Thacker, C. | bioRxiv Science

bioRxiv2023

Paranannizziopsis spp. associated with skin lesions in wild snakes in North America and development of a real-time PCR assay for rapid detection of the fungus in clinical samples

The emergence of ophidiomycosis (or snake fungal disease) in snakes has prompted increased awareness of the potential effects of fungal infections on wild reptile populations. Yet, aside from Ophidiomyces ophidiicola, little is known about other mycoses affecting wild reptiles. The closely related genus Paranannizziopsis has been associated with dermatomycosis in snakes and tuataras in captive collections, and P. australasiensis was recently identified as the cause of skin infections in non-native wild panther chameleons (Furcifer pardalis) in Florida, USA. Here we describe five cases of Paranannizziopsis spp. associated with skin lesions in wild snakes in North America and one additional case from a captive snake from Connecticut, USA. In addition to demonstrating that wild Nearctic snakes can serve as a host for these fungi, we also provide evidence that the genus Paranannizziopsis is widespread in wild snakes, with cases being identified in Louisiana (USA), Minnesota (USA), Virginia (USA), and British Columbia (Canada). Phylogenetic analyses conducted on multiple loci of the fungal strains we isolated identified P. australasiensis in Louisiana and Virginia; the remaining strains from Minnesota and British Columbia did not cluster with any of the described species of Paranannizziopsis, although the strains from British Columbia appear to represent a single lineage. Finally, we designed a pan-Paranannizziopsis real-time PCR assay targeting the internal transcribed spacer region 2. This assay successfully detected DNA of all described species of Paranannizziopsis and the two potentially novel taxa isolated in this study and did not cross-react with closely related fungi or other fungi commonly found on the skin of snakes. The assay was 100% sensitive and specific when screening clinical (skin tissue or skin swab) samples, although full determination of the assays performance will require additional follow up due to the small number of clinical samples (n=14 from 11 snakes) available for testing in our study. Nonetheless, the PCR assay can provide an important tool in further investigating the prevalence, distribution, and host range of Paranannizziopsis spp. and facilitate more rapid diagnosis of Paranannizziopsis spp. infections that are otherwise difficult to differentiate from other dermatomycoses.

microbiology↗

bioRxiv2022

Continent-wide phylogenomic framework reveals introgression as a driver of intra-specific diversity and enriched molecular pathways in caribou

High intra-specific genetic diversity is associated with adaptive potential which is key for resilience to global change. However, high variation may also support deleterious alleles through genetic load, unless purged, thereby increasing the risk of inbreeding depression if population sizes decrease rapidly. Purging of deleterious variation has now been demonstrated in some threatened species. However, less is known about the costs of population declines and inbreeding in species with large population sizes and high genetic diversity even though this encompasses many species globally that have or are expected to undergo rapid population declines. Caribou is a species of ecological and cultural significance in North America with a continental-wide distribution supporting extensive phenotypic variation, but with some populations undergoing significant declines resulting in their at-risk status in Canada. We assessed intra-specific genetic variation, adaptive divergence, inbreeding, and genetic load across populations with different demographic histories using an annotated chromosome-scale reference genome and 66 whole genome sequences. We found high genetic diversity and nine phylogenomic lineages across the continent with adaptive diversification of genes, but also high genetic load among lineages. We also found highly divergent levels of inbreeding across individuals including the loss of alleles by drift (genetic erosion) but not purging, likely due to rapid population declines not allowing time for purging of deleterious alleles. As a result, further inbreeding may need to be mitigated through conservation efforts. Our results highlight the double-edged sword of genetic diversity that may be representative of other species-at-risk affected by anthropogenic activities.

genomics↗