Reconstructing Reticulate Evolution in Species—Theory and Practice

Reconstructing patterns of reticulate evolution in plants.

Until recently, rigorously reconstructing the many hybrid speciation events in plants has not been practical because of the limited number of molecular markers available for plant phylogenetic reconstruction and the lack of good, biologically based methods for inferring reticulation (network) events. This situation should change rapidly with the development of multiple nuclear markers for phylo...

Phylogenetic analysis under reticulate evolution.

The usual assumption that species have evolved from a common ancestor by a simple branching process--where each branch is genetically isolated--has been challenged by the observation of frequent hybridization between species in natural populations. In fact, most plant species are thought to have hybrid origins. This reticulate pattern of species evolution has posed problems in the definition of...

Network (Reticulate) Evolution: Biology, Models, and Algorithms

The Role of Reticulate Evolution in Creating Innovation and Complexity

Reticulate evolution encompasses processes that conflict with traditional Tree of Life efforts. These processes, horizontal gene transfer (HGT), gene and whole-genome duplications through allopolyploidization, are some of the main driving forces for generating innovation and complexity. HGT has a profound impact on prokaryotic and eukaryotic evolution. HGTs can lead to the invention of new meta...

A Framework for Representing Reticulate Evolution

Acyclic directed graphs (ADGs) are increasingly being viewed as more appropriate for representing certain evolutionary relationships, particularly in biology, than rooted trees. In this paper, we develop a framework for the analysis of these graphs which we call hybrid phylogenies. We are particularly interested in the problem whereby one is given a set of phylogenetic trees and wishes to deter...