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 ~110,000 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（PCE，Preponderant Clonal Evolution）提出，诸多具备有性重组能力的病原体中频繁发生的克隆繁殖（两个克隆体间的有性交配）会引发强烈的连锁不平衡，以及以偶发基因流为特征的离散遗传分化类群的形成。本研究对该假说进行拓展，预测更高的克隆繁殖速率将催生三类特征：（1）形态隐存种；（2）较低的种内变异水平；（3）较近的种间分化时间。我们以加勒比蜥蜴疟原虫（Plasmodium floridense）为研究材料，采集了覆盖该病原体分布全域的63份蜥蜴单感染样本，对其2个线粒体基因、1个顶质体（apicoplast）基因以及5个核基因进行测序。我们在P. floridense中共鉴定出11个暂定隐存种，每个类群均表现出较低的种内变异以及较近的种间分化时间（部分类群的分化时间约为11万年前）。本研究结果与"克隆繁殖可显著影响具备有性重组能力的物种的分化进程"这一假说一致，并表明克隆繁殖可能催生了大量未被识别的病原体物种。目前尚不清楚调控病原体克隆繁殖速率的具体因素，本文还探讨了流行率与毒力如何与克隆繁殖产生关联。