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

Two new species of Annonaceae from Bolivia

Two new tree species of Annonaceae are described here: Ephedranthus boliviensis CHATROU & PIRIE and Klarobelia pandoensis CHATROU. Ephedranthus boliviensis is the only species in the genus occurring in Bolivia (departments of Beni, Pando, and Santa Cruz). Next to Klarobelia inundata CHATROU, only known from one collection in Bolivia, Klarobelia pandoensis is the second recorded species of Klarobelia for Bolivia. Klarobelia pandoensis is endemic for Bolivia (department of Pando), Ephedranthus boliviensis is also known from one collection from the Brazilian state of Acre

Dating clades with fossils and molecules: The case of Annonaceae

This article addresses the challenges involved in estimating the ages of clades using fossils and DNA sequences. We review the principles and problems of placing fossils in trees of extant taxa and using them to constrain the ages of nodes in molecular dating analyses. Endressinia and Futabanthus provide minimum ages of 112Mya for the stem lineage and 89Mya for the crown group of Annonaceae, and the diversity of endosperm ruminations in seeds from the London Clay indicates that the four main clades of Annonaceae had diverged by 50Mya. Ages inferred using these minimum constraints and a plastid phylogenetic tree for Annonaceae, particularly crown ages of the two main clades (Malmeoideae and Annonoideae), depend on assumptions regarding the pattern of variation in rates of molecular evolution. Our results using methods that assume rate autocorrelation or log-normal distribution of rates suggest that neither assumption fits well the apparently abrupt changes in rates in Annonaceae. Instead of soft-bounded age constraints, we argue for the use of only well-substantiated fossil evidence by means of priors with hard bounds. Thus, we can infer ages that take into account both palaeontological and phylogenetic uncertainty, without confounding the different factors involved. © 2012 The Linnean Society of London

Three new rarely collected or endangered species of Annonaceae from Venezuela

Three new species of Annonaceae from Venezuela are described here: Cremastosperma venezuelanum Pirie, Klarobelia subglobosa Chatrou, and Pseudomalmea wingfieldii Chatrou. All three are represented by few collections (in comparison to those of other Neotropical species of Annonaceae). Klarobelia subglobosa and P. wingfieldii in particular are only known from a few individual specimens collected in areas vulnerable to habitat destruction. IUCN threat categories are assigned to these species

Dating clades with fossils and molecules: The case of Annonaceae

This article addresses the challenges involved in estimating the ages of clades using fossils and DNA sequences. We review the principles and problems of placing fossils in trees of extant taxa and using them to constrain the ages of nodes in molecular dating analyses. Endressinia and Futabanthus provide minimum ages of 112Mya for the stem lineage and 89Mya for the crown group of Annonaceae, and the diversity of endosperm ruminations in seeds from the London Clay indicates that the four main clades of Annonaceae had diverged by 50Mya. Ages inferred using these minimum constraints and a plastid phylogenetic tree for Annonaceae, particularly crown ages of the two main clades (Malmeoideae and Annonoideae), depend on assumptions regarding the pattern of variation in rates of molecular evolution. Our results using methods that assume rate autocorrelation or log-normal distribution of rates suggest that neither assumption fits well the apparently abrupt changes in rates in Annonaceae. Instead of soft-bounded age constraints, we argue for the use of only well-substantiated fossil evidence by means of priors with hard bounds. Thus, we can infer ages that take into account both palaeontological and phylogenetic uncertainty, without confounding the different factors involved. © 2012 The Linnean Society of London

Three new rarely collected or endangered species of Annonaceae from Venezuela

Three new species of Annonaceae from Venezuela are described here: Cremastosperma venezuelanum Pirie, Klarobelia subglobosa Chatrou, and Pseudomalmea wingfieldii Chatrou. All three are represented by few collections (in comparison to those of other Neotropical species of Annonaceae). Klarobelia subglobosa and P. wingfieldii in particular are only known from a few individual specimens collected in areas vulnerable to habitat destruction. IUCN threat categories are assigned to these specie

A densely sampled ITS phylogeny of the Cape flagship genus Erica L. suggests numerous shifts in floral macro-morphology

Erica L. is the largest of the 'Cape' clades that together comprise around half of the disproportionately high species richness of the Cape Floristic Region (CFR) of South Africa. Around 840 species of Erica are currently recognised, C.680 of which are found in the CFR, the rest distributed across the rest of Southern Africa, the highlands of Tropical Africa and Madagascar, and Europe. Erica is taxonomically well documented, but very little is known about species-level relationships. We present the first densely sampled phylogenetic analysis of Erica, using nuclear ribosomal DNA sequences (internal transcribed spacers; ITS) of c. 45% of the species from across the full geographic range of the genus, both Calluna and Daboecia (Ericeae; monotypic genera and putative sister groups of Erica), and further Ericoideae outgroups. Our results show both morphological and geographic coherence of some clades, but numerous shifts in floral macro-morphology as represented by variation in individual morphological characters and pollination syndromes. European Ericeae is a paraphyletic grade subtending a monophyletic African/Malagasy Erica. Given the limited resolution of this single gene tree, more data are needed for further conclusions. Clades are identified that will serve as an effective guide for targeted sampling from multiple linkage groups. © 2011 Elsevier Inc.Articl