Study sites and overall dynamics of environmental DNA (eDNA) concentrations and the number of fish species detected.

(a) Study sites in the Boso Peninsula. The study sites are influenced by the Kuroshio current (red arrow; left panel) and distributed along the coastal line in the Boso Peninsula (right panel). (b) Total eDNA copy numbers estimated by quantitative eDNA metabarcoding (see Methods for detail). (c) Fish species richness detected by eDNA metabarcoding. Points and lines indicate raw values and LOESS smoothing lines, respectively. The line color indicates the sampling site. Warmer colors generally correspond to study sites with a higher mean water temperature.

Primer sequences used in the present study

Interaction networks of the fish community in the Boso Peninsula coastal region.

The “average” interaction network reconstructed by quantifying information transfer between eDNA time series. Transfer entropy (TE) was quantified by leveraging all eDNA time series from multiple study sites to draw this network. Only information flow larger than 80% quantiles (i.e., strong interaction) was shown as interspecific interactions for visualization. The edge color indicates scaled transfer entropy values, and fish illustration colors represent their ecology (e.g., habitat and feeding behavior). Node colors and node sizes indicate the fish family and fish abundance (total eDNA copy numbers of the fish species), respectively.

Dependence of interaction strengths on biotic and abiotic variables (50 dominant fish species and 11 study sites were leveraged).

The panels show the overall effects of biotic and abiotic variables on interaction strengths of the 50 dominant fish species: Effects of (a, d) water temperature, (b, e) species richness, and (c, f) total eDNA copy numbers. The Y-axis indicates the effects of the variables on fish-fish interaction strengths quantified by the MDR S-map method. a–c show the effects on the species interactions that a focal species receives (i.e., In-strength), and d–f show the effects on the species interactions that a focal species gives (i.e., Out-strength). The line indicates the average effects estimated by the general additive model (GAM), and the grey region indicates 95% confidential intervals. LME and GAM indicate the statistical clarity of the linear mixed model portion and GAM portion, respectively. Detailed statistical results and raw data are shown in Table S4 and Fig. S5, respectively.

Temperature dependence of fish species interactions at the species level.

a and b show temperature effects on fish species interactions quantified by the MDR S-map method. Note that the MDR S-map enables quantifications of interaction strengths at each time point, and thus the number of data points is large. (a) Points indicate the species interactions that a focal species (indicated by the strip label and fish image) receives (i.e., In-strength). (b) Points indicate the species interactions that a focal species (indicated by the strip label and fish image) gives (i.e., Out-strength). For a and b, only fish species of which interactions are statistically clearly affected by water temperature are shown (to exclude fish species with relatively weak temperature effects, P < 0.0001 was used as a criterion here). Point color indicates the study site. Gray line is drawn by GAM (the study sites were averaged for visualization purpose).