Alain Franc

Biodiversity, disturbances, ecosystem function and management of European forests

Abstract We review the effects of human impact on biodiversity of European forests in the light of recent views on disturbances and succession in ecosystems, and discuss recent ideas on how biodiversity affects ecosystem functions such as productivity and ecosystem stability. With this as a background we discuss how to better manage European forests for both production and biodiversity. We argue that the next generation of forestry practices need to understand and mimic natural disturbance dynamics much better than the present ones. Of particular importance is the fact that most species in European forests have evolved in forests that were to a large extent influenced by large grazers, first by megaherbivores and later, in historic times, by domestic animals. We highlight several areas where new knowledge and management tools are urgently needed: (i) How do species survive and adapt to the natural disturbance regimes in different regions and forest types? (ii) How can new and imaginative forest management practices be devised that take natural disturbance regimes into account? (iii) How does forest biodiversity affect ecosystem function and stability in a changing world, in particular in the light of predicted climate changes? (iv) How are ecological processes at different levels and scales related to diversity, and how do different management practices affect biodiversity? (v) How can efficient agroforestry methods be developed to preserve biodiversity? (vi) What is the role of humans and human behaviour for sustainable management of ecosystems?

Temporal Changes in the Ectomycorrhizal Community in Two Soil Horizons of a Temperate Oak Forest

ABSTRACT The species structure of an ectomycorrhizal (ECM) community was assessed monthly for 15 months in the two horizons (A1 and A2) of an oak temperate forest in northeastern France. Ectomycorrhizal species were identified each month by internal transcribed spacer sequencing. Seventy-five fungal symbionts were identified. The community was dominated by Tomentellaceae, Russulaceae, Cortinariaceae, and Boletales. Four species are abundant in the study site: Lactarius quietus, Tomentella sublilacina, Cenococcum geophilum, and Russula sp1. The relative abundance of each species varied depending on the soil horizon and over time. Some species, such as L. quietus, were present in the A1 and A2 horizons. C. geophilum was located particularly in the A2 horizon, whereas T. sublilacina was more abundant in A1. Some species, such as Clavulina sp., were detected in winter, while T. sublilacina and L. quietus were present all year long. Our results support the hypothesis that a rapid turnover of species composition of the ECM community occurs over the course of a month. The spatial and temporal unequal distribution of ECM species could be explained by their ecological preferences, driven by such factors as root longevity, competition for resources, and resistance to environmental variability.

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.

A next-generation sequencing approach to river biomonitoring using benthic diatoms

Abstract: Diatoms are main bioindicators used to assess the ecological quality of rivers, but their identification is difficult and time-consuming. Next Generation Sequencing (NGS) can be used to study communities of microorganisms, so we carried out a test of the reliability of 454 pyrosequencing for estimating diatom inventories in environmental samples. We used small subunit ribosomal deoxyribonucleic acid (SSU rDNA), ribulose-1, 5-bisphosphate carboxylase (rbcL), and cytochrome oxidase I (COI) markers and examined reference libraries to define thresholds between the intra- and interspecific and intra- and intergeneric genetic distances. Based on tests of 1 mock community, we used a threshold of 99% identity for SSU rDNA and rbcL sequences to study freshwater diatoms at the species level. We applied 454 pyrosequencing to 4 contrasting environmental samples (with one in duplicate), assigned taxon names to environmental sequences, and compared the qualitative and quantitative molecular inventories to those obtained by microscopy. Species richness detected by microscopy was always higher than that detected by pyrosequencing. Some morphologically detected taxa may have been persistent frustules from dead cells. Some taxa detected by molecular analysis were not detected by morphology and vice versa. The main source of divergence appears to be inadequate taxonomic coverage in DNA reference libraries. Only a small percentage of species (but almost all genera) in morphological inventories were included in DNA reference libraries. DNA reference libraries contained a smaller percentage of species from tropical (27.1–38.1%) than from temperate samples (53.7–77.8%). Agreement between morphological and molecular inventories was better for species with relative abundance >1% than for rare species. The rbcL marker appeared to provide more reproducible results (94.9% species similarity between the 2 duplicates) and was very useful for molecular identification, but procedural standardization is needed. The water-quality ranking assigned to a site via the Pollution Sensitivity diatom index was the same whether calculated with molecular or morphological data. Pyrosequencing is a promising approach for detecting all species, even rare ones, once reference libraries have been developed.

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

Abstract 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.

Aggregation of an individual-based space-dependent model of forest dynamics into distribution-based and space-independent models

A question addressed in forest modelling is: which level of detail is required to reproduce the ecosystem function? In this paper four versions of the same model of a natural rain-forest are compared. The most detailed is an individual-based distance-dependent model, where every individual is described and interacts with other trees through a spatially explicit neighbourhood. Performing aggregation on the stand description yields a distribution-based distance-dependent model. Applying the mean field approximation brings two distance-dependent models. Three of the four models appear to predict the same stationary state in the limit where the number of trees is infinite (individual-based distance-independent+distribution-based models). The individual-based distance-dependent model differs because of the occurrence of space-dependent effects. An alternative aggregation method based on moment equations is then suggested to render the space-dependent effects.

Tectonic-driven climate change and the diversification of angiosperms

Significance Angiosperm range expansion and diversification have been major biotic upheavals in the Earth history. Mechanisms involved in their successful diversification have mainly called upon intrinsic processes at the plant level, leaving the influence of the global tectonics poorly explored. We investigate evolution of paleogeography and climate and correlate it with the diversification of angiosperms by using a general circulation model. We show that Pangea breakup induced an important expansion of temperate zones during the late Cretaceous which was concomitant to the rise of angiosperms. We suggest that the breakup of Pangea led to the onset of new humid bioclimatic continents, which in turn may have provided new external conditions for ecological expansion of the angiosperms and their diversification. 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.

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.

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.

Are ecological groups of species optimal for forest dynamics modelling

The huge diversity of tree species in tropical rain-forests makes the modelling of its dynamics a difficult task. One-way to deal with it is to define species groups. A classical approach for building species groups consists in grouping species with nearby characteristics, using cluster analysis. A group of species is then characterized by the same list of attributes as a single species, and it is incorporated in the model of forest dynamics in the same way as a single species. In this paper, a new approach for building species group is proposed. It relies on the discrepancy between model predictions when all species are considered separately, and model predictions when species groups are used. An aggregation error that quantifies the bias in model predictions that results from species grouping is thus defined. We then define the optimal species grouping as the one that minimizes the aggregation error. Using data from a tropical rain-forest in French Guiana and a toy model of forest dynamics, this new method for species grouping is confronted to the classical method based on cluster analysis of the species characteristics, and to a combined method based on a cluster analysis that uses the aggregation error as a dissimilarity between species. The optimal species grouping is quite different from the classical species grouping. The ecological interpretation of the optimal groups is difficult, as there is no direct linkage between the species characteristics and the way that they are grouped. The combined approach yields species groups that are closed to the optimal ones, with much less computations. The optimal species groups are thus specific to the model of forest dynamics and lack the generality of those of the classical method, that in turn are not optimal.