相关论文: Invariants for level-1 phylogenetic networks under…

Algebraic techniques in phylogenetics have historically been successful at proving identifiability results and have also led to novel reconstruction algorithms. In this paper, we study the ideal of phylogenetic invariants of the…

Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees, such as hybridization, introgression, and lateral gene transfer. Studying phylogenetic networks under a statistical model of DNA…

Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…

In phylogenetics, it is important for the phylogenetic network model parameters to be identifiable so that the evolutionary histories of a group of species can be consistently inferred. However, as the complexity of the phylogenetic network…

An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…

The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…

When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several…

Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…

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…

We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…

Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…

Less rigid than phylogenetic trees, phylogenetic networks allow the description of a wider range of evolutionary events. In this note, we explain how to extend the rank invariants from phylogenetic trees to phylogenetic networks evolving…

Stochastic models of evolution (Markov random fields on trivalent trees) generally assume that different characters (different runs of the stochastic process) are independent and identically distributed. In this paper we take the first…

Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer.…

Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…

Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…

We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…

An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…