PhD: decline of European bats

This PhD thesis is part of an ANR project (REPAST, 2019-2024): “Retro-observatories of animal biodiversity during the Anthropocene: how have global changes affected populations and communities?”.
 
Context
The populations of many European bat species experienced a dramatic decline in the 1950s-1970s, and most of them are currently considered to be vulnerable or endangered species. Several species, widespread in all Europe before the 1940s, became locally extinct. Scientists failed to clearly identify the causes of such a decline. In the absence of long-term data, international groups of bat experts listed the most likely causes of bat decline. This hypothetical list of causes of decline includes land-use changes, disturbance and loss of roosts, environmental pollution, climate changes, decline of insect preys, loss of genetic diversity, and infectious diseases. Although these are credible, they are poorly supported by field data, and are geographically and temporally variable. Moreover, these causes may act simultaneously, as none of them can explain alone the decline.
In this context, REPAST propose to crossbreed methods generally used in paleoecology, environmental history and ecology to reconstruct long-term history of bat populations and some of the hypothetical causes of their decline, using three types of archives:
1) Bat guano accumulations. All bat populations exhibit a yearly life cycle: the location of their roosts varies in time (i.e. season) and space. However, bats are known to be highly philopatric: individuals, at least females, come back every year in their natal roost where they can form large (and sometimes multispecies) colonies. Some roosts have been sheltering hundreds of bats for decades, centuries or even millennia. In these roosts, the droppings (guano) fall to the ground and accumulate chronologically until reaching substantial thickness over time. If these guano accumulations have not been disturbed (trampled or mixed for instance), they can constitute historical archives containing temporally situated information about bat populations, environmental context, and human pressures.
2) Historical archives. The scientific literature does not contain global long-term surveys of bat populations before the 1990s, for most of the >40 European species, and most of the European countries. Bat decline was first reported in the literature in 1970, after some scientists demonstrated that colonies of several species decreased or disappeared in all European countries. Before the 1970s, scientists essentially focused on bat biology and reproduction, and not on the dynamics of populations and their long-term health evolution. However, some historical archives can help to reconstitute global patterns of bat demography from the 1940s to nowadays. Information about colony size, population distribution range, and global demographic trends can be found in atlases, national specialized journals, archives of natural history museum reports or naturalist society reports, etc.
3) Museum specimens. During the last decade, the use of museum specimens for biological conservation purposes has substantially increased, mainly due to the advent of molecular genetic approaches. Because most specimens stored in collections are from the 19th and the beginning of the 20th Century, museum specimens offer unique opportunities to quantify evolutionary or microevolutionnary changes that occurred since the 19th Century, for the reconstruction of population history. Particularly, the study of gene pools in museum specimens and nowadays samples can help to determine whether a low genetic variability is the consequence of recent population declines, or represents an ancestral state.
 
REPAST will (i) use biological archives (both guano accumulation and museum specimens) for reconstituting the temporal dynamics of populations and environmental parameters explaining the loss of animal biodiversity, (ii) use methods of monitoring that inform about key population and environment features that scientists failed to assess by regular monitoring over time. Overall, the underlying hypothesis of REPAST is that one or several stressors (habitat or climate changes, exposure to pollutants) will be associated to temporal variations of biological responses (pathogen prevalence, shift in diet, genetic diversity, bat richness). The nature and the pattern of this association (what stressor(s) is(are) linked to what response(s) and how (from long and continuous associations to sudden shifts) will improve our understanding of the mechanism(s) of bat decline. As some past environmental stressors still persist nowadays, this project will contribute to the prioritization of the current threats to animal species and their habitats and will ultimately guide conservation measures. This retrospective study will be used to parameterise predictive scenarios of the evolution of animal population dynamics in relation to the long-term predictions of different stressors.
 
PhD student tasks
           The PhD student will be mainly involved in work packages aiming to relate human pressure indices and some descriptors of bat colonies through the study of guano cores. Human pressures measured will be:
- Modifications in foraging areas: through pollen composition, pollutant concentrations, and historical data about landscapes.
- Climate changes, through the assessment of microclimate data (using data generated by meteorological stations).
           These human pressures will be related to longitudinal data on: 1) bat specific richness in colonies, the composition of bat assemblages, shift in bat diet, and bat genetic diversity; 2) exposure to parasites.
 
Student
 
The candidate should hold a Master degree or equivalent in ecology with a strong interest for biological conservation and interdisciplinary research at the interface of molecular ecology, ecotoxicology, and history (landscape evolution). The candidate should have advanced knowledges in statistical analyses (using the R software). A solid knowledge in molecular ecology (in particular population genetics) and/or ecotoxicology will be an advantage. Concerning the laboratory analyzes (molecular analyses and analytical chemistry), the student will be supported by technical staff, but will have to show the qualities necessary for the correct interpretation of the data.
The candidate should be rigorous, proactive, with a reasonable degree of autonomy, with good organizational skills and be willing to evolve in an interdisciplinary project. Moreover she/he should have a solid English level and good writing skills. 
The student will be based at the Chrono-environment laboratory, Besançon (Franche-Comté):  https://chrono-environnement.univ-fcomte.fr/
 
 
 
Application
 
                  The application should include 1) a cover letter describing the candidate, her/his research interests and her/his motivation to do a PhD, 2) a CV, 3) a copy of the undergraduate and master degree, and a copy of the master report, and 4) the names and contact information of at least two reference persons (e-mail address and phone number). The application should be written in French or English.

Please submit your application by sending it to eve.afonso@univ-fcomte.fr and renaud.scheifler@univ-fcomte.fr before September 15th.
 
Ideally, the thesis should start at the beginning of November 2019.

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