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A recent paper (Manceau and Lambert, 2016) developed a novel approach for describing two well-defined notions of species based on a phylogenetic tree and a phenotypic partition. In this paper, we explore some further combinatorial properties of this approach and describe an extension that allows an arbitrary number of phenotypic partitions to be combined with a phylogenetic tree for these two species notions.
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the recursive comput
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with
Rooted phylogenetic networks provide a way to describe species relationships when evolution departs from the simple model of a tree. However, networks inferred from genomic data can be highly tangled, making it difficult to discern the main reticulat
Measures of tree balance play an important role in the analysis of phylogenetic trees. One of the oldest and most popular indices in this regard is the Colless index for rooted bifurcating trees, introduced by Colless (1982). While many of its statis
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if $mathcal{T