10.5061/DRYAD.66F8C
Wham, Drew C.
Pennsylvania State University
LaJeunesse, Todd C.
Pennsylvania State University
Data from: Symbiodinium population genetics: testing for species
boundaries and analyzing samples with mixed genotypes
Dryad
dataset
2015
2015-11-12T16:57:14Z
2015-11-12T16:57:14Z
en
https://doi.org/10.1111/mec.13623
286944 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
Simulated.dataS1Simulated species 1 data, input to simulation R
fileSimulated.dataS2Simulated species 2 file to input into R Simulation
fileSimulating dataR script for processing the pure simulated genotypes
into mixed sexual and clonal samples as would be sampled naturallyfdataraw
unprocessed output of Simulated data processing script with mixed
MLGsSimulated dataData processing of simulated dataC1and3Processed
Symbiodinium C1 and C1 dataHowellsetal2013Presence/absence file from
Howells et al. 2013 processed into a list of alleles observed in each
sample used to create Figure 4Wirshingetal 2013 PartitionedData from
Wirshing et al. 2013 after partitioning into the two species ( Figure 5c)