Maximum likelihood phylogenetic trees.

<p>(A) RdRp domain sequences of representative members of the <i>Coronaviridae</i>. (B) pp1ab sequences of members of the <i>Torovirus</i> genus, <i>Bafinivirus</i> genus, suggested <i>Barnivirus</i> genus and possum nidovirus. Trees are rooted on Cavally virus. The tree with the highest log likelihood is shown. Bootstrap support values are displayed above the branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Viral GenBank accession numbers are as follows: Ball python nidovirus (a), AIM19602; Ball python nidovirus (b), YP_009052475; Beluga whale coronavirus SW1, YP_001876435; Berne virus, CAA36601; Bottlenose dolphin coronavirus HKU22, AHB63494; Bovine nidovirus TCH5, YP_009142787; Bovine respiratory coronavirus, ACT11016; Bovine torovirus, BAU21404; Breda virus, YP_337905; Cavally virus, YP_004598981.2; Chinook salmon bafinivirus, YP009130641; Fathead minnow nidovirus, ADN95978; Human coronavirus OC43, AAD32993; Infectious bronchitis virus, AAP92673; MERS coronavirus, AGN70927; Munia coronavirus, YP_002308505; Murine hepatitis virus, AAA46458; Porcine epidemic diarrhoea virus, AFC98503; Porcine haemagglutinating encephalyomelitis virus, AAD32992; Porcine torovirus, AIU41583; Possum nidovirus, AEU12347.2; Python nidovirus, AII00825; Rhinolophus bat coronavirus HKU2, ABB77027; SARS coronavirus Frankfurt 1, AAP33696; Thrush coronavirus, YP_002308496.1; White bream virus, YP_803213.</p

Results of oropharyngeal swab testing for shingleback nidovirus 1.

<p>Results of oropharyngeal swab testing for shingleback nidovirus 1.</p

Partial genomic organization of Shingleback nidovirus 1.

<p>Nucleotide position is indicated along the top. Open reading frames (ORFs) and direction are represented by large block arrows. RFS indicates the position of the ribosomal frameshift site. Conserved nidovirus domains and their position within pp 1ab are indicated in an expanded view of the amino acid sequence below.</p

Pair-wise associations between viral pp1ab amino acid sequences in the <i>Torovirus</i>, <i>Bafinivirus</i> and proposed <i>Barnivirus</i> genera and possum nidovirus.

<p>Percentage level of similarity as calculated using the BLOSUM62 matrix is indicated. All GenBank accession numbers for viral sequences are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165209#pone.0165209.g002" target="_blank">Fig 2</a>.</p

Additional file 2: of Can the intake of antiparasitic secondary metabolites explain the low prevalence of hemoparasites among wild Psittaciformes?

Figure S1. Locations of the sampled population at Rasa I., Palawan, Philippines, in the Indo-Malayan zoogeographical region. Figure S2. Locations of the sampled populations in New Caledonia, Australasian zoogeographical region. Figure S3. Locations of the sampled population in the Chatham Is., Australasian zoogeographical region. Figure S4. Locations of the sampled populations in New Zealand, Australasian zoogeographical region. Figure S5. Locations of the sampled populations in the Neotropical zoogeographical region. (PDF 1271 kb

Additional file 4: of Can the intake of antiparasitic secondary metabolites explain the low prevalence of hemoparasites among wild Psittaciformes?

Scripts and combined dataset to analyse the presence of hemoparasites in Psittaciformes. Analyses and the combined dataset for the effects of diet, habitat, climate, screening method (as factors) and species (as a random variable) on the presence of parasites in the studied individuals using a binomial General Lineal Mixed-Effects Model and model averaging based on Akaike information criterion (AIC) with R. Scripts for the 10-fold cross validation and the calculations of parasite detection probability are also provided. (TXT 34 kb

Additional file 1: of Can the intake of antiparasitic secondary metabolites explain the low prevalence of hemoparasites among wild Psittaciformes?

Table S1. Hemoparasites in wild Psittaciformes. Malaria parasites (Plasmodium), related intracellular haemosporidians (Haemoproteus and Leucocytozoon), the unicellular parasitic flagellate protozoans (Trypanosoma), and microfilaria reported in wild populations of Psittaciformes. The probability of detection for adults is based on a simulation (see Additional file 4) of the probability that the parasites will actually be detected given the sample size and an expected true prevalence based on the prevalences observed in wild Psittaciformes. The habitat and climate classification follow the references in Table 1. (XLSX 34 kb

Additional file 3: of Can the intake of antiparasitic secondary metabolites explain the low prevalence of hemoparasites among wild Psittaciformes?

Table S2. Main food items consumed by the Psittaciformes species in the localities where the blood parasite sampling was carried out. Details on the species, main food items and parts consumed are provided. The presence of secondary metabolites with antimalarial/general antiparasitic plant secondary metabolites, anthelmintic, antimicrobial, and antioxidant properties is indicated. Source references are provided. (XLSX 29 kb