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1.  Development of microsatellite primers in the protected species Viola elatior (Violaceae) using next-generation sequencing1 
Applications in Plant Sciences  2015;3(5):apps.1500011.
Premise of the study:
Viola elatior (Violaceae) is a Eurasian perennial plant species in which French populations are threatened by anthropogenic pressures. Microsatellite primers were developed to investigate its genetic structure and diversity.
Methods and Results:
Eight microsatellite markers were isolated using next-generation sequencing. Loci were amplified and screened for 138 individuals in 17 populations from France. Two of the eight polymorphic loci presented no variability across populations. The total number of alleles per locus varied from two to four. Observed heterozygosity ranged from 0.051 to 1.000. All primers amplified successfully in the closely related species V. pumila.
This set of microsatellites offers a valuable tool for assessing population genetic diversity of the species to improve its conservation and base management efforts. High observed heterozygosity values probably reflect the particular mating system of the species and suggest an important tendency to clonality.
PMCID: PMC4435467  PMID: 25995977
conservation; microsatellites; next-generation sequencing; population genetics; Viola elatior; Violaceae
2.  Ecological specialization and rarity indices estimated for a large number of plant species in France 
Data in Brief  2015;3:165-168.
The biological diversity of the Earth is being rapidly depleted due to the direct and indirect consequences of human activities. Specialist or rare species are generally thought to be more extinction prone than generalist or common species. Testing this assumption however requires that the rarity and ecological specialization of the species are quantified. Many indices have been developed to classify species as generalists vs. specialists or as rare vs. common, but large data sets are needed to calculate these indices.
Here, we present a list of specialization and rarity values for more than 2800 plant species of continental France, which were computed from the large botanical and ecological dataset SOPHY. Three specialization indices were calculated using species co-occurrence data. All three indices are based on (dis)similarity among plant communities containing a focal species, quantified either as beta diversity in an additive (Fridley et al., 2007 [6]) or multiplicative (Zeleny, 2008 [15]) partitioning of diversity or as the multiple site similarity of Baselga et al. (2007) [1]. Species rarity was calculated as the inverse of a species occurrence.
PMCID: PMC4510126  PMID: 26217738
Ecological specialization indices; Rarity; Species co-occurrence; Flora of France
3.  The Influence of Low Intensities of Light Pollution on Bat Communities in a Semi-Natural Context 
PLoS ONE  2014;9(10):e103042.
Anthropogenic light pollution is an increasingly significant issue worldwide. Over the past century, the use of artificial lighting has increased in association with human activity. Artificial lights are suspected to have substantial effects on the ecology of many species, e.g., by producing discontinuities in the territories of nocturnal animals. We analyzed the potential influence of the intensity and type of artificial light on bat activity in a semi-natural landscape in France. We used a species approach, followed by a trait-based approach, to light sensitivity. We also investigated whether the effect of light could be related to foraging traits. We performed acoustic surveys at sites located along a gradient of light intensities to assess the activity of 15 species of bats. We identified 2 functional response groups of species: one group that was light-tolerant and one group that was light-intolerant. Among the species in the latter group that appear to be disadvantaged by lighting conditions, many are rare and threatened in Europe, whereas the species from the former group are better able to thrive in disturbed habitats such as lighted areas and may actually benefit from artificial lighting. Finally, several methods of controlling light pollution are suggested for the conservation of bat communities. Recommendations for light management and the creation of dim-light corridors are proposed; these strategies may play an important role in protecting against the impact of light pollution on nocturnal animals.
PMCID: PMC4215844  PMID: 25360638
4.  Mixing Plants from Different Origins to Restore a Declining Population: Ecological Outcomes and Local Perceptions 10 Years Later 
PLoS ONE  2013;8(1):e50934.
Populations of the Large-flowered Sandwort (Arenaria grandiflora L.) in the Fontainebleau forest (France) have declined rapidly during the last century. Despite the initiation of a protection program in 1991, less than twenty individuals remained by the late 1990s. The low fitness of these last plants, which is likely associated with genetic disorders and inbreeding depression, highlighted the need for the introduction of non-local genetic material to increase genetic diversity and thus restore Fontainebleau populations. Consequently, A. grandiflora was introduced at three distant sites in the Fontainebleau forest in 1999. Each of these populations was composed of an identical mix of individuals of both local and non-local origin that were obtained through in vitro multiplication. After establishment, the population status (number of individuals, diameter of the plants, and number of flowers) of the introduced populations was monitored. At present, two populations (one of which is much larger than the other) persist, while the third one became extinct in 2004. Analyses of the ecological parameters of the introduction sites indicated that differences in soil pH and moisture might have contributed to the differences in population dynamics. This introduction plan and its outcome attracted interest of local community, with those who supported the plan and regarded its 10-year result as a biological success (i.e., persistent populations were created), but also those who expressed reservations or disapproval of the plan and its outcome. To understand this controversy, a sociological study involving 27 semi-structured interviews was carried out. From these interviews emerged three areas of controversy: alteration of the identity of the plant, alteration of the identity of its territory, and the biological and ethical consequences of the techniques used for the experimental conservation.
PMCID: PMC3549913  PMID: 23349668
5.  Morphological versus molecular markers to describe variability in Juniperus excelsa subsp. excelsa (Cupressaceae) 
AoB Plants  2012;2012:pls013.
This is a large scale investigation of morphological diversity in Juniperus excelsa excelsa. It offers complementary results to those obtained for the same populations using molecular markers. These two approaches are complementary and should be considered together in order to obtain a comprehensive view of the variability of J. excelsa excelsa.
Background and aims
Juniperus excelsa M.-Bieb. is a major forest element in the mountains of the eastern part of Mediterranean and sub-Mediterranean regions. This study comprises the first morphological investigation covering a large part of the geographical range of J. excelsa and aims to verify the congruency between the morphological results and molecular results of a previous study.
We studied 14 populations sampled from Greece, Cyprus, Ukraine, Turkey and Lebanon, 11 of which have previously been investigated using molecular markers. Three hundred and ninety-four individuals of J. excelsa were examined using nine biometric features characterizing cones, seeds and shoots, and eight derived ratios. Statistical analyses were conducted in order to evaluate the intra- and inter-population morphological variability.
Principal results
The level of intra-population variability observed did not show any geographical trends. The total variation mostly depended on the ratios of cone diameter/seed width and seed width/seed length. The discrimination analysis, the Ward agglomeration method and barrier analysis results showed a separation of the sampled populations into three main clusters. These results confirmed, in part, the geographical differentiation revealed by molecular markers with a lower level of differentiation and a less clear geographical pattern. The most differentiated populations using both markers corresponded to old, isolated populations in the high altitudes of Lebanon (>2000 m). Moreover, a separation of the northern Turkish population from the southern Turkish populations was observed using both markers.
Morphological variation together with genetic and biogeographic studies make an effective tool for detecting relict plant populations and also populations subjected to more intensive selection.
PMCID: PMC3357054  PMID: 22822421
6.  High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region 
AoB Plants  2011;2011:plr003.
Juniperus excelsa constitutes a precious woody species of high ecological value able to grow up to Mountain treeline around the Mediterranean. Nuclear microsatellites were used to shed light on genetic diversity and differentiation of different Mediterranean populations. This information is essential in planning conservation strategies and reforestation programs.
Background and aims
Juniperus excelsa is an important woody species in the high mountain ecosystems of the eastern Mediterranean Basin where it constitutes the only coniferous species found at the tree line. The genetic diversity within and among J. excelsa populations of the eastern Mediterranean Basin is studied in the light of their historical fragmentation.
Nuclear microsatellites originally developed for Juniperus communis and J. przewalskii were tested on 320 individuals from 12 different populations originating from Lebanon, Turkey, Cyprus, Greece and the Ukraine.
Principal results
Among the 31 nuclear microsatellite primers tested, only three produced specific amplification products, with orthology confirmed by sequence analysis. They were then used for genetic diversity studies. The mean number of alleles and the expected heterozygosity means were Na=8.78 and He=0.76, respectively. The fixation index showed a significant deviation from Hardy–Weinberg equilibrium and an excess of homozygotes (FIS=0.27–0.56). A moderate level of genetic differentiation was observed among the populations (FST=0.075, P<0.001). The most differentiated populations corresponded to old vestigial stands found at the tree line (>2000 m) in Lebanon. These populations were differentiated from the other populations that are grouped into three sub-clusters.
High levels of genetic diversity were observed at species and population levels. The high level of differentiation in the high-mountain Lebanese populations reflects a long period of isolation or possibly a different origin. The admixture observed in other populations from Lebanon suggests a more recent separation from the Turkish–southeastern European populations.
PMCID: PMC3064508  PMID: 22476474
7.  No Genetic Diversity at Molecular Markers and Strong Phenotypic Plasticity in Populations of Ranunculus nodiflorus, an Endangered Plant Species in France 
Annals of Botany  2007;99(6):1203-1212.
Background and Aims
Although conservation biology has long focused on population dynamics and genetics, phenotypic plasticity is likely to play a significant role in population viability. Here, an investigation is made into the relative contribution of genetic diversity and phenotypic plasticity to the phenotypic variation in natural populations of Ranunculus nodiflorus, a rare annual plant inhabiting temporary puddles in the Fontainebleau forest (Paris region, France) and exhibiting metapopulation dynamics.
The genetic diversity and phenotypic plasticity of quantitative traits (morphological and fitness components) were measured in five populations, using a combination of field measurements, common garden experiments and genotyping at microsatellite loci.
Key Results
It is shown that populations exhibit almost undetectable genetic diversity at molecular markers, and that the variation in quantitative traits observed among populations is due to a high level of phenotypic plasticity. Despite the lack of genetic diversity, the natural population of R. nodiflorus exhibits large population sizes and does not appear threatened by extinction; this may be attributable to large phenotypic plasticity, enabling the production of numerous seeds under a wide range of environmental conditions.
Efficient conservation of the populations can only be based on habitat management, to favour the maintenance of microenvironmental variation and the resulting strong phenotypic plasticity. In contrast, classical actions aiming to improve genetic diversity are useless in the present case.
PMCID: PMC3244344  PMID: 17468109
Metapopulation; Ranunculus nodiflorus; phenotypic plasticity; quantitative trait; genetic diversity; conservation

Results 1-7 (7)