# A microbial view on secondary contact between two Alpine butterflies

## TL;DR

This study explores how gut microbes differ between two closely related Alpine butterflies, suggesting they help define ecological niches during secondary contact.

## Contribution

The study introduces gut microbial communities as a novel proxy for biotic niche differentiation in secondary contact zones.

## Key findings

- Gut microbial communities significantly differ between the two butterfly species but not between sexes.
- The abundance of Wolbachia, a heritable endosymbiont, varies between species and suppresses the diversity of other microbes.
- Microbial communities on nectar plants partially overlap with those in butterflies, indicating partial environmental filtering.

## Abstract

Widespread sympatry between sibling species can be limited if they are ecologically too close, potentially leading to the formation of narrow zones of secondary contact. While the ecological niche is commonly estimated using abiotic factors, the potential differentiation in gut microbial communities as a proxy for biotic niche differentiation is less well studied. We address this gap in research, focusing on two Alpine butterfly species of the genus Erebia that form a stable and very narrow contact zone.

Using a metabarcoding approach to sequence the adult gut microbial communities of our two focal species as well as capturing the microbial diversity found on three nectar plant species, we found that the microbial community i) significantly differed between species but not between sexes, that ii) the abundance of the heritable endosymbiont Wolbachia differed between species, where its high abundance resulted in the detection of fewer other microbial taxa, and that iii) microbes found on flowers largely but not completely overlapped with the ones found in the butterfly hosts, suggesting that intestinal environmental filtering occurs only to some degree.

Consistent with biotic niche differentiation, we uncovered species specific differences in the gut microbial communities, further highlighting the complex interactions between host biology and environmental factors in shaping the gut microbiota. The observed microbial differences could reflect local adaptation to different resources or microhabitats. Overall, our study highlights the utility of gut microbial metabarcoding to study ecological niche differentiation, also during secondary contact.

The online version contains supplementary material available at 10.1186/s12862-026-02503-1.