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Ecological networks allow us to study the structure and function of ecosystems and gain insights on species resilience/stability. The study of this ecological networks is usually a snapshop focused in a limited specific range of space and…
During the last two decades, ecological speciation has been a major research theme in evolutionary biology. Ecological speciation occurs when reproductive isolation between populations evolves as a result of niche differentiation.…
Interactive networks representing user participation and interactions in specific "events" are highly dynamic, with communities reflecting collective behaviors that evolve over time. Predicting these community evolutions is crucial for…
Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
To comprehend the multipartite organization of large-scale biological and social systems, we introduce a new information theoretic approach that reveals community structure in weighted and directed networks. The method decomposes a network…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…
With growing exchanges of people and merchandise between countries, epidemics have become an issue of increasing importance and huge amounts of data are being collected every day. Hence, analyses that were usually run in personal computers…
When dealing with evolving or multi-dimensional complex systems, network theory provides with elegant ways of describing their constituting components, through respectively time-varying and multi-layer complex networks. Nevertheless, the…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
Network ecologists investigate the structure, function, and evolution of ecological systems using network models and analyses. For example, network techniques have been used to study community interactions (i.e., food-webs, mutualisms),…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that…
Data acquisition in animal ecology is rapidly accelerating due to inexpensive and accessible sensors such as smartphones, drones, satellites, audio recorders and bio-logging devices. These new technologies and the data they generate hold…
This paper presents a robotic mowing framework that actively enhances garden biodiversity through visual perception and adaptive decision-making. Unlike passive rewilding approaches, the proposed system uses deep feature-space analysis to…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…