arXiv subjects

Marta Casanellas

Publications and source records attributed to Marta Casanellas.

31 records · Page 2Linked to original sources

arXiv2014

Local description of phylogenetic group-based models

Motivated by phylogenetics, our aim is to obtain a system of equations that define a phylogenetic variety on an open set containing the biologically meaningful points. In this paper we consider phylogenetic varieties defined via group-based models. For any finite abelian group $G$, we provide an explicit construction of $codim X$ phylogenetic invariants (polynomial equations) of degree at most $|G|$ that define the variety $X$ on a Zariski open set $U$. The set $U$ contains all biologically meaningful points when $G$ is the group of the Kimura 3-parameter model. In particular, our main result confirms a conjecture by the third author and, on the set $U$, a couple of conjectures by Bernd Sturmfels and Seth Sullivant.

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arXiv2012

The space of phylogenetic mixtures for equivariant models

The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected probabilities of patterns observed at the leaves of a phylogenetic tree could be used for model selection. It remained open the question regarding whether these equations were enough for characterizing the evolutionary model. Here we prove that, for equivariant models of evolution, the space of distributions satisfying these linear equations coincides with the space of distributions arising from mixtures of trees on a set of taxa. In other words, we prove that an alignment is produced from a mixture of phylogenetic trees under an equivariant evolutionary model if and only if its distribution of column patterns satisfies the linear equations mentioned above. Moreover, for each equivariant model and for any number of taxa, we provide a set of linearly independent equations defining this space of phylogenetic mixtures. This is a powerful tool that has already been successfully used in model selection. We also use the results obtained to study identifiability issues for phylogenetic mixtures.

q-bio.PE↗

arXiv2012

Empar: EM-based algorithm for parameter estimation of Markov models on trees

The goal of branch length estimation in phylogenetic inference is to estimate the divergence time between a set of sequences based on compositional differences between them. A number of software is currently available facilitating branch lengths estimation for homogeneous and stationary evolutionary models. Homogeneity of the evolutionary process imposes fixed rates of evolution throughout the tree. In complex data problems this assumption is likely to put the results of the analyses in question. In this work we propose an algorithm for parameter and branch lengths inference in the discrete-time Markov processes on trees. This broad class of nonhomogeneous models comprises the general Markov model and all its submodels, including both stationary and nonstationary models. Here, we adapted the well-known Expectation-Maximization algorithm and present a detailed performance study of this approach for a selection of nonhomogeneous evolutionary models. We conducted an extensive performance assessment on multiple sequence alignments simulated under a variety of settings. We demonstrated high accuracy of the tool in parameter estimation and branch lengths recovery, proving the method to be a valuable tool for phylogenetic inference in real life problems. $\empar$ is an open-source C++ implementation of the methods introduced in this paper and is the first tool designed to handle nonhomogeneous data.

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arXiv2011

Generating Markov evolutionary matrices for a given branch length

Under a markovian evolutionary process, the expected number of substitutions per site (also called branch length) that have occurred when a sequence has evolved from another according to a transition matrix $P$ can be approximated by $-1/4log det P.$ When the Markov process is assumed to be continuous in time, i.e. $P=\exp Qt$ it is easy to simulate this evolutionary process for a given branch length (this amounts to requiring $Q$ of a certain trace). For the more general case (what we call discrete-time models), it is not trivial to generate a substitution matrix $P$ of given determinant (i.e. corresponding to a process of given branch length). In this paper we solve this problem for the most well-known discrete-time models JC*, K80*, K81*, SSM and GMM. These models lie in the class of nonhomogeneous evolutionary models. For any of these models we provide concise algorithms to generate matrices $P$ of given determinant. Moreover, in the first four models, our results prove that any of these matrices can be generated in this way. Our techniques are mainly based on algebraic tools.

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arXiv2011

Stable Ulrich bundles

The existence of stable ACM vector bundles of high rank on algebraic varieties is a challenging problem. In this paper, we study stable Ulrich bundles (that is, stable ACM bundles whose corresponding module has the maximum number of generators) on nonsingular cubic surfaces $X \subset \mathbb{P}^3.$ We give necessary and sufficient conditions on the first Chern class $D$ for the existence of stable Ulrich bundles on $X$ of rank $r$ and $c_1=D$. When such bundles exist, we prove that that the corresponding moduli space of stable bundles is smooth and irreducible of dimension $D^2-2r^2+1$ and consists entirely of stable Ulrich bundles (see Theorem 1.1). As a consequence, we are also able to prove the existence of stable Ulrich bundles of any rank on nonsingular cubic threefolds in $\mathbb{P}^4$.

math.AG↗

arXiv2009

Relevant phylogenetic invariants of evolutionary models

Recently there have been several attempts to provide a whole set of generators of the ideal of the algebraic variety associated to a phylogenetic tree evolving under an algebraic model. These algebraic varieties have been proven to be useful in phylogenetics. In this paper we prove that, for phylogenetic reconstruction purposes, it is enough to consider generators coming from the edges of the tree, the so-called edge invariants. This is the algebraic analogous to Buneman's Splits Equivalence Theorem. The interest of this result relies on its potential applications in phylogenetics for the widely used evolutionary models such as Jukes-Cantor, Kimura 2 and 3 parameters, and General Markov models.

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arXiv2008

ACM bundles on cubic surfaces

In this paper we prove that, for every $r \geq 2$, the moduli space $M^s_X(r;c_1,c_2)$ of rank $r$ stable vector bundles with Chern classes $c_1=rH$ and $c_2=(3r^2-r)/2$ on a nonsingular cubic surface $X \subset \mathbb{P}^3$ contains a nonempty smooth open subset formed by ACM bundles, i.e. vector bundles with no intermediate cohomology. The bundles we consider for this study are extremal for the number of generators of the corresponding module (these are known as Ulrich bundles), so we also prove the existence of indecomposable Ulrich bundles of arbitrarily high rank on $X$.

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arXiv2007

Geometry of the Kimura 3-parameter model

The Kimura 3-parameter model on a tree of n leaves is one of the most used in phylogenetics. The affine algebraic variety W associated to it is a toric variety. We study its geometry and we prove that it is isomorphic to a geometric quotient of the affine space by a finite group acting on it. As a consequence, we are able to study the singularities of W and prove that the biologically meaningful points are smooth points. Then we give an algorithm for constructing a set of minimal generators of the localized ideal at these points, for an arbitrary number of leaves n. This leads to a major improvement of phylogenetic reconstruction methods based on algebraic geometry.

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arXiv2006

The minimal resolution conjecture for points on the cubic surface

In this paper we prove that the generalized version of the Minimal Resolution Conjecture stated by Mustata holds for certain general sets of points on a smooth cubic surface $X \subset \mathbb{P}^3$. The main tool used is Gorenstein liaison theory and, more precisely, the relationship between the free resolutions of two linked schemes.

math.AC↗

arXiv2006

Performance of a new invariants method on homogeneous and non-homogeneous quartet trees

An attempt to use phylogenetic invariants for tree reconstruction was made at the end of the 80s and the beginning of the 90s by several authors (the initial idea due to Lake and Cavender and Felsenstein in 1987. However, the efficiency of methods based on invariants is still in doubt, probably because these methods only used few generators of the set of phylogenetic invariants. The method studied in this paper was first introduced by Casanellas, Garcia and Sullivant and it is the first method based on invariants that uses the whole set of generators for DNA data. The simulation studies performed in this paper prove that it is a very competitive and highly efficient phylogenetic reconstruction method, especially for non-homogeneous models on phylogenetic trees.

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arXiv2003

Hilbert functions of irreducible arithmetically Gorenstein schemes

In this paper we compute the Hilbert functions of irreducible (or smooth) and reduced arithmetically Gorenstein schemes that are twisted anti-canonical divisors on arithmetically Cohen-Macaulay schemes. We also prove some folklore results characterizing the Hilbert functions of irreducible standard determinantal schemes, and we use them to produce a new class of functions that occur as Hilbert functions of irreducible (or smooth) and reduced arithmetically Gorenstein schemes in any codimension.

math.AG↗

arXiv2003

Gorenstein Liaison and ACM Sheaves

We study Gorenstein liaison of codimension two subschemes of an arithmetically Gorenstein scheme X. Our main result is a criterion for two such subschemes to be in the same Gorenstein liaison class, in terms of the category of ACM sheaves on X. As a consequence we obtain a criterion for X to have the property that every codimension 2 arithmetically Cohen-Macaulay subscheme is in the Gorenstein liaison class of a complete intersection. Using these tools we prove that every arithmetically Gorenstein subscheme of $\mathbb{P}^n$ is in the Gorenstein liaison class of a complete intesection and we are able to characterize the Gorenstein liaison classes of curves on a nonsingular quadric threefold in $\mathbb{P}^4$.

math.AG↗

arXiv2003

Gorenstein Biliaison and ACM Sheaves

Let $X$ be a normal arithmetically Gorenstein scheme in ${\mathbb P}^n$. We give a criterion for all codimension two ACM subschemes of $X$ to be in the same Gorenstein biliaison class on $X$, in terms of the category of ACM sheaves on $X$. These are sheaves that correspond to the graded maximal Cohen--Macaulay modules on the homogeneous coordinate ring of $X$. Using known results on MCM modules, we are able to determine the Gorenstein biliaison classes of codimension two subschemes of certain varieties, including the nonsingular quadric surface in ${\mathbb P}^3$, and the cone over it in ${\mathbb P}^4$. As an application we obtain a new proof of some theorems of Lesperance about curves in ${\mathbb P}^4$, and answer some questions be raised.

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