Data from: Genomic sequence capture of haemosporidian parasites: methods and prospects for enhanced study of host-parasite evolution

Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus,
and Leucocytoozoon) represent an exciting multi-host, multi-parasite
system in ecology and evolution. Global research in this field accelerated
after 1) the publication in 2000 of PCR protocols to sequence a
haemosporidian mitochondrial (mtDNA) barcode, and 2) the development in
2009 of an open-access database to document the geographic and host ranges
of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from
bird hosts, however, has been technically challenging, slowing the
transition to genomic-scale sequencing techniques. We extend a
recently-developed sequence capture method to obtain hundreds of
haemosporidian nuclear loci from wild bird samples, which typically have
low levels of infection, or parasitemia. We tested 51 infected birds from
Peru and New Mexico and evaluated locus recovery in light of variation in
parasitemia, divergence from reference sequences, and pooling strategies.
Our method was successful for samples with parasitemia as low as ~0.02% (2
of 10,000 blood cells infected) and mtDNA divergence as high as 15.9% (one
Leucocytozoon sample), and using the most cost-effective pooling strategy
tested. Phylogenetic relationships estimated with >300 nuclear loci
were well resolved, providing substantial improvement over the mtDNA
barcode. We provide protocols for sample preparation and sequence capture
including custom probe sequences, and describe our bioinformatics pipeline
using aTRAM 2.0, PHYLUCE, and custom Perl/Python scripts. This approach
can be applied to thousands of avian samples that have already been found
to have haemosporidian infections of at least moderate intensity, greatly
improving our understanding of parasite speciation, biogeography, and
evolutionary dynamics.