. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 . . . . . . . . . . ....

Deforestation and forest fragmentation are known major causes of nonrandom extinction, but there is no information about their impact on the phylogenetic diversity of the remaining species assemblages. Using a large vegetation dataset from an old hyper-fragmented landscape in the Brazilian Atlantic rainforest we assess whether the local extirpation of tree species and functional impoverishment ...

The evolutionary history of a set of species is commonly represented by a phylogenetic tree. Often, however, the data contain conflicting signals, which can be better represented by a more general structure, namely a phylogenetic network. Such networks allow the display of several alternative evolutionary scenarios simultaneously but this can come at the price of complex visual representations....

different species of gazelles are among the most endangered mammals on the asian steppes and occur in the central, southern and northwestern regions of iran. the previous conservation efforts in this region have been incomplete due to confusion about the phylogenetic relationship among various populations. so that, different conservation programs such as ex-situ breeding and transfer of captive...

Answering a problem posed by Nakhleh, we prove that counting the number of phylogenetic trees inferred by a (binary) phylogenetic network is #P-complete. An immediate consequence of this result is that counting the number of phylogenetic trees commonly inferred by two (binary) phylogenetic networks is also #P-complete.

There exist several methods dealing with the reconstruction of rooted phylogenetic networks explaining different evolutionary histories given by rooted binary phylogenetic trees. In practice, however, due to insufficient information of the underlying data, phylogenetic trees are in general not completely resolved and, thus, those methods can often not be applied to biological data. In this work...

A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not tree-like. In a seminal paper, Wang et al.(1) studied the problem of constructing a phylogenetic network, allowing recombination between sequences, with the constraint that the resulting cycles must be disjoint. We call such a phylogenetic network a "galled-tree". They gave a polynomia...

A phylogenetic algorithm computes a tree of distance relationships on a set, S, of phylogenetic descriptions (which may not be complete), given a phylogenetic-description transformation function, D, defined on S. Maximum Parsimony (MP) is a widely used phylogenetic algorithm that computes the shortest phylogenetic tree that represents the tree distances on S determined by D. To date, the sensit...

Phylogenetic analysis of the class 'Alphaproteobacteria', including physiologically diverse species, was conducted by using small-subunit rRNA gene sequences. The 16S rRNA gene sequences of 261 species in the class 'Alphaproteobacteria' were obtained from GenBank/EMBL/DDBJ for constructing a phylogenetic tree by using maximum-likelihood analysis. In the resulting tree, members of the class 'Alp...

Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on the analysis of multiple genes. Thus, it has become necessary to devise statistical methods to combine multiple molecular datasets. Here, we compare several models for combining different genes for ...