Microsatellite markers for Dictyochloropsis reticulata (Trebouxiophyceae), the symbiotic alga of the lichen Lobaria pulmonaria (L.)

We isolated and characterized eight microsatellite markers for Dictyochloropsis reticulata, the primary photosynthetic partner of the epiphytic lichen Lobaria pulmonaria. These are the first microsatellite loci reported for a lichen symbiotic alga. These polymorphic markers will be useful for investigating spatial genetic structure, biogeography and dispersal of this eukaryotic alga and will generally shed light on the coevolution of the green-algal lichen symbiose

Remnants fragments preserve genetic diversity of the old forest lichen Lobaria pulmonaria in a fragmented Mediterranean mountain forest

Fragmentation represents a serious threat to biodiversity worldwide, however its effects on epiphytic organisms is still poorly understood. We study the effect of habitat fragmentation on the genetic population structure and diversity of the red-listed epiphytic lichen, Lobaria pulmonaria, in a Mediterranean forest landscape. We tested the relative importance of forest patch quality, matrix surrounding fragments and connectivity on the genetic variation within populations and the differentiation among them. A total of 855 thalli were sampled in 44 plots (400m2) of 31 suitable forest fragments (beeches and oaks), in the Sierra de Ayllón in central Spain. Variables related to landscape attributes of the remnant forest patches such as size and connectivity and also the nature of the matrix or tree species had no significant effects on the genetic diversity of L. pulmonaria. Values of genetic diversity (Nei's) were only affected by habitat quality estimated as the age patches. Most of the variation (76%) in all populations was observed at the smallest sampled unit (plots). Using multiple regression analysis, we found that habitat quality is more important in explaining the genetic structure of the L. pulmonaria populations than spatial distance. The relatively high level of genetic diversity of the species in old forest patches regardless of patch size indicates that habitat quality in a highly structured forest stand determines the population size and distribution pattern of this species and its associated lichen community. Thus, conservation programmes of Mediterranean mountain forests have to prioritize area and habitat quality of old forest patche

Dispersal ecology of the endangered woodland lichen Lobaria pulmonaria in managed hemiboreal forest landscape

Changes in the forest management practices have strongly influenced the distribution of species inhabiting old-growth forests. The epiphytic woodland lichen Lobaria pulmonaria is frequently used as a model species to study the factors affecting the population biology of lichens. We sampled 252 L. pulmonaria individuals from 12 populations representing three woodland types differing in their ecological continuity and management intensity in Estonia. We used eight mycobiont-specific microsatellite loci to quantify genetic diversity among the populations. We calculated the Sørensen distance to estimate genetic dissimilarity among individuals within populations. We revealed that L. pulmonaria populations have significantly higher genetic diversity in old-growth forests than in managed forests and wooded meadows. We detected a significant woodland-type-specific pattern of genetic dissimilarity among neighbouring L. pulmonaria individuals, which suggests that in wooded meadows and managed forests dominating is vegetative reproduction. The vegetative dispersal distance between the host trees of L. pulmonaria was found to be only 15-30m. Genetic dissimilarity among individuals was also dependent on tree species and trunk diameter. Lobaria pulmonaria populations in managed forests included less juveniles compared to old-growth forests and wooded meadows, indicating that forest management influences life stage structure within populations. We conclude that as intensive stand management reduces the genetic diversity of threatened species in woodland habitats, particular attention should be paid to the preservation of remnant populations in old-growth habitats. Within managed habitats, conservation management should target on maintenance of the stand's structural diversity and availability of potential host tree

Simple rules for an efficient use of geographic information systems in molecular ecology

Geographic Information Systems (GIS) are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and livestock species is becoming a trend with many researchers publishing genomic data that is specifically suitable for landscape studies. GIS uniquely reveal the possibility to overlay genetic information with environmental data and, as such, allow us to locate and analyze genetic boundaries of various plant and animal species or to study gene-environment associations (GEA). This means that, using GIS, we can potentially identify the genetic bases of species adaptation to particular geographic conditions or to climate change. However, many biologists are not familiar with the use of GIS and underlying concepts and thus experience difficulties in finding relevant information and instructions on how to use them. In this paper, we illustrate the power of free and open source GIS approaches and provide essential information for their successful application in molecular ecology. First, we introduce key concepts related to GIS that are too often overlooked in the literature, for example coordinate systems, GPS accuracy and scale. We then provide an overview of the most employed open-source GIS-related software, file formats and refer to major environmental databases. We also reconsider sampling strategies as high costs of Next Generation Sequencing (NGS) data currently diminish the number of samples that can be sequenced per location. Thereafter, we detail methods of data exploration and spatial statistics suited for the analysis of large genetic datasets. Finally, we provide suggestions to properly edit maps and to make them as comprehensive as possible, either manually or trough programming languages

Impact of the urbanization process on connectivity and genetic diversity - a spatially explicit simulation approach

Urbanization leads to fragmentation, degradation or loss of natural environments and reduces connectivity between remaining habitat patches. This affects dispersal and establishment of species and their genes and might have adverse effects on biodiversity in urban areas. Here we assess functional connectivity between green spaces for one plant (Plantago major) and one insect (Pieris rapae) model species in the Geneva urban area. We also estimate the impact of future urbanization projects planned until 2030 in Geneva (constructions and road projects) on the connectivity network. We show that the connectivity between small green spaces in the urban centres and larger ones in peripheral areas is fragile and unstable. Potential barriers to dispersal for the study species are mainly buildings, roads, but also large areas of forests, crops and vineyards. Furthermore and based on spatially explicit simulations of gene flow, we test how the distribution of genetic variation among populations along rural-urban gradients is affected by urban landscape elements. We compare these results to empirically observed population responses of the butterfly species P. rapae in the region of Marseille, France. For different dispersal scenarios and taking into account the effect of future intensification of urbanization, results show a decrease in genetic diversity in areas characterized by medium to high urban densities. In order to conserve and promote genetically stable and diverse populations, it is therefore important to maintain or increase landscape connectivity, especially between green spaces in dense urban centres and those in more natural peripheral areas

A participatory WebGIS platform to support biodiversity inventory in the Geneva cross-border area

The context is the URBANGENE project which aims at estimating the impact of urbanization on biodiversity using genetic information. The paper discusses the opportunities to involve citizens in a conservation process through the development of a participatory platform based on user-friendly, specially adapted and reusable crowdsourcing tools

A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON)

Background In 2007, the Food and Agriculture Organization of the United Nations (FAO) initiated the Global plan of action for Farm Animal Genetic Resources (FAnGR). The main goal of this plan is to reduce further loss of genetic diversity in farm animals, so as to protect and promote the diversity of farm animal resources. An important step to reach this goal is to monitor and prioritize endangered breeds in the context of conservation programs. Methodology/Web portal implementation The GENMON WebGIS platform is able to monitor FAnGR and to evaluate the degree of endangerment of livestock breeds. The system takes into account pedigree and introgression information, the geographical concentration of animals, the cryo-conservation plan and the sustainability of breeding activities based on socio-economic data as well as present and future land use conditions. A multi-criteria decision tool supports the aggregation of the multi-thematic indices mentioned above using the MACBETH method, which is based on a weighted average using satisfaction thresholds. GENMON is a monitoring tool to reach subjective decisions made by a government agency. It relies on open source software and is available at http://lasigsrv2.epfl.ch/genmon-ch. Results/Significance GENMON allows users to upload pedigree-information (animal ID, parents, birthdate, sex, location and introgression) from a specific livestock breed and to define species and/or region-specific weighting parameters and thresholds. The program then completes a pedigree analysis and derives several indices that are used to calculate an integrated score of conservation prioritization for the breeds under investigation. The score can be visualized on a geographic map and allows a fast, intuitive and regional identification of breeds in danger. Appropriate conservation actions and breeding programs can thus be undertaken in order to promote the recovery of the genetic diversity in livestock breeds in need. The use of the platform is illustrated by means of an example based on three local livestock breeds from different species in Switzerland

Biodiversity dynamics and the effect of urban environment on the distribution of genetic variation in the Geneva cross-border area

Population growth, urbanization and agriculture lead to degradation and loss of natural environment. This has an adverse effect on the diversity of habitats, species and genes and might cause decline in the quality of life of the resident population. In this context and in the densely populated Geneva cross-border area, we study biodiversity dynamics and the effect of the environment on the distribution of genetic variation (URBANGENE project). We use genetic information of three model species (a plant, an insect and an amphibian) in combination with environmental and landscape data to evaluate their potential to disperse and adapt to urban environments. Based on a representative population survey, we further investigate how urban residents perceive their quality of life with a local biodiversity perspective, compared with health data measured in the same areas. Using genome-wide SNP data, we assessed genome-environment associations for Plantago major, a synanthropic plant, in order to obtain information on its ability to disperse among habitats and to adapt to the urban environment. Butterfly (Pieris rapae) and amphibian model species (Bufo bufo) will be sampled in 2015. As regards the amphibians, we developed a WebGIS participatory platform, making it possible for Geneva residents to indicate the geographic location of amphibian habitats on an interactive map, and to transmit information on the species they observed in this area. The integration of results from this interdisciplinary project should allow for a more sustainable urban development and a better conservation and management of biodiversity in urban areas

Relationship between land cover type and Body Mass Index in Geneva

Past studies conducted in urban areas analyzed the impact of the presence of green spaces on public health, and highlighted in particular the psychological benefits of interacting with nature. To investigate a supposed relationship between overweight and dense built environment, we focused on the State of Geneva, Switzerland, and calculated the correlation between Body Mass Index (BMI) in a representative sample of 6663 adults and the percentage of natural areas at the locations where these individuals were living. To this end, we used populationbased health data from the “Bus Sante” study (Geneva University Hospitals) and multi-scale land cover maps obtained by means of satellite images and LiDAR data classification. We found little correlation between BMI (as a proxy for health) and land cover data and were not able to verify the working hypothesis at local and regional scales. However, an important phenomenon highlighted here is the difference in the results obtained between the city center and the whole State