arXiv subjects

Andrew Francis

Publications and source records attributed to Andrew Francis.

31 records · Page 2Linked to original sources

arXiv2018

Lattice consensus: A partial order on phylogenetic trees that induces an associatively stable consensus method

There is a long tradition of the axiomatic study of consensus methods in phylogenetics that satisfy certain desirable properties. One recently-introduced property is associative stability, which is desirable because it confers a computational advantage, in that the consensus method only needs to be computed "pairwise". In this paper, we introduce a phylogenetic consensus method that satisfies this property, in addition to being "regular". The method is based on the introduction of a partial order on the set of rooted phylogenetic trees, itself based on the notion of a hierarchy-preserving map between trees. This partial order may be of independent interest. We call the method "lattice consensus", because it takes the unique maximal element in a lattice of trees defined by the partial order. Aside from being associatively stable, lattice consensus also satisfies the property of being Pareto on rooted triples, answering in the affirmative a question of Bryant et al (2017). We conclude the paper with an answer to another question of Bryant et al, showing that there is no regular extension stable consensus method for binary trees.

q-bio.PE↗

arXiv2017

Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution

Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is that of identifiability, which essentially asks under what circumstances can we reliably identify the phylogenetic network that gave rise to the observed data? Recently, identifiability results have appeared for networks relative to a model of sequence evolution that generalizes the standard Markov models used for phylogenetic trees. However, these results are quite limited in terms of the complexity of the networks that are considered. In this paper, by introducing an alternative probabilistic model for evolution along a network that is based on some ground-breaking work by Thatte for pedigrees, we are able to obtain an identifiability result for a much larger class of phylogenetic networks (essentially the class of so-called tree-child networks). To prove our main theorem, we derive some new results for identifying tree-child networks combinatorially, and then adapt some techniques developed by Thatte for pedigrees to show that our combinatorial results imply identifiability in the probabilistic setting. We hope that the introduction of our new model for networks could lead to new approaches to reliably construct phylogenetic networks.

q-bio.PE↗

arXiv2017

Tree-based unrooted phylogenetic networks

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An \emph{unrooted} phylogenetic network on a nonempty, finite set $X$ of taxa, or \emph{network}, is a connected graph in which every vertex has degree 1 or 3 and whose leaf-set is $X$. It is called a \emph{phylogenetic tree} if the underlying graph is a tree. In this paper we consider properties of \emph{tree-based networks}, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hyrbridization which are important factors in the evolution of many organisms.

q-bio.PE↗

arXiv2017

New Characterisations of Tree-Based Networks and Proximity Measures

Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution, such networks are simply phylogenetic (evolutionary) trees. Moreover, phylogenetic networks that are not trees can sometimes be represented as phylogenetic trees with additional directed edges placed between their edges. Such networks are called {\em tree based}, and the class of phylogenetic networks that are tree based has recently been characterised. In this paper, we establish a number of new characterisations of tree-based networks in terms of path partitions and antichains (in the spirit of Dilworth's theorem), as well as via matchings in a bipartite graph. We also show that a temporal network is tree based if and only if it satisfies an antichain-to-leaf condition. In the second part of the paper, we define three indices that measure the extent to which an arbitrary phylogenetic network deviates from being tree based. We describe how these three indices can be described exactly and computed efficiently using classical results concerning maximum-sized matchings in bipartite graphs.

math.CO↗

arXiv2017

Bounds for phylogenetic network space metrics

Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which every vertex has degree 1 or 3 and whose leaf-set is a fixed set $X$ of taxa. This space, denoted $\mathcal{N}(X)$, is defined in terms of two operations on networks -- the nearest neighbor interchange and triangle operations -- which can be used to transform any network with leaf set $X$ into any other network with that leaf set. In particular, it gives rise to a metric $d$ on $\mathcal N(X)$ which is given by the smallest number of operations required to transform one network in $\mathcal N(X)$ into another in $\mathcal N(X)$. The metric generalizes the well-known NNI-metric on phylogenetic trees which has been intensively studied in the literature. In this paper, we derive a bound for the metric $d$ as well as a related metric $d_{N\!N\!I}$ which arises when restricting $d$ to the subset of $\mathcal{N}(X)$ consisting of all networks with $2(|X|-1+i)$ vertices, $i \ge 1$. We also introduce two new metrics on networks -- the SPR and TBR metrics -- which generalize the metrics on phylogenetic trees with the same name and give bounds for these new metrics. We expect our results to eventually have applications to the development and understanding of network search algorithms.

q-bio.PE↗

arXiv2017

Can we 'future-proof' consensus trees?

Consensus methods are widely used for combining phylogenetic trees into a single estimate of the evolutionary tree for a group of species. As more taxa are added, the new source trees may begin to tell a different evolutionary story when restricted to the original set of taxa. However, if the new trees, restricted to the original set of taxa, were to agree exactly with the earlier trees, then we might hope that their consensus would either agree with or resolve the original consensus tree. In this paper, we ask under what conditions consensus methods exist that are 'future proof' in this sense. While we show that some methods (e.g. Adams consensus) have this property for specific types of input, we also establish a rather surprising `no-go' theorem: there is no 'reasonable' consensus method that satisfies the future-proofing property in general. We then investigate a second notion of 'future proofing' for consensus methods, in which trees (rather than taxa) are added, and establish some positive and negative results. We end with some questions for future work.

q-bio.PE↗

arXiv2012

Multiplicative Bases for the Centres of the Group Algebra and Iwahori-Hecke Algebra of the Symmetric Group

Let $\H_n$ be the Iwahori-Hecke algebra of the symmetric group $S_n$, and let $Z(\H_n)$ denote its centre. Let $B={b_1,b_2,...,b_t}$ be a basis for $Z(\H_n)$ over $R=\Z[q,q^{-1}]$. Then $B$ is called \emph{multiplicative} if, for every $i$ and $j$, there exists $k$ such that $b_ib_j= b_k$. In this article we prove that there are no multiplicative bases for $Z(\Z S_n)$ and $Z(\H_n)$ when $n\ge 3$. In addition, we prove that there exist exactly two multiplicative bases for $Z(\Z S_2)$ and none for $Z(\H_2)$.

math.RT↗

arXiv2008

The centers of Iwahori-Hecke algebras are filtered

We show that the center of the Iwahori--Hecke algebra of the symmetric group $S_n$ carries a natural filtered algebra structure, and that the structure constants of the associated graded algebra are independent of $n$. A series of conjectures and open problems are also included.

math.RT↗

arXiv2007

Monomial bases for the centres of the group algebra and Iwahori--Hecke algebra of S_4

G. E. Murphy showed in 1983 that the centre of every symmetric group algebra has an integral basis consisting of a specific set of monomial symmetric polynomials in the Jucys--Murphy elements. While we have shown in earlier work that the centre of the group algebra of S_3 has exactly three additional such bases, we show in this paper that the centre of the group algebra of S_4 has infinitely many bases consisting of monomial symmetric polynomials in Jucys--Murphy elements, which we characterize completely. The proof of this result involves establishing closed forms for coefficients of class sums in the monomial symmetric polynomials in Jucys--Murphy elements, and solving several resulting exponential Diophantine equations with the aid of a computer. Our initial motivation was in finding integral bases for the centre of the Iwahori--Hecke algebra, and we address this question also, by finding several integral bases of monomial symmetric polynomials in Jucys--Murphy elements for the centre of the Iwahori--Hecke algebra of S_4.

math.GR↗

arXiv2007

Centralizers in the Hecke algebras of complex reflection groups

How far can the elementary description of centralizers of parabolic subalgebras of Hecke algebras of finite real reflection groups be generalized to the complex reflection group case? In this paper we begin to answer this question by establishing results in two directions. First, under conditions closely analogous to those existing for the real case, we give explicit relations between coefficients in an element centralizing a generator. Second, we introduce a tool for dealing with a major challenge of the complex case -- the ``instability'' of certain double cosets -- through the definition and use of a double coset graph. We use these results to find integral bases for the centralizers of generators as well as the centres of the Hecke algebras of types $G_4$ and $G(4,1,2)$. Keywords: complex reflection group; Hecke algebra; centre; centralizer; modular; double coset.

math.RT↗

arXiv2007

A new integral basis for the centre of the Hecke algebra of type A

We describe a recursive algorithm that produces an integral basis for the centre of the Hecke algebra of type A consisting of linear combinations of monomial symmetric polynomials of Jucys--Murphy elements. We also discuss the existence of integral bases for the centre of the Hecke algebra that consist solely of monomial symmetric polynomials of Jucys--Murphy elements. Finally, for n=3, we show that only one such basis exists for the centre of the Hecke algebra, by proving that there are exactly four bases for the centre of the corresponding symmetric group algebra which consist solely of monomial symmetric polynomials of Jucys--Murphy elements.

math.RT↗

arXiv2007

On the square root of the centre of the Hecke algebra of type A

In this paper we investigate non-central elements of the Iwahori-Hecke algebra of the symmetric group whose squares are central. In particular, we describe a commutative subalgebra generated by certain non-central square roots of central elements, and the generic existence of a rank-three submodule of the Hecke algebra contained in the square root of the centre but not in the centre. The generators for this commutative subalgebra include the longest word and elements related to trivial and sign characters of the Hecke algebra. We find elegant expressions for the squares of such generators in terms of both the minimal basis of the centre and the elementary symmetric functions of Murphy elements.

math.RT↗

arXiv2005

On bases of centres of Iwahori-Hecke algebras of the symmetric group

Using norms, the second author constructed a basis for the centre of the Hecke algebra of the symmetric group over $\Q[ξ]$ in 1990. An integral "minimal" basis was later given by the first author in 1999, following work of Geck and Rouquier. In principle one can then write elements of the norm basis as integral linear combinations of minimal basis elements. In this paper we find an explicit non-recursive expression for the coefficients appearing in these linear combinations. These coefficients are expressed in terms of readily computable numbers involving orders of symmetric groups and conjugacy classes. In the process of establishing this main theorem, we prove the following items of independent interest: a result on the projection of the norms onto parabolic subalgebras, the existence of an inner product on the Hecke algebra with some interesting properties, and the existence of a partial ordering on the norms.

math.QA↗