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.

种群遗传标记（population genetic markers）正日益被用于研究虫黄藻属（Symbiodinium）的多样性、生态学与演化——该类群为一类真核微生物，通常与造礁珊瑚形成互利共生关系。种群遗传标记可从宿主组织样本中区分单个克隆或株系，但样本中可能包含不同物种，这会干扰对基因流（gene flow）与遗传结构（genetic structure）的解读结果。本文提出一种基于遗传重组检测的方法，可从种群遗传数据中区分物种。在开展后续分析前，将个体划归至发生遗传重组的种群，可避免基因流与扩散（dispersal）解读中的关键性误差。为验证本方法的有效性，我们首先将其应用于模拟数据集（simulated dataset）。随后利用该方法对两种宿主泛化型虫黄藻属物种进行区分，这类物种常见于采自印度-西太平洋（Indo-West Pacific）礁区的造礁珊瑚样本中。研究证实，即便部分宿主携带两种不同物种的基因型（genotype），本方法依然具备稳健性。最后，我们分析了发表于《分子生态学》（Molecular Ecology）的两篇近期论文中的种群遗传数据集。结果显示，两篇数据集均强烈支持双物种解读结论，这显著修正了两项研究原本的研究结论。结合现有系统发育（phylogenetic）与生态学证据，利用种群遗传数据可为明确界定形态隐存种（morphologically cryptic species）提供一种稳健的研究方法。