intron-containing taxa. We then compared the congruence of intron (Fig. 3A) and “organismal” (Fig. 3B) phylogenies to assess the relative contributions of vertical and horizontal transmission to the intron's evolutionary history in angiosperms. These phylogenies are highly incongruent. From this, we concluded that the intron had been independently acquired, by cross-species horizontal transfer, many times separately among the examined plants. For example, consider the closely related rosids Bursera and Melia, whose intron-hybridizing DNAs are in adjacent lanes in Fig. 1 (lanes 46 and 47; recall that DNAs are arranged according to presumptive phylogenetic order in these blots) and which group with 100% bootstrap support in the organismal tree of Fig. 3B. Their cox1 intron sequences do not, however, group together (Fig. 3A), suggesting that Bursera and Melia acquired their introns independently of one another. Three, more convincing pairs of examples of phylogenetic evidence for independent acquisition consist of Ilex/Hydrocotyle, Symplocus/Diospyros, and Maranta/Hedychium. Each pair again receives 100% bootstrap support in Fig. 3B, and in each case the two members of the pair are now separated by multiple, well supported nodes in the intron tree (Fig. 3A).
All told, we inferred at least 32 separate cases of intron gain to account for the intron's presence in the 48 angiosperms revealed to contain the intron by the 281-taxa Southern blot survey (Cho et al., 1998). Some 25 of these cases are marked on Fig. 3A by plus signs, while 7 additional gains were inferred by criterion ii, as we shall now describe. Overall, the inferences of independent intron gain were based on four criteria: (i) the many incongruencies, some strongly supported, some less so, between intron and organismal phylogenies (Fig. 3); (ii) the highly disjunct phylogenetic distribution of intron-containing plants; (iii) different lengths of co-conversion tracts among otherwise related introns (Fig. 3); and (iv) the existence of ancestrally intron-lacking taxa within families containing the intron. This last form of evidence also relates to co-conversion, the process by which donor exonic sequences flanking the intron replace recipient exonic sequences when the intron is inserted into the cox1 gene. Space limitations preclude any meaningful discussion of the complicated logic behind the two criteria that are largely or entirely based on co-conversion tract evidence; the interested reader is instead referred to Cho et al. (1998) and Cho and Palmer (1999).
More extensive sampling within the monocot family Araceae showed that 6 of the 14 Araceae sampled contain the intron and that these 6 taxa probably acquired their introns by at least 3 and quite possibly 5 separate horizontal transfers (Cho et al., 1998; Cho and Palmer, 1999). In addition, unpublished studies from our lab and that of Claude dePamphilis reveal many more cases of independent gain of this promiscuous group I intron. Given that we have still sampled only a tiny fraction of the >300,000