Eva Czabarka , Steven Kelk , Vincent Moulton , László A. Székely
{"title":"系统发育树集合上的共凸特征","authors":"Eva Czabarka , Steven Kelk , Vincent Moulton , László A. Székely","doi":"10.1016/j.aam.2025.102952","DOIUrl":null,"url":null,"abstract":"<div><div>In phylogenetics, a key problem is to construct evolutionary trees from collections of characters where, for a set <em>X</em> of species, a character is simply a function from <em>X</em> onto a set of states. In this context, a key concept is convexity, where a character is convex on a tree with leaf set <em>X</em> if the collection of subtrees spanned by the leaves of the tree that have the same state are pairwise disjoint. Although collections of convex characters on a single tree have been extensively studied over the past few decades, very little is known about <em>coconvex characters</em>, that is, characters that are simultaneously convex on a collection of trees. As a starting point to better understand coconvexity, in this paper we prove a number of extremal results for the following question: <em>What is the minimal number of coconvex characters on a collection of n-leaved trees taken over all collections of size</em> <span><math><mi>t</mi><mo>≥</mo><mn>2</mn></math></span><em>, also if we restrict to coconvex characters which map to k states?</em> As an application of coconvexity, we introduce a new one-parameter family of tree metrics, which range between the coarse Robinson-Foulds distance and the much finer quartet distance. We show that bounds on the quantities in the above question translate into bounds for the diameter of the tree space for the new distances. Our results open up several new interesting directions and questions which have potential applications to, for example, tree spaces and phylogenomics.</div></div>","PeriodicalId":50877,"journal":{"name":"Advances in Applied Mathematics","volume":"172 ","pages":"Article 102952"},"PeriodicalIF":1.3000,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Coconvex characters on collections of phylogenetic trees\",\"authors\":\"Eva Czabarka , Steven Kelk , Vincent Moulton , László A. Székely\",\"doi\":\"10.1016/j.aam.2025.102952\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>In phylogenetics, a key problem is to construct evolutionary trees from collections of characters where, for a set <em>X</em> of species, a character is simply a function from <em>X</em> onto a set of states. In this context, a key concept is convexity, where a character is convex on a tree with leaf set <em>X</em> if the collection of subtrees spanned by the leaves of the tree that have the same state are pairwise disjoint. Although collections of convex characters on a single tree have been extensively studied over the past few decades, very little is known about <em>coconvex characters</em>, that is, characters that are simultaneously convex on a collection of trees. As a starting point to better understand coconvexity, in this paper we prove a number of extremal results for the following question: <em>What is the minimal number of coconvex characters on a collection of n-leaved trees taken over all collections of size</em> <span><math><mi>t</mi><mo>≥</mo><mn>2</mn></math></span><em>, also if we restrict to coconvex characters which map to k states?</em> As an application of coconvexity, we introduce a new one-parameter family of tree metrics, which range between the coarse Robinson-Foulds distance and the much finer quartet distance. We show that bounds on the quantities in the above question translate into bounds for the diameter of the tree space for the new distances. Our results open up several new interesting directions and questions which have potential applications to, for example, tree spaces and phylogenomics.</div></div>\",\"PeriodicalId\":50877,\"journal\":{\"name\":\"Advances in Applied Mathematics\",\"volume\":\"172 \",\"pages\":\"Article 102952\"},\"PeriodicalIF\":1.3000,\"publicationDate\":\"2025-08-19\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Advances in Applied Mathematics\",\"FirstCategoryId\":\"100\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0196885825001149\",\"RegionNum\":3,\"RegionCategory\":\"数学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"MATHEMATICS, APPLIED\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Advances in Applied Mathematics","FirstCategoryId":"100","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0196885825001149","RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"MATHEMATICS, APPLIED","Score":null,"Total":0}
Coconvex characters on collections of phylogenetic trees
In phylogenetics, a key problem is to construct evolutionary trees from collections of characters where, for a set X of species, a character is simply a function from X onto a set of states. In this context, a key concept is convexity, where a character is convex on a tree with leaf set X if the collection of subtrees spanned by the leaves of the tree that have the same state are pairwise disjoint. Although collections of convex characters on a single tree have been extensively studied over the past few decades, very little is known about coconvex characters, that is, characters that are simultaneously convex on a collection of trees. As a starting point to better understand coconvexity, in this paper we prove a number of extremal results for the following question: What is the minimal number of coconvex characters on a collection of n-leaved trees taken over all collections of size, also if we restrict to coconvex characters which map to k states? As an application of coconvexity, we introduce a new one-parameter family of tree metrics, which range between the coarse Robinson-Foulds distance and the much finer quartet distance. We show that bounds on the quantities in the above question translate into bounds for the diameter of the tree space for the new distances. Our results open up several new interesting directions and questions which have potential applications to, for example, tree spaces and phylogenomics.
期刊介绍:
Interdisciplinary in its coverage, Advances in Applied Mathematics is dedicated to the publication of original and survey articles on rigorous methods and results in applied mathematics. The journal features articles on discrete mathematics, discrete probability theory, theoretical statistics, mathematical biology and bioinformatics, applied commutative algebra and algebraic geometry, convexity theory, experimental mathematics, theoretical computer science, and other areas.
Emphasizing papers that represent a substantial mathematical advance in their field, the journal is an excellent source of current information for mathematicians, computer scientists, applied mathematicians, physicists, statisticians, and biologists. Over the past ten years, Advances in Applied Mathematics has published research papers written by many of the foremost mathematicians of our time.