M/F Ecology of squamates interacting with road infrastructures

21 Mar 2024
Job Information

Organisation/Company

CNRS

Department

Centre d'études biologiques de Chizé

Research Field

Biological sciences
Environmental science

Researcher Profile

First Stage Researcher (R1)

Country

France

Application Deadline

10 Apr 2024 - 23:59 (UTC)

Type of Contract

Temporary

Job Status

Full-time

Hours Per Week

35

Offer Starting Date

22 May 2024

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme

Is the Job related to staff position within a Research Infrastructure?

No

Offer Description

Host laboratories and supervision. The thesis will be supervised by Xavier Bonnet (CEBC, CNRS) and Jonathan Jumeau (CERISE, CeA). Funding for this thesis has been secured. You will be enrolled in the Euclide Doctoral School at La Rochelle University. As a doctoral student, you will be a member of the Ecophy team at the Centre d'Etudes Biologiques de Chizé (CEBC), but physically based at the Collectivité Européenne d'Alsace (CeA) in Strasbourg. As far as the fieldwork is concerned, the thesis work will take place in the Bas-Rhin. As far as scientific development is concerned, and for certain training courses (e.g. animal experimentation designer), the Centre d'Etudes Biologiques de Chizé (CEBC, UMR 7372 CNRS-Université La Rochelle), located in the Nouvelle-Aquitaine region in the Deux-Sèvres department, 25 km south of Niort, will be the host structure. The unit is structured into three research teams: Ecophy, Prédateurs Marins and Résilience. The Ecophy team studies how animals respond to environmental stressors (climate change, habitat degradation, pollution). The link between the environment (e.g. alteration of habitats) and ecological and demographic responses is studied using various biological models, particularly reptiles. The European Collectivity of Alsace, which will be the host site, is the departmental level of local government in Alsace. It is the merger of the Bas-Rhin and Haut-Rhin départements. One of its missions is to manage the departmental and national road network within its territory. This includes project management for road projects, which are regularly confronted with environmental issues. With 6,000 hectares of roadside verges managed as grassland, around a hundred storm water basins serving as refuge habitats for numerous wetland species, and 48,000 trees lining the roads, the CeA has a major responsibility for preserving biodiversity in Alsace. In order to gain a better understanding of the interaction between roads and biodiversity, in 2014 the local authority launched a research programme called CERISE, which includes this research project.
Profile and skills required
We are looking for a motivated candidate who is keen to take part in a research project focusing on conservation biology.
Skills required:
Strong ability to work in the field and monitor experimental set-ups.
Good drafting and summarising skills.
English fluent in reading, speaking and writing.
Experience in population monitoring, preferably herpetofauna.
Ability to supervise trainees.
Driving licence essential.
Hosting conditions
The PhD student will be based at the Collectivité européenne d'Alsace in Strasbourg.
Fieldwork will take place within a radius of approximately 30 km from the place of work. Travel expenses will be covered and company cars will be made available.
The doctoral student will be temporarily hosted at the CEBC for sessions to promote the work, to prepare conferences and for specific training courses.

The growing development of road infrastructure is having major ecological consequences (Forman & Alexander, 1998). These impacts are varied in their temporality, since they begin during the construction phase and continue during the operating phase (Andrews et al., 2006). Road impacts are also varied in terms of the nature of the effect, because in addition to direct mortality from vehicle-wildlife collisions, roads also lead to habitat loss through destruction, changes in connectivity, and indirect disturbances such as the introduction of invasive alien species, which are major causes of biodiversity erosion (Wood et al., 2000). These impacts are significant, affecting many species (more than 1,200 continental species are threatened directly by roads, 4,000 by invasive alien species, etc.; IUCN, 2023) and extending beyond roads. This is clearly visible in the "road-effect zone" in which distant effects such as pollution (light, noise, chemical, etc.) operate (Forman & Alexander, 1998). The size and intensity of this zone depend on the habitats present and the species concerned (Boarman & Sazaki, 2006; Bissonette & Rosa, 2009, Shanley & Pyare, 2011). Reptiles are a taxon particularly impacted by human activities (Aburrow et al., 2023), with 21% of species assessed as threatened with extinction (IUCN, 2022). In addition to mortality directly linked to the destruction of habitat during construction, reptiles are particularly prone to vehicle-wildlife collisions because of their small size, poor mobility and immobility in the face of traffic (Andrews & Gibbons, 2005). The use of asphalt pavements as a substrate for thermoregulation and as hunting areas, as well as post-natal dispersal behaviour, can increase this mortality (Blouin-Demers & Weatherhead, 2002; Meylan et al., 2002). The low dispersal capacity of reptiles also makes them sensitive to the loss of connectivity caused by road construction (Andrews et al., 2006), which acts as a barrier to the movement of individuals and therefore to gene flow (Herrmann et al., 2017). Consequently, habitat fragmentation linked to human activities is one of the major causes of the decline in herpetofauna populations (Teixido et al., 2021). In addition, the various types of pollution (i.e. chemical, light and noise) associated with road use cause physiological and behavioural changes in reptiles (Brattstrom & Bondello, 1983; Mautz & Dohm, 2004). The construction of roads is legally accompanied by the implementation of measures to avoid, reduce and compensate for environmental impacts (the ERC sequence). This sequence is based on effective methods for detecting individuals and knowledge of the ecology of the target species, so as not to underestimate the impact of the project and to implement appropriate mitigation measures. However, in the case of reptiles, the inventory methods commonly used (i.e. plate surveys alone) can greatly underestimate species diversity (Hutchens & DePemo, 2009) and the anti-fence barriers put in place are not always effective (Baxter-Gilbert et al., 2015). Furthermore, the effectiveness of wildlife crossings in re-establishing connectivity is poorly documented for reptiles. Road projects may therefore present threats with underestimated impacts for the reptiles present. Despite the threats they present, roadsides and in particular, the neighbouring herbaceous strips are attractive habitats for reptiles, which can then be found there in large numbers (Wells et al., 1996; (Meek, 2009; Cartbew et al., 2013; Homyack et al., 2016; Mi broda et al., 2017)). They generally have low vegetation, good exposure to sunlight and areas of bare soil, making them particularly suitable for thermoregulatory behaviour (Blouin-Demers & Weatherhead, 2002) and egg-laying (Steen et al., 2006). Herbaceous areas along roadsides can harbour significant biodiversity of invertebrates that serve as prey for reptiles (Jakobsson et al., 2018). Finally, roadsides offer a variety of habitats in the form of grass strips, ditches and stone embankments, providing a good supply of resources (Van der Ree et al., 2015).
Research objectives: Roadsides offer a variety of attractive habitats for reptiles. However, they are exposed to direct threats (e.g. mortality linked to vehicle-wildlife collisions) and indirect threats (e.g. genetic barriers, behavioural changes, etc.). The quality of these habitats is therefore uncertain. It is possible that in some cases they act as ecological traps, i.e. habitats that are attractive to individuals but in which their selective value is diminished, particularly because of low survival or reproduction rates (Robertson & Hutto, 2006). It is therefore important to study the ecology of reptiles interacting with roads in order to assess whether or not these habitats are of good quality for these species and to provide recommendations in terms of management and consideration in environmental assessments. It is with this objective in mind that this thesis project aims to: (i) evaluate the current methods used for monitoring individuals and populations, particularly of small squamates; (ii) determine whether roadside developments are effective in reducing road mortality and improving landscape connectivity; (iii) study the quality of roadside habitats for squamates in terms of individual quality, demography and habitat use.
Protocol: This thesis project focuses on squamates present in the Bas-Rhin plain (Grand-Est, France). This region has a landscape dominated by intensive agriculture with a dense road network (2 km/km2 in 201 7) that is constantly expanding (MTE, 201 7). The various reptile species, all of which are protected at national level, present a major challenge when road projects are implemented, making it even more important to improve our knowledge of their interactions with road infrastructure. This will be achieved by studying various species of squamate, lacertidae and colubridae present in the study area.
The aim of the project is to obtain new knowledge about the ecology of squamates, but also to optimise monitoring and development methods, in order to establish ERC measures that can be applied to these species in future development projects. The project is divided into 3 sections:
I - Individual and population monitoring methods for squamates. The aim of this first section is to assess the methods currently used to study the species richness and population monitoring of squamates.
a - Evaluation of biodiversity monitoring methods for squamates Environmental assessments are carried out as part of development projects. They aim to determine the pre-development state of ecosystems, then the impacts and effectiveness of environmental measures, in particular by assessing species richness and monitoring populations. Habitats are visited to observe the species present. Squamates are often detected using sunlight plots or "reptile plates". These installations consist of a dark material and are placed randomly or along a transect in the landscapes to be studied in order to attract the animals, as they represent a good substrate for increasing their body temperature (i.e. thermoregulation).
The aim of this first phase is to determine whether these studies are representative of the species richness and population trends of squamates. To begin with, the protocols of the various environmental consultancies and associations will be studied in order to determine the points in common and the differences, in particular the number of visits, their frequency and the field observation protocol. Sunlight plots will then be set up at several sites along transects or at random. Different materials will be used to determine whether they attract different species to the same habitat. The sites will be visited once a week from March to July. The transect will first be walked, observing and counting the individuals of different species present on the plots and along the route. On the return journey, the plots will be lifted to observe the individuals present underneath.
These data will be used to model changes in species richness, population estimates according to the sampling effort (frequency of visits and number of plots), and the materials used, in order to determine whether the protocols currently in use provide reliable estimates. It is hypothesised that they underestimate populations and do not always allow for the detection of rarer species (Hutchens & DePemo, 2009). The individuals observed as part of this study will also be captured and used for other protocols and analyses.
b - Photo-identification: an effective method for monitoring small squamates? Individual identification is essential for monitoring populations. It often requires the use of expensive and invasive methods (e.g. PIT-tags). Photo-identification could enable inexpensive and minimally invasive monitoring, which is possible for small species for which the use of PIT-tags is not recommended. The aim of this study is therefore to evaluate the effectiveness of this method for squamates, and to compare commonly used software in order to optimise the monitoring of these species. During the detection study described above (1.a.), individuals of the various species observed will be captured and photographed twice using a standardised protocol, enabling similar photographs to be taken of all the individuals. This bank of photographs of known individuals will then be used to assess the efficiency of different software (l3S, WildID, APHIS, Hotspotter) for individual identification. Individuals identified by PIT-tags as part of study III.a. will also be photographed at each capture, enabling the method to be evaluated over the longer term. The results of this study will be of particular interest for small species such as the viviparous lizard, potentially enabling population monitoring by capture-mark-recapture using photo-identification.
II - Effectiveness of mitigation measures for squamates
In the context of road projects, the "avoid, reduce and compensate" doctrine is implemented. This involves, among other things, the addition of barriers and wildlife crossings designed to preserve ecological connectivity and reduce mortality linked to wildlife vehicle collisions. However, little is known about their effectiveness for squamates. The aim of this second section is therefore to determine whether these structures are suitable and what features would make them more effective.
a - Effectiveness of small wildlife barriers in reducing squamate mortality Roadside barriers are usually made of fine mesh. However, little is known about their effectiveness in preventing squamates from crossing them. The aim of this study is therefore to investigate the effectiveness of various commonly used barriers (wire mesh, sheet metal, concrete, with or without a flap) and at different heights. Transparent and opaque barriers have been selected in order to assess whether opacity plays a role in the number of attempts made by individuals to cross the barrier, which could result in deleterious energy expenditure. Different species will be tested under controlled conditions in order to assess their crossing capacities and their behaviour when faced with barriers. Species with different sizes and modes of locomotion will be selected (i.e. Stumped Lizard, Snapping Lizard, Fragile Orvet and Helvetic Snake). The individuals will be placed in an arena that has already been used for similar studies on amphibians (Conan et al., 2023), set up at the VRPV enclosure ("Voie Rapide du Piémont des Vosges"; Coordinates: 48.512303, 7.582014).
b - Use of wildlife crossings by squamates
When road infrastructure is being built, wildlife crossings are put in place to preserve ecological connectivity. Their effectiveness depends entirely on the behaviour of the target species when faced with these structures (i.e. whether or not they enter the crossing, whether or not they complete the crossing, etc.), something that has not been studied very much in squamates. This study is based on the design of effective photo traps for poikilothermic species (i.e. species whose body temperature varies with that of the environment) in order to study their use of wildlife crossings in situ. The photo-traps commonly used operate using infrared radiation to detect objects whose temperature is different from that of the environment, and therefore do not work for our target species. Systems using laser triggers ('HAL T' type) are being considered. The photo traps will be evaluated ex situ before being installed at various wildlife crossings near the sites monitored in l.a., l.b., Ill.a. They will be lifted every week in order to change the SD card and analyse the photos taken. The passage data collected can be compared with the specific richness known at the sites monitored in the vicinity. This will make it possible to determine whether this monitoring is representative of the specific diversity of reptiles living in the vicinity, i.e. to assess whether certain species use the structures more or less than others. The data will also be analysed temporally in order to determine the periods of use for different species, and potentially migration peaks.
111 - Ecology in interaction with road infrastructure. Roadsides provide attractive habitats for reptiles, but their quality for these species is poorly understood. This final section will study the quality of roadside habitats for squamates by looking at population dynamics, individual quality and habitat use.
a - Is living by the roadside a good situation?
A first method of assessing the quality of habitats for a species is to study the quality of the populations present in them. The quality of a habitat (presence or absence of resources, sources of stress, pollution, etc.) can have an impact on the selective value of individuals and the dynamics of the populations present there. The first aim of this study is to assess individual quality and stress indices (body condition, proportion of autotomy, fluctuating asymmetry, nuptial coloration, etc.) in different squamate populations. As part of the monitoring on plates (1.a.), individuals will be captured and biometric measurements will be taken in order to obtain these various indices. The relationship between these indices and proximity to road infrastructure will be studied in order to determine whether individual quality and population dynamics are influenced by distance from the road and landscape characteristics. In order to study population dynamics, the individuals will also be marked by PIT-tags (except for the viviparous lizard because of its small size) and photographed (l.b. ). This individual identification will enable Capture-Marking-Recapture monitoring to be carried out at the various sites. The capture data obtained will be used to model the dynamics of the different populations (growth or decline indices). In order to determine whether roads influence populations, the relationship between these dynamics and the proximity of road infrastructures and landscape characteristics will be studied.
b - Habitat use by the viviparous lizard
Improving our knowledge of the species' habitat use is essential in order to optimise development and compensation during the construction of road infrastructures. The aim of this project is to study the habitat preferences, and if possible the home range, of the viviparous lizard. In order to assess whether external telemetry transmitters have an impact on locomotion, body condition and behaviour for this species, 10 individuals will be fitted with objects of identical shape and weight to a transmitter and monitored under controlled conditions. l O control individuals will be monitored under the same conditions for the planned monitoring period of l months. If the dummy transmitters do not have a significant negative impact on the individuals (i.e. on their locomotion and body condition), telemetry monitoring will be carried out in the second year of the thesis. Individuals will be located twice a day in order to monitor their movements. The study sites will be mapped in order to study the habitat preferences of the individuals monitored. The locations will be used to model their home ranges. The habitat preferences observed can be used to model ecological niches and ecological networks. These results will provide a better understanding of the ecology of this species and thus help to improve management.
Organisation
Year 1 - 2024:
Winter:
Site preparation.
Implementation of the necessary derogations.
Spring and Summer:
Monitoring of sites for studies I.a., l.b. and III.a. From March to July with a Master 2 trainee.
Evaluation of the effectiveness of the barriers for squamates (II.a.) 2 days a week from March, depending on the specimens captured.
Locomotion test and body condition for study IIl.b. From August.
Autumn:
Publication of results.
Conference presentations.
Conceptualisation of equipment for study 11.b.
Year 2 - 2025:
Winter:
Site preparation.
Ex situ testing of camera traps for study 11.b.
Spring and Summer:
Monitoring of sites for studies I.a., I.b. and III.a. From March to July with a Master 2 trainee.
Telemetric monitoring of the Viviparous Lizard in May (III.b.) with a Master 2 trainee.
Setting up photo-trap monitoring of wildlife crossings (11.b.).
Autumn:
Publication of results.
Presentations at conferences.
Year 3 - 2026:
Publication of results and drafting of manuscript.
Possibility of additional fieldwork if necessary for study 111.b.
Bibliography
Aburrow, K., Moffat, D., Bega, S., & Clarke, K. (2023). What is wrong with wildlife fencing and what should we do? A review of fencing guidance for reptiles and amphibians.
Andrews, K. M., & Gibbons, J. W. (2005). How do highways influence snake movement? Behavioral responses to roads and vehicles. Copeia, 2005(4), 772-782.
Andrews, K. M., Gibbons, J. W., & Jochimsen, D. M. (2006). Literature synthesis of the effects of roads and vehicles on amphibians and reptiles. Synthesis, 2006.
-Antrop, M. (2004). Landscape change and the urbanization process in Europe. Landscape and urban planning, 67(1-4), 9-26.
Baxter-Gilbert, J. H., Riley, J. L., Lesbarrères, D., & Litzgus, J. D. (2015). Mitigating reptile road mortality: fence failures compromise ecopassage effectiveness. PLos one, I 0(3), e0120537.
Bissonette, J. A., & Rosa, S. A. (2009). Road zone effects in small-mammal communities. Ecology and society, 14( 1 ).
Blouin-Demers, G., & Weatherhead, P. J. (2002). Habitat-specific behavioural thermoregulation by black rat snakes (Elaphe obsoleta obsoleta). Oikos, 97(1), 59-68.
Boarman, W. I., & Sazaki, M. (2006). A highway's road-effect zone for desert tortoises (Gopherus agassizii). Journal of Arid Environments, 65(1), 94-101.
Brattstrom, B. H., & Bondello, M. C. ( 1983 ). Effects of off-road vehicle noise on desert vertebrates. Environmental ejfects of off-road vehicles: impacts and management in arid regions, 167-206.
Carthew, S. M., Garrett, L. A., & Ruykys, L.(2013). Roadside vegetation can provide valuable habitat for small, terrestrial fatma in South Australia. Biodiversity and conservation, 22, 737- 754.
Forman, R. T., & Alexander, L. E. (1998). Roads and their major ecological effects. Annual review of ecology and systematics, 29(1), 207-231.
Herrmann, H. W., Pozarowski, K. M., Ochoa, A., & Schuett, G. W. (2017). An interstate highway affects gene flow in a top reptilian predator (Crotalus atrox) of the Sonoran Desert. Conservation Genetics, 18, 911-924.
Homyack, J. A., O'Bryan, C. J., Thomton, J. E., & Baldwin, R. F. (2016). Community occupancy of herpetofauna in roadside ditches in a managed pine landscape. Forest Ecology and Management, 361, 346-357.
Hutchens, S. J., & DePemo, C. S. (2009). Efficacy of sampling techniques for determining species richness estimates ofreptiles and amphibians. Wildlife Biology, 15(2), 113-122.
International Road Federation (2022). World Road Statistics 2015-2020.
IUCN (2022). The IUCN Red List of Threatened Species. Version 2022-2. https://www.iucnredlist.org . Accessed on 27/06/2023
Jakobsson, S., Bernes, C., Bullock, J. M., Verheyen, K., & Lindborg, R. (2018). How does roadside vegetation management affect the diversity of vascular plants and invertebrates? A systematic review. Environmental Evidence, 7, 1-14.
Mautz, W. J., & Dohm, M. R. (2004). Respiratory and behavioral effects of ozone on a lizard and a frog. Comparative Biochemistry and Physiology Part A: Molecular & Jntegrative Physiology, 139(3), 371-377.
Meek, R. (2009). Patterns of reptile road-kills in the Vendée region of western France. The Herpetological Journal, 19(3), 135-142.
Meylan, S., Belliure, J., Clobert, J., & de Fraipont, M. (2002). Stress and body condition as prenatal and postnatal deterrninants of dispersal in the common lizard (Lacerta vivipara). Hormones and Behavior, 42(3), 319-326.
Mibroda, J., Duchamp, J., McNeil, D. J., Townsend, J., & Larkin, J. L. (2017). Roadside habitat use by the endemic Short-headed Gartersnake (Thamnophis brachystoma) in northwestern Pennsylvania, USA. Herpetological Conservation and Biology, 12(3), 655-663.
Ministère de la Transition Ecologique et solidaire (2017). Memento of urban and road transport 2017.
Robertson, B. A., & Hutto, R. L. (2006). A framework for understanding ecological traps and an evaluation of existing evidence. Ecology, 87(5), 1075-1085.
Shanley, C. S., & Pyare, S. (2011). Evaluating the road-effect zone on wildlife distribution in a rural landscape. Ecosphere, 2(2), 1-16.
Steen, D. A., Aresco, M. J., Beilke, S. G., Compton, B. W., Condon, E. P., Kenneth Dodd Jr, C., ... & Gibbs, J. P. (2006). Relative vulnerability of female turtles to road mortality. Animal Conservation, 9(3), 269-273.
Teixido, A. L., Sehn, H., Quintanilla, L. G., Gonçalves, S. R., Férnandez-Arellano, G. J., Dàttilo, W., ... & Moreira, L. F. (2021). A meta-analysis of the effects of fragmentation on the megadiverse herpetofauna of Brazil. Biotropica, 53(3), 726-737.
UICN (2023). Red list of threatened species (https://www.iucnredlist.org/ )
UNDESA (2019). World urbanization prospects: The 2018 revision.
Van Der Ree, R., Smith, D. J., & Grilo, C. (2015). Handbook ofroad ecology. John Wiley & Sons.
Wells, M., Langton, T., Garland, L., & Wilson, G. (1995, November). The value of motorway verges for reptiles-a case study. In Reptile survey methods: proceedings of a seminar (Vol. 7, pp. 174-181).
Wood, A., Stedman-Edwards, P., & Mang, J. (Eds.). (2000). The root causes of biodiversity loss. Earthscan. 21

Requirements

Research Field

Biological sciences

Education Level

Bachelor Degree or equivalent

Research Field

Environmental science

Education Level

Bachelor Degree or equivalent

Languages

FRENCH

Level

Basic

Research Field

Biological sciences

Years of Research Experience

1 - 4

Research Field

Environmental science

Years of Research Experience

1 - 4

Additional Information
Additional comments

NA

Website for additional job details

https://emploi.cnrs.fr/Offres/Doctorant/UMR7372-XAVBON0-001/Default.aspx

Work Location(s)

Number of offers available

1

Company/Institute

Centre d'études biologiques de Chizé

Country

France

City

STRASBOURG

Geofield

Where to apply

Website

https://emploi.cnrs.fr/Candidat/Offre/UMR7372-XAVBON0-001/Candidater.aspx

Contact

City

STRASBOURG

Website

http://www.cebc.cnrs.fr/

STATUS: EXPIRED