# Large-scale environmental DNA survey reveals niche axes of a regional coastal fish community

## TL;DR

This study uses environmental DNA data to uncover hidden ecological niches shaping the distribution of coastal fish in Japan, revealing how ocean currents influence biodiversity patterns.

## Contribution

The study identifies hidden niche axes in a large coastal fish community using eDNA data and species distribution modeling.

## Key findings

- The hidden niche axes explained most of the variation in fish biodiversity and revealed five biogeographic boundaries.
- Response diversity to niche axes was positively correlated with species richness but was geographically biased.
- Niche axes are likely influenced by ocean currents, including environmental filters and dispersal barriers.

## Abstract

The concept of the ecological niche, defined as the basic habitat requirements for a species, is central to understanding species geographic distributions and predicting their responses to environmental change. However, identifying the essential niche for large regional communities remains a challenge because niche axes can be “hidden” by the complexity of the underlying ecological processes. Here, applying advanced species distribution modelling to nationwide environmental DNA survey data, we identified hidden niche axes of the Japanese coastal fish community and investigated the response diversity to these axes. Our survey detected 1,220 coastal fish species. The hidden niche axes collectively explained most of the variation in fish biodiversity and revealed five biogeographic boundaries for the regional community. These niches of the Japanese fish community may primarily relate to several processes due to ocean currents, such as environmental filters, transport from source areas and dispersal barriers. We also found that the response diversity to niche axes was positively correlated with species richness, although local communities with particularly high response diversity were geographically biased. A better understanding of the niche axes of the regional ecological community should help to mitigate the loss of biodiversity and ecosystem services caused by ongoing environmental change.

The online version contains supplementary material available at 10.1038/s41598-025-31307-4.