Detection of lineage-specific evolutionary changes among primate species

Table 1 Average accuracy (shown as a percentage) of DivE (dE) and DLESS (dl) to detect conservation and accelerated evolution computed on all primate subtrees for simulated data of different lengths.

		50 bp		100 bp		200 bp		500 bp		1000 bp
		dE	dl	dE	dl	dE	dl	dE	dl	dE	dl
gain	0.01	4.4	1.6	15.0	5.3	32.3	15.6	59.6	40.0	80.7	66.0
	0.02	5.2	1.7	15.1	6.3	32.7	15.9	58.7	40.0	81.5	63.7
	0.05	3.8	1.6	13.0	5.6	30.5	15.6	56.0	39.9	79.6	62.2
	0.1	4.7	0.9	12.2	3.8	27.5	14.6	54.0	37.8	77.2	58.6
	0.2	2.0	1.6	8.7	2.7	22.7	10.5	48.6	33.6	70.7	53.8
	0.3	2.1	0.2	6.6	2.0	18.3	8.9	40.7	28.0	62.1	48.4
	0.4	1.3	0.3	5.2	1.8	13.6	5.8	33.8	21.5	54.2	36.6
	0.5	0	0.2	1.9	0.1	13.0	4.1	25.4	13.8	45.4	26.0
loss	0.01	85.6	73.6	93.9	86.5	97.4	93.5	99.1	97.2	99.5	98.8
	0.02	85.7	72.7	93.7	86.8	97.3	93.5	99.0	97.3	99.5	98.6
	0.05	84.3	69.3	93.4	86.9	97.2	93.6	99.0	97.3	99.5	98.7
	0.1	82.2	61.5	91.8	86.3	96.7	93.1	98.9	97.4	99.5	98.9
	0.2	70.6	43.9	87.5	84.1	94.2	91.9	98.1	97.3	99.2	98.7
	0.3	53.9	29.8	81.6	72.3	90.5	90.4	96.2	96.7	98.3	98.3
	0.4	41.2	22.8	70.7	52.6	85.7	80.7	93.7	94.0	96.7	96.6
	0.5	31.3	12.5	55.1	37.0	77.3	58.9	89.8	80.8	94.4	87.6
acc	0.01^-1	71.0	-	80.4	-	88.0	-	93.6	-	96.4	-
	0.02^-1	69.5	-	79.8	-	87.1	-	93.5	-	96.1	-
	0.05^-1	54.4	-	73.7	-	84.8	-	92.7	-	95.9	-
	0.1^-1	35.8	-	58.7	-	78.7	-	90.7	-	95.2	-
	0.2^-1	16.4	-	33.2	-	56.1	-	80.9	-	90.2	-
	0.3^-1	6.1	-	20.4	-	36.8	-	61.5	-	80.3	-
	0.4^-1	3.0	-	8.6	-	24.2	-	47.1	-	66.6	-
	0.5^-1	1.8	-	3.7	-	10.7	-	31.9	-	47.0	-

Accuracy was computed as the average of precision and recall. The first column in table shows the type of selection (gain, loss, or acceleration), and the value of the scaling parameter ρ. Smaller values of ρ correspond to stronger selection pressure, which is easier to detect. Results in bold show the larger accuracy value for each comparison between DivE and DLESS.