Ecological divergence is marked by species specific plastic gene expression and distinct rhizosphere among sibling allopolyploid marsh orchids (Dactylorhiza)

Abstract

AbstractPhenotypic plasticity, the dynamic adjustment of traits to environmental variations, is pivotal to enabling species to exploit broader niches and withstand suboptimal conditions. This adaptability is expected to be particularly relevant for newly formed allopolyploids, which have redundant gene copies and must establish themselves in diverse environments, distinct from their parents and other relatives.Here we investigate ecologically divergent sibling allopolyploid marsh orchids (Dactylorhiza) through reciprocal transplantation experiments at two localities to understand the drivers of ecological divergence and species persistence in the face of interspecific gene flow.Although consistent abiotic differences characterise the alternative environments, the great majority of gene expression differences between the sibling allopolyploids is plastic. Few genes exhibit fixed expression differences, suggesting that despite ecological divergence, plasticity may mediate gene flow between sibling allopolyploids, thereby preventing differentiation. Extending our investigations to the rhizosphere, we uncover a much more diverse root mycobiome for either species when growing in the environment with nutrient-poor soils.Our finding suggests that both biotic and abiotic factors contribute to the distribution and delimitation ofDactylorhizasibling allopolyploids. Altogether, our results indicate that plasticity can simultaneously promote diversification and homogenization of lineages, influencing the establishment and persistence of recurrently formed allopolyploid species.Plain language summaryA duplicated genome can enhance plasticity in polyploids, widening their environmental tolerance, but the long term effects of this plasticity remain unclear. Studying ecologically distinct marsh orchids, we show that sibling allopolyploids exhibit high plasticity with only very few fixed transcriptomic differences. Instead, we observe divergent mycobiomes associated with each orchid’s environment, revealing a complex interplay in polyploid speciation.