The composition vector (CV) method is an alignment-free method for phylogenetics. Because of its simplicity when compared with the alignment-based methods, the method has been widely discussed lately. There are mainly four steps in the CV method: (1) count the frequency of each k-string in the sequence; (2) construct the composition vector for the sequence; (3) compute the distance between ever...

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix CHAPTER 1. General Introduction . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 Computational Phylogenetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1.1 The Perfect Phylogeny Problem . . . . . . . . . . . . . . . . . . . . . . . 2 1.1.2 The Tree Compatibility Problem . . . . . . . . . . ....

Anthracnose is a general term for sunken lesions and blights on stems, leaves and fruits which causes economic damage to agricultural products. This study, conducted to identify Colletotrichum species associated with anthracnose symptoms on some plants in Khuzestan province (Iran) using morphological and molecular methods. During 2016–17, 40 leaf and fruit samples showing anthracnose symptoms (...

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The development of comparative phylogenetic methods has provided a powerful toolkit for addressing adaptive hypotheses, and researchers have begun to apply these methods to test the role of pollinators in floral evolution and diversification. One approach is to reconstruct the history of both floral traits and pollination systems to determine if floral trait change is spurred by shifts in polli...

It is widely accepted that the rate of evolution (substitution rate) at neutral genes is unaffected by population size fluctuations. This result has implications for the analysis of genetic data in population genetics and phylogenetics, and provides, in particular, a justification for the concept of the molecular clock. Here, we show that the substitution rate at neutral genes does depend on po...

Studying the shape of phylogenetic trees under different random models is an important issue in evolutionary biology. In this paper, we propose a general framework for deriving detailed statistical results for patterns in phylogenetic trees under the Yule-Harding model and the uniform model, two of the most fundamental random models considered in phylogenetics. Our framework will unify several ...

Science and society would benefit enormously from detailed and well-supported knowledge of the Tree of Life (TOL). At present, however, we know relatively little about the phylogenetic relationships of most of the species on Earth, or even among many of the major branches of the Tree. Fortunately, we have reached a turning point. Owing to fundamental theoretical advances, to the development of ...

Recent advances in the field of plant community phylogenetics and invasion phylogenetics are mostly based on plot-level data, which do not take into consideration the spatial arrangement of individual plants within the plot. Here we use within-plot plant coordinates to investigate the link between the physical distance separating plants, and their phylogenetic relatedness. We look at two vegeta...