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Detecting selection using time-series data of allele frequencies with multiple independent reference Loci.

Nishino J - G3 (Bethesda) (2013)

Bottom Line: Recently, in 2013 Feder et al. proposed the frequency increment test (FIT), which evaluates natural selection at a single diallelic locus by the use of time-series data of allele frequencies.Here, we expand upon the FIT by introducing a test that explicitly allows for changes in population size by using information from independent reference loci.Various demographic models suggest that our proposed test is unbiased irrespective of fluctuations in population size when sampling noise can be ignored and that it has greater power to detect selection than the FIT if sufficient reference loci are used.

View Article: PubMed Central - PubMed

Affiliation: Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan.

ABSTRACT
Recently, in 2013 Feder et al. proposed the frequency increment test (FIT), which evaluates natural selection at a single diallelic locus by the use of time-series data of allele frequencies. This test is unbiased under conditions of constant population size and no sampling noise. Here, we expand upon the FIT by introducing a test that explicitly allows for changes in population size by using information from independent reference loci. Various demographic models suggest that our proposed test is unbiased irrespective of fluctuations in population size when sampling noise can be ignored and that it has greater power to detect selection than the FIT if sufficient reference loci are used.

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Related in: MedlinePlus

The effects of selection at reference loci on the power of the FITR. The powers of the FITR under various selection strengths, s0, at focal loci are shown as functions of the selection coefficient, , at reference loci for demographic models 1 and 5. Each point corresponds to the power obtained by 100,000 simulations at the 5% significance level. The number of reference loci, the duration of sampling time, and the number of sampled points were R = 10, T = 1000, and (L + 1) = 11, respectively. The intervals between any two adjacent sampled points were the same at . The initial frequency for all  loci, , was assumed to be 0.5.
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fig4: The effects of selection at reference loci on the power of the FITR. The powers of the FITR under various selection strengths, s0, at focal loci are shown as functions of the selection coefficient, , at reference loci for demographic models 1 and 5. Each point corresponds to the power obtained by 100,000 simulations at the 5% significance level. The number of reference loci, the duration of sampling time, and the number of sampled points were R = 10, T = 1000, and (L + 1) = 11, respectively. The intervals between any two adjacent sampled points were the same at . The initial frequency for all loci, , was assumed to be 0.5.

Mentions: A case in which the reference loci are under selection is evaluated in Figure 4. The selection model is the same because the focal loci and R loci are under the same degree of selection. That is, for all loci, the fitnesses of genotypes AhAh, Ahah, and ahah are assumed to be 1, 1 + 0.5sh, and 1 + sh (s1 = s2 = ··· = sR), respectively. The effects of selection at the reference loci are conservative for type I error rates (see the case of s0 = 0 in Figure 4). The results of Model 1 suggest that if , there is little difference in rejection rates compared to the neutral case. Including Model 5, if the condition sh ≤ 1/2s0 is met, the power is not decreased. That is, the power is not highly sensitive to selection at the reference loci. Nevertheless, we recommend using synonymous sites or noncoding regions as references.


Detecting selection using time-series data of allele frequencies with multiple independent reference Loci.

Nishino J - G3 (Bethesda) (2013)

The effects of selection at reference loci on the power of the FITR. The powers of the FITR under various selection strengths, s0, at focal loci are shown as functions of the selection coefficient, , at reference loci for demographic models 1 and 5. Each point corresponds to the power obtained by 100,000 simulations at the 5% significance level. The number of reference loci, the duration of sampling time, and the number of sampled points were R = 10, T = 1000, and (L + 1) = 11, respectively. The intervals between any two adjacent sampled points were the same at . The initial frequency for all  loci, , was assumed to be 0.5.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852378&req=5

fig4: The effects of selection at reference loci on the power of the FITR. The powers of the FITR under various selection strengths, s0, at focal loci are shown as functions of the selection coefficient, , at reference loci for demographic models 1 and 5. Each point corresponds to the power obtained by 100,000 simulations at the 5% significance level. The number of reference loci, the duration of sampling time, and the number of sampled points were R = 10, T = 1000, and (L + 1) = 11, respectively. The intervals between any two adjacent sampled points were the same at . The initial frequency for all loci, , was assumed to be 0.5.
Mentions: A case in which the reference loci are under selection is evaluated in Figure 4. The selection model is the same because the focal loci and R loci are under the same degree of selection. That is, for all loci, the fitnesses of genotypes AhAh, Ahah, and ahah are assumed to be 1, 1 + 0.5sh, and 1 + sh (s1 = s2 = ··· = sR), respectively. The effects of selection at the reference loci are conservative for type I error rates (see the case of s0 = 0 in Figure 4). The results of Model 1 suggest that if , there is little difference in rejection rates compared to the neutral case. Including Model 5, if the condition sh ≤ 1/2s0 is met, the power is not decreased. That is, the power is not highly sensitive to selection at the reference loci. Nevertheless, we recommend using synonymous sites or noncoding regions as references.

Bottom Line: Recently, in 2013 Feder et al. proposed the frequency increment test (FIT), which evaluates natural selection at a single diallelic locus by the use of time-series data of allele frequencies.Here, we expand upon the FIT by introducing a test that explicitly allows for changes in population size by using information from independent reference loci.Various demographic models suggest that our proposed test is unbiased irrespective of fluctuations in population size when sampling noise can be ignored and that it has greater power to detect selection than the FIT if sufficient reference loci are used.

View Article: PubMed Central - PubMed

Affiliation: Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan.

ABSTRACT
Recently, in 2013 Feder et al. proposed the frequency increment test (FIT), which evaluates natural selection at a single diallelic locus by the use of time-series data of allele frequencies. This test is unbiased under conditions of constant population size and no sampling noise. Here, we expand upon the FIT by introducing a test that explicitly allows for changes in population size by using information from independent reference loci. Various demographic models suggest that our proposed test is unbiased irrespective of fluctuations in population size when sampling noise can be ignored and that it has greater power to detect selection than the FIT if sufficient reference loci are used.

Show MeSH
Related in: MedlinePlus