DOI: 10.5061/dryad.72fg9
title: Data from: Phylogeny of haemosporidian blood parasites revealed by a multi-gene approach

description: 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.
description: Single gene amino acid
 alignments of the 21 nuclear genesFasta files containing
 the single amino acid nucleotide alignments of the 21 nuclear genes. The
 alignments were created using MAFFT L-INS-i v7.013.single_genes_aa.zipSingle gene amino acid alignments of the 21 nuclear genes Glocks processedFasta files containing the single gene amino acid alignments of the 21 nuclear genes after processing by Gblocks 0.91b (allowing for smaller final blocks, gap positions within the final blocks, and less strict flanking positions).single_genes_aa_gblocks.zipSingle gene nucleotide alignments of the 21 nuclear genesFasta files containing the single gene nucleotide alignments of the 21 nuclear genes. The nucleotide (codon) alignments are based on the amino acid alignments.single_genes_codons.zipSingle gene nucleotide alignments of the 21 nuclear genes Glocks processedFasta files containing the single gene nucleotide alignments of the 21 nuclear genes after processing by Gblocks. The nucleotide (codon) alignments are based on the Gblocks processed amino acid alignments.single_genes_codons_gblocks.zipSingle gene nucleotide alignments of the combined datasetFasta files containing the single gene nucleotide alignments comprising data for five genes from the studies of Martinsen et al. (2008), Schaer et al. (2013) and Borner et al. (2015).single_genes_martinsen_schaer_borner_combined.zipConcatenated multigene aignmentsFasta files containing the concatenated multigene aignments of the datasets listed in Supplemental Table S4.super_alignments.zipreadme