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Molecular-Clock Dating Using MrBayes – Seminar and Workshop

Publicerat av Johan Nylander --

Molecular-Clock Dating Using MrBayes – Seminar and Workshop

  • 22 April – Stockholm: 09:30-11:30, Rum 540, Botaniska Institutionen, Stockholms universitet
  • 23 April – Uppsala: 13:15-15:15, Lärosal 4, Evolutionsbiologiskt Centrum, Uppsala universitet

Chi Zhang*, Swedish Museum of Natural History, Stockholm
Johan Nylander, BILS/Swedish Museum of Natural History, Stockholm

MrBayes – the most often used software for Bayesian phylogenetic analysis – has included many new features since version 3.2. In this seminar, we will highlight some newly implemented functionality, with focus on the molecular-clock dating capacities of the current version (v.3.2.4). The seminar will consist of two parts, where following a presentation* giving the necessary backrground information, there will be a hands-on tutorial where participants are encouraged to bring their own data (and computers).

Abstract
There are two approaches on dating using molecular data: node dating and total-evidence dating. Node dating calibrates the internal nodes of the tree by assigning distributions using information from external sources, such as the fossil record. Total-evidence dating uses the morphological data from fossil record and morphological and sequence data from recent organisms together to infer the dates. Several steps involve in Bayesian dating analysis, including data partitioning, node or fossil age calibration, and setting priors for the tree and the molecular clock model. I will describe the available calibration probability distributions, clock tree priors – especially the fossilized birth-death prior for total-evidence dating, and relaxed clock models, through a step-by-step tutorial of MrBayes.

The program (MrBayes v.3.2.4) is available from http://mrbayes.net (alternatively https://sourceforge.net/projects/mrbayes/files/mrbayes)

Participants in the practical part are encouraged to bring their own computers with the software installed from the above mentioned URL’s.

Stockholm Phylogenomics Group – Talk at NRM 24 March: SUPERSMART. Change in time!

Publicerat av Johan Nylander --

Dear All!

Reminder and change of starting time!

Stockholm Phylogenomics Group announces – Upcoming talk at the Naturhistoriska riksmuseet, Stockholm, March 24.

Speakers: Alexandre Antonelli (University of Gothenburg),
Hannes Hettling and Rutger Vos (Naturalis Biodiversity Center,
the Netherlands)

Title: SUPERSMART: Ecology and evolution in the era of big data

Time: March 24 at 15:30-16:30

Venue: Room 525, Naturhistoriska riksmuseet, Stockholm

Host: Fredrik Ronquist

Abstract: Rapidly growing biological data volumes – including
molecular sequences and fossil records – hold an unprecedented
potential to reveal how evolutionary processes generate and
maintain biodiversity. However, most studies integrating these
data use an idiosyncratic step-by-step approach for the
reconstruction of time-calibrated phylogenies. We will present a
novel conceptual framework, termed SUPERSMART (Self-Updating
Platform for Estimating Rates of Speciation and Migration, Ages,
and Relationships of Taxa), and present our proof of concept for
dealing with the moving targets of biodiversity research. This
framework reconstructs dated phylogenies based on the assembly
of molecular and genomic datasets. The data handled for each step
are continuously updated as databases accumulate new records. We
believe that this emerging framework will provide an invaluable
tool for a wide range of hypothesis-driven research questions in
systematics and evolution. For more information please see

http://www.supersmart-project.org.

Stockholm Phylogenomics Group – Talk at NRM 24 March: SUPERSMART

Publicerat av Johan Nylander --

Stockholm Phylogenomics Group announces – Upcoming talk at the Naturhistoriska riksmuseet, Stockholm, March 24.

Speakers: Alexandre Antonelli (University of Gothenburg),
Hannes Hettling and Rutger Vos (Naturalis Biodiversity Center,
the Netherlands)

Title: SUPERSMART: Ecology and evolution in the era of big data

Time: March 24 at 15:00-16:00

Venue: Room 525, Naturhistoriska riksmuseet, Stockholm

Host: Fredrik Ronquist

Abstract: Rapidly growing biological data volumes – including
molecular sequences and fossil records – hold an unprecedented
potential to reveal how evolutionary processes generate and
maintain biodiversity. However, most studies integrating these
data use an idiosyncratic step-by-step approach for the
reconstruction of time-calibrated phylogenies. We will present a
novel conceptual framework, termed SUPERSMART (Self-Updating
Platform for Estimating Rates of Speciation and Migration, Ages,
and Relationships of Taxa), and present our proof of concept for
dealing with the moving targets of biodiversity research. This
framework reconstructs dated phylogenies based on the assembly
of molecular and genomic datasets. The data handled for each step
are continuously updated as databases accumulate new records. We
believe that this emerging framework will provide an invaluable
tool for a wide range of hypothesis-driven research questions in
systematics and evolution. For more information please see

http://www.supersmart-project.org.

Researcher in Evolutionary Biology (Plant Speciation)

Publicerat av Magnus Popp --

A 3-year research position is available at the Natural History Museum (NHM), University of Oslo. The position is connected to the project SpArc (High speciation rates in Arctic plants: genomic mechanisms and relevance to the latitudinal diversity gradient), funded by the Research Council of Norway for four years from 2015.

More info at: http://uio.easycruit.com/vacancy/1336993/71922?iso=no