Population structure shapes copy number variation in malaria parasites. Plasmodium falciparum

If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in 7 countries in Africa, SE Asia and S. America using a high density SNP/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500bp to 59kb, as well as 10,107 flanking, biallelic SNPs. Overall, CNVs were rare, small and skewed towards low frequency variants, consistent with the deleterious model. Relative to African and SE Asian populations, CNVs were significantly more common in S. America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g. DNA helicase, and 3 conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen. Overall design: SNP/CGH hybridisation of 175 malaria parasite samples

若拷贝数变异（copy number variants, CNVs）大多为有害型，那么我们可以预期，相较于有效种群大小（effective population size, Ne）较小的种群，这类变异会在有效种群较大的种群中被更高效地清除。
恶性疟原虫（Plasmodium falciparum）为验证这一预测提供了绝佳的研究模型：该原生动物在单一物种种群内展现出广泛的种群结构谱系——非洲地区存在规模庞大且稳定的远交种群，南美洲地区则为规模较小且不稳定的近交种群，东南亚地区的种群特征则介于两者之间。
本研究使用高密度单核苷酸多态性（single nucleotide polymorphism, SNP）/拷贝数变异微阵列，对来自非洲、东南亚及南美洲7个国家的疟疾病患者体内的122株未经过预先实验室培养的单克隆疟原虫进行了特征分析。
我们在该疟原虫的外显子组中共鉴定出134个高可信度CNVs，其中包括33个缺失变异与102个扩增变异，变异片段长度介于小于500bp至59kb之间；同时还鉴定出10107个侧翼双等位基因SNPs。
整体而言，CNVs呈现出稀有性、片段短小且偏向低频变异的特征，这与有害变异模型的预期相符。
与非洲及东南亚种群相比，南美洲种群中的CNVs出现频率显著更高，等位基因频率的偏移程度显著更低，且变异片段长度显著更长。
在CNVs整体为低频变异的背景下，我们通过FST离群值分析，还鉴定出数个处于推测正选择作用下的高频CNVs。
这些高频CNVs包括已知的适应性CNVs（携带rh2b与pfmdr1基因），以及另外数个有待进一步研究的CNVs（例如DNA解旋酶编码基因及3个保守蛋白编码基因所在的变异区域）。
本研究的数据表明，种群遗传结构对这一重要人类病原体的CNV负荷具有显著影响。
实验整体设计：对175株疟原虫样本进行SNP/比较基因组杂交（comparative genomic hybridization, CGH）分析。