Internship Opportunity in Landscape Genetics: Assessing Gene Flow among Populations of 2 Contrasting Herbaceous Plants within a Fragmented System

Habitat fragmentation is a major threat to biodiversity. Nonetheless, habitat fragmentation may have an unequal influence over genetic flow depending on specie life history traits and dispersion capacities (Baguette et al., 2013). Generally, the effects of fragmentation on genetic flow is more pronounced for sessile organisms, compared with more mobile or vagile ones (Callens et al., 2011), and for specialists compared with generalists (Bonte et al., 2003; Entling et al., 2011). The plant species Geum urbanum (wood avens: on the left picture below) and Primula elatior (true oxlip: on the right picture below) are common within highly fragmented European temperate forests. They are nonetheless two contrasting models in terms of dispersion abilities and ecological specialisation: P. elatior being a notorious forest specialist with limited dispersal abilities.

The proposed internship aims at evaluating functional connectivity in a fragmented system (temperate deciduous forests) by means of indirect estimators for this two contrasting model species. Contemporary and past genetic diversity will be measured using cytoplasmic genes (cpDNA – historic genetic variation) and microsatellites loci (contemporary gene flow) (Arens et al., 2004; Van Geert et al., 2006; Seino et al., 2014). Two landscape windows were selected for both the Hauts-de-France region (Thiérache) and the Brittany region (Zone Atelier Armorique): one window is characterized by forest patches interconnected through a dense hedgerow network (locally called ‘bocage’) while the other window is characterized by a highly fragmented system with few to no hedgerows. For the Hauts-de-France region, a third landscape window was selected as a control or baseline unfragmented system based on ‘virtual forest patches’ spread out across a forest matrix. Individuals were sampled in forest patches (or virtual forest patches) and in hedgerows during two field seasons (i.e. in 2017 and 2018). Functional connectivity and population genetic structure will be investigated using classic methods (DAPC) (Jombart et al., 2008) and Bayesian assigning tests (Pritchard et al., 2000; Guillot et al., 2005) for characterizing genetic structure. The role of landscape features on genetic structure will be assessed by means of correlative approaches and graph-theory methods. The successful applicant will be highly encouraged to propose other analytical methods if he/she deems fit.

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We seek a highly motivated and curious candidate. The successful candidate will be closely supervised by Professor Annie Guiller, Senior Researcher Jonathan Lenoir and PhD student Pedro Poli during his/her internship. He/She should be able to work independently. Strong interest in population genetics, landscape ecology, evolution and biostatistics are recommended, meaning that a good background in those domains is desired, but not mandatory. Those skills will be developed during the internship.

Funding: We acknowledge a grant from the “Fondation pour la Recherche sur la Biodiversité” (FRB, AO 2018).

Internship stipend: About 500 EUR per month during 6 months (January-June 2019).

Starting date and duration: The succesful applicant is expected to start his/her internship on the 7th of January 2019 for a 6 month duration.

Host Institute: Edysan is a mixed research unit involving the CNRS and Université de Picardie Jules Verne institutes. The research work developed in Edysan aims at understanding natural and semi-natural ecosystem functioning and impacts environment changes over those systems. We are well placed in Amiens, a nice and active city in the Picardy region. The laboratory has an ongoing partnership with Regional Molecular Biology Centre (CRRBM) that dispose of state of the art equipment and infrastructure.

Supervisors: Annie Guiller (Professeur), Jonathan Lenoir (CR CNRS) and Pedro Poli (PhD student).

Application deadline: 30th November 2018. Potential candidates should send a CV and a cover letter (in English or French) to: annie.guiller@u-picardie.fr, jonathan.lenoir@u-picardie.fr and pedro.poli@u-picardie.fr

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Call for a 3-yr PhD Position in Ecology, Phylogeography and Landscape Genetics

Title

Incorporating Phylogeographic infOrmation into niche moDels to improve species re-distribution projections under climAte waRming and habitat fragmentation: the Case of forest-dwelling specIes across European agricultural landscapeS [PODARCIS]

Aim

Climate warming and habitat fragmentation are two key components of global change that push species to redistribute or evolve to adapt to the new conditions (Lenoir & Svenning, 2015; Pecl et al., 2017). To hindcast and forecast species redistribution under past and future environmental conditions, respectively, the state-of-the-art is to use species distribution models (SDMs) (Guisan & Zimmermann, 2000). However, traditional SDMs assume that individuals from all populations of a given species respond equally to environmental changes although different populations from the same species may respond differently to environmental changes (Valladares et al., 2014). The most recent scientific literature on SDMs suggests that incorporating intraspecific variation into SDMs leads to less pessimistic redistribution projections (Pearman et al., 2010; Oney et al., 2013). Both phylogeography (Guiller & Madec, 2010; Guiller et al., 2012) and landscape genetics can provide spatially and temporally explicit information on the genetic structure and differences among populations of the same species that could be used to incorporate intraspecific variation into SDMs and thus improve redistribution projections under climate change. This PhD project entitled PODARCIS specifically aims at incorporating intraspecific variation data obtained from a union of phylogeography and landscape genetics (Rissler, 2016) into SDMs. PODARCIS is part of the EU (BiodivERsA) project Woodnet and the regional (Hauts-de-France) project Pegase. Three model species of European temperate forests will be studied throughout the PhD project: the plants Geum urbanum and Oxalis acetosella characterized by different dispersal capacities as well as the tick Ixodes ricinus considered as the main vector of the Lyme Borreliosis in Western Europe and thus implying potential public health hazards. PODARCIS rests on three basic pillars:

  • Phylogeography and historical demography to determine the phylogeographic structure of each species and to disentangle the relative impacts of past versus current climatic changes in shaping the geographic distributions of genealogical lineages;
  • Fundamental ecology to develop SDMs adapted to each genealogical lineage and to compare these lineage-specific SDMs to classical SDMs at different periods (Pleistocene and Anthropocene);
  • Landscape genetics to identify landscape and environmental features that constrain genetic connectivity and thus to account for dispersal and gene flow across the landscape.

Keywords

Climate change, ecoepidemiology, forest ecosystems, landscape genetics, phylogeography, population genetics, spatial statistics, species distribution modelling

Qualifications

The candidate is expected to have good training in statistics or mathematical modelling and have a strong background in ecology or evolutionary biology (population genetics and phylogeography). Typical PhD candidates will have a master degree in ecology or evolutionary biology. Basic knowledge and interest in ecology and landscape genetics is required. Experience in molecular genetics and GIS knowledge will be further appreciated. Programming skills in Free and Open Source Software (FOSS) such as in the R and GRASS environments will be a clear advantage. Teamwork skills, curiosity, autonomy at work as well as good oral and written communication skills in English will also be valued.

Supervision

The student will be hosted within the research unit EDYSAN (Ecologie et Dynamique des Systèmes Anthropisés, FRE 3498 CNRS – UPJV, head Prof. Guillaume Decocq), 33 rue Saint Leu, 80000 Amiens, France. EDYSAN is a young, diverse, vibrant and international research community with strong collaborative interdisciplinary ties within and beyond Amiens.

Application

Applications (letter, CV and 2 contacts for references) should be sent to Annie Guiller, Jonathan Lenoir and Guillaume Decocq (guillaume.decocq@u-picardie.fr) no later than June 15. The selected candidate will have an audition with the Doctoral Department at UPJV (Université de Picardie Jules Verne, Amiens) in the beginning of July and, if successful, will start in September 2017.

References

  • Guiller & Madec (2010). Historical biogeography of the land snail Cornu aspersum: a new scenario inferred from haplotype distribution in the Western Mediterranean Basin. BMC Evolutionary Biology, 10: 18
  • Guiller et al. (2012) Tracing the invasion of the Mediterranean land snail Cornu aspersum aspersum becoming an agricultural and garden pest in areas recently introduced. PLoS ONE, 7: e49674
  • Guisan & Zimmermann (2000) Predictive habitat distribution models in ecology. Ecological Modelling, 135: 147–186
  • Lenoir & Svenning (2015). Climate-related range shifts – a global multidimensional synthesis and new research directions. Ecography, 38: 15–28
  • Oney et al. (2013). Intraspecific variation buffers projected climate change impacts on Pinus contorta. Ecology and Evolution, 3: 437–449
  • Pearman et al. (2010). Within-taxon niche structure: niche conservatism, divergence and predicted effects of climate change. Ecography, 33: 990–1003
  • Pecl et al. (2017). Biodiversity redistribution under climate change: Impacts on ecosystems and human well-being. Science, 355: eaai9214
  • Rissler (2016). Union of phylogeography and landscape genetics. PNAS, 113: 8079–8086
  • Valladares et al. (2014). The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change. Ecology Letters, 17: 1351–1364