Annonaceae substitution rates: a codon model perspective

The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

Diversidade e caracterização das Annonaceae do Brasil

Há, no Brasil, 29 gêneros e 386 espécies de Annonaceae, distribuídas principalmente na Amazônia, mas também na Mata Atlântica e no Cerrado. As Annonaceae estão classificadas em quatro subfamílias, Anaxagoreoideae, Annonoideae, Ambavioideae e Malmeoideae. Anaxagoreoideae inclui apenas Anaxagorea, com 14 espécies no Brasil. Ambavioideae é composto por nove gêneros, mas apenas Tetrameranthus ocorre no Brasil, com três espécies. Annonoideae é a maior subfamília, com 51 gêneros, dos quais 12 ocorrem no Brasil. Estão aqui incluídos Annona, Duguetia, Guatteria e Xylopia, os gêneros mais representativos da família na flora brasileira. Malmeoideae inclui principalmente gêneros asiáticos, e apenas os representantes da tribo Malmeeae, com 13 gêneros, ocorrem no Brasil.