Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila

Table 1 Variation in the 5' and 3' ends of R1 and R2 elements

	Major copy type: mean divergence* (maximum)		Atypical sequences: number (divergence)
	5' end	3' end	Variant copies^†	Variant 5' ends^‡
R1 elements
D. simulans R1A	0.000 (0.000)	0.002 (0.003)		4 (0.01-0.03)
D. sechellia R1A	<0.001 (0.003)	<0.001 (0.002)
D. melanogaster R1A	0.001 (0.008)	0.003 (0.015)	2 (0.07)
D. yakuba R1A	0.001 (0.005)	0.000 (0.000)	1 (0.02)
D. erecta R1A	0.002 (0.005)	0.001 (0.007)
D. ananassae R1A	0.013 (0.043)	<0.001 (0.003)		1 (0.08-0.11)
D. ananassae R1B	0.000 (0.000)	0.002 (0.005)		3 (0.15-0.22)
D. pseudoobscura R1A	0.000 (0.000)	0.002 (0.010)		1 (0.04)
D. persimilis R1A	ND	0.000 (0.000)	1 (0.02)
D. willistoni R1A	0.002 (0.005)	0.001 (0.003)
D. mojavensis R1A	0.000 (0.000)	0.000 (0.000)
D. virilis R1B	0.001 (0.008)	<0.001 (0.003)	6 (0.01-0.05)
D. grimshawi R1B₁	0.000 (0.000)	0.001 (0.005)
D. grimshawi R1B₂	0.000 (0.000)	0.000 (0.000)
R2 elements
D. simulans R2	0.001 (0.008)	0.000 (0.000)
D. sechellia R2	0.000 (0.000)	<0.001 (0.003)
D. melanogaster R2	0.002 (0.005)	0.001 (0.015)	6 (0.02-0.05)
D. yakuba R2	0.002 (0.013)	0.006 (0.018)
D. ananassae R2	0.004 (0.008)	0.001 (0.005)
D. persimilis R2	ND	ND
D. pseudoobscura R2	ND	0.005 (0.010)
D. willistoni R2 sub1	0.001 (0.003)	0.002 (0.008)
D. willistoni R2 sub2^§	0.003 (0.006)	0.015 (0.028)

*Average nucleotide divergence from the consensus. The maximum divergence observed is shown in parentheses. ^†Divergence detected at both the 5' and 3' ends except for the insertion in D. yakuba, where divergence was detected only at the 3' end. ^‡The number of distinct 5' ends excludes the majority (consensus) sequence used in the previous columns. The divergence of additional 5' ends is calculated from the consensus. ^§There may be only two copies of this lineage. ND indicates that these numbers were not included because sequencing reads with variant sequences had poor quality scores.

ISSN: 1474-760X