Non-hereditary Minimum Deep Coalescence trees
One of the goals of phylogenetic research is to find the species tree describing the evolutionary history of a set of species. But the trees derived from geneti data with the help of tree inference methods are gene trees that need not coincide with the species tree. This can for example happen when so-called deep coalescence events take place. It is also known that species trees can differ from their most likely gene trees. Therefore, as a means to find the species tree, it has been suggested to use subtrees of the gene trees, for example triples, and to puzzle them together in order to find the species tree. In this paper, we will show that this approach may lead to wrong trees regarding the minimum deep coalescence criterion (MDC). In particular, we present an example in which the optimal MDC tree is unique, but none of its triple subtrees fulfills the MDC criterion. In this sense, MDC is a non-hereditary tree reconstruction method.
Code (0)
등록된 구현이 없습니다.
Similar Papers 제목 키워드 기반
In the Light of Deep Coalescence: Revisiting Trees Within Networks
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing th…
Roadblocked monotonic paths and the enumeration of coalescent histories for non-matching caterpillar gene trees and species trees
Given a gene tree topology and a species tree topology, a coalescent history represents a possible mapping of the list of gene tree coalescences to associated branches of a species tree on which those coalescences take p…
Structural Learning of Simple Staged Trees
Bayesian networks faithfully represent the symmetric conditional independences existing between the components of a random vector. Staged trees are an extension of Bayesian networks for categorical random vectors whose g…
Reducibility among NP-Hard graph problems and boundary classes
Many NP-hard graph problems become easy for some classes of graphs, such as coloring is easy for bipartite graphs, but NP-hard in general. So we can ask question like when does a hard problem become easy? What is the min…
Coalescent histories for lodgepole species trees
Coalescent histories are combinatorial structures that describe for a given gene tree and species tree the possible lists of branches of the species tree on which the gene tree coalescences take place. Properties of the …