Publisher Correction: Ophidiomycosis surveillance of snakes in Georgia, USA reveals new host species and taxonomic associations with disease.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Ophidiomycosis surveillance of snakes in Georgia, USA reveals new host species and taxonomic associations with disease.

Ophidiomycosis (snake fungal disease) is caused by the fungus Ophidiomyces ophiodiicola and threatens snake health worldwide. It has been documented throughout the eastern United States and severe cases have recently been reported in Georgia, USA. To evaluate disease distribution and prevalence in this state, 786 free-ranging snakes were examined for skin lesions consistent with ophidiomycosis and swabbed to detect O. ophiodiicola DNA using qPCR. Sampled snakes represented 34 species and 4 families; 27.5% had skin lesions, 13.3% were positive for O. ophiodiicola DNA, and 77.8% of the qPCR positive individuals had skin lesions. This is the first report of O. ophiodiicola in five of the 22 species that were qPCR positive. Multinomial logistic regression modeling indicated that Drymarchon couperi had a higher relative risk of apparent ophidiomycosis (lesions present and qPCR positive), and the best models predicting qPCR result and ophidiomycosis category included individual factors and excluded temporal and spatial factors. Phylogeny-based bipartite network analysis showed that Nerodia erythrogaster, Nerodia taxispilota, and D. couperi had the highest prevalence of apparent ophidiomycosis; this category was more prevalent in the subfamily Colubrinae and less prevalent in Natricinae. These results provide important information about ophidiomycosis epidemiology, which has implications for snake conservation.

Patterns of head shape and scutellation in Drymarchon couperi (Squamata: Colubridae) reveal a single species.

Krysko et al. (2016a) used analyses of DNA sequence data to reveal two genetic lineages of Drymarchon couperi. The Atlantic lineage contained specimens from southeastern Georgia and eastern peninsular Florida, and the Gulf Coast lineage contained specimens from western and southern peninsular Florida as well as western Florida, southern Alabama, and southern Mississippi. In a second paper Krysko et al. (2016b) analyzed morphological variation of the two lineages, which allowed them to restrict D. couperi to the Atlantic lineage and to describe the Gulf Coast lineage as a new species, Drymarchon kolpobasileus. This taxonomic discovery was remarkable for such a large, wide-ranging species and was notable for its impact on conservation. Because of population declines, particularly in western Florida, southern Alabama, and southern Mississippi, D. couperi (sensu lato) was listed as Threatened under the Endangered Species Act (United States Fish and Wildlife Service 1978, 2008) and repatriation of the species to areas where it had been extirpated was listed as a priority conservation goal (United States Fish and Wildlife Service 1982, 2008). Such repatriation efforts were attempted in Alabama, Florida, Georgia, and South Carolina, starting in 1977 (Speake et al. 1987), but failed to create viable populations, likely because too few snakes were released at too many sites (Guyer et al. 2019; Folt et al. 2019a). A second attempt at repatriation was started in 2010 and concentrated on release of snakes at a single site in Alabama (Stiles et al. 2013). However, Krysko et al. (2016a) criticized this repatriation effort because it appeared to involve release of D. couperi (sensu stricto) into the geographic region occupied by D. kolpobasileus (as diagnosed in Krysko et al. 2016b).

Ophidiomycosis prevalence in Georgia's Eastern Indigo Snake (Drymarchon couperi) populations.

Wildlife diseases have posed a significant challenge to the conservation of many species in recent years. Diseases have been implicated in population declines over large geographic areas, with severe disease outbreaks leading to either local or complete extinctions of wild populations. Ophidiomycosis, commonly known as snake fungal disease, is caused by the fungus Ophidiomyces ophiodiicola, which has been documented in snake populations across the eastern and southern United States. We collected swab samples from the federally threatened Eastern Indigo Snake (Drymarchon couperi) in populations across the species' Georgia range. We used quantitative PCR to determine the presence of O. ophiodiicola DNA and also recorded skin abnormalities characteristic of ophidiomycosis. From 1 September 2016 to 4 August 2018, Eastern Indigo Snakes tested positive for O. ophiodiicola DNA on 47 of 107 occasions (43.9%) and tested negative for fungal DNA but had skin lesions consistent with ophidiomycosis on 42 occasions (39.3%). Symptomatic and qPCR positive individuals were more likely to be encountered during January and February when compared to November and December. We found no effect of sex (p = 0.517), age-class (p = 0.106), or body size (snout-vent length: p = 0.083; mass: p = 0.206; body condition: p = 0.063) on ophidiomycosis status. Over the two-year study, we encountered individuals in which infection was clearly negatively impacting overall health and also documented individuals in which infection apparently cleared from one year to the next. These results demonstrate that O. ophiodiicola and lesions characteristic of ophidiomycosis are widespread in Georgia's Eastern Indigo Snake populations. However, there are many unanswered questions regarding this disease, including the effects of disease on populations and individuals, the presence of infection vectors, and the change in prevalence over time. More research is needed to address ophidiomycosis and understand its impacts on ongoing conservation efforts.

Taxonomic and conservation implications of population genetic admixture, mito-nuclear discordance, and male-biased dispersal of a large endangered snake, Drymarchon couperi.

Accurate species delimitation and description are necessary to guide effective conservation of imperiled species, and this synergy is maximized when multiple data sources are used to delimit species. We illustrate this point by examining Drymarchon couperi (Eastern Indigo Snake), a large, federally-protected species in North America that was recently divided into two species based on gene sequence data from three loci and heuristic morphological assessment. Here, we re-evaluate the two-species hypothesis for D. couperi by evaluating both population genetic and gene sequence data. Our analyses of 14 microsatellite markers revealed 6-8 genetic population clusters with significant admixture, particularly across the contact zone between the two hypothesized species. Phylogenetic analyses of gene sequence data with maximum-likelihood methods suggested discordance between mitochondrial and nuclear markers and provided phylogenetic support for one species rather than two. For these reasons, we place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA are driven by high dispersal of males relative to females. We advocate for species delimitation exercises that evaluate admixture and gene flow in addition to phylogenetic analyses, particularly when the latter reveal monophyletic lineages. This is particularly important for taxa, such as squamates, that exhibit strong sex-biased dispersal. Problems associated with over-delimitation of species richness can become particularly acute for threatened and endangered species, because of high costs to conservation when taxonomy demands protection of more individual species than are supported by accumulating data.

HEALTH AND NUTRITIONAL ASSESSMENT OF FREE-RANGING EASTERN INDIGO SNAKES (DRYMARCHON COUPERI) IN GEORGIA, UNITED STATES.

Clinical pathology and nutritional parameters are useful in evaluating and monitoring threatened and endangered wildlife populations, but reference ranges for most snake species are lacking. From 2001 to 2005, health assessments were performed on 58 eastern indigo snakes (EIS) (Drymarchon couperi) captured in the wild in southeastern Georgia, United States. Health and nutritional assessments performed included hematology, serum biochemistry, fat-soluble vitamins, heavy metals, pesticide contaminants, parasitology, and surveys of other pathogens. Significant differences in total solids, packed cell volume, glucose, blood urea nitrogen, albumin : globulin ratio, amylase, triglycerides, and bile acids between males and females were observed. Additionally, there was a significant difference between liver and kidney concentrations for vitamins A and E. As previously noted in captive EIS, total Ca was elevated in comparison to concentrations reported in other snake species. Parasitism was a common finding in sampled EIS, but the overall health status of this free-ranging population appeared good. A winter-time dermatitis was found in most snakes, which resolved in the summer months. This study represents the first health and nutritional assessment of free-ranging EIS, and provides needed data to guide monitoring and conservation efforts.

Snake co-occurrence patterns are best explained by habitat and hypothesized effects of interspecific interactions.

Snakes often occur in species-rich assemblages, and sympatry is thought to be facilitated primarily by low diet overlap, not interspecific interactions. We selected, a priori, three species pairs consisting of species that are morphologically and taxonomically similar and may therefore be likely to engage in interspecific, consumptive competition. We then examined a large-scale database of snake detection/nondetection data and used occupancy modelling to determine whether these species occur together more or less frequently than expected by chance while accounting for variation in detection probability among species and incorporating important habitat categories in the models. For some snakes, we obtained evidence that the probabilities that habitat patches are used are influenced by the presence of potentially competing congeneric species. Specifically, timber rattlesnakes (Crotalus horridus) were less likely than expected by chance to use areas that also contained eastern diamond-backed rattlesnakes (Crotalus adamanteus) when the proportion of evergreen forest was relatively high. Otherwise, they occurred together more often than expected by chance. Complex relationships were revealed between habitat use, detection probabilities and occupancy probabilities of North American racers (Coluber constrictor) and coachwhips (Coluber flagellum) that indicated the probability of competitive exclusion increased with increasing area of grassland habitat, although there was some model uncertainty. Cornsnakes (Pantherophis guttatus or Pantherophis slowinskii) and ratsnakes (Pantherophis alleghaniensis, Pantherophis spiloides, or Pantherophis obsoletus) exhibited differences in habitat selection, but we obtained no evidence that patterns of use for this species pair were influenced by current interspecific interactions. Overall, our results are consistent with the hypothesis that competitive interactions influence snake assemblage composition; the strength of these effects was affected by landscape-scale habitat features. Furthermore, we suggest that current interspecific interactions may influence snake occupancy, challenging the paradigm that contemporary patterns of snake co-occurrence are largely a function of diet partitioning that arose over evolutionary time.

Landscape-level influences of terrestrial snake occupancy within the southeastern United States.

Habitat loss and degradation are thought to be the primary drivers of species extirpations, but for many species we have little information regarding specific habitats that influence occupancy. Snakes are of conservation concern throughout North America, but effective management and conservation are hindered by a lack of basic natural history information and the small number of large-scale studies designed to assess general population trends. To address this information gap, we compiled detection/nondetection data for 13 large terrestrial species from 449 traps located across the southeastern United States, and we characterized the land cover surrounding each trap at multiple spatial scales (250-, 500-, and 1000-m buffers). We used occupancy modeling, while accounting for heterogeneity in detection probability, to identify habitat variables that were influential in determining the presence of a particular species. We evaluated 12 competing models for each species, representing various hypotheses pertaining to important habitat features for terrestrial snakes. Overall, considerable interspecific variation existed in important habitat variables and relevant spatial scales. For example, kingsnakes (Lampropeltis getula) were negatively associated with evergreen forests, whereas Louisiana pinesnake (Pituophis ruthveni) occupancy increased with increasing coverage of this forest type. Some species were positively associated with grassland and scrub/shrub (e.g., Slowinski's cornsnake, Elaphe slowinskii) whereas others, (e.g., copperhead, Agkistrodon contortrix, and eastern diamond-backed rattlesnake, Crotalus adamanteus) were positively associated with forested habitats. Although the species that we studied may persist in varied landscapes other than those we identified as important, our data were collected in relatively undeveloped areas. Thus, our findings may be relevant when generating conservation plans or restoration goals. Maintaining or restoring landscapes that are most consistent with the ancestral habitat preferences of terrestrial snake assemblages will require a diverse habitat matrix over large spatial scales.

Widespread occurrence of the amphibian chytrid fungus Batrachochytrium dendrobatidis in the southeastern USA.

From 1999 to 2006, we sampled > 1200 amphibians for the fungal pathogen Batrachochytrium dendrobatidis (Bd) at 30 sites in the southeastern USA. Using histological techniques or PCR assays, we detected chytrid infection in 10 species of aquatic-breeding amphibians in 6 states. The prevalence of chytrid infection was 17.8% for samples of postmetamorphic amphibians examined using skin swab-PCR assays (n = 202 samples from 12 species at 4 sites). In this subset of samples, anurans had a much higher prevalence of infection than caudates (39.2% vs. 5.5%, respectively). Mean prevalence in ranid frogs was 40.7%. The only infected salamanders were Notophthalmus viridescens at 3 sites. We found infected amphibians from late winter through late spring and in 1 autumn sample. Although we encountered moribund or dead amphibians at 9 sites, most mortality events were not attributed to Bd. Chytridiomycosis was established as the probable cause of illness or death in fewer than 10 individuals. Our observations suggest a pattern of widespread and subclinical infections. However, because most of the sites in our study were visited only once, we cannot dismiss the possibility that chytridiomycosis is adversely affecting some populations. Furthermore, although there is no evidence of chytrid-associated declines in our region, the presence of this pathogen is cause for concern given global climate change and other stressors. Although presence-absence surveys may still be needed for some taxa, such as bufonids, we recommend that future researchers focus on potential population-level effects at sites where Bd is now known to occur.