The Ediacaran Penumbra of Animal Origins and the Limits of Phylogenetic Inference


Knowledge of the early metazoan diversification dates can provide important insights into the underlying processes of animal evolution. Recent fossil findings have suggested a possible divergence of Metazoa >100 Ma before the Cambrian. However, the evidence remains controversial, especially concerning the origin of bilaterian phyla where the first definitive evidence of crown-group bilaterians appears in the geological record only after the Ediacaran-Cambrian boundary. Most previous molecular clock dating studies, however, have suffered from limitations and biases in methodologies, and the estimated ages are often inconsistent.Here, a Bayesian dating technique was used to estimate the divergence times of main metazoan clades. Four fossil calibration strategies, that reflect different interpretations of the fossil information, were used to calibrate the molecular phylogeny and estimate divergence times. The results suggest that the divergence of Metazoa occurred 834–681 Ma during the Cryogenian, whereas most of the crown-group bilaterian phyla diverged during the Ediacaran, implying a long, cryptic history of animals before the Cambrian. While this Cryogenian origin of crown-Metazoa agrees with current geological interpretations and recent molecular findings, the divergences of bilaterians remain controversial. These conclusions are broadly consistent with previous dating studies, although our estimates are generally younger and more precise. Time estimates are sensitive to the fossil calibrations, phylogenetic hypotheses and data partitioning. A better-resolved animal phylogeny, updated fossil evidence of early animals, and more molecular sequence data are likely to improve the accuracy and precision of the divergence time estimates.



The global spread of HIV-1 subtype B epidemic


Human immunodeficiency virus type 1 (HIV-1) was discovered in the early 1980’s when the virus had already established a pandemic. For at least three decades the epidemic in the Western World has been dominated by subtype B infections, as part of a sub-epidemic that traveled from Africa through Haiti to United States. However, the pattern of the subsequent spread still remains poorly understood. Here we analyze a large dataset of globally representative HIV-1 subtype B strains to map their mobility around the world over the last 50 years and describe significant mobility patterns. We show that North America was an active hub of dispersal; Western Europe was a passive receiver while Central/Eastern Europe was isolated. Looking with more detail in Europe, United Kingdom, France and Switzerland interacted more with non-European countries than within Europe. The observed pattern is likely to mirror geopolitical landmarks in the post World War II era, namely the rise and the fall of the Iron Curtain and the European colonialism. If human activities drive the dispersal of HIV-1 subtype B then the knowledge of viral dispersal pathways could be important in designing interventions to prevent onward transmissions.



An evaluation of different partitioning strategies for Bayesian estimation of species divergence times


The explosive growth of molecular data has allowed the estimation of species divergence times using large data sets with multiple loci. In these data sets it is important to account for variation in the evolutionary patterns across the genomic parts and partitioning is a commonly used approach. The method involves the grouping of sites that have been evolved under similar processes and the estimation of independent substitution models for each group. There are several ways to partition a data set into groups and the choice of partitioning scheme might affect the inference of divergence times. Here, we use computer simulation and real data analysis to study differences in divergence time estimates applying five commonly used partitioning schemes. Results from simulations indicate that differences in the accuracy of the estimates are small when the prior assumptions are correct and the clock is not seriously violated. The concatenation scheme is not bad but may produce very imprecise estimates. The use of many partitions increases the precision but the 95% high posterior density intervals may not include the true ages in case of incorrect priors. Differences among partitioning schemes are more apparent when the clock is seriously violated. We analyzed a data set of 78 plastid genes from 15 plant species with serious clock violation and show that the time estimates could differ significantly in both accuracy and precision among schemes, irrespective of the clock-model used. Multiple and precise fossil calibrations reduce the differences among partitioning schemes and are important to improve precision of divergence times.