High Local Diversity of <i>Trypanosoma</i> in a Common Bat Species, and Implications for the Biogeography and Taxonomy of the <i>T. cruzi</i> Clade

<div><p>The <i>Trypanosoma cruzi</i> clade is a group of parasites that comprises <i>T. cruzi</i> sensu lato and its closest relatives. Although several species have been confirmed phylogenetically to belong to this clade, it is uncertain how many more species can be expected to belong into this group. Here, we present the results of a survey of trypanosome parasites of the bat <i>Artibeus jamaicensis</i> from the Panamá Canal Zone, an important seed disperser. Using a genealogical species delimitation approach, the Poisson tree processes (PTP), we tentatively identified five species of trypanosomes – all belonging to the <i>T. cruzi</i> clade. A small monophyletic group of three putative <i>Trypanosoma</i> species places at the base of the clade phylogeny, providing evidence for at least five independent colonization events of these parasites into the New World. <i>Artibeus jamaicensis</i> presents a high diversity of these blood parasites and is the vertebrate with the highest number of putative trypanosome species reported from a single locality. Our results emphasize the need for continued efforts to survey mammalian trypanosomes.</p></div

Phylogeny of the <i>Trypanosoma cruzi</i> clade.

<p>Maximum likelihood tree constructed with concatenated 18S rRNA and gGAPDH genes. Numbers on the branches represent support values corresponding to bootstrap replicates (right) and Bayesian posterior probabilities (left). Clades highlighted with colored boxes correspond to trypanosomes detected in Panamá. Collapsed branches at the base of the phylogeny indicate low support for the placement of the three Panamian lineages. The symbol//on the branch to the outgroup indicates a shortened branch. GenBank accession numbers of the samples used in this phylogeny are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108603#pone.0108603.s001" target="_blank">Table S1</a>.</p

Putative species delimitation of members of the <i>Trypanosoma cruzi</i> clade.

<p>Maximum likelihood phylogeny with Bayesian support values presented for all 18 lineages recognized as species for the PTP analyses. Monophyletic groups in red indicate a single putative species as well as terminal branches in blue. Names of terminals indicate codes of the samples. Names in bold after a | symbol are taxonomic or geographic identifiers of the putative species. Arrows indicate the 5 putative species found in <i>Artibeus jamaicensis</i> in Panamá.</p

Five independent colonization events of <i>Trypanosoma cruzi</i> clade members to the New World.

<p>Cladogram of species belonging to the <i>Trypanosoma cruzi</i> clade, depicting in red are the branches that indicate dispersal events to the Americas with grey branches denoting the species that are not present in the New World. Note that <i>T. dionisii</i> 2 and <i>T. conorhini</i> are distributed in the New and Old Worlds <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108603#pone.0108603-Hamilton3" target="_blank">[20]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108603#pone.0108603-Hamilton4" target="_blank">[43]</a>. Branch lengths in the cladogram are not proportional to divergence; for branch length estimates refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108603#pone-0108603-g001" target="_blank">Figures 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108603#pone-0108603-g002" target="_blank">2</a>.</p

Concatenated multigene aignments

Fasta files containing the concatenated multigene aignments of the datasets listed in Supplemental Table S4

Single gene nucleotide alignments of the combined dataset

Fasta 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 gene nucleotide alignments of the 21 nuclear genes Glocks processed

Fasta 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 gene amino acid alignments of the 21 nuclear genes Glocks processed

Fasta 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)

readme

readm

Single gene amino acid alignments of the 21 nuclear genes

Fasta files containing the single amino acid nucleotide alignments of the 21 nuclear genes. The alignments were created using MAFFT L-INS-i v7.013