Selection on Horizontally Transferred and Duplicated Genes in Sinorhizobium (Ensifer), the Root-Nodule Symbionts of Medicago

Genome Biol. Evol. 6(5):1199–1209. doi: 10.1093/gbe/evu090

The sentence in the Results at the top of page 1204 that begins, “For all three replicons in S. meliloti, D_Tdup was more negative than D_{T nonsyn}…” should read “For all three replicons combined, and for the chromosome and pSymA separately in S. meliloti, D_Tdup was more negative than D_{T nonsyn}…”

In addition, tables 1, 3, and supplementary table S3 contained some erroneous values. In table 1, the values for θ_π and D_T for S. meliloti SNPs were calculated based on 24 S. meliloti strains, rather than the 20 strains used for the rest of the results. Similarly, the S. meliloti row in table 3 presents results for 24 strains, rather than for the 20 strain subset. The numbers presented in table S3 were based on an earlier version of the duplication detection pipeline—we neglected to update this table when we updated our pipeline. Corrected values are presented below. As a consequence of these corrections, the sentence at the bottom of page 1204 that reads, “Based on the minor allele frequency spectrum, 10% of nonsynonymous mutations in S. meliloti are effectively neutral, whereas two-thirds are subject to very strong (probably negative) selection (table 3)” should read “Based on the minor allele frequency spectrum, 10% of nonsynonymous mutations in S. meliloti are effectively neutral, whereas three-quarters are subject to very strong (probably negative) selection (table 3).”

Table S3.

MinimumCoverage	Reference strain	min.	mean	median
1.5	286	226	830	579
1.8	14	136	486	361
2.0	8	95	323	266

Table 1.

Mean Per cent of Genes Duplicated (among Strain Range Shown in Parentheses), Number of HT Genes, and Pairwise Diversity of Segregating Duplicates and Nucleotide Variants

	% Duplicates	HT Genes	θπ dup	θπ rep	θπ syn	DT dup	DT rep	DT syn
S. meliloti	0.6 (0.4–0.9)	10,247	0.010	0.0013	0.0095	−1.14	−1.02	−0.95
chr. - full	0.1 (0–0.5)	2,318	0.003	0.0008	0.0067	−1.80	−1.14	−1.19
chr. - 1a	0.1 (0–0.6)	804c	0.002	0.0012	0.0098	−1.88	−0.89	−0.71
chr. - 2b	0.2 (0–0.7)	1,014c	0.003	0.0006	0.0043	−1.64	−1.34	−1.56
pSymA	1.3 (0.6–2.6)	1,985	0.023	0.0025	0.0159	−1.30	−0.91	−0.50
pSymB	0.8 (0–1.4)	1,271	0.011	0.0023	0.0165	−0.12	−0.73	−0.38
S. medicae	0.8 (0.2–1.4)	4,521	0.012	0.0008	0.0038	−0.13	−0.28	−0.12
chr.	0.7 (0.1–1.6)	1,399	0.009	0.0007	0.0025	0.66	−0.06	0.15
pSymA	1.9 (0.4–3.8)	823	0.030	0.0019	0.0082	−0.46	−0.09	0.15
pSymB	0.2 (0.1–0.4)	515	0.003	0.0012	0.0070	−1.38	−0.71	−0.82

^aBefore position 1735000.

^bDoes not sum to 2,318 because some HT genes assigned to the chromosome had an ambiguous location.

^cAfter position 1735000.

Table 3.

DFE of Nonsynonymous Mutations: Per cent of Sites in Each Selection Bin (Standard Error)

	Nes
Species	0 – 1	1 – 10	10 – 100	>100
S. meliloti	10 (0.4)	5.7 (0.4)	8.9 (0.8)	75 (1.0)
S. medicae	19 (0.7)	6.7 (0.8)	9 (1.5)	65 (2)

The corrected values are similar to the erroneous values and do not affect any of the other tables, figures, or results, and they do not alter our principal finding—that duplications and horizontally transferred genes tend to segregate at low frequency relative to SNPs. The authors regret these errors and apologize for any inconvenience they may have caused.