Land use and life history constrain adaptive genetic variation and reduce the capacity for climate change adaptation in turtles

Background Rapid anthropogenic climate change will require species to adapt to shifting environmental conditions, with successful adaptation dependent upon current patterns of genetic variation. While landscape genomic approaches allow for exploration of local adaptation in non-model systems, most landscape genomics studies of adaptive capacity are limited to exploratory identification of potentially important functional genes, often without a priori expectations as to the gene functions that may be most important for climate change responses. In this study, we integrated targeted sequencing of genes of known function and genotyping of single-nucleotide polymorphisms to examine spatial, environmental, and species-specific patterns of potential local adaptation in two co-occuring turtle species: the Blanding’s turtle (Emydoidea blandingii) and the snapping turtle (Chelydra serpentina). Results We documented divergent patterns of spatial clustering between neutral and putatively adaptive genetic variation in both species. Environmental associations varied among gene regions and between species, with stronger environmental associations detected for genes involved in stress response and for the more specialized Blanding’s turtle. Land cover appeared to be more important than climate in shaping spatial variation in functional genes, indicating that human landscape alterations may affect adaptive capacity important for climate change responses. Conclusions Our study provides evidence that responses to climate change will be contingent on species-specific adaptive capacity and past history of exposure to human land cover change.

Blanding’s Turtle Demography and Population Viability

In anticipation of US federal status classification (warranted, warranted but precluded, not warranted), scheduled for 2023, we provide population viability analysis of the Blanding’s turtle Emydoidea blandingii , a long-lived, late-maturing, semi-aquatic species of conservation concern throughout its range. We present demographic data from long-term study of a population in northeastern Illinois and use these data as the basis for viability and sensitivity analyses focused on parameter uncertainty and geographic parameter variation. We use population viability analysis to identify population sizes necessary to provide population resiliency to stochastic disturbance events and catastrophes and demonstrate how alternative definitions of ‘foreseeable future’ might affect status decisions. Demographic parameters within our focal population resulted in optimistic population projections (probability of extinction = 0% over 100 years) but results were less optimistic when catastrophes or uncertainty in parameter estimates were incorporated (probability of extinction = 3% and 16%, respectively). Uncertainty in estimates of age-specific mortality had the biggest impact on population viability analysis outcomes but uncertainty in other parameters (age of first reproduction, environmental variation in age-specific mortality, % females reproducing, clutch size) also contributed. Blanding’s turtle demography varies geographically and incorporating this variation resulted in both mortality- and fecundity-related parameters affecting population viability analysis outcomes. Possibly, compensatory variation among demographic parameters allows for persistence across a wide range of parameter values. We found that extinction risk decreased and retention of genetic diversity increased rapidly with increasing initial population size. In the absence of catastrophes, demographic conservation goals could be met with a smaller initial population size than could genetic conservation goals; ≥20-50 adults were necessary for extinction risk <5% whereas ≥50-110 adults were necessary to retain >95% of existing genetic diversity over 100 yrs. These thresholds shifted upward when catastrophes were included; ≥50-200 adults were necessary for extinction risk <5% and ≥110 to more than 200 adults were necessary to retain >95% of existing genetic diversity over 100 yrs. Impediments to Blanding’s turtle conservation include an incomplete understanding of geographic covariation among demographic parameters, the large amount of effort necessary to estimate and monitor abundance, and uncertainty regarding the impacts of increasingly frequent extreme weather events.

Detection of a novel herpesvirus associated with squamous cell carcinoma in a free-ranging Blanding’s turtle

The spread of both infectious and noninfectious diseases through wildlife populations is of increasing concern. Neoplastic diseases are rarely associated with population-level impacts in wildlife; however, impacts on individual health can be severe and might reflect deteriorating environmental conditions. An adult male free-ranging Blanding’s turtle ( Emydoidea blandingii) originally captured in 2005 and deemed healthy, was recaptured in 2018 with a 1 × 1.5 cm intra-oral broad-based right mandibular mass. An excisional biopsy was performed, and histopathology revealed squamous cell carcinoma (SCC). Consensus herpesvirus PCR identified a novel herpesvirus (proposed name Emydoidea herpesvirus 2 [EBHV-2]) within the tumor. EBHV-2 shares 85% sequence homology with Terrapene herpesvirus 2 (TerHV-2), a herpesvirus linked to fibropapillomas in eastern box turtles ( Terrapene carolina carolina). Virus-associated fibropapillomas have been identified in multiple marine turtle species and have had debilitating effects on their populations, but to date, virus-associated SCCs are rarely reported.

Environmental DNA detection of endangered and invasive species in Kejimkujik National Park and Historic Site

The use of environmental DNA (eDNA) allows the early detection of aquatic species at low densities (e.g. elusive and invasive species), which otherwise could be challenging to monitor using conventional techniques. Here, we assess the ability of eDNA sampling to detect the presence/absence of one species-at-risk (Blanding’s Turtle) and two invasive species (Chain Pickerel and Smallmouth Bass) in Kejimkujik National Park and National Historic site, Nova Scotia, where the aquatic system is highly acidic and rich in organic compounds. Five replicates of 1L water samples were taken per sampling site. Water filtration and eDNA extractions were performed on-site, while qPCR reactions were performed in the laboratory using species-specific assays. Samples were treated with an inhibition removal kit and analyzed pre- and post-inhibition removal. Despite the low pH and PCR inhibitors in water samples, our results showed positive eDNA detections in almost all expected positive sites (except in one site for Blanding’s Turtle). Detections of the target species were also observed at sites where their presence was previously unknown. Our study supports the advantage of eDNA to monitor species at low densities, revealing new distributions or recently invaded areas. We also demonstrate how eDNA can directly instruct management strategies in Kejimkujik.