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Biology subjects

Kondoh, M.

Publications and source records attributed to Kondoh, M..

6 recordsLinked to original sources
bioRxiv2025

Shifts in spring migration phenology are greater in northern wintering species

Climate change is significantly affecting animal distributions and phenology, with migratory birds experiencing notable shifts in migration timing. There are complexities to changes in migration timing, considering variations due to monitoring locations or definitions of migration timing. Previous studies have focused on differences between traits in the magnitude of change and agreed that migration distance has an effect, although distribution has not been considered. This study investigates the factors influencing phenological changes in spring migration, focusing on First Arrival Date (FAD) and Last Departure Date (LDD) in eastern Japan. Using community science data from Sendai and Tokyo, we examine the effects of species characteristics, including trophic level, migration distance, and breeding and wintering areas, in addition to climatic variables. Consistent with other studies, FAD was advanced and LDD was delayed with climate. Notably, the magnitude of change in FAD differed depending on the distribution of wintering areas. Birds use many areas during their life cycle, and our results suggest that distribution, as a simple indicator, may be key to predicting responses to climate change.

animal behavior and cognition↗
bioRxiv2020

A model ecosystem of twelve cryopreservable microbial species allowing for a non-invasive approach

Simultaneous understanding of both individual and ecosystem dynamics is crucial in an era marked by the degradation of ecosystem services. Herein, we present a high-throughput synthetic microcosm system comprising 12 functionally and phylogenetically diverse microbial species. These species are axenically culturable, cryopreservable, and can be measured noninvasively via microscopy, aided by machine learning. This system includes prokaryotic and eukaryotic producers and decomposers, and eukaryotic consumers to ensure functional redundancy. Our model system displayed both positive and negative interspecific interactions and higher-order interactions that surpassed the scope of any two-species interaction. Although complete species coexistence was not our primary objective, we identified several conditions under which at least one species from the producers, consumers, and decomposers groups, and one functionally redundant species, persisted for over six months. These conditions set the stage for detailed investigations in the future. Given its designability and experimental replicability, our model ecosystem offers a promising platform for deeper insights into both individual and ecosystem dynamics, including evolution and species interactions.

microbiology↗
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

Evolutionary stability of plant-pollinator networks: efficient communities, hysteresis, and a pollination dilemma

Mutualistic interactions between species such as pollination and plant-mycorrhiza interactions are ubiquitous in nature and essential for ecosystem functioning. Often dozens or even hundreds of species with different degree of specialization form complex networks of interdependence. How the complexity evolved and is maintained are fundamental questions in ecology. Here, we present a new game theoretical approach to model complex mutualistic interactions, which we apply to pollination networks. The theoretical analysis revealed multiple evolutionary stable network structures that form a gradient from generalism toward specialism with increasing availability of pollination service. In particular, we found that efficient communities evolve only under pollination oversupply, but that pollination shortage selects for inefficient network structures due to a pollination dilemma. These results suggest that availability of pollination services is a key factor structuring pollination networks and offer a new explanation for the geographical differences in pollination faunas that have long been recognized by ecologists. The study bridges the gap between network studies, game theory, and the natural history of pollination, which have hitherto been studied largely independently.

ecology↗
bioRxiv2017

Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing

Effective ecosystem conservation and resource management require quantitative monitoring of biodiversity, including accurate descriptions of species composition and temporal variations of species abundance. Therefore, quantitative monitoring of biodiversity has been performed for many ecosystems, but it is often time- and effort-consuming and costly. Recent studies have shown that environmental DNA (eDNA), which is released to the environment from macro-organisms living in a habitat, contains information about species identity and abundance. Thus, analyzing eDNA would be a promising approach for more efficient biodiversity monitoring. In the present study, we added internal standard DNAs (i.e., known amounts of short DNA fragments from fish species that have never been observed in a sampling area) to eDNA samples, which were collected weekly from a coastal marine ecosystem in Maizuru-Bay, Kyoto, Japan (from April 2015 to March 2016), and performed metabarcoding analysis using Illumina MiSeq to simultaneously identify fish species and quantify fish eDNA copy numbers. A correction equation was obtained for each sample using the relationship between the number of sequence reads and the added amount of the standard DNAs, and this equation was used to estimate the copy numbers from the sequence reads of non-standard fish eDNA. The calculated copy numbers showed significant positive correlation with those determined by quantitative PCR, suggesting that eDNA metabarcoding with standard DNA enabled useful quantification of eDNA. Furthermore, for samples that show a high level of PCR inhibition, our method might allow more accurate quantification than qPCR because the correction equations generated using internal standard DNAs would include the effect of PCR inhibition. A single run of Illumina MiSeq produced > 70 quantitative fish eDNA time series in our study, showing that our method could contribute to more efficient and quantitative monitoring of biodiversity.

ecology↗