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等距系统发育仙人掌空间

The Space of Equidistant Phylogenetic Cactuses.

作者信息

Huber Katharina T, Moulton Vincent, Owen Megan, Spillner Andreas, St John Katherine

机构信息

School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ UK.

Department of Mathematics, Lehman College, CUNY, New York, NY 10468 USA.

出版信息

Ann Comb. 2024;28(1):1-32. doi: 10.1007/s00026-023-00656-0. Epub 2023 Jun 9.

Abstract

An - is a type of rooted, arc-weighted, directed acyclic graph with leaf set , that is used in biology to represent the evolutionary history of a set  of species. In this paper, we introduce and investigate the space of equidistant -cactuses. This space contains, as a subset, the space of ultrametric trees on that was introduced by Gavryushkin and Drummond. We show that equidistant-cactus space is a CAT(0)-metric space which implies, for example, that there are unique geodesic paths between points. As a key step to proving this, we present a combinatorial result concerning rooted -cactuses. In particular, we show that such graphs can be encoded in terms of a pairwise compatibility condition arising from a poset of collections of pairs of subsets of  that satisfy certain set-theoretic properties. As a corollary, we also obtain an encoding of ranked, rooted -trees in terms of partitions of , which provides an alternative proof that the space of ultrametric trees on is CAT(0). We expect that our results will provide the basis for novel ways to perform statistical analyses on collections of equidistant -cactuses, as well as new directions for defining and understanding spaces of more general, arc-weighted phylogenetic networks.

摘要

一个[具体术语未给出]是一种有根的、带弧权重的、有向无环图,其叶集为[具体集合未给出],在生物学中用于表示一组物种的进化历史。在本文中,我们引入并研究等距[具体术语未给出]仙人掌的空间。这个空间作为一个子集包含了由加夫留什金和德拉蒙德引入的关于[具体集合未给出]的超度量树的空间。我们证明等距仙人掌空间是一个CAT(0)度量空间,这意味着例如在点之间存在唯一的测地线。作为证明这一点的关键步骤,我们给出了一个关于有根[具体术语未给出]仙人掌的组合结果。特别地,我们表明这样的图可以根据由满足某些集合论性质的[具体集合未给出]的子集对的集合的偏序集产生的成对兼容性条件进行编码。作为一个推论,我们还得到了根据[具体集合未给出]的划分对有等级的、有根的[具体术语未给出]树的编码,这为关于[具体集合未给出]的超度量树的空间是CAT(0)提供了另一种证明。我们期望我们的结果将为对等距[具体术语未给出]仙人掌集合进行统计分析的新方法提供基础,以及为定义和理解更一般的、带弧权重的系统发育网络的空间提供新的方向。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c6e5/10904525/0fb326b263ac/26_2023_656_Fig1_HTML.jpg

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