Data from: Clonal reproduction shapes evolution in the lizard malaria parasite Plasmodium floridense

The preponderant clonal evolution hypothesis (PCE) predicts that frequent clonal reproduction (sex between two clones) in many pathogens capable of sexual recombination results in strong linkage disequilibrium and the presence of discrete genetic subdivisions characterized by occasional gene flow. We expand on the PCE and predict that higher rates of clonal reproduction will result in: (1) morphologically cryptic species that exhibit (2) low within-species variation and (3) recent between-species divergence. We tested these predictions in the Caribbean lizard malaria parasite Plasmodium floridense using 63 single-infection samples in lizards collected from across the parasite's range, and sequenced them at two mitochondrial, one apicoplast, and five nuclear genes. We identified 11 provisionally cryptic species within P. floridense, each of which exhibits low intraspecific variation and recent divergence times between species (some diverged ∼110000 years ago). Our results are consistent with the hypothesis that clonal reproduction can profoundly affect diversification of species capable of sexual recombination, and suggest that clonal reproduction may have led to a large number of unrecognized pathogen species. The factors that may influence the rates of clonal reproduction among pathogens are unclear, and we discuss how prevalence and virulence may relate to clonal reproduction.

优势克隆进化假说（Preponderant Clonal Evolution, PCE）预测，在诸多具备有性重组（sexual recombination）能力的病原体中，高频的克隆繁殖（clonal reproduction，即两个克隆个体间的有性生殖）会产生强烈的连锁不平衡（linkage disequilibrium），并形成以偶发基因流动为特征的离散遗传亚群。我们对该假说进行了拓展，提出更高的克隆繁殖率将带来三类特征：（1）形态上隐蔽的物种（cryptic species）；（2）较低的种内变异（intraspecific variation）水平；（3）较近的种间分化时间。我们以加勒比地区的蜥蜴疟原虫——佛罗里达疟原虫（Plasmodium floridense）为研究对象，利用采集自该寄生虫整个分布范围的63份蜥蜴单感染样本对上述预测进行验证，并对其2个线粒体基因（mitochondrial gene）、1个顶质体（apicoplast）基因以及5个核基因（nuclear gene）进行了测序。我们在佛罗里达疟原虫中共鉴定出11个暂定隐蔽物种，每个物种均表现出较低的种内变异，且物种间分化时间较近（部分物种的分化时间约为11万年前）。我们的研究结果与“克隆繁殖可深刻影响具备有性重组能力的物种的物种多样化过程”这一假说相符，并提示克隆繁殖可能催生了大量未被识别的病原体物种。目前尚不明确影响病原体克隆繁殖率的具体因素，我们还讨论了流行率（prevalence）与毒力（virulence）如何与克隆繁殖相关联。