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Estimation of the neutrality index
journal contribution
posted on 2023-06-08, 08:59 authored by Nina Stoletzki, Adam Eyre-WalkerAdam Eyre-WalkerThe McDonaldKreitman (MK) test is a simple and widely used test of selection in which the numbers of nonsilent and silent substitutions (Dn and Ds) are compared with the numbers of nonsilent and silent polymorphisms (Pn and Ps). The neutrality index (NI 5 DsPn/DnPs), the odds ratio (OR) of the MK table, measures the direction and degree of departure from neutral evolution. The mean of NI values across genes is often taken to summarize patterns of selection in a species. Here, we show that this leads to statistical bias in both simulated and real data to the extent that species, which show a pattern of adaptive evolution, can apparently be subject to weak purifying selection and vice versa. We show that this bias can be removed by using a variant of the CochranMantelHaenszel procedure for estimating a weighted average OR. We also show that several point estimators of NI are statistically biased even when cutoff values are employed. We therefore suggest that a new statistic be used to study patterns of selection when data are sparse, the direction of selection: DoS 5 Dn/(Dn Ds) Pn/(Pn Ps).
History
Publication status
- Published
Journal
Molecular Biology and EvolutionISSN
0737-4038Publisher
Oxford University PressExternal DOI
Issue
1Volume
28Page range
63-70Department affiliated with
- Evolution, Behaviour and Environment Publications
Full text available
- No
Peer reviewed?
- Yes
Legacy Posted Date
2012-02-06Usage metrics
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