Section: Application Domains

Community ecology and population genetics

Community assembly models how species can assemble or diassemble to build stable or metastable communities. It has grown out of inventories of countable organisms. Using metagenomics one can produce molecular based inventories at rates never reached before. Most communities can be understood as pathways of carbon exchange, mostly in the form of sugar, between species. Even a plant cannot exist without carbon exchange with its rhizosphere. Two main routes for carbon exchange have been recognized: predation and parasitism. In predation, interactions–even if sometimes dramatic–may be loose and infrequent, whereas parasitism requires what Claude Combes has called intimate and sustainable interactions [19]. About one decade ago, some works [25] have proposed a comprehensive framework to link the studies of biodiversity with community assembly. This is still incipient research, connecting community ecology and biogeography.

We aim at developping graph-based models of co-occurence between species from NGS inventories in metagenomics, i.e. recognition of patterns in community assembly, and as a further layer to study links, if any, between diversity at different scales and community assemblies, starting from current, but oversimplified theories, where species assemble from a regional pool either randomly, as in neutral models, or by environmental filtering, as in niche modeling. We propose to study community assembly as a multiscale process between nested pools, both in tree communities in Amazonia, and diatom communities in freshwaters. This will be a step towards community genomics, which adds an ecological flavour to metagenomics.

Convergence between the processes that shape genetic diversity and community diversity–drift, selection, mutation/speciation and migration–has been noted for decades and is now a paradigm, establishing a continuous scale between levels of diversity patterns, beyond classical approaches based on iconic levels like species and populations. We will aim at deciphering diversity pattern along these gradients, connecting population and community genetics. Therefore, some key points must be adressed on reliability of tools.

Next-generation sequencing technologies are now an essential tool in population and community genomics, either for making evolutionary inferences or for developing SNPs for population genotyping analyses. Two problems are highlighted in the literature related to the use of those technologies for population genomics: variable sequence coverage and higher sequencing error in comparison to the Sanger sequencing technology. Methods are developed to develop unbiased estimates of key parameters, especially integrating sequencing errors [23]. An additional problem can be created when sequences are mapped on a reference sequence, either the sequenced species or an heterologous one, since paralogous genes are then considered to be the same physical position, creating a false signal of diversity [20]. Several approaches were proposed to correct for paralogy, either by working directly on the sequences issued from mapped reads [20] or by filtering detected SNPs. Finally, an increasingly popular method (RADseq) is used to develop SNP markers, but it was shown that using RADseq data to estimate diversity directly biases estimates [11]. Workflows to implement statistical methods that correct for diversity biases estimates now need an implementation for biologists.