Molecular Dating, Evolutionary Rates, and the Age of the Grasses

Many questions in evolutionary biology require an estimate of divergence times but, for groups with a sparse fossil record, such estimates rely heavily on molecular dating methods. The accuracy of these methods depends on both an adequate underlying model and the appropriate implementation of fossil evidence as calibration points. We explore the effect of these in Poaceae (grasses), a diverse plant lineage with a very limited fossil record, focusing particularly on dating the early divergences in the group. We show that molecular dating based on a data set of plastid markers is strongly dependent on the model assumptions. In particular, an acceleration of evolutionary rates at the base of Poaceae followed by a deceleration in the descendants strongly biases methods that assume an autocorrelation of rates. This problem can be circumvented by using markers that have lower rate variation, and we show that phylogenetic markers extracted from complete nuclear genomes can be a useful complement to the more commonly used plastid markers. However, estimates of divergence times remain strongly affected by different implementations of fossil calibration points. Analyses calibrated with only macrofossils lead to estimates for the age of core Poaceae ∼51-55 Ma, but the inclusion of microfossil evidence pushes this age to 74-82 Ma and leads to lower estimated evolutionary rates in grasses. These results emphasize the importance of considering markers from multiple genomes and alternative fossil placements when addressing evolutionary issues that depend on ages estimated for important group

La bibliothèque sans bibliothécaire: l'autogestion comme outil de communication à la Cité du Genévrier

La Cité du Genévrier, située à Saint-Légier sur Vevey, dans le canton de Vaud, est une institution qui accueille des personnes physiquement et/ou mentalement polyhandicapées. Cet établissement fait partie de la Fondation Eben-Hezer qui compte également deux institutions-soeurs, les Maisons des Chavannes et le Home Salem. Un nouveau bâtiment a été construit; il accueillera notamment l’administration de l’institution. La bibliothèque y disposera d’un local bien éclairé, à proximité directe de la réception. A l’occasion du déménagement s’est posée la question suivante : cela vaut-il la peine de déménager la bibliothèque, ou le moment est-il venu de la supprimer? Le changement de lieu est présenté comme une opportunité de régler définitivement le problème de sa gestion. Nous avons donc été mandatées pour juger de l’utilité ou non de la bibliothèque d’après les besoins des collaborateurs, puis pour élaborer des scenarii, qui puissent être présentés au Conseil de direction. Tels sont les objectifs généraux fixés au départ

Integrating an online information literacy module in all students' curriculum: teaching across the disciplines in a technical university

The EPFL Library recently took part in the creation of a new educational offer, called Global Issues, targeting 1st year Bachelor students across all disciplines taught at EPFL, which represents 1,600 people. This course is a multidisciplinary approach of global challenges, bringing humanities and technical sciences together, encouraging students to go beyond their core discipline. For the first time, information literacy is embedded in an EPFL credited course. Due to the number of students, we had to find new ways to pass on knowledge and skills. We shaped an online course completed with exercises, tutorials and a forum, in order to deal with this constraint. Thanks to this innovative experience, bridges were built between the Library and the Center for Digital Education - experts in the production of MOOCs -, the Teaching Support Center and the Faculty. At the end of the semester, each group of students was required to present a poster in front of a panel of judges. Thus, our teaching focused on efficient research techniques, reference management and proper use of information provides students with a set of concrete tools to be used straight away, and to be studied more in-depth throughout their curriculum. Despite the rather important role we played in this teaching, we have the feeling that we will need to keep arguing for the importance of the information literacy skills in the years to come

genomes_beast_2

This file contains the consensus tree inferred on nuclear markers by BEAST with the topology fixed. External calibration plus phytoliths were used. Each time unit corresponds to 20 million years

FigureS8

Supplementary Figure 8: Detailed comparison of methods and datasets. For calibration #1, the age estimates (in million years ago) are represented for nodes that were shared between phylogenetic trees of plastid and nuclear markers. The ages are represented independently when produced by BEAST and MULTIDIVTIME. Black circles are ages based on the whole plastid dataset, red squares are ages based on plastid markers for 28 species only, black triangles are aged based on the whole nuclear dataset, and red bars indicate the interval between the 1st and 3rd quartiles of 100 replicates of the nuclear dataset decreased to the size of the plastid dataset. Taxonomic groups are indicated on the bottom. The last point corresponds to the crown of BEP, and the horizontal bar indicates the minimal age for the clade that would be congruent with the 67 Ma phytolith fossil (Prasad et al. 2011). Numbers can be used to identify the corresponding nodes in Supplementary Figure 9

Data from: Molecular dating, evolutionary rates, and the age of the grasses

Many questions in evolutionary biology require an estimate of divergence times but, for groups with a sparse fossil record, such estimates rely heavily on molecular dating methods. The accuracy of these methods depends on both an adequate underlying model and the appropriate implementation of fossil evidence as calibration points. We explore the effect of these in Poaceae (grasses), a diverse plant lineage with a very limited fossil record, focusing particularly on dating the early divergences in the group. We show that molecular dating based on a dataset of plastid markers is strongly dependent on the model assumptions. In particular, an acceleration of evolutionary rates at the base of Poaceae followed by a deceleration in the descendants strongly biases methods that assume an autocorrelation of rates. This problem can be circumvented by using markers that have lower rate variation, and we show that phylogenetic markers extracted from complete nuclear genomes can be a useful complement to the more commonly used plastid markers. However, estimates of divergence times remain strongly affected by different implementations of fossil calibration points. Analyses calibrated with only macrofossils lead to estimates for the age of core Poaceae around 51-55 Ma, but the inclusion of microfossil evidence pushes this age to 74-82 Ma and leads to lower estimated evolutionary rates in grasses. These results emphasize the importance of considering markers from multiple genomes and alternative fossil placements when addressing evolutionary issues that depend on ages estimated for important groups

FigureS1

Supplementary Figure 1: Comparison of concatenated and partitioned analyses. Ages are plotted in million years ago for a) plastid markers and b) nuclear markers. Analyses were performed with BEAST and the dataset was partitioned by codon position. Black lines indicate 1:1 relationships

plastid245_beast_2

This file contains the consensus tree inferred on plastid markers by BEAST with the topology fixed. External calibration plus phytoliths were used. Each time unit corresponds to 20 million years