Bonnici, I. | bioRxiv Science

bioRxiv2024

EcologicalNetworksDynamics.jl: A Julia package to simulate the temporal dynamics of complex ecological networks

O_LISpecies interactions play a crucial role in shaping biodiversity, species coexistence, population dynamics, community stability and ecosystem functioning. Our understanding of the role of the diversity of species interactions driving these species, community and ecosystem features is limited because current approaches often focus only on trophic interactions. This is why a new modelling framework that includes a greater diversity of interactions between species is crucially needed. C_LIO_LIWe developed a modular, user-friendly, and extensible Julia package that delivers the core functionality of the bio-energetic food web model. Moreover, it embeds several ecological interaction types alongside the capacity to manipulate external drivers of ecological dynamics like temperature. These new features represent important processes known to influence biodiversity, coexistence, functioning and stability in natural communities. Specifically, they include: a) an explicit multiple nutrient intake model for producers, b) competition among producers, c) temperature dependence implemented via the Boltzmann-Arhennius rule, and d) the ability to model several non-trophic interactions including competition for space, plant facilitation, predator interference and refuge provisioning. C_LIO_LIThe inclusion of the various features provides users with the ability to ask questions about multiple simultaneous processes and stressor impacts, and thus develop theory relevant to real world scenarios facing complex ecological communities in the Anthropocene. It will allow researchers to quantify the relative importance of different mechanisms to stability and functioning of complex communities. C_LIO_LIThe package was build for theoreticians seeking to explore the effects of different types of species interactions on the dynamics of complex ecological communities, but also for empiricists seeking to confront their empirical findings with theoretical expectations. The package provides a straightforward framework to model explicitly complex ecological communities or provide tools to generate those communities from few parameters. C_LI

ecology↗

bioRxiv2022

Nanopore sequencing enables multigenic family reconstruction despite highly frequent PCR-induced recombination

This study developed a new bioinformatics pipeline to acquire all the different copies of multi-copy gene families based on Oxford Nanopore Technologies sequencing of PCR products. We used this pipeline to acquire the sequences of highly similar copies of the cidA and cidB genes present in the genomes of Wolbachia pipientis (wPip) bacteria infecting the cells of Culex pipiens mosquitoes. The approach is based on read mapping, SNP calling and haplotyping, using our already wide existing reference database for the cid genes obtained by cloning and Sanger sequencing. We addressed problems commonly faced when using mapping approaches for multi-copy gene families with highly similar variants (or haplotypes). In addition, we confirmed that PCR amplification causes frequent chimeras which have to be carefully considered when working on families of recombinant genes. We tested the robustness of the pipeline through a combination of analyses of simulated reads and of gene sequence acquisitions through cloning and Sanger sequencing. For genes of which the haplotype cannot be reconstructed from short reads sequencing, this pipeline confers a high throughput acquisition, gives reliable results as well as insights of the relative copy numbers of the different variants.

genomics↗