element in the ith row, the jth column of the population projection matrix, and the jth element of the normalized stable stage distribution. C_LIO_LIThe sum of the interstage flow matrix elements is equal to the population growth rate, which is the dominant eigenvalue of the population projection matrix. The interstage flow matrix elements allow decomposition of population growth rate into component contributions made by transitions between developmental stages. C_LIO_LIWe demonstrate the utility of interstage flow matrices using matrix population models from the COMPADRE plant matrix database. We compared interstage flows among four life history/functional groups (semelparous herbs, iteroparous herbs, shrubs, and trees) and described how population growth rate reflected individual transitions related to stasis, fecundity, and growth. We found that the individual flows are different among functional groups. C_LIO_LISynthesis: The proposed population statistic, the interstage flow matrix, describes the contribution of individual developmental stage transitions to the population growth rate. The flow of individuals between developmental stages differs in distinctive ways among different life histories and functional groups. The interstage flow matrix is a valuable statistic for describing these differences. C_LI

ecology↗

bioRxiv2022

Albatrosses employ orientation and routing strategies similar to yacht racers

The way goal-oriented birds adjust their travel direction and route in response to wind significantly affects their travel costs. This is expected to be particularly pronounced in pelagic seabirds, which utilize a wind-dependent flight style called dynamic soaring. Dynamic soaring seabirds in situations without a definite goal, e.g. searching for prey, are known to preferentially fly with tail-to-side winds to increase the speed and search area, and reduce travel costs. However, little is known about their reaction to wind when heading to a definite goal, such as homing. Homing tracks of wandering albatrosses (Diomedea exulans) vary from beelines to zigzags, which are similar to those of sailboats. Here, given that both albatrosses and sailboats travel slower in headwinds and tailwinds, we tested whether the time-minimizing strategies used by yacht racers can be compared to the locomotion patterns of wandering albatrosses. We predicted that when the goal is located upwind or downwind, albatrosses should deviate their travel directions from the goal on the microscale and increase the number of turns on the macroscale. Both hypotheses were supported by track data from albatrosses and racing yachts in the Southern Ocean confirming that albatrosses qualitatively employ the same strategy as yacht racers. Nevertheless, albatrosses did not strictly minimize their travel time, likely making their flight robust against wind fluctuations to reduce flight costs. Our study provides the first empirical evidence of tacking in albatrosses and demonstrates that man-made movement strategies provide a new perspective on the laws underlying wildlife movement.

animal behavior and cognition↗

bioRxiv2021

Multispecies site occupancy modeling and study design for spatially replicated environmental DNA metabarcoding

O_LIEnvironmental DNA (eDNA) metabarcoding has become widely applied to gauge biodiversity in a noninvasive and cost-efficient manner. The detection of species using eDNA metabarcoding is, however, imperfect owing to various factors that can cause false negatives in the inherent multi-stage workflow. C_LIO_LIImperfect detection in the multi-stage workflow of eDNA metabarcoding also raises an issue of study design: namely, how available resources should be allocated among the different stages to optimize survey efficiency. C_LIO_LIHere, we propose a variant of the multispecies site occupancy model for eDNA metabar-coding studies where samples are collected at multiple sites within a region of interest. This model describes the variation in sequence reads, the unique output of the high-throughput sequencers, in terms of the hierarchical workflow of eDNA metabarcoding and interspecific heterogeneity, allowing the decomposition of the sources of variation in the detectability of species throughout the different stages of the workflow. We also introduced a Bayesian decision analysis framework to identify the study design that optimizes the efficiency of species detection with a limited budget. C_LIO_LIAn application of the model to freshwater fish communities in the Lake Kasumigaura watershed, in Japan, highlighted a remarkable inhomogeneity in the detectability of species, indicating a potential risk of the biased detection of specific species. Species with lower site occupancy probabilities tended to be difficult to detect as they had lower capture probabilities and lower dominance of the sequences. The expected abundance of sequence reads was predicted to vary by up to 23.5 times between species. C_LIO_LIAn analysis of the study design suggested that ensuring multiple within-site replications of the environmental samples is preferred in order to achieve better species detection efficiency, provided that a throughput of tens of thousands of sequence reads was secured. C_LIO_LIThe proposed framework makes the application of eDNA metabarcoding more error-tolerant, allowing ecologists to monitor ecological communities more efficiently. C_LI

ecology↗

bioRxiv2018

Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling

We propose a general framework of abundance estimation based on spatially replicated quantitative measurements of environmental DNA in which production, transport, and degradation of DNA are explicitly accounted for. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. These findings indicate the ability of environmental DNA to reliably reflect population abundance of aquatic macroorganisms and may o[ff]er a new avenue for population monitoring based on the fast, cost-e[ff]ective, and non-invasive sampling of genetic information.

ecology↗

bioRxiv2018

Macroscale estimates of species abundance reveal evolutionary drivers of biodiversity

Evolutionary processes underpin the biodiversity on the planet. Theories advocate that the form of the species abundance distribution (SAD), presented by the number of individuals for each species within an ecological community, is intimately linked to speciation modes such as point mutation and random fission. This prediction has rarely been, however, verified empirically; the fact that species abundance data can be obtained only from local communities critically limits our ability to infer the role of macroevolution in shaping ecological patterns. Here, we developed a novel statistical model to estimate macroscale SADs, the hidden macroecological property, by integrating spatially replicated multispecies detection-nondetection observations and the data on species geographic distributions. We determined abundance of 1,248 woody plant species at a 10 km grid square resolution over East Asian islands across subtropical to temperate biomes, which produced a metacommunity (i.e. species pool) SAD in four insular ecoregions along with its absolute size. The metacommunity SADs indicated lognormal-like distributions, which were well explained by the unified neutral theory of biodiversity and biogeography (UNTB) with protracted speciation, a mode of speciation intermediate between point mutation and random fission. Furthermore, the analyses yielded an estimate of speciation rate in each region that highlighted the importance of geographic characteristics in macroevolutionary processes and predicted the average species lifetime that was congruent with previous estimates. The estimation of macroscale SADs plays a remarkable role in revealing evolutionary diversification of regional species pools.

ecology↗