Abstract
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.
Highlights
A variety of properties of Annonaceae that are useful to humans have been acknowledged for centuries
In the 19th an 20th century, an era of many natural history explorations in the tropics, scientist documented the use of Annonaceae and showed the large extent to which species of this family are used on a local scale as food, medicine, construction material (e.g. BAILLON, 1868; FRIES, 1959)
First we assessed whether clock differences across our tree can be inferred using branch lengths from codon models
Summary
A variety of properties of Annonaceae that are useful to humans have been acknowledged for centuries. Edible fruits, such as cherimoya (Annona cherimola Mill.) have been transported in pre-Columbian times across tropical America (POZORSKI and POZORSKI, 1997). In the 19th an 20th century, an era of many natural history explorations in the tropics, scientist documented the use of Annonaceae and showed the large extent to which species of this family are used on a local scale as food, medicine, construction material Many applied studies have focused on the cultivation of Annonas species and hybrids (e.g. GEORGE and NISSEN, 1987), providing a wealth of observations on patterns of variation, crossability of species, and selection of traits
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