Saturation of the PCR Survey

Saturation Curves

The completeness of the sample can be estimated using a first order saturation model

Nnew(n) = Ntotal [ 1 - exp(-K n) ]

where Nnew(n) is the number of distinct Hox genes encountered after sequencing n clones. Saturation curves are shown below:


Figure. Saturation curve for the three PCR series.


Probability of Missing a Gene

The probability of missing a gene given the expected number Ntotal of distinct genes and a sample size of n sequences PCR products (which Hox genes) is

Prob[miss] = ( 1-1/Ntotal )n

PCR series n Ntotal Nfound K corr. chi2 Prob[miss]
5E5/3F 29 8.02 8 0.1575 0.988 2.55 0.021
5E5-2/3F 64 14.52 14 0.080 0.991 18.15 0.010
5E/3F 144 22.88 24 0.027 0.972 283.82 0.002
Note that the E/F series does not fit well to the saturation curve. This was noted earlier, see also [Misof, M.Y. and Wagner G.P., Evidence for Four Hox Clusters in the Killifish Fundulus Heteroclitus (Teleostei), Mol. Phyl. Evol. 5: 309-322 (1996).


The survey is fairly well saturated in the sense that it is unlikely that:
(1) any further sequences would be found in 5E5/3F,
(2) more than one more sequence would be found in 5E5-2/3F,
(3) any further sequences would be found in 5E/3F.