Data from: Symbiodinium population genetics: testing for species boundaries and analyzing samples with mixed genotypes

Population genetic markers are increasingly being used to study the diversity, ecology, and evolution of Symbiodinium, a group of eukaryotic microbes that are often mutualistic with reef-building corals. Population genetic markers can resolve individual clones, or strains, from samples of host tissue, however samples may comprise different species that may confound interpretations of gene flow and genetic structure. Here we propose a method for resolving species from population genetic data using tests of genetic recombination. Assigning individuals to genetically recombining populations prior to further analyses avoids critical errors in the interpretation of gene flow and dispersal. To demonstrate the effectiveness of the approach we first apply this method to a simulated dataset. We then use the method to resolve two species of host-generalist Symbiodinium that commonly co-occur in reef-building corals collected from Indo-West Pacific reefs. We demonstrate that the method is robust even when some hosts contain genotypes of two distinct species. Finally, we examine population genetic datasets from two recently published papers in Molecular Ecology. We show that each strongly supports a two species interpretation, which significantly changes the original conclusions presented in these studies. When combined with available phylogenetic and ecological evidence, the use of population genetic data offers a robust method for unambiguously delimiting morphologically cryptic species