Tying up loose strands: defining equations of the strand symmetric model

DOI10.18409/JAS.V6I1.34zbMATH Open1346.92047arXiv1410.3344OpenAlexW2964343649MaRDI QIDQ2820006FDOQ2820006

Authors: Colby Long, Seth Sullivant 

Publication date: 13 September 2016

Published in: Journal of Algebraic Statistics (Search for Journal in Brave)

Abstract: The strand symmetric model is a phylogenetic model designed to reflect the symmetry inherent in the double-stranded structure of DNA. We show that the set of known phylogenetic invariants for the general strand symmetric model of the three leaf claw tree entirely defines the ideal. This knowledge allows one to determine the vanishing ideal of the general strand symmetric model of any trivalent tree. Our proof of the main result is computational. We use the fact that the Zariski closure of the strand symmetric model is the secant variety of a toric variety to compute the dimension of the variety. We then show that the known equations generate a prime ideal of the correct dimension using elimination theory.

Full work available at URL: https://arxiv.org/abs/1410.3344

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zbMATH Keywords

algebraic statisticsphylogenetic invariantsstrand symmetric model

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Genetics and epigenetics (92D10) Problems related to evolution (92D15)

Cited In (4)

• Invariants for level-1 phylogenetic networks under the Cavendar-Farris-Neyman model
• Tensor decomposition and homotopy continuation
• Calculating two-strand jellyfish relations
• Phylogenetic complexity of the Kimura 3-parameter model

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