Data from: Phylogeny of haemosporidian blood parasites revealed by a multi-gene approach

The apicomplexan order Haemosporida is a clade of unicellular blood parasites that infect a variety of reptilian, avian and mammalian hosts. Among them are the agents of human malaria, parasites of the genus Plasmodium, which pose a major threat to human health. Illuminating the evolutionary history of Haemosporida may help us in understanding their enormous biological diversity, as well as tracing the multiple host switches and associated acquisitions of novel life-history traits. However, the deep-level phylogenetic relationships among major haemosporidian clades have remained enigmatic because the datasets employed in phylogenetic analyses were severely limited in either gene coverage or taxon sampling. Using a PCR-based approach that employs a novel set of primers, we sequenced fragments of 21 nuclear genes from seven haemosporidian parasites of the genera Leucocytozoon, Haemoproteus, Parahaemoproteus, Polychromophilus and Plasmodium. After addition of genomic data from 25 apicomplexan species, the unreduced alignment comprised 20,580 bp from 32 species. Phylogenetic analyses were performed based on nucleotide, codon and amino acid data employing Bayesian inference, maximum likelihood and maximum parsimony. All analyses resulted in highly congruent topologies. We found consistent support for a basal position of Leucocytozoon within Haemosporida. In contrast to all previous studies, we recovered a sister group relationship between the genera Polychromophilus and Plasmodium. Within Plasmodium, the sauropsid and mammal-infecting lineages were recovered as sister clades. Support for these relationships was high in nearly all trees, revealing a novel phylogeny of Haemosporida, which is robust to the choice of the outgroup and the method of tree inference.顶复门（Apicomplexa）血孢子虫目（Haemosporida）是一类单细胞血液寄生虫，可感染爬行类、鸟类与哺乳类等多种宿主。其中包含引发人类疟疾的疟原虫属（Plasmodium）寄生虫，这类病原体对人类健康构成重大威胁。阐明血孢子虫目的演化历史，有助于我们理解其极为丰富的生物多样性，同时亦可追溯其多次宿主转换事件以及伴随产生的全新生活史特征。然而，由于过往系统发育分析所采用的数据集在基因覆盖度或类群采样层面均存在严重局限，血孢子虫主要演化支间的深层系统发育关系长期以来悬而未决。本研究采用一套新型引物建立的聚合酶链式反应（PCR）扩增策略，对来自白细胞孢子虫属（Leucocytozoon）、血变虫属（Haemoproteus）、副血变虫属（Parahaemoproteus）、多孢虫属（Polychromophilus）及疟原虫属（Plasmodium）的7种血孢子虫的21个核基因片段完成了测序。在纳入25种顶复门生物的基因组数据后，未经过删减的序列比对总长达到20580 bp，涵盖32个物种类群。研究分别基于核苷酸、密码子与氨基酸数据，采用贝叶斯推断（Bayesian inference）、最大似然法（maximum likelihood）及最大简约法（maximum parsimony）开展系统发育分析。所有分析得到的拓扑结构高度一致。研究结果一致支持白细胞孢子虫属位于血孢子虫目的基部分支。与此前所有研究结论不同的是，本研究发现多孢虫属与疟原虫属构成姊妹群关系。在疟原虫属内部，感染蜥形类与哺乳类的演化支互为姊妹演化支。几乎所有系统发育树均对上述关系提供了高支持度，表明本研究得到的血孢子虫目全新系统发育关系不受外类群选择与树推断方法的影响，具备较强稳健性。