ESTIMATING DIVERSIFICATION RATES: HOW USEFUL ARE DIVERGENCE TIMES?

The dynamics of species diversification rates are a key component of macroevolutionary patterns. Although not absolutely necessary, the use of divergence times inferred from sequence data has led to development of more powerful methods for inferring diversification rates. However, it is unclear what impact uncertainty in age estimates have on diversification rate inferences. Here, we quantify these effects using both Bayesian and frequentist methodology. Through simulation, we demonstrate that adding sequence data results in more precise estimates of internal node ages, but a reasonable approximation of these node ages is often sufficient to approach the theoretical minimum variance in speciation rate estimates. We also find that even crude estimates of divergence times increase the power of tests of diversification rate differences between sister clades. Finally, because Bayesian and frequentist methods provided similar assessments of error, novel Bayesian approaches may provide a useful framework for tests of diversification rates in more complex contexts than are addressed here.     

Using DNA taxonomy to investigate the ecological determinants of plankton diversity: explaining the occurrence of Synchaeta spp. (Rotifera,Monogononta) in mountain lakes

1. The occurrence of unresolved complexes of cryptic species may hinder the identification of the main ecological drivers of biodiversity when different cryptic taxa have different ecological requirements. 2. We assessed factors influencing the occurrence of Synchaeta species (monogonont rotifers) in 17 waterbodies of the Trentino‐South Tyrol region in the Eastern Alps. To do so, we compared the results of using unresolved complexes of cryptic species, as is common practice in limnological studies based on morphological taxonomy, and having resolved cryptic complexes, made possible by DNA taxonomy. 3. To identify cryptic species, we used the generalised mixed Yule coalescent (GMYC) model. We investigated the relationship between the environment and the occurrence of Synchaeta spp. by multivariate ordination using two definitions of the units of diversity, namely (i) unresolved species complexes (morphospecies) and (ii) putative cryptic species (GMYC entities). Our expectation was that resolving complexes of cryptic species could provide more information than using morphospecies. 4. As expected, DNA taxonomy provided greater taxonomic resolution than morphological taxonomy. Further, environmental‐based multivariate ordination on cryptic species explained a significantly higher proportion of variance than that based on morphospecies. Occurrence of GMYC entities was related to total phosphorus (TP), whereas no relationship could be found between morphospecies and the environment. Moreover, different cryptic species within the same morphospecies showed different, and even opposite, preferences for TP. In addition, the wide geographical distribution of haplotypes and cryptic species indicated the absence of barriers to dispersal in Synchaeta.     

A rosette by any other name: species diversity in the Bangiales (Rhodophyta) along the South African coast

The Bangiales is an order of Rhodophyta, widely distributed around the globe and best known for its economic value in the nori industry. The morphological simplicity of the group offers limited distinguishing characters for species identification. We therefore delimited species of the Bangiales along the South African coast based on two unlinked loci, the mitochondrial cox1 gene and the plastid rbcL gene, supplemented with additional sequence data from a third gene, the nuclear nSSU. Application of DNA-based species delimitation methods including the Automatic Barcode Gap Discovery (ABGD), General Mixed Yule Coalescent (GYMC) and Poisson Tree Processes (PTP), resulted in the recognition of 10 Porphyra and three Pyropia species in South Africa, only three of which had been previously described. Additional species of Bangiales previously recorded along the South African coast were added to our final species list despite not being found in the present study, resulting in an estimate of 14–16 Bangiales species occurring along this shoreline. Most of this extensive genetic diversity has been misidentified as the commonly rosette-forming species P. capensis. The name P. capensis currently refers to a species complex and cannot be attached to any one species with certainty. All species in this complex, confirmed using genetic data, are endemic to South Africa. Our results compare well with other Southern Hemisphere countries, such as Chile and New Zealand, where high genetic diversity, species richness and endemicity have also been found.     

The prior probabilities of phylogenetic trees

Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance and bias are. I then consider different methods of assigning prior probabilities to trees. I argue that priors need to be derived from an understanding of how distinct taxa have evolved and that the appropriate evolutionary model is captured by the Yule birth–death process. This process leads to a well-known statistical distribution over trees. Though further modifications may be necessary to model more complex aspects of the branching process, they must be modifications to parameters in an underlying Yule model. Ignoring these Yule priors commits a fallacy leading to mistaken inferences both about the trees themselves and about macroevolutionary processes more generally.     

DNA barcode‐based delineation of putative species: efficient start for taxonomic workflows

The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies.