Polyploidy—whole genome duplication—is common in plants. Studies over the last several decades have documented numerous mixed-ploidy populations. Whether arising via recurrent whole genome duplication events within a population, or from secondary contact, the persistence of mixed populations is possible by niche differentiation. Specifically, one mechanism facilitating ploidy co-occurrence is microbially-mediated niche differentiation (MMND), wherein cytotypes occupy different niches via interactions with different sets of microbes. Inherently cryptic, MMND is underexplored in polyploid plant populations. Here, we search for evidence of MMND in creosotebush (Larrea tridentata), a dominant desert shrub of the southwestern U.S. and northern Mexico. We sequenced root-associated fungal taxa in soil diploid, autotetraploid, and autohexaploid plants growing in two naturally-occurring mixed-cytotype populations. Within populations, we found substantial fungal assemblage overlap across host plant cytotypes. However, using indicator species analysis, we identified some fungi that are differentiated by host plant cytotype, satisfying a precondition for MMND. Future study is needed to determine the degree of niche differentiation conferred, if any, and whether the identified fungi play a role in the long-term persistence of multiple cytotypes within populations.

These data come from root-associated soils from 50+ Larrea tridentata of various ploidies collected in mixed-ploidy populations. DNA was extracted and fungal ITS amplifed and sequenced. The data has been cleaned to be a list of fungal OTUs and the scripts further filter out none fungal OTUs.

All scripts can be run using Rstudio and .txt files can be read with any text editor.