Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK.
Department of Aquaculture, Chattogram Veterinary and Animal Sciences University, Chattogram, 4225, Bangladesh.
Nat Commun. 2024 Jun 3;15(1):4725. doi: 10.1038/s41467-024-49162-8.
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.
表型变异的非遗传来源，如表观基因组和微生物组，可能是遗传多样性低的物种适应变异的重要贡献者。然而，人们对这些因素与宿主遗传多样性之间的复杂相互作用知之甚少，特别是在野生种群中。在这里，我们研究了在同域和异域条件下两种具有不同交配系统（自交和杂交）的亲缘关系密切的红树林食蚊鱼的皮肤微生物组组成。这使我们能够将基因型和环境对其微生物组和（先前描述的）表观遗传特征的影响分开。我们发现皮肤微生物组的多样性和群落组成主要受环境影响，其次受物种特异性影响。杂合性和微生物组α多样性，但不是表观遗传变化，与与表现（视觉）和行为（攻击性）相关的性状的波动不对称相关。我们的研究表明，一部分表观遗传多样性和微生物组分化与遗传变异无关，并且我们在这些野生种群中发现了微生物组和表观遗传多样性之间关联关系的证据。这表明这两种机制都可能有助于遗传多样性低的物种的变异。
