Phylogenetic tree and community structure from a Tangled Nature model

• Published in: Journal of theoretical biology Vol. 382; pp. 216 - 222
• Main Authors: Canko, Osman, Taşkın, Ferhat, Argın, Kamil
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 07.10.2015
• Subjects: Ecosystem; Food-web; Genome; Likelihood Functions; Maximum likelihood method; Models, Genetic; Modularity; Neighbor-joining method; Phylogenetic tree; Phylogeny; Species Specificity; Time Factors; Food-web; Maximum likelihood method; Modularity; Phylogenetic tree; Neighbor-joining method
• ISSN: 0022-5193; 1095-8541; 1095-8541
• DOI: 10.1016/j.jtbi.2015.07.005

In evolutionary biology, the taxonomy and origination of species are widely studied subjects. An estimation of the evolutionary tree can be done via available DNA sequence data. The calculation of the tree is made by well-known and frequently used methods such as maximum likelihood and neighbor-joining. In order to examine the results of these methods, an evolutionary tree is pursued computationally by a mathematical model, called Tangled Nature. A relatively small genome space is investigated due to computational burden and it is found that the actual and predicted trees are in reasonably good agreement in terms of shape. Moreover, the speciation and the resulting community structure of the food-web are investigated by modularity. •Phylogenetic trees (pt) estimated from genomes (or morphologies) of extant species cannot be compared with real pt, which is at best imperfectly known from the fossil record.•One way to assess the accuracy of common estimation methods, such as ML or NJ, would be to apply them to data from in silico evolution models, for which the pt is exactly known.•The quasi-evolutionary stable strategies׳ communities are very highly connected and there are no obvious fragmented subgroups among the species in a habitat.