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

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

Authors Colby Long, Seth Sullivant

Publication date 13 September 2016

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

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

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)

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.

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