TY - JOUR AU - Azevedo, Ricardo B AU - Lohaus, Rolf AU - Tiago Paixao ID - 2900 IS - 5 JF - Evolution & Development TI - Networking networks VL - 10 ER - TY - CONF AB - Motivated by an application in cell biology, we describe an extension of the kinetic data structures framework from Delaunay triangulations to fixed-radius alpha complexes. Our algorithm is implemented using CGAL, following the exact geometric computation paradigm. We report on several techniques to accelerate the computation that turn our implementation applicable to the underlying biological problem. AU - Kerber, Michael AU - Edelsbrunner, Herbert ID - 2906 T2 - 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments TI - 3D kinetic alpha complexes and their implementation ER - TY - JOUR AB - Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation by distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module. AU - Kelleher, Jerome AU - Barton, Nicholas H AU - Etheridge, Alison ID - 2910 IS - 7 JF - Bioinformatics TI - Coalescent simulation in continuous space VL - 29 ER - TY - JOUR AB - We survey a class of models for spatially structured populations which we have called spatial Λ-Fleming–Viot processes. They arise from a flexible framework for modelling in which the key innovation is that random genetic drift is driven by a Poisson point process of spatial ‘events’. We demonstrate how this overcomes some of the obstructions to modelling populations which evolve in two- (and higher-) dimensional spatial continua, how its predictions match phenomena observed in data and how it fits with classical models. Finally we outline some directions for future research. AU - Barton, Nicholas H AU - Etheridge, Alison AU - Véber, Amandine ID - 2909 IS - 1 JF - Journal of Statistical Mechanics Theory and Experiment TI - Modelling evolution in a spatial continuum VL - 2013 ER - TY - JOUR AB - Hybridization is an almost inevitable component of speciation, and its study can tell us much about that process. However, hybridization itself may have a negligible influence on the origin of species: on the one hand, universally favoured alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional hybridisation may hardly affect the process of divergence. AU - Barton, Nicholas H ID - 2908 IS - 2 JF - Journal of Evolutionary Biology TI - Does hybridisation influence speciation? VL - 26 ER -