Related papers: Evolutionary and Ecological Trees and Networks

Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…

Innovation and its complement exnovation describe the progression of realized possibilities from the past to the future, and the process depends on the structure of the underlying graph. For example, the phylogenetic tree represents the…

A biologically motivated individual-based framework for evolution in network-structured populations is developed that can accommodate eco-evolutionary dynamics. This framework is used to construct a network birth and death model. The…

It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…

A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…

Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…

The architecture of bipartite networks linking two classes of constituents is affected by the interactions within each class. For the bipartite networks representing the mutualistic relationship between pollinating animals and plants, it…

Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…

Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…

A mathematical model of interacting species filling ecological niches left by the extinction of others is introduced. Species organize themselves into genera of all sizes. The size of a genus on average grows linearly with its age,…

We investigate the formation of stable ecological networks where many species share the same resource. We show that such stable ecosystem naturally occurs as a result of extinctions. We obtain an analytical relation for the number of…

We study the behavior of phylogenetic tree shapes in the tropical geometric interpretation of tree space. Tree shapes are formally referred to as tree topologies; a tree topology can also be thought of as a tree combinatorial type, which is…

Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…

Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…

We consider an evolving network of a fixed number of nodes. The allocation of edges is a dynamical stochastic process inspired by biological reproduction dynamics, namely by deleting and duplicating existing nodes and their edges. The…

It is well-known that population structure is a catalyst for the evolution of cooperation since individuals can reciprocate with their neighbors through local interactions defined by network structures. Previous research typically relies on…

We study the role of phylogenetic trees on correlations in mutation processes. Generally, correlations decay exponentially with the generation number. We find that two distinct regimes of behavior exist. For mutation rates smaller than a…

Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…

The identification of key populations shaping the structure and connectivity of metapopulation systems is a major challenge in population ecology. The use of molecular markers in the theoretical framework of population genetics has allowed…

We consider models for growing networks incorporating two effects not previously considered: (i) different species of nodes, with each species having different properties (such as different attachment probabilities to other node species);…