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.