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、生态学特征与演化历程——该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出单个克隆株或菌株，但样本中可能包含不同物种，这会干扰基因流与遗传结构的解读结果。为此，我们提出一种基于遗传重组（genetic recombination）检测的方法，可从种群遗传数据中区分物种。在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模式解读中的关键误差。为验证该方法的有效性，我们首先将其应用于模拟数据集。随后，我们利用该方法区分了两类常见共生于印度-西太平洋海域造礁珊瑚中的宿主泛化型虫黄藻属物种。实验结果表明，即便部分宿主体内同时存在两种不同物种的基因型，该方法依然具备稳健性。最后，我们针对《分子生态学（Molecular Ecology）》期刊近期发表的两篇论文中的种群遗传数据集展开分析。分析结果显示，两类数据集均强烈支持双物种假说，这一结论极大修正了两项研究的原有推断。结合现有系统发育与生态学证据，种群遗传数据的应用可为形态隐存种的明确界定提供一种稳健可靠的方法。