CERoPath

Rodent populations and individuals are confronted to several environmental stressors including landscape changes, rodent community composition, and the nature and diversity of parasites and pathogens. Phenotypic and genetic markers reveal the strength of the stress and the potential of adaptation. Geometric morphometrics [17] and immunogenetics [12] are the two methodologies that will be used for investigating local adaptation and maladaptation.

WP2.1. Geometric morphometrics (GM) and Fluctuating Asymmetry (FA) of rodents

The recent emergence of the statistical analysis of shape and size and methods of GM allows an exploration and a quantification of patterns of biological variation considering the geometric architecture of phenotypes [17]. GM allied with a comparative approach will be used for identifying morphological component of phenotypes linked to adaptation to new environments and for estimating how much phenotypes can be constrained by their phylogenetic history [16] (WP1). These methods can be applied for quantifying difference in skeletal morphologies between species of rodents [3] [20]. Moreover, they offer a way to detect even small shift in morphology between populations, and a cheap diagnostic tool for taxonomic identification of species.

Fluctuating asymmetry (random deviations from perfect bilateral symmetry) is commonly used as a measure of developmental stability . Elevated levels of FA are potentially relevant as indicator of demographic bottlenecks, environmental stress or habitat disturbance [4] [41] [46] [56]. GM has been adapted for measuring amount of fluctuating asymmetry in integrating the complexity of the architecture of organisms [2]. We hypothesise to find elevated FA in individuals less able to buffer environmental stress  during development. Moreover, as increase of FA has been reported in hosts when infested by parasites [5], we will measure levels of asymmetries in relation to parasitic load, parasite diversity and parasite life-history traits, using the methods developed by partner 1. Changes and perturbations in developmental patterns can be analyzed in a comparative way in rodent communities taking into account potential phylogenetic inertia [16] using the methodology developed by [24].

WP2.2. Population genetics and immunogenetics of rodents

Interaction among species may affect genetic diversity and natural selection of a focal species through indirect genetic effects (IGE) [14]. Pathogens affect the genetic variation controlling genes involved in the interaction, ie. the immune genes. Several studies have established associations between particular MHC (Major Histocomptability Complex) alleles/haplotypes  and resistance or susceptibility to single parasite infections [48], although it has been shown that single associations cannot explain the high genetic diversity of the MHC genes [59] [70]. Demographic changes induced by landscape changes may have significant impact on the adaptive genetics  [44]. Primers and molecular techniques used for the laboratory rat (R. norvegicus ), for which the MHC genes have been completely sequenced [38], will be adapted to other Rattus species and close relatives by partner 2. MHC diversity and MHC gene expression will be investigated according to methods developed by partner 2 [8] [9]. Associations between alleles and pathogens will be performed.

WP2.3. Population genetics and virulence of pathogens

  Interaction between species is a dual action which involves reaction form the host but also active and adaptive mechanisms  of virulence and pathogenicity from the pathogen. Virulence and selected mechanisms often result from adaptive genetics or co-evolution of host and pathogen [10] [29]. It might also reflect recent movements of populations of pathogens and emergence. Biodiversity related to virulence of pathogens is therefore a key aspect to investigate which can shed light on population structure, functional diversity, phylogeny and evolution. MLST and MLVA provide markers for analyzing genetic diversity, both neutral and selected, using precise genotyping. MLST and MLVA  were proved very efficient to identify pathotypes and characterize populations of Leptospira  [1] [58] [61]. This same proven approach will be applied here to type and characterize the biodiversity of both Leptospira  and Rickettsia .

Specific outputs regarding this WP2

  1/ relationships between FA and environmental stress (habitat, parasites) in Mus spp and Rattus  spp.

  2/ Diversity of MHC genes in Rattus spp and its relationship to pathogen diversity

  3/ Diversity and genotyping of virulent genes in Leptospira and Rickettsia