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Extra-organismal DNA (eoDNA) from material left behind by organisms (noninvasive DNA, e.g., feces, hair) or from environmental samples (eDNA, e.g., water, soil) is a valuable source of genetic information. However, the relatively low quality and quantity of eoDNA, which can be further degraded by environmental factors, results in reduced amplification and sequencing success. This is often compensated for through cost- and time-intensive replications of genotyping/sequencing procedures. Therefore, system- and site-specific quantifications of environmental degradation are needed to maximize sampling efficiency (e.g., fewer replicates, shorter sampling durations), and to improve species detection and abundance estimates. Using 10 environmentally diverse bat roosts as a case study, we developed a robust modeling pipeline to quantify the environmental factors degrading eoDNA, predict eoDNA quality, and estimate sampling-site-specific ideal exposure duration. Maximum humidity was the strongest eoDNA-degrading factor, followed by exposure duration and then maximum temperature. We also found a positive effect when hottest days occurred later. The strength of this effect fell between the strength of the effects of exposure duration and maximum temperature. With those predictors and information on sampling period (before or after offspring were born), we reliably predicted mean eoDNA quality per sampling visit at new sites with a mean squared error of 0.0349. Site-specific simulations revealed that reducing exposure duration to 2–8 days could substantially improve eoDNA quality for future sampling. Our pipeline identified high humidity and temperature as strong drivers of eoDNA degradation even in the absence of rain and direct sunlight. Furthermore, we outline the pipeline's utility for other systems and study goals, such as estimating sample age, improving eDNA-based species detection, and increasing the accuracy of abundance estimates.
Species persistence in the face of rapidly progressing environmental change requires adaptive responses that allow organisms to either cope with the novel conditions in their habitat or to follow their environmental niche in space. A poleward range shift due to global warming induced habitat loss in the south has been predicted for the lesser horseshoe bat, Rhinolophus hipposideros. Theoretical as well as numerous empirical studies link range expansion success to increased dispersal and reproduction rates due to spatial sorting and r-selection resulting from low population densities at the expansion front. R. hipposideros females however are highly philopatric and the species’ life history reflects a K- rather than an r-strategy, encompassing a long life span and limited individual annual reproductive output. I therefore investigated if adaptations in these traits determining range expansion success (dispersal and reproduction) can be observed in this bat species of high conservation concern. Genetic diversity presents a critical factor for adaptive responses to global change, both for range expansion and for coping with novel environmental conditions. I hence explored the genetic diversity levels of European R. hipposideros leading edge populations and their drivers for an assessment of these populations’ evolutionary potential and the development of conservation recommendations.
Comparing range expansion traits between an expanding R. hipposideros metapopulation in Germany and a non-expanding one in France revealed that range expansion was associated with an increase in juvenile survival and fecundity, and no decrease in adult survival. These results demonstrate than an increase in reproduction and growth rates is generally possible in R. hipposideros, indicating a potential adaptation (sensu lato) to range expansion. A positive correlation between adult and juvenile survival in the expanding metapopulation suggests higher resource acquisition in the expanding metapopulation, giving rise to the question if the observed demographic changes have a genetic basis or if they are rather induced by differences in environmental conditions between the two metapopulations. Long-term range expansion success requires adaptive evolutionary changes. The relative contribution of the former and that of undirected changes resulting e.g. from differences in resource availability therefore will have to be investigated in more detail in the future to allow predictions about range expansion dynamics in R. hipposideros.
The number of individuals within a radius of approximately 60 to 90 km around a population (as a measure of connectivity) was identified as the main positive driver of the studied populations’ genetic diversity. Overall genetic diversity levels in German R. hipposideros populations were found to be reduced compared to populations in France as a legacy of demographic bottlenecks resulting from severe population declines in the mid-20th century. This finding is alarming as future range expansion can be expected to entail a further decrease in genetic diversity. The resulting loss of genetic diversity can be expected to be particularly strong in R. hipposideros due to the detected dependence of genetic diversity on connectivity, because range expansion often results in small and patchy populations.
Protecting and ideally re-installing genetic diversity in R. hipposideros leading edge populations therefore presents a conservation goal of utmost importance. To achieve this endeavour, conservation efforts should target the protection of extensive networks of well-connected populations. Geographical concentration of individuals should be avoided and populations in key locations that connect clusters must be protected particularly well to prevent populations from becoming isolated. Continuous, regular monitoring of population trends is also important for a quick registration of disturbances or threats, and the subsequent rapid development of countermeasures to preclude further demographic declines.
The reduced levels of genetic diversity in the German metapopulation precluded a reliable quantification of dispersal rates due to the reduced power of discrimination between individuals. While ongoing re-colonization and the establishment of new maternity colonies provide evidence for increased dispersal in the expanding metapopulation, evaluating the expected range expansion velocity of R. hipposideros in relation to the estimated velocity of global warming induced habitat loss will require the confirmation of the existing preliminary dispersal data by employing more genetic markers.