Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri

Table 1 Validation of array-CGH results against highly conserved^a genes predicted to be copy number expanded (CNEs) in A. lyrata

Array-CGH prediction method	Total number of CNEs detected	No. of CNEs detected (117 ; 98)^b		Sensitivity (% positives detected out of predicted positives)		Specificity (% negatives detected out of predicted negatives)		Precision (% true positives out of total no. detected)^c
		E	E-A	E	E-A	E	E-A	E	E-A
Present manuscript	217	12	12	10.3	12.2	99.5	99.6	5.3	5.3
Darby et al. 2011^d	949	10	8	8.5	8.2	99.5	99.6	1.3	1.1
Machado et al. 2010^e	298	7	5	5.9	5.1	99.5	99.6	2.9	2.1

^a A. lyrata genes sharing ≥ 95% sequence identity with their closest A. thaliana homologue [68] are termed highly conserved (compare Additional file 7)
^bHeaders of half-columns refer to total number of CNEs predicted by Ensembl Plants (E; Vilella et al. 2009) alone or additionally by A. lyrata genome analysis (E-A; Hu et al. 2011), respectively, as given in parentheses here. Shown are commonalities with these two groups of genes (same column, below) or data referring to these two groups of genes (columns to the right)
^cTrue positive is a CNE detected based on array-CGH that was previously predicted to be a CNE by Ensembl Plants [68] alone, or additionally by A. lyrata genome [35] analysis
^d[42]
^e[43]

ISSN: 1471-2164