The problem of constructing an optimal rooted phylogenetic network from an arbitrary set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet, which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes from an arbitrary set of rooted triplets. Despite of current methods that work for dense set of roote...

Although polyploidy plays a fundamental role in plant evolution, the elucidation of polyploid origins is fraught with methodological challenges. For example, allopolyploid species may confound phylogenetic reconstruction because commonly used methods are designed to trace divergent, rather than reticulate patterns. Recently developed techniques of phylogenetic network estimation allow for a mor...

Chalinidae is a family of haplosclerid sponges with a delicate reticulated chaonosomal skeleton of uni-, paucior multispicular primary lines which are connected by unispicular secondary lines, and with an ectosomal skeleton, if present, formed by a regular hexagonal, unispicular, tangential reticulation (Weerdt 2002). Currently, the family harbors only five valid genera (Chalinula, Cladocroce, ...

Reticulate evolution is a fundamental process in the evolution of certain groups of taxa. Consequently, conflicting signals in a data set may not be the result of sampling or modelling errors, but due to the fact that reticulation has played a role in the evolutionary history of the species under consideration. However, despite its occurrence, such processes are still relatively rare, and so, a...

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree based on a model of speciation and duplication where duplications are clustered in duplication episodes. The goal is to minimize the number of such episodes. T...

Reticulation events occur frequently in many types of species. Therefore, to develop accurate methods for reconstructing phylogenetic networks in order to describe evolutionary history in the presence of reticulation events is important. Previous work has suggested that constructing phylogenetic networks by merging gene trees is a biologically meaningful approach. This paper presents two new ef...

In higher plants, the development of functional chloroplasts is essential for photosynthesis and many other physiological processes. With a long-term goal of elucidating the genetic regulation of chloroplast development, we identified two allelic leaf variegation mutants, variegated5-1 (var5-1) and var5-2. Both mutants showed a distinct leaf reticulation phenotype of yellow paraveinal regions a...

The present paper proposes to investigate the links between the microstructure of polyurethane foams and their sound absorbing efficiency, and more specifically the effect of membranes closing the cells. This study is based on the complete characterization of 15 polyurethane foam with various cell sizes and reticulation rates (i.e., open pore content): (i) characterization of the microstructure...

A phylogenetic network is a model for reticulate evolution. A hybridization network is one type of phylogenetic network for a set of discordant gene trees and "displays" each gene tree. A central computational problem on hybridization networks is: given a set of gene trees, reconstruct the minimum (i.e., most parsimonious) hybridization network that displays each given gene tree. This problem i...

Straightforward semi-phenomenological models have been developed for highly porous polyurethane foams to predict the macroscopic nonacoustic parameters involved in the classical Johnson-Champoux-Allard model (i.e., porosity, airflow resistivity...) from microstructure properties (i.e, strut length, strut thickness and reticulation rate). These microstructure properties are measured using sophis...