Species-specific responses to landscape fragmentation: implications for management strategies

Habitat fragmentation affects the integrity of many species, but little is known about species-specific sensitivity to fragmentation. Here, we compared the genetic structure of four freshwater fish species differing in their body size (Leuciscus cephalus; Leuciscus leuciscus; Gobio gobio and Phoxinus phoxinus) between a fragmented and a continuous landscape. We tested if, overall, fragmentation affected the genetic structure of these fish species, and if these species differed in their sensitivity to fragmentation. Fragmentation negatively affected the genetic structure of these species. Indeed, irrespective of the species identity, allelic richness and heterozygosity were lower, and population divergence was higher in the fragmented than in the continuous landscape. This response to fragmentation was highly species-specific, with the smallest fish species (P. phoxinus) being slightly affected by fragmentation. On the contrary, fish species of intermediate body size (L. leuciscus and G. gobio) were highly affected, whereas the largest fish species (L. cephalus) was intermediately affected by fragmentation. We discuss the relative role of dispersal ability and effective population size on the responses to fragmentation we report here. The weirs studied here are of considerable historical importance. We therefore conclude that restoration programmes will need to consider both this societal context and the biological characteristics of the species sharing this ecosyste

Using metabarcoding to reveal and quantify plant-pollinator interactions.

12 pagesInternational audienceGiven the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole

Spatial genetic structure of Lissotriton helveticus L. following the restoration of a forest ponds network

International audiencePreserving amphibian genetic diversity through ecological restoration and conservation actions is a major challenge since their populations are declining worldwide. We studied the genetic diversity and spatial genetic structure of the palmate newt (Lissotriton helveticus) 2 years after the restoration of a pond network in northwestern France with the aim of reconstructing fine-scale genetic structure and patterns of colonization. We sampled newts from 29 forest ponds including both restored and non-degraded reference ponds, and genotyped 391 individuals at 12 microsatellite loci. We used two Bayesian clustering methods to spatially delineate genetic clusters, and we also detected potential recent migrants within the network. All ponds showed low levels of observed heterozygosity (Ho = 0.534) and a mean F IS of 0.251, possibly indicating a Wahlund or bottleneck effect. Pairwise F ST suggested limited evidence of genetic differentiation among ponds. Within the pond network, we identified 3 to 4 genetic clusters. Combined with the detection of migrants, the results suggest an increase in gene flow within the restored pond network and that a high number of migrants came from the reference ponds. Our findings indicate an unexpected high dispersal ability for this small-bodied species. Overall, the absence of population structure represents a positive beginning for the restoration project. It also emphasizes the importance of spatial design in restoring a pond network and that such genetic data and methods should be used to monitor amphibians in restored habitats

Sampling site data

A table with 1) site name, 2) drainage basin belonging, 3) coordinates, 4) dates of traditional and eDNA sampling, 5) sample PCR code and 6) site map number

Analyse R script

A R script of the analyses conducted in the manuscrit

Run4

Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file; 3) File with experiment name, sample name and the tags, the forward primer and the reverse primer sequence associate

Run3

Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file; 3) File with experiment name, sample name and the tags, the forward primer and the reverse primer sequence associate

Data from: Unlocking biodiversity and conservation studies in high diversity environments using environmental DNA (eDNA): a test with Guianese freshwater fishes

Determining the species compositions of local assemblages is a prerequisite to understanding how anthropogenic disturbances affect biodiversity. However, biodiversity measurements often remain incomplete due to the limited efficiency of sampling methods. This is particularly true in freshwater tropical environments that host rich fish assemblages, for which assessments are uncertain and often rely on destructive methods. Developing an efficient and non-destructive method to assess biodiversity in tropical freshwaters is highly important. In this study, we tested the efficiency of environmental DNA (eDNA) metabarcoding to assess the fish diversity of 39 Guianese sites. We compared the diversity and composition of assemblages obtained using traditional and metabarcoding methods. More than 7,000 individual fish belonging to 203 Guianese fish species were collected by traditional sampling methods, and ~17 million reads were produced by metabarcoding, among which ~8 million reads were assigned to 148 fish taxonomic units, including 132 fish species. The two methods detected a similar number of species at each site, but the species identities partially matched. The assemblage compositions from the different drainage basins were better discriminated using metabarcoding, revealing that while traditional methods provide a more complete but spatially limited inventory of fish assemblages, metabarcoding provides a more partial but spatially extensive inventory. eDNA metabarcoding can therefore be used for rapid and large-scale biodiversity assessments, while at a local scale, the two approaches are complementary and enable an understanding of realistic fish biodiversity

Hypercalcemia and inactive mutation of CYP24A1. Case-study and literature review

We present the case of a family whose members have high levels of serum calcium (hypercalcaemia) by loss of function of the enzyme vitamin D 24-hydroxylase due to bi-allelic mutations in the CYP24A1 gene: c.443 T>C (p.Leu148Pro) and c.1187 G>A (p.Arg396Gln). 24-VITD hydroxylase is a key player in regulating the circulating calcitriol, its tissue concentration and its biological effects. Transmission is recessive. The estimated prevalence of stones in the affected subjects is estimated between 10 and 15%. The loss of peripheral catabolism of vitamin D metabolites in patients with an inactivating mutation of CYP24A1 is responsible for persistent high levels of 1,25-dihydroxyvitamin D especially after sun exposure and a charge of native vitamin D. Although there are currently no recommendations (French review) on this subject, this disease should be suspected in association with recurrent calcium stones with nephrocalcinosis, and a calcitriol-dependent hypercalcaemia with adapted low parathyroid hormone levels. Resistance to corticosteroid therapy distinguishes it from other calcitriol-dependent hypercalcemia. A ratio of 25-hydroxyvitamin D/24.25 hydroxyvitamin D>50, is in favor of hypercalcemia with vitamin D deficiency 24-hydroxylase. Genetic analysis of CYP24A1 should be performed at the second step. The current therapeutic management includes the restriction native vitamin D supplementation and the limitation of sun exposure. Biological monitoring will be based on serum calcium control and modulation of parathyroid hormone concentrations