Descartes' rule of signs and the identifiability of population demographic models from genomic variation data

DOI10.1214/14-AOS1264zbMATH Open1305.62027arXiv1309.5056OpenAlexW1991564538WikidataQ31151279 ScholiaQ31151279MaRDI QIDQ482900FDOQ482900

Authors: Anand Bhaskar, Yun S. Song 

Publication date: 6 January 2015

Published in: The Annals of Statistics (Search for Journal in Brave)

Abstract: The sample frequency spectrum (SFS) is a widely-used summary statistic of genomic variation in a sample of homologous DNA sequences. It provides a highly efficient dimensional reduction of large-scale population genomic data and its mathematical dependence on the underlying population demography is well understood, thus enabling the development of efficient inference algorithms. However, it has been recently shown that very different population demographies can actually generate the same SFS for arbitrarily large sample sizes. Although in principle this nonidentifiability issue poses a thorny challenge to statistical inference, the population size functions involved in the counterexamples are arguably not so biologically realistic. Here, we revisit this problem and examine the identifiability of demographic models under the restriction that the population sizes are piecewise-defined where each piece belongs to some family of biologically-motivated functions. Under this assumption, we prove that the expected SFS of a sample uniquely determines the underlying demographic model, provided that the sample is sufficiently large. We obtain a general bound on the sample size sufficient for identifiability; the bound depends on the number of pieces in the demographic model and also on the type of population size function in each piece. In the cases of piecewise-constant, piecewise-exponential and piecewise-generalized-exponential models, which are often assumed in population genomic inferences, we provide explicit formulas for the bounds as simple functions of the number of pieces. Lastly, we obtain analogous results for the "folded" SFS, which is often used when there is ambiguity as to which allelic type is ancestral. Our results are proved using a generalization of Descartes' rule of signs for polynomials to the Laplace transform of piecewise continuous functions.

Full work available at URL: https://arxiv.org/abs/1309.5056

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zbMATH Keywords

identifiabilitypopulation geneticspopulation sizefrequency spectrumcoalescent theory

Mathematics Subject Classification ID

Statistical aspects of information-theoretic topics (62B10) Applications of statistics to biology and medical sciences; meta analysis (62P10) Problems related to evolution (92D15)

Cites Work

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Cited In (7)

• Coalescence times for three genes provide sufficient information to distinguish population structure from population size changes
• On the decidability of population size histories from finite allele frequency spectra
• Rates of convergence in the two-island and isolation-with-migration models
• Non-parametric estimation of population size changes from the site frequency spectrum
• Sparse moments of univariate step functions and allele frequency spectra
• Can one hear the shape of a population history?
• Efficiently inferring the demographic history of many populations with allele count data

Uses Software

• FTEC
• Eigenstrat

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