TAJIMA'S D AND SITE-SPECIFIC NUCLEOTIDE FREQUENCY IN A POPULATION DURING AN INFECTIOUS DISEASE OUTBREAK

Omori, Ryosuke; Wu, Jianhong

SIAM journal on applied mathematics, 2017, 77(6), 2156-2171

Permalink : https://hdl.handle.net/2115/70807

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アクセス権
open access
URI
https://hdl.handle.net/2115/70807
タイトル
TAJIMA'S D AND SITE-SPECIFIC NUCLEOTIDE FREQUENCY IN A POPULATION DURING AN INFECTIOUS DISEASE OUTBREAK
著者
e-Rad_Researcher
10746952
著者名
Omori, Ryosuke
著者名
Wu, Jianhong
言語
英語
キーワード
Tajima's D
SIR model
evolution
infectious disease
発行日
2017
出版者
Society for Industrial and Applied Mathematics(SIAM)
収録物名
SIAM journal on applied mathematics
巻(号)
77(6)
ページ
2156-2171
抄録
Tajima's D measures the difference between two estimates of genetic diversity in a given set of nucleic acid sequences. Here we show how Tajima's D can be calculated/estimated by developing an inductive algorithm for calculating the site-specific nucleotide frequencies from a standard multistrain susceptible-infective-removed (SIR) model (both deterministic and stochastic). We show that these frequencies are fully determined by the mutation rate and the initial condition of the frequencies. We prove that the sign of Tajima's D is independent of the disease population dynamics and that the negative sign does not imply an expansion of the infected population in the deterministic model. Using individual-based simulations, we also show that dependence of Tajima's D on the disease transmission and evolution dynamics is a result of the stochasticity of those dynamics. The same is true for the dependence related to genetic diversity of a pathogen.
資源タイプ
学術雑誌論文
出版タイプ
Version of Record
権利情報
Creative Commons Attribution 4.0 International
権利情報
© 2017, Society for Industrial and Applied Mathematics
PISSN
0036-1399
関連情報 (isIdenticalTo)
出版社版DOI
https://doi.org/10.1137/17M1114946