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. 2012 Oct 3;4(11):1176–1187. doi: 10.1093/gbe/evs081

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Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2012.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 7.— — Distribution of diversity statistics compared between ORFans and non-ORFan controls. The three rows show the distributions for pi (upper), dS (middle) and dN (lower), for both t1 (left column) and t2 (right column) control sets. To understand the shape of the distribution of population statistics for ORFans, values for ORFans were gathered into decile bins defined by the non-ORFan control clusters, that is, each bin comprises 10% of the distribution of non-ORFan values. The value on the Y axis for the first decile bin in (A), for instance, represents the frequency with which the Pi value for an ORFan ranks in the top 10% of the values in its customized t1 control group. (C, E) The same comparison for dN and dS; (B, D, and F) the distribution of Pi, dN, and dS (respectively) relative to the t2 comparison group. The null expectation is a straight line at a value of 10%, with a slight anomaly at the low (right) end of the distribution due to zero values (in cases where zero values exceed 10% of the control distribution, zero values in the ORFan distribution will be placed in whichever bin is counted first, which in this case tends to leave a shortage in the last bin). The symmetric but slightly U-shaped distribution of dS values indicates that ORFans exhibit greater variance, but otherwise have the same distribution of synonymous differences as non-ORFans. However, the deviation from the distribution of dN (and Pi) values is asymmetric, with a 2-fold or more excess of ORFan clusters with diversity in the top 10% or 20% of the distribution relative to non-ORFan controls.