Bassam AlKindy

Reem Alsrraj, Bassam AlKindy, Christophe Guyeux et al.

The number of complete chloroplastic genomes increases day after day, making it possible to rethink plants phylogeny at the biomolecular era. Given a set of close plants sharing in the order of one hundred of core chloroplastic genes, this article focuses on how to extract the largest subset of sequences in order to obtain the most supported species tree. Due to computational complexity, a discrete and distributed Particle Swarm Optimization (DPSO) is proposed. It is finally applied to the core genes of Rosales order.

Bassam AlKindy, Bashar Al-Nuaimi, Christophe Guyeux et al.

The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their chloroplasts, the phylogenetic tree that can be inferred by their core genes is not necessarily well supported, due to the possible occurrence of problematic genes (i.e., homoplasy, incomplete lineage sorting, horizontal gene transfers, etc.) which may blur the phylogenetic signal. However, a trustworthy phylogenetic tree can still be obtained provided such a number of blurring genes is reduced. The problem is thus to determine the largest subset of core genes that produces the best-supported tree. To discard problematic genes and due to the overwhelming number of possible combinations, this article focuses on how to extract the largest subset of sequences in order to obtain the most supported species tree. Due to computational complexity, a distributed Binary Particle Swarm Optimization (BPSO) is proposed in sequential and distributed fashions. Obtained results from both versions of the BPSO are compared with those computed using an hybrid approach embedding both genetic algorithms and statistical tests. The proposal has been applied to different cases of plant families, leading to encouraging results for these families.

Bassam AlKindy, Christophe Guyeux, Jean-François Couchot et al.

The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their chloroplasts, the phylogenetic tree that can be inferred by their core genes is not necessarily well supported, due to the possible occurrence of "problematic" genes (i.e., homoplasy, incomplete lineage sorting, horizontal gene transfers, etc.) which may blur phylogenetic signal. However, a trustworthy phylogenetic tree can still be obtained if the number of problematic genes is low, the problem being to determine the largest subset of core genes that produces the best supported tree. To discard problematic genes and due to the overwhelming number of possible combinations, we propose an hybrid approach that embeds both genetic algorithms and statistical tests. Given a set of organisms, the result is a pipeline of many stages for the production of well supported phylogenetic trees. The proposal has been applied to different cases of plant families, leading to encouraging results for these families.