Annonaceae substitution rates: a codon model perspective

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 nonsynonymous 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. Index terms: Annonaceae, Branch lengths, Codon models, Non-synonymous substitution rate, Phylogenetics, Synonymous substitution rate. TAXAS DE SUBSTITUIÇÕES DAS ANNONACEAS -UMA PERSPECTIVA DO MODELO CÓDONRESUMO -A Família Annonaceae inclui espécies cultivadas de interesse econômico e representa uma importante fonte de informação para uma melhor compreensão da evolução das florestas tropicais. Em análises filogenéticas de dados de sequências de DNA que são utilizados para tratar de questões evolutivas, é imperativo usar modelos estatísticos apropriados. As Anonáceas são casos em questão: Dois clados irmãos, as subfamílias Annonoideae e Malmeoideae, contêm a maioria da diversidade da espécie anonáceas. As Annonoideae geralmente apresentam um maior grau de divergência de seqüência em relação às Malmeoideae, resultando em diferenças acentuadas nos comprimentos dos ramos em árvores filogenéticas. Incerteza sobre como interpretar e analisar essas diferenças levou a resultados inconsistentes ao estimar as idades de clados em Anonáceas utilizando-se técnicas de datação molecular. Foi perguntado se estas diferenças podem ser atribuídas a hipóteses de modelagem inadequadas nas análises filogenéticas. Especificamente, foi testado para (clado específico) diferenças nas taxas de substituições não sinônimas e s...

Disentangling lianas : The systematics of Monanthotaxis (Annonaceae)

“…Any of these examples are unlikely to be the cause of the difference in the rate of evolution in Annonoideae and Malmeoideae as these differences are visible in both the chloroplast and the nuclear genome as well as in the introns and spacers (chapter 2, . However there is an indication of different levels of selection pressure between the Annonoideae and Malmeoideae as the ratio of nonsynonymous versus synonymous substitutions is higher in the Annonoideae than in the Malmeoideae (a pattern not found by Chatrou et al 2014). Small effective population sizes could cause a pattern like this.…”

“…In the family Annonaceae the two most species-rich subfamilies, the Annonoideae and the Malmeoideae, show a remarkable lineage-specific rate heterogeneity in phylogenetic trees (Chatrou et al 2014, Richardson et al 2004). The Annonoideae have a much wider variation in branch lengths than the Malmeoideae and these two sister subfamilies account together to almost 95% of the species of Annonaceae.…”

“…No obvious differences in generation time or in life traits are visible between those two subfamilies, which could explain this heterogeneity. All previous studies on this group only focused on a few chloroplast markers (Chatrou et al 2014, Pirie & Doyle 2012, Richardson et al 2004, leaving the question open if this heterogeneity is only confined to the chloroplast or the entire genome. Therefore there is a huge number of possibilities which could explain the rate heterogeneity in the two major subfamilies of the Annonaceae.…”

“…Studies which shown and/or further analysed the molecular rate heterogeneity in Annonaceae only used a small number of chloroplast markers (e.g. Chatrou et al 2014, Pirie & Doyle 2012, Richardson et al 2004, leaving open the question as to whether lineage-specific rate differences run in parallel across the three plant genomes. In this study, we use next-generation sequence data to investigate the molecular rate of evolution in Annonaceae.…”