Wednesday, February 25, 2015

The fossil calibration database

Fossils are not only fascinating finds that allow a glimpse into past biodiversity, they also provide the age data needed to unlock the timing of major evolutionary events. Very often fossil data are used to calibrate molecular clocks which can reveal the ages of groups that lack good fossil records. An example is shown in the image on the left. I did this analysis about 10 years ago and some values in the tree are marked with an asterisk. These represent calibration points based on fossil records. I also remember quite well but not fondly that finding these dates required a substantial amount of literature research hindered by the fact that a good number of the publications wasn't easily accessible.

Gladly things have changed. This week a new resource for researchers went live, and it is designed to help answer just those kinds of questions. The Fossil Calibration Database is a free, open-access resource that stores vetted fossil data. More than twenty paleontologists, molecular biologists, and computer programmers from five different countries contributed to the design and implementation of this new database.

The launch of the database was accompanied by five peer-reviewed papers and an editorial on the topic published in Palaeontologia Electronica:

  1. Constraints on the timescale of animal evolutionary history
  2. Fossil calibration of Magnoliidae, an ancient lineage of angiosperms
  3. Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves
  4. Sixteen vetted fossil calibrations for divergence dating of Charadriiformes (Aves, Neognathae)
  5. Four mammal fossil calibrations: balancing competing palaeontological and molecular considerations

This exciting field of study, known as 'divergence dating,' is important for understanding the origin and evolution of biodiversity, but has been hindered by the improper use of data from the fossil record. The Fossil Calibration Database addresses this issue by providing molecular biologists with paleontologist-approved data for organisms across the Tree of Life. 

The authors also promote best practices for justifying fossil calibrations and citing calibrations properly. These best practices have been published a couple of years ago and I would encourage anyone who plans to do some molecular clock work to read that paper before jumping into any analysis.

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