Paleogeographic reconstructions using raw paleobiology data

Authors: Nicky Wright and Sabin Zahirovic

EarthByte Research Group, School of Geosciences, University of Sydney, Australia

Paleogeographic reconstructions using raw paleobiology data



        Included Files

Exercise 1: Loading and preparing fossil data for reconstruction

Exercise 2: Reconstructing the fossil data



This tutorial is designed to teach the user how to load, prepare and reconstruct fossil data in GPlates.


The following tutorial describes loading and reconstructing data from the Paleobiology Database in GPlates. The shapefiles provided can be directly loaded into GPlates as Begin/End ages have been assigned.


Note: If importing your own fossil data, create a shapefile of the points in ArcGIS or the open-source equivalent QGIS. Make sure the fossil data has “Begin” and “End” ages representing the age range.

Included Files

Click here to download the data bundle for this tutorial.

The tutorial dataset includes the following files:

        Coastlines file: Seton_etal_ESR2012_Coastlines_2012.1

        Rotation file: Seton_etal_ESR2012_2012.1

        Static polygons: Seton_etal_ESR2012_StaticPolygons_2012.1

`It also includes a folder of fossil locations as shapefiles:

        Marine Carbonates

        Marine Siliclastics

        Terrestrial Fossils

        General Fossils

Exercise 1: Loading and preparing raw fossil data for reconstruction

1. Open GPlates > Open Feature Collections > Navigate to your folder and select the marine carbonates shapefile (Figure 1)

Figure 1. Open files in GPlates

2. The first time the shapefile is loaded, GPlates will ask you what properties it should associate with the different shapefile attributes (Figure 2a). Make sure you assign Begin: ma_max and End: ma_min, otherwise your fossil data will exist at all times. You can also attach fields that represent ‘Name’ and ‘Description’ of each datapoint, if so desired (Figure 2b). Click OK (this may sometimes take a few seconds, do not quit!).

Figure 2. Assigning shapefile attributes in GPlates. (a) The ‘Associate shapefile attributes with GPlates model properties’ window with default settings and (b) with Begin and End attributes defined as ma_max and ma_min respectively

Note: If an attribute is assigned incorrectly we can change the associated properties by File > Manage Feature Collections > ‘Configure’ (the first option next to the shapefile in question)

3. The fossils will appear as yellow dots in GPlates 1.4. You may like to add the coastlines file so we can see the fossil locations with more context. If we slide the time slider back to 100 Ma, we will see these fossil points appear and disappear, indicating that we’ve assigned their ages correctly. However, they do not yet move because they need to be linked to the plate motions.

4. Select any fossil point to see how no Plate ID has been assigned yet. We will need to cookie-cut (i.e. Assign Plate IDs) to the fossil data, in order to get them to reconstruct according to our rotation file. Here we will use the polygons provided in the GPlates 1.3 sample data; alternatively, your own polygons with associated Plate IDs could be used.

Load the Static polygons from our Sample Data: Go to File > Open Feature Collection > Navigate to folder and load:

- Seton_etal_ESR2012_StaticPolygons_2012.1.gpmlz

You will now also see some coloured polygons in the GPlates main window. (Figure 3).


Figure 3. Static polygons in GPlates (coloured by Plate ID) and fossil datapoints with no Plate IDs assigned.

5. To assign Plate IDs: Go to Features > Assign Plate IDs…


Figure 4. Features menu

6. Specify the partitioning layer: this is generally a Static Polygon file – ours is the ‘Seton_etal_ESR2012_StaticPolygons_2012.1’ file. Click Next.

Figure 5. Select partitioning layers in the Assign Plate IDs process

7. Specify the layer to be partitioned. In the example, it is the carbonate marine data from 100 Ma to 0 Ma. Click Next.

Figure 6. Assign the feature to be partitioned in the Assign plate ID process

8. The next screen allows you to decide whether you want to cookie-cut your data at present-day or some other reconstruction time. For the purposes of reconstructing fossils and other similar data, you would normally choose ‘Present Day’.

Leave options as their defaults (Figure 7) and click Apply.

Figure 7. Options required for Assigning Plate IDs for fossil data

9. Your data is now ready to reconstruct. If you deselect the Static Polygons in the Layers window, you will see the data points will have a range of colours, assigned by Plate ID (Figure 8).

Save the changes to your shapefile, or save out to a new shapefile or other format in File > Manage Feature Collections > “Save As” or “Save A Copy”

Figure 8. Fossil Data assigned by Plate ID

Exercise 2: Reconstructing the fossil data

1. Load up the included plate motion model. Go to File > Open Feature Collection > navigate to folder > Select the following files (Figure 9):

- Seton_etal_ESR2012_2012.1.rot

- Seton_etal_ESR2012_Coastlines_2012.1.gpmlz

Figure 9. Open plate motion model files in GPlates

2. We can repeat steps 1-8 for the remaining fossil shapefiles (siliciclastic, terrestrial, and general). We can cookie cut multiple shapefiles at once by ticking multiple features (this is one of the most useful and efficient features on GPlates).

Once we have a full range of environments uploaded, it is more useful to colour the fossil environment groups based on a single colour, rather than Plate ID: Go to Feature > Manage Colouring > select layer (i.e. a single shapefile layer) and ‘Single Colour’. Choose colour of your choice.

We should also colour the coastline a single colour (e.g. grey).


3. You can now reconstruct to any desired time, and choose to export animations as JPGs files or any other files.

Go to Reconstruction > Export > Select your time range (100 Ma – 0 Ma) > Click “Add Export Type” and choose Colour Raster > (*.jpg) or any other image type. Configure your image resolution if desired. Click OK, and then click “Begin Animation”. GPlates will output your data into your specified directory.

Note:  It is common to export Reconstructed Geometries as GMT XY or ESRI Shapefiles to create detailed maps.

Figure 10. Export animations as image files such as JPGs

4. Now that we can have reconstructed fossil data, we can see how the fossil environment (e.g. paleogeography) relates to our reconstructions.

- Terrestrial (green) – General (red) – Siliciclastic (yellow) – Carbonates (blue)

Figure 11. Reconstructed fossil data at 0 Ma, 50 Ma and 100 Ma. The terrestrial fossils are coloured green, general fossils red, siliciclastic fossils yellow and carbonate fossils blue.