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"Gilles, André"
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Unsuspected prevalence of Pinus cembra in the high-elevation sky islands of the western Alps
A survey of Pinus cembra (Arolla pine) growing above 2800-m elevation was conducted in an ecoregion of the western Alps, where the highest treeline is at ~ 2650 m. The concepts of treeline and species line are discussed based on these field observations. The species line is the biological limit of a species, with inherited nested historical and current processes of high-mountain socio-ecosystems, while the treeline strictly concerns the limit of erect trees. Arolla pines were located and described (height, physiognomy) and their habitats recorded (elevation, slope, aspect). Individuals occurred up to 3200 m on east-facing steep and rocky slopes, with density decreasing exponentially with increasing elevation (halving every 40 m). East-facing habitats benefit from the main atmospheric moisture coming from the east (Italy). Individuals were mostly dwarf-shaped/prostrate (58%) or trees (39%; max height 3.8 m). They usually do not bear female cones, and needles are smaller by half compared to those of pines growing in lower elevation forests. Their morphology indicates harsh growing conditions due to elevation (aridity, frost) and disturbances (wind, snow, rockfall). Habitat preference primarily on grass-free steep rocky slopes and cliffs at high elevation is likely explained by the exclusion of livestock impacts (grazing, trampling). These pines constitute noteworthy “sky island” populations. Larix decidua and Pinus uncinata were also recorded above the treeline, but with lower maximum elevation and density than Pinus cembra. These observations highlight a complex pattern of species treeline in the western Alps, and probably beyond, with relevance to issues in conservation science.
Journal Article
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
Background
The rapid evolution of 454 GS-FLX sequencing technology has not been accompanied by a reassessment of the quality and accuracy of the sequences obtained. Current strategies for decision-making and error-correction are based on an initial analysis by Huse
et al.
in 2007, for the older GS20 system based on experimental sequences. We analyze here the quality of 454 sequencing data and identify factors playing a role in sequencing error, through the use of an extensive dataset for Roche control DNA fragments.
Results
We obtained a mean error rate for 454 sequences of 1.07%. More importantly, the error rate is not randomly distributed; it occasionally rose to more than 50% in certain positions, and its distribution was linked to several experimental variables. The main factors related to error are the presence of homopolymers, position in the sequence, size of the sequence and spatial localization in PT plates for insertion and deletion errors. These factors can be described by considering seven variables. No single variable can account for the error rate distribution, but most of the variation is explained by the combination of all seven variables.
Conclusions
The pattern identified here calls for the use of internal controls and error-correcting base callers, to correct for errors, when available (e.g. when sequencing amplicons). For shotgun libraries, the use of both sequencing primers and deep coverage, combined with the use of random sequencing primer sites should partly compensate for even high error rates, although it may prove more difficult than previous thought to distinguish between low-frequency alleles and errors.
Journal Article
Underestimation of Species Richness in Neotropical Frogs Revealed by mtDNA Analyses
Amphibians are rapidly vanishing. At the same time, it is most likely that the number of amphibian species is highly underestimated. Recent DNA barcoding work has attempted to define a threshold between intra- and inter-specific genetic distances to help identify candidate species. In groups with high extinction rates and poorly known species boundaries, like amphibians, such tools may provide a way to rapidly evaluate species richness.
Here we analyse published and new 16S rDNA sequences from 60 frog species of Amazonia-Guianas to obtain a minimum estimate of the number of undescribed species in this region. We combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs.
In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contrary to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species.
Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia-Guianas.
As a consequence the global amphibian decline detected especially in the Neotropics may be worse than realised.
Journal Article
Correction: Phylogenetic Analysis of Thecosomata Blainville, 1824 (Holoplanktonic Opisthobranchia) Using Morphological and Molecular Data
In Figure 7, there is an error related to the schematized shell morphology and genus correspondence. Please see the corrected Figure 7 here: thumbnail Download: * PPT PowerPoint slide * PNG larger image * TIFF original image Figures Citation: Corse E, Rampal J, Cuoc C, Pech N, Perez Y, Gilles A (2013) Correction: Phylogenetic Analysis of Thecosomata Blainville, 1824 (Holoplanktonic Opisthobranchia) Using Morphological and Molecular Data.
Journal Article
Challenges and advances for transcriptome assembly in non-model species
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence). Here we focus on gene identification and not on resolving the whole set of transcripts (i.e. the complete transcriptome). For simulated datasets, the transcriptome-guided assembly based on blastn recovers 94.8% of genes irrespective of read length at 0% divergence; however, assignment rate of reads is negatively correlated with both increasing divergence level and reducing read lengths. Nevertheless, we still observe 92.6% of recovered genes at 30% divergence irrespective of read length. This analysis also produces a categorization of genes relative to their assignment, and suggests guidelines for data processing prior to analyses of comparative transcriptomics and gene expression to minimize potential inferential bias associated with incorrect transcript assignment. We also compare the performances of de novo assembly alone vs in combination with a transcriptome-guided assembly based on blastn both via simulation and empirically, using data from a cyprinid fish species and from an oak species. For any simulated scenario, the transcriptome-guided assembly using blastn outperforms the de novo approach alone, including when the divergence level is beyond the reach of traditional mapping methods. Combining de novo assembly and a related reference transcriptome for read assignment also addresses the bias/error in contigs caused by the dependence on a related reference alone. Empirical data corroborate these findings when assembling transcriptomes from the two non-model organisms: Parachondrostoma toxostoma (fish) and Quercus pubescens (plant). For the fish species, out of the 31,944 genes known from D. rerio, the guided and de novo assemblies recover respectively 20,605 and 20,032 genes but the performance of the guided assembly approach is much higher for both the contiguity and completeness metrics. For the oak, out of the 29,971 genes known from Vitis vinifera, the transcriptome-guided and de novo assemblies display similar performance, but the new guided approach detects 16,326 genes where the de novo assembly only detects 9,385 genes.
Journal Article
A systematic revision of the five-spotted Hemichromis complex (Cichliformes: Cichlidae) from West Africa and Lower Guinea, with the description of a new species from Cameroon
The group of large five-spotted Hemichromis species from West Africa and Lower Guinea was revised using an integrative approach combining morphometry (measurements, meristics and colour patterns) and genetics (cytochrome b gene). Specimens from 100 populations were sorted into three main groups on the basis of morphological criteria. Samples from Lake Bosumtwi clustered together with others from West Africa in a large well-supported clade (bootstrap values and posterior probabilities: 98/96/100), both in morphometric and genetic analyses, raising again the hypothesis of synonymy of H. frempongi with H. fasciatus. Samples from southern Lower Guinea, including the type locality (Gabon) of H. elongatus, constituted a second weakly resolved cluster (64/38/51), resulting from a potential admixture of populations of diverse origins which share common morphological traits. Populations from northern Lower Guinea (Atlantic coastal basins) and the upper Chad basin in Cameroon formed a third strongly supported clade (99/100/100), which corresponds to a new species, Hemichromis camerounensis sp. nov., herein described.
Journal Article
Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion Zone
Background
Individual functional modifications shape the ability of wildlife populations to cope with anthropogenic environmental changes. But instead of adaptive response, human-altered environments can generate a succession of deleterious functional changes leading to the extinction of the population. To study how persistent anthropogenic changes impacted local species’ population status, we characterised population structure, genetic diversity and individual response of gene expression in the tree frog
Hyla orientalis
along a gradient of radioactive contamination around the Chernobyl nuclear power plant.
Results
We detected lower effective population size in populations most exposed to ionizing radiation in the Chernobyl Exclusion Zone that is not compensated by migrations from surrounding areas. We also highlighted a decreased body condition of frogs living in the most contaminated area, a distinctive transcriptomics signature and stop-gained mutations in genes involved in energy metabolism. While the association with dose will remain correlational until further experiments, a body of evidence suggests the direct or indirect involvement of radiation exposure in these changes.
Conclusions
Despite ongoing migration and lower total dose rates absorbed than at the time of the accident, our results demonstrate that
Hyla orientalis
specimens living in the Chernobyl Exclusion Zone are still undergoing deleterious changes, emphasizing the long-term impacts of the nuclear disaster.
Journal Article
Irrigation canals as tools for climate change adaptation and fish biodiversity management in Southern France
This paper is based on the interdisciplinary research conducted in the south of France that analyses the different economic, social and environmental roles played by agricultural irrigation canals. We argue that beyond their productive role, which is to supply farmers with water, they fulfil other environmental services and play an important role in the context of future climate change to face challenges of adaptation. We point up several ecosystem services provided by such canals, e.g. replenishing the groundwater table, the development of riparian vegetation and wet areas in the Mediterranean zone, tools for regulating flooding and drought, the bases for new cultural approaches to nature. Moreover, they play an important role in the maintenance of an ichthyological biodiversity that is indispensable for the persistence of natural ecosystem. Functioning as an ecological corridor, they display interesting capacities as refuges for certain fish species under stress. Indeed, they can potentially connect upstream and downstream zones over a continuum of more than 300 km and thus covering very contrasted climatic zones (alpine versus Mediterranean). For now, most of these services remain largely unknown and underestimated. However, they serve as assets for territorial development since they combine economic, ecological and social factors whose remodelling is becoming increasingly necessary in the face of climate change.
Journal Article
Multiple Quaternary Refugia in the Eastern Guiana Shield Revealed by Comparative Phylogeography of 12 Frog Species
The Guiana Shield (GS) is one of the most pristine regions of Amazonia and biologically one of the richest areas on Earth. How and when this massive diversity arose remains the subject of considerable debate. The prevailing hypothesis of Quaternary glacial refugia suggests that a part of the eastern GS, among other areas in Amazonia, served as stable forested refugia during periods of aridity. However, the recently proposed disturbance–vicariance hypothesis proposes that fluctuations in temperature on orbital timescales, with some associated aridity, have driven Neotropical diversification. The expectations of the temporal and spatial organization of biodiversity differ between these two hypotheses. Here, we compare the genetic structure of 12 leaf-litter inhabiting frog species from the GS lowlands using a combination of mitochondrial and nuclear sequences in an integrative analytical approach that includes phylogenetic reconstructions, molecular dating, and Geographic Information System methods. This comparative and integrated approach overcomes the well-known limitations of phylogeographic inference based on single species and single loci. All of the focal species exhibit distinct phylogeographic patterns highlighting taxon-specific historical distributions, ecological tolerances to climatic disturbance, and dispersal abilities. Nevertheless, all but one species exhibit a history of fragmentation/isolation within the eastern GS during the Quaternary with spatial and temporal concordance among species. The signature of isolation in northern French Guiana (FG) during the early Pleistocene is particularly clear. Approximate Bayesian Computation supports the synchrony of the divergence between northern FG and other GS lineages. Substructure observed throughout the GS suggests further Quaternary fragmentation and a role for rivers. Our findings support fragmentation of moist tropical forest in the eastern GS during this period when the refuge hypothesis would have the region serving as a contiguous wet-forest refuge.
Journal Article