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Microbiome and epigenetic variation in wild fish with low genetic diversity
Journal article   Open access   Peer reviewed

Microbiome and epigenetic variation in wild fish with low genetic diversity

Ishrat Z. Anka, Tamsyn M. Uren Webster, Waldir M. Berbel-Filho, Matthew Hitchings, Benjamin Overland, Sarah Weller, Carlos Garcia de Leaniz and Sofia Consuegra
Nature communications, Vol.15, 4725
06/03/2024
DOI: https://doi.org/10.1038/s41467-024-49162-8
PMID: 38830879
Web of Science ID: WOS:001238270100008

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Abstract

Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity. Species with low genetic diversity have limited capacity to adapt to environmental change. This study finds that the skin microbiome and non-genetic (epigenetic) modifications of the DNA represent additional sources of variation that could help low diversity fish survive environmental challenges.
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