Dataset of Phanerozoic continental climate and Köppen-Geiger climate classes.

This article describes a suite of global climate model output files that provide continental climatic conditions (monthly temperatures, precipitation, evaporation, precipitation minus evaporation balance, runoff) together with the calculated Köppen-Geiger climate classes and topography, for 28 evenly spaced time slices through the Phanerozoic (Cambrian to Quaternary, 540 Ma to 0 Ma). Climatic variables were simulated with the Fast Ocean Atmosphere Model (FOAM), using a recent set of open-access continental reconstructions with paleotopography and recent atmospheric CO2 and solar luminosity estimates. FOAM is a general circulation model frequently used in paleoclimate studies, especially in the Palaeozoic. Köppen-Geiger climate classes were calculated based on simulated temperature and precipitation fields using Wong Hearing et al.'s [1] implementation of Peel et al.'s [2] updated classification. This dataset provides a unique window onto changing continental climate throughout the Phanerozoic that accounts for the simultaneous evolution of paleogeography (continental configuration and topography), atmospheric composition and greenhouse gas forcing, and solar luminosity.

Does clustering of DNA barcodes agree with botanical classification directly at high taxonomic levels? Trees in French Guiana as a case study.

Characterizing biodiversity is one of the main challenges for the coming decades. Most diversity has not been morphologically described, and barcoding is now complementing morphological-based taxonomy to further develop inventories. Both approaches have been cross-validated at the level of species and OTUs. However, many known species are not listed in reference databases. One path to speed up inventories using barcoding is to directly identify individuals at coarser taxonomic levels. We therefore studied in barcoding of plants whether morphological-based and molecular-based approaches are in agreement at genus, family and order levels. We used Agglomerative Hierarchical Clustering (with Ward, Complete and Single Linkage) and Stochastic Block Models (SBM), with two dissimilarity measures (Smith-Waterman scores, kmers). The agreement between morphological-based and molecular-based classifications ranges in most of the cases from good to very good at taxonomic levels above species, even though it decreases when taxonomic levels increase, or when using the tetramer-based distance. Agreement is correlated with the entropy of morphological-based classification and with the ratio of the mean within- and mean between-groups dissimilarities. The Ward method globally leads to the best agreement, whereas Single Linkage can show poor behaviours. SBM provides a useful tool to test whether or not the dissimilarities are structured by the botanical groups. These results suggest that automatic clustering and group identification at taxonomic levels above species are possible in barcoding.

The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts.

Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity in seven neotropical rodent species living in four types of habitats and (b) exploring how the extent of environmental disturbance influences this diversity. Through a metagenomic approach, we identified 77,767 viral sequences from spleen, kidney, and serum samples. These viral sequences were attributed to 27 viral families known to infect vertebrates, invertebrates, plants, and amoeba. Viral diversities were greater in pristine habitats compared with disturbed ones, and lowest in peri-urban areas. High viral richness was observed in savannah areas. Differences in these diversities were explained by rare viruses that were generally more frequent in pristine forest and savannah habitats. Moreover, changes in the ecology and behavior of rodent hosts, in a given habitat, such as modifications to the diet in disturbed vs. pristine forests, are major determinants of viral composition. Lastly, the phylogenetic relationships of four vertebrate-related viral families (Polyomaviridae, Flaviviridae, Togaviridae, and Phenuiviridae) highlighted the wide diversity of these viral families, and in some cases, a potential risk of transmission to humans. All these findings provide significant insights into the diversity of rodent viruses in Amazonia, and emphasize that habitats and the host's dietary ecology may drive viral diversity. Linking viral richness and abundance to the ecology of their hosts and their responses to habitat disturbance could be the starting point for a better understanding of viral emergence and for future management of ecosystems.

Quantitative comparison of geological data and model simulations constrains early Cambrian geography and climate.

Marine ecosystems with a diverse range of animal groups became established during the early Cambrian (~541 to ~509 Ma). However, Earth's environmental parameters and palaeogeography in this interval of major macro-evolutionary change remain poorly constrained. Here, we test contrasting hypotheses of continental configuration and climate that have profound implications for interpreting Cambrian environmental proxies. We integrate general circulation models and geological observations to test three variants of the 'Antarctocentric' paradigm, with a southern polar continent, and an 'equatorial' configuration that lacks polar continents. This quantitative framework can be applied to other deep-time intervals when environmental proxy data are scarce. Our results show that the Antarctocentric palaeogeographic paradigm can reconcile geological data and simulated Cambrian climate. Our analyses indicate a greenhouse climate during the Cambrian animal radiation, with mean annual sea-surface temperatures between ~9 °C to ~19 °C and ~30 °C to ~38 °C for polar and tropical palaeolatitudes, respectively.

Ecology, evolution, and epidemiology of zoonotic and vector-borne infectious diseases in French Guiana: Transdisciplinarity does matter to tackle new emerging threats.

French Guiana is a European ultraperipheric region located on the northern Atlantic coast of South America. It constitutes an important forested region for biological conservation in the Neotropics. Although very sparsely populated, with its inhabitants mainly concentrated on the Atlantic coastal strip and along the two main rivers, it is marked by the presence and development of old and new epidemic disease outbreaks, both research and health priorities. In this review paper, we synthetize 15 years of multidisciplinary and integrative research at the interface between wildlife, ecosystem modification, human activities and sociodemographic development, and human health. This study reveals a complex epidemiological landscape marked by important transitional changes, facilitated by increased interconnections between wildlife, land-use change and human occupation and activity, human and trade transportation, demography with substantial immigration, and identified vector and parasite pharmacological resistance. Among other French Guianese characteristics, we demonstrate herein the existence of more complex multi-host disease life cycles than previously described for several disease systems in Central and South America, which clearly indicates that today the greater promiscuity between wildlife and humans due to demographic and economic pressures may offer novel settings for microbes and their hosts to circulate and spread. French Guiana is a microcosm that crystallizes all the current global environmental, demographic and socioeconomic change conditions, which may favor the development of ancient and future infectious diseases.

Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization.

Ecological assessment of lakes and rivers using benthic diatom assemblages currently requires considerable taxonomic expertise to identify species using light microscopy. This traditional approach is also time-consuming. Diatom metabarcoding is a promising alternative and there is increasing interest in using this approach for routine assessment. However, until now, analysis protocols for diatom metabarcoding have been developed and optimised by research groups working in isolation. The diversity of existing bioinformatics methods highlights the need for an assessment of the performance and comparability of results of different methods. The aim of this study was to test the correspondence of outputs from six bioinformatics pipelines currently in use for diatom metabarcoding in different European countries. Raw sequence data from 29 biofilm samples were treated by each of the bioinformatics pipelines, five of them using the same curated reference database. The outputs of the pipelines were compared in terms of sequence unit assemblages, taxonomic assignment, biotic index score and ecological assessment outcomes. The three last components were also compared to outputs from traditional light microscopy, which is currently accepted for ecological assessment of phytobenthos, as required by the Water Framework Directive. We also tested the performance of the pipelines on the two DNA markers (rbcL and 18S-V4) that are currently used by the working groups participating in this study. The sequence unit assemblages produced by different pipelines showed significant differences in terms of assigned and unassigned read numbers and sequence unit numbers. When comparing the taxonomic assignments at genus and species level, correspondence of the taxonomic assemblages between pipelines was weak. Most discrepancies were linked to differential detection or quantification of taxa, despite the use of the same reference database. Subsequent calculation of biotic index scores also showed significant differences between approaches, which were reflected in the final ecological assessment. Use of the rbcL marker always resulted in better correlation among molecular datasets and also in results closer to these generated using traditional microscopy. This study shows that decisions made in pipeline design have implications for the dataset's structure and the taxonomic assemblage, which in turn may affect biotic index calculation and ecological assessment. There is a need to define best-practice bioinformatics parameters in order to ensure the best representation of diatom assemblages. Only the use of similar parameters will ensure the compatibility of data from different working groups. The future of diatom metabarcoding for ecological assessment may also lie in the development of new metrics using, for example, presence/absence instead of relative abundance data.

Chloroplast DNA variation in a hyperdiverse tropical tree community.

We investigate chloroplast DNA variation in a hyperdiverse community of tropical rainforest trees in French Guiana, focusing on patterns of intraspecific and interspecific variation. We test whether a species genetic diversity is higher when it has congeners in the community with which it can exchange genes and if shared haplotypes are more frequent in genetically diverse species, as expected in the presence of introgression.We sampled a total of 1,681 individual trees from 472 species corresponding to 198 genera and sequenced them at a noncoding chloroplast DNA fragment.Polymorphism was more frequent in species that have congeneric species in the study site than in those without congeners (30% vs. 12%). Moreover, more chloroplast haplotypes were shared with congeners in polymorphic species than in monomorphic ones (44% vs. 28%).Despite large heterogeneities caused by genus-specific behaviors in patterns of hybridization, these results suggest that the higher polymorphism in the presence of congeners is caused by local introgression rather than by incomplete lineage sorting. Our findings suggest that introgression has the potential to drive intraspecific genetic diversity in species-rich tropical forests.

Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana.

Environmental disturbances in the Neotropics (e.g., deforestation, agriculture intensification, urbanization) contribute to an increasing risk of cross-species transmission of microorganisms and to disease outbreaks due to changing ecosystems of reservoir hosts. Although Amazonia encompasses the greatest diversity of reservoir species, the outsized viral population diversity (virome) has yet to be investigated. Here, through a metagenomic approach, we identified 10,991 viral sequences in the saliva and feces of two bat species, Desmodus rotundus (hematophagous), trapped in two different caves surrounded by primary lowland forest, and Molossus molossus (insectivorous), trapped in forest and urban habitats. These sequences are related to 51 viral families known to infect a wide range of hosts (i.e., bacteria, plants, insects and vertebrates). Most viruses detected reflected the diet of bat species, with a high proportion of plant and insect-related viral families for M. molossus and a high proportion of vertebrate-related viral families for D. rotundus, highlighting its influence in shaping the viral diversity of bats. Lastly, we reconstructed the phylogenetic relationships for five vertebrate-related viral families (Nairoviridae, Circoviridae, Retroviridae, Herpesviridae, Papillomaviridae). The results showed highly supported clustering with other viral sequences of the same viral family hosted by other bat species, highlighting the potential association of viral diversity with the host's diet. These findings provide significant insight into viral bat diversity in French Guiana belonging to the Amazonian biome and emphasize that habitats and the host's dietary ecology may drive the viral diversity in the bat communities investigated.

The impact of parasitism on resource allocation in a fungal host: the case of Cryphonectria parasitica and its mycovirus, Cryphonectria Hypovirus 1.

Parasites are known to profoundly affect resource allocation in their host. In order to investigate the effects of Cryphonectria Hypovirus 1 (CHV1) on the life-history traits of its fungal host Cryphonectria parasitica, an infection matrix was completed with the cross-infection of six fungal isolates by six different viruses. Mycelial growth, asexual sporulation, and spore size were measured in the 36 combinations, for which horizontal and vertical transmission of the viruses was also assessed. As expected by life-history theory, a significant negative correlation was found between host somatic growth and asexual reproduction in virus-free isolates. Interestingly this trade-off was found to be positive in infected isolates, illustrating the profound changes in host resource allocation induced by CHV1 infection. A significant and positive relationship was also found in infected isolates between vertical transmission and somatic growth. This last relationship suggests that in this system, high levels of virulence could be detrimental to the vertical transmission of the parasite. Those results underscore the interest of studying host-parasite interaction within the life-history theory framework, which might permit a more accurate understanding of the nature of the modifications triggered by parasite infection on host biology.

Phylogenetic signal in diatom ecology: perspectives for aquatic ecosystems biomonitoring.

Diatoms include a great diversity of taxa and are recognized as powerful bioindicators in rivers. However using diatoms for monitoring programs is costly and time consuming because most of the methodologies necessitate species-level identification. This raises the question of the optimal trade-off between taxonomic resolution and bioassessment quality. Phylogenetic tools may form the bases of new, more efficient approaches for biomonitoring if relationships between ecology and phylogeny can be demonstrated. We estimated the ecological optima of 127 diatom species for 19 environmental parameters using count data from 2119 diatom communities sampled during eight years in eastern France. Using uni- and multivariate analyses, we explored the relationships between freshwater diatom phylogeny and ecology (i.e., the phylogenetic signal). We found a significant phylogenetic signal for many of the ecological optima that were tested, but the strength of the signal varied significantly from one trait to another. Multivariate analysis also showed that the multidimensional ecological niche of diatoms can be strongly related to phylogeny. The presence of clades containing species that exhibit homogeneous ecology suggests that phylogenetic information can be useful for aquatic biomonitoring. This study highlights the presence of significant patterns of ecological optima for freshwater diatoms in relation to their phylogeny. These results suggest the presence of a signal above the species level, which is encouraging for the development of simplified methods for biomonitoring survey.

phylosignal: an R package to measure, test, and explore the phylogenetic signal.

Phylogenetic signal is the tendency for closely related species to display similar trait values as a consequence of their phylogenetic proximity. Ecologists and evolutionary biologists are becoming increasingly interested in studying the phylogenetic signal and the processes which drive patterns of trait values in the phylogeny. Here, we present a new R package, phylosignal which provides a collection of tools to explore the phylogenetic signal for continuous biological traits. These tools are mainly based on the concept of autocorrelation and have been first developed in the field of spatial statistics. To illustrate the use of the package, we analyze the phylogenetic signal in pollution sensitivity for 17 species of diatoms.

Plastome data reveal multiple geographic origins of Quercus Group Ilex.

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members of Quercus Group Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.

R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring.

Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts…), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom. Database URL: http://www.rsyst.inra.fr/.

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.

With the increasingly rapid growth of data in life sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. Such approaches necessitate the use of large-scale computational resources and e-infrastructures, such as the European Grid Infrastructure (EGI). EGI, one of key the enablers of the digital European Research Area, is a federation of resource providers set up to deliver sustainable, integrated and secure computing services to European researchers and their international partners. Here we aim to provide the state of the art of Grid/Cloud computing in EU research as viewed from within the field of life sciences, focusing on key infrastructures and projects within the life sciences community. Rather than focusing purely on the technical aspects underlying the currently provided solutions, we outline the design aspects and key characteristics that can be identified across major research approaches. Overall, we aim to provide significant insights into the road ahead by establishing ever-strengthening connections between EGI as a whole and the life sciences community.

Tectonic-driven climate change and the diversification of angiosperms.

In 1879, Charles Darwin characterized the sudden and unexplained rise of angiosperms during the Cretaceous as an "abominable mystery." The diversification of this clade marked the beginning of a rapid transition among Mesozoic ecosystems and floras formerly dominated by ferns, conifers, and cycads. Although the role of environmental factors has been suggested [Coiffard C, Gómez B (2012) Geol Acta 10(2):181-188], Cretaceous global climate change has barely been considered as a contributor to angiosperm radiation, and focus was put on biotic factors to explain this transition. Here we use a fully coupled climate model driven by Mesozoic paleogeographic maps to quantify and discuss the impact of continental drift on angiosperm expansion and diversification. We show that the decrease of desertic belts between the Triassic and the Cretaceous and the subsequent onset of long-lasting humid conditions during the Late Cretaceous were driven by the breakup of Pangea and were contemporaneous with the first rise of angiosperm diversification. Positioning angiosperm-bearing fossil sites on our paleobioclimatic maps shows a strong match between the location of fossil-rich outcrops and temperate humid zones, indicating that climate change from arid to temperate dominance may have set the stage for the ecological expansion of flowering plants.

When is sampling complete? The effects of geographical range and marker choice on perceived diversity in Nitzschia palea (Bacillariophyta).

DNA barcoding, being developed for biomonitoring, requires a database of reference sequences and knowledge of how much sequences can deviate before they are assigned to separate species. The molecular hunt for hidden species also raises the question of species definitions. We examined whether there are objective criteria for sequence-based species delimitation in diatoms, using Nitzschia palea, an important monophyletic indicator species already known to contain cryptic diversity. Strains from a wide geographical range were sequenced for 28S rRNA, COI and rbcL. Homogeneity indices and the Chao index failed to objectively select a precise number of species existing in N. palea as well as an evolutionary method based on coalescence theory. COI always gave higher diversity estimations than 28S rRNA or rbcL. Mating data did not provide a precise calibration of molecular species thresholds. Rarefaction curves indicated that further MOTUs would be detected with more isolates than we sampled (81 clones, 42 localities). Although some genotypes had intercontinental distributions, there was a positive relationship between genetic and geographical distance, suggesting even higher richness than we assessed, given that many regions were not sampled. Overall, no objective criteria were found for species separation; instead barcoding will need a consensual approach to molecular species limits.

Community genetics in the time of next-generation molecular technologies.

Understanding the interactions of co-occurring species within and across trophic levels provides key information needed for understanding the ecological and evolutionary processes that underlie biological diversity. As genetics has only recently been integrated into the study of community-level interactions, the time is right for a critical evaluation of potential new, gene-based approaches to studying communities. Next-generation molecular techniques, used in parallel with field-based observations and manipulative experiments across spatio-temporal gradients, are key to expanding our understanding of community-level processes. Here, we introduce a variety of '-omics' tools, with recent studies of plant-insect herbivores and of ectomycorrhizal systems providing detailed examples of how next-generation approaches can revolutionize our understanding of interspecific interactions. We suggest ways that novel technologies may convert community genetics from a field that relies on correlative inference to one that reveals causal mechanisms of genetic co-variation and adaptations within communities.

Parasitism and maintenance of diversity in a fungal vegetative incompatibility system: the role of selection by deleterious cytoplasmic elements.

In fungi, horizontal transmission of deleterious cytoplasmic elements is reduced by the vegetative incompatibility system. This self/non-self recognition system may select for greater diversity of fungal incompatibility phenotypes in a frequency-dependent manner but the link between the diversity of fungal phenotypes and the virulence of cytoplasmic parasites has been poorly studied. We used an epidemiological model to show that even when transmission between incompatibility types is permitted, parasite pressure can lead to high levels of polymorphism for vegetative incompatibility systems. Moreover, high levels of polymorphism in host populations can select for less virulent cytoplasmic parasites. This feedback mechanism between parasite virulence and vegetative incompatibility system polymorphism of host populations may account for the general avirulence of most known mycoviruses. Furthermore, this mechanism provides a new perspective on the particular ecology and evolution of the host/parasite interactions acting between fungi and their cytoplasmic parasites.

Optimized assay and storage conditions for enzyme activity profiling of ectomycorrhizae.

The aim of a joint effort by different research teams was to provide an improved procedure for enzyme activity profiling of field-sampled ectomycorrhizae, including recommendations on the best conditions and maximum duration for storage of ectomycorrhizal samples. A more simplified and efficient protocol compared to formerly published procedures was achieved by using manufactured 96-filter plates in combination with a vacuum manifold and by optimizing incubation times. Major improvements were achieved by performing the series of eight enzyme assays with a single series of root samples instead of two series, reducing the time needed for sample preparation, minimizing error-prone steps such as pipetting and morphotyping, and facilitating subsequent DNA analyses due to the reduced sequencing effort. The best preservation of samples proved to be storage in soil at 4-6 °C in the form of undisturbed soil cores containing roots. Enzyme activities were maintained for up to 4 weeks under these conditions. Short-term storage of washed roots and ectomycorrhizal tips overnight in water did not cause substantial changes in enzyme activity profiles. No optimal means for longer-term storage by freezing at -20 °C or storage in 100% ethanol were recommended.

Robust scaling in ecosystems and the meltdown of patch size distributions before extinction.

Robust critical systems are characterized by power laws which occur over a broad range of conditions. Their robust behaviour has been explained by local interactions. While such systems could be widespread in nature, their properties are not well understood. Here, we study three robust critical ecosystem models and a null model that lacks spatial interactions. In all these models, individuals aggregate in patches whose size distributions follow power laws which melt down under increasing external stress. We propose that this power-law decay associated with the connectivity of the system can be used to evaluate the level of stress exerted on the ecosystem. We identify several indicators along the transition to extinction. These indicators give us a relative measure of the distance to extinction, and have therefore potential application to conservation biology, especially for ecosystems with self-organization and critical transitions.