Additional file 3: Figure S2. of Spatial pattern of genetic diversity and selection in the MHC class II DRB of three Neotropical bat species

Positions of PCR primers used to amplify the indicated fragments of the MHC class II loci in C. perspicillata, D. rotundus and M. molossus, based on cDNA. The structure of the cDNA of the MHC class II DRB gene is based on [50]. According to each species, boxes indicate the amplified region using each couple of primers. The shaded region represents the region of interest, namely exon 2. Sequences and references of all primers used are given in Table 1. (PDF 26 kb

Additional file 1: Table S1. of Spatial pattern of genetic diversity and selection in the MHC class II DRB of three Neotropical bat species

Supplementary methods, including the characteristics of all capture sites (Table S1)ďťż, the list of samples successfully amplified for the MHC class II DRB loci (Table S2), the distribution of DRB alleles per species (Table S3-5), the pairwise differentiation computations per species (Table S6-8), as well as the correlations of genetics and geographic distance (Table S9). (XLS 179 kb

French Guiana study sites, with the protected areas.

<p>Protected areas: nature reserves and national parks, in green. Locations of the sites where camera-trap surveys were implemented (1, Montagne de Fer; 2, Counami; 3, Montagne de Kaw; 4, Nouragues) in light brown; locations of the areas where line-transects were implemented in dark brown; and jaguar habitats from less favorable (light grey) to more favorable (dark grey).</p

Biomass Index (kg^-1 × km of transect) of a selected set of terrestrial birds and mammals, according to the Human Footprint Index, and associated correlation curves.

<p>The four study sites for jaguar density assessment are given on the index scale, according to their mean value. The two pictures show sites with a 5–10 Index value (left) and a 15–20 Index value (right).</p

French Guiana more favorable habitats of prey.

<p>Protected areas: nature reserves and national parks, in green. Hatchings: area with Human Footprint Index < 15 (thresold value allowing maintenance of the abundance of most of prey species). Dark grey: forest areas with canopy roughness > 12, favoring higher biomass of prey.</p

Field surveys required to assess abundance of ungulates and two frugivorous birds, based on 40 surveys (up), and the number of jaguars based on four study areas (down).

<p>Top: the r coefficient correlation shows the correlation between the stabilized abundance (sampling effort > 100 km) and abundance assessed with a lesser sampling effort. The correlation is derived from 40 surveys.</p

Results of four camera-trapping surveys in French Guiana for jaguars.

<p>Results of four camera-trapping surveys in French Guiana for jaguars.</p

Fauna communities on the four study sites with implementation of both camera-trapping and linear transects: jaguar density, biomass index of mammal prey, biomass index of terrestrial bird prey.

<p>Fauna communities on the four study sites with implementation of both camera-trapping and linear transects: jaguar density, biomass index of mammal prey, biomass index of terrestrial bird prey.</p

Heatmap based on the viral-associated contigs of 51 families of insect, phage, plant/protozoan and vertebrate viruses in each pooled sample.

<p>Location information is provided above each column (Caves F and M for <i>D</i>. <i>rotundus</i>, Urban and Forest for <i>M</i>. <i>molossus</i>). The names of the viral families are presented in alphabetical order in the middle. The boxes colored from green to dark red represent the number of contigs observed. Contigs varied between 1 and 450 for the saliva samples and between 1 and 1465 for feces. The scales are given for each type of sample.</p

Phylogenetic analysis of partial RdRp protein sequences (alignment of 341 amino acids) directly obtained from the metagenomic data of pooled fecal samples of <i>M</i>. <i>molossus</i> with other representative members of the <i>Nairoviridae</i> family.

<p>The tree was inferred using the Bayesian method with the WAG + G model. Sequence identifiers include the NCBI accession number and the isolate name. The blue arrows indicate the bat-sourced nairovirus sequence obtained in the present study. Posterior probabilities of the Bayesian analysis (>50%) are shown next to each node. The scale bar indicates amino acid substitutions per site.</p