Seminar by Sebastian Höhna, Wed 26 Sept, SU


Onsdagen den 26 september klockan 15.15 håller Sebastian Höhna, Stockholms universitet, ett seminarium med titeln / On Wednesday September 26 at 15.15, Sebastina Höhna from Stockholm University will give a seminar with the title:

Estimating non-constant species diversification rates and patterns under incomplete, systematic species sampling.

Sammanfattning / Abstact:
The macro-evolutionary process of species diversity is commonly modeled using a birth-death branching process. Here I consider the class of processes where each species alive at time t has the same speciation rate lambda(t) and the extinction rate mu(t). The questions I aim to answer are: Did the rates change over time? How did the rates change over time? Where there times of mass-extinction and/or rapid radiations?

Recent extensions include specific rate functions (e.g. exponential decreasing/increasing) and random species sampling. In this talk I will present the likelihood equations for any time-dependent rate function (e.g. with one or several modes) and systematic species sampling (e.g. one species per family). I will show the estimates of the speciation rate and extinction rate over time for the complete order of mammals. Additionally, I will present a second approach for the derivation of the likelihood which can be used for fast simulation of reconstructed phylogenetic trees for:

a) a fixed time of the process,
b) a fixed number of sampled species and
c) a fixed number of sampled species and time of the process.

Lokal  /  Place: Cramerrummet (rum 306)  /  Cramér room (room 306), hus /  house 6; Kräftriket. Karta/Directions:



PhyloBayes workshop NRM June 5 – reminder

Dear All,

We are happy host Dr. Nicolas Lartillot (University of Montreal, Canada) for a one day workshop on Bayesian phylogenetics here at the Museum of Natural History (Stockholm).
Nicolas will lead a morning software session (PhyloBayes software) and give a talk (”Bayesian Integrative Models for Macroevolutionary Studies”) in the afternoon.

Date: Tuesday June 5.
Venue: Natural History Museum, Stockholm.
Time: 9am – 12pm (software session), 3:00pm – 4:30pm (seminar)

More information can be found on

Nicolas home page:

PhyloBayes software:


Fwd: Postdoctoral fellowships in Australia (CSIRO, Canberra)

Dear Johan,

Could I ask you to draw the following two vacancies to the attention of potential applicants in your group (and beyond).

All the best, Lars

Two exciting postdoctoral fellowships in Computational Biology and Molecular Phylogenetics are currently available in CSIRO Ecosystem Sciences’s Bioinformatics & Phylogenomics team, which is led by Lars Jermiin.

  1. Computational Biology – Bioinformatics-driven design of novel enzymes: The aim of this position is for the appointee to develop, implement, and use computational methods to predict intramolecular interactions reliably in enzymes. For further details, (1) go to, (2) click on Positions Vacant, (3) click on Job Search, (4) enter ACT12/00960 under Reference Number, and (5) click Search. Closing date: 31 May 2012
  2. Molecular Phylogeny – Optimising the fit of phylogenetic estimates: The aim of this position is for the appointee to develop, implement, and use phylogenetic methods that provide a better fit between phylogenetic data and the phylogenetic estimates. For further details, (1) go to, (2) click on Positions Vacant, (3) click on Job Search, (4) enter ACT12/00962 under Reference Number, and (5) click Search. Closing date: 4 June 2012

For details about how to apply, follow the links given above and submit your application online via CSIRO’s Online Application Portal. For further details about the research, please send an email<>.

Dr Lars Jermiin OCE Science Leader – Bioinformatics & Phylogenomics Team CSIRO Ecosystem Sciences Phone: +61 2 6246 4043 | Fax: 61 2 6246 4094 | Mobile: +61 467 776 866 | |

Address: CSIRO – Ecosystem Sciences, GPO Box 1700, Canberra, ACT 2601, Australia

Stockholm Phylogenomics Group – Aktiviteter 2012


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Johan Nylander

Enheten för Biodiversitetsinformatik, Naturhistoriska riksmuseet (BI/NRM)

Bioinformatics Infrastructure for Life Sciences (BILS)