Habitat fragmentation in the Brazilian Atlantic Forest is associated with erosion of frog immunogenetic diversity and increased fungal infections

Abstract

Habitat fragmentation and infectious diseases threaten wildlife globally, but the interactions of these threats are poorly understood. For instance, while habitat fragmentation can impact genetic diversity at neutral loci, the impacts on disease-relevant loci are less well-studied. We examined the effects of habitat fragmentation in Brazil's Atlantic Forest on amphibian genetic diversity at an immune locus related to antigen presentation and detection (MHC IIB Exon 2). We used a custom high-throughput assay to sequence a fragment of MHC IIB and quantified Batrachochytrium dendrobatidis (Bd) infections in six frog species in two Atlantic Forest regions. Habitat fragmentation was associated with genetic erosion at MHC IIB Exon 2. This erosion was most severe in forest specialists. Significant Bd infections were detected only in one Atlantic Forest region, potentially due to relatively higher elevation. In this region, forest specialists showed an increase in both Bd prevalence and infection loads in fragmented habitats. Reduced population-level MHC IIB diversity was associated with increased Bd infection risk. On the individual level, MHC IIB heterozygotes exhibited a trend toward reduced Bd infection risk, although this was marginally non-significant. Our results suggest that habitat fragmentation increases Bd infection susceptibility in amphibians, mediated at least in part through erosion of immunogenetic diversity. Our findings have implications for management of fragmented populations in the face of emerging infectious diseases.

Keywords: Amphibians; Batrachochytrium dendrobatidis; Brazil’s Atlantic Forest; Disease susceptibility; Habitat fragmentation; Immunogenetics.

Figure 1.. Sampling locations.

Preserved continuous forests (CO1 and CO2) are denoted with white circles, and forest fragments (FR1-FR4) are denoted with red triangles. For each of the six focal species for genetic analyses, two populations were sampled, one from a continuous site and one from a fragmented site. See Table S2 for sample sizes and species associated with each site.

Figure 2.. MHC IIB haplotype network for four focal species.

Circle size is proportional to haplotype frequency, colors correspond to the populations in which each haplotype is found, and the length of the links between haplotype circles correspond to the genetic distance between haplotypes. XL was the only haplotype found in more than one species (B. semilineata and D. branneri). Photos by A. M. Belasen and T. Y. James.

Figure 3.. MHC IIB summary statistics across all focal species.

Sampling region (SP = São Paulo, BA = Bahia) is specified in parentheses after each species’ name. (A, B) MHC IIB immunogenetic diversity erodes in fragmented populations as measured by both expected heterozygosity (A) and nucleotide diversity (B). Dark green bars represent populations from continuous forests and light green bars represent populations from fragmented forests. Asterisks represent a significant difference according 95% Confidence Intervals shown by error bars. (C) Genetic differentiation (fixation index, F_ST) at MHC IIB vs. ddRAD markers. ddRAD F_ST mean values are shown by red bars with 95% CI error bars and MHC IIB F_ST values are shown by pink bars.

Figure 4.. Bd incidence across populations and MHC IIB genotypes.

A and B include data from six São Paulo amphibian species, while C only includes data from the four species that were genotyped for MHC IIB (see text for details). (A) Bd prevalence in São Paulo across habitat types and species ecologies (forest specialists in dark gray, habitat generalists in light gray). (B) Log-transformed Bd infection loads across species ecologies ecologies (forest specialists in dark gray, habitat generalists in light gray). (C) Proportion of Bd-infected (black) versus uninfected (white) frogs according the MHC IIB allelic genotype.