Abstract
In order to clarify the relationships among southern South American (sSA) representatives of the genus Ilex, an amplified fragment length polymorphism (AFLP) analysis was accomplished. In addition, the phylogenetic relationships of the species were studied using ribosomal internal transcribed spacer (ITS) sequence data alone and in combination with AFLP data, taking into account the possible existence of paralogous sequences and the influence of alignment parameters. To explore stability of phylogenetic hypotheses, a sensitivity analysis was performed using 15 indel-substitution models. Within each species assayed, the AFLPs allowed the recognition of several diagnostic bands. Furthermore, the AFLP analysis revealed that individuals belonging to the same morpho-species formed coherent clades. In addition, some cases of geographical association were noted. Studies on ITS sequences revealed divergence between data obtained herein and sequence data downloaded from GenBank. The sensitivity analyses yielded different interspecific hypotheses of relationships. Notwithstanding, analyses of the ITS data alone and in combination with AFLPs, rendered clades stable to variation in the analytical parameters. Topologies obtained for the AFLPs, the ITS data alone and the combined analyses, demonstrated the existence of a group formed by I. argentina, I. brasiliensis, I. brevicuspis, I. integerrima, and I. theezans, and that I. dumosa and I. paraguariensis were distantly related to the former. Incongruence with traditional taxonomical treatments was found.
Highlights
In order to clarify the relationships among southern South American representatives of the genus Ilex, an amplified fragment length polymorphism (AFLP) analysis was accomplished
Topologies obtained for the AFLPs, the internal transcribed spacer (ITS) data alone and the combined analyses, demonstrated the existence of a group formed by I. argentina, I. brasiliensis, I. brevicuspis, L integerrima, and L theezans, and that L dumosa and I. paraguariensis were distantly related to the former
Clades found throughout combining AFLP data for eight taxa and nucleotide sequences the parameter space explored are marked with thick lines
Summary
Gene conversion, unequal crossing over, and perhaps repeat amplification (Baldwin et al, 1995). A. As a res The u formatiol n andt placem, ent of subcs lade (I.e brevicuv spis + I. er iliensis AJ492661, I. brevicuspis AJ492663, I. dumosa taubertiana) was dependent on analytical conditions; it was AJ492656, I. integerrima AJ492664, and I. pseudobuxus found in 80% of the conditions, and it formed a monophyletic AJ492660, could be considered as pseudogenes: the high nu- group with (I. microdonta + I. pseudobuxus + L microdonta cleotide divergence with co-specific data, the low G + C con- AJ492665) in only 53% of the conditions. The sister sequence tent, the departure from the conserved motif in ITS 1, the less to the sSA clade, in 67% of the parameters sets assayed, was thermodynamic stability in the RNA structure, and their basal represented solely by Asian L pedunculosa, but with low Breposition on phylogenetic trees with respect to sSA counter- mer support values. I. decidua 260 58.08 - 101.4 -97.3 10 D 234 56.84 -96.2 -92.1 5 I. glabra 261 58.62 -94.1 -89.5 17 D 243 58.02 -101.8 -96.9 14 L. mucronata 256 59.38 -102.6 -97.8 9 B 242 54.13 -87.6 -83.8 5 L opaca 259 58.69 -105.7 -100.5 14 D 243 59.26 -91.5 -88.1 3
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