UGA Stratigraphy Lab

The data is in the strata

A Guide to Biostrat 1.7

Note: Biostrat 1.7 is not compatible with OS X 10.6 (Snow Leopard)

Simulating the stratigraphic occurrences of fossils

First, generate a water depth history. This can just be a text file in which you specify the water depths through successive equally spaced points in time. Use TextEdit to make this file, or you can use a word processor like Word, provided you use Save As… to save the file as a text-only or ASCII file. Each water depth should go on its own line, with the water depth of the oldest horizon at the top of the page and the water depth of the youngest horizon at the bottom. Save the file with a .wd suffix to remind you that it’s a water depth history file. Alternatively, you can use STRATA to generate a water depth file (see below).

Second, create species to be simulated. Use Create Database…Species to generate the characteristics of species, including times of origination and extinction, as well as the three ecological characteristics, preferred depth, depth tolerance, and peak abundance. This file should be saved with a .spe suffix to remind you that it is a species database. This file can also be modified with TextEdit.

Third, simulate the occurrences of the species. Use Create Database…Occurrences to read the species file and the water depth history file and to generate two files, one listing all occurrences of every species in the section and another file listing all of the species characteristics including times of first and last occurrence. The first file should be saved with .occ suffix to indicate that it is an occurrences file, and the second file should be saved with a .mod suffix to indicate that it is a modified species file. A modified species file (.mod) contains exactly the same data as the species file (.spe), plus the times of first and last occurrence for each species.

Create Database menu

Species (Command-1)

This module will generate species characteristics to be used in subsequent modules of BIOSTRAT. A dialog box will ask for minimum and maximum values of preferred depth, depth tolerance, and peak abundance. These three ecologic characteristics of each species are randomly generated from an even probability distribution between the specified minimum and maximum values. The dialog box will also ask for the starting number of species, a per-million year probability of extinction, the number of time steps in the model, and the duration of the time steps. Species originate and go extinct according to a random-branching model in which the probability of speciation equals the probability of extinction. Because of this random branching, the number of species generated by this model will be larger than the number of starting species. The number of time steps should be at least equal to the number of time steps in the water depth history file, or alternatively the number of time steps multiplied by the duration of the time steps should equal or exceed the length of the STRATA run to be simulated.

The module will ask for the name of the species database file in which the data should be written. It is recommended that you add .spe to the file name to indicate that it is a species database file.

As the module runs, it will display its progress in a window and repeat the inputted values to the run. In some cases, it may be possible for the program to run out of memory if too many species are generated. This is most likely when starting with a large number of initial species, a large extinction (and hence origination) rate, or a large number of time steps. If this happens, the program should inform you to quit and increase program size in Get Info; this is not necessary in OS X.

Occurrences (Command-2)

This module will read a species database file and a water depth history file and determine the horizons at which each species occurs. The module will then write an occurrence file containing every occurrence of every species. It will also write a modified species file that consists of the species file in its entirety, plus the first and last occurrences of each species. Note that these are the first and last occurrences in terms of time, not rock thickness.

The module will ask for the names of the four files (species database, water depth history, occurrence file, and modified species file). It is recommended that .occ be appended to the occurrence file name and that .mod be appended to the modified species file name.

The progress of the module will be displayed in a window.

Horizons (Command-3)

If desired, the program can also tally the total number of first occurrences, last occurrences, originations, and extinctions at each time horizon. This module will ask for the name of the modified species file (.mod) containing the necessary data. The module will then ask for the name of the horizon file to be created. It is recommended that the horizon file have a .hor suffix. This module will only work on occurrences that are expressed in terms of time, not in terms of rock thickness.

As for the other modules, progress will be displayed in a window.

STRATA menu

The original biostrat model used water depth histories that were hand-made. Since then, STRATA has been modified (see below) to produce water depth histories. Several utilities have been added to ease the connection between STRATA and BIOSTRAT.

Make depth files…

This module reads the water depth file supplied by STRATA (“biostrat.dat” or “mark.plt”), and parses it into a pair of files for each node or position across the basin.

The first file for each node is given a name “name.node#”, and you are asked for an 8 character prefix which will become the “name”. This file is just a parsed version of the original biostrat.dat file, and consists of the following four columns: node, age, elevation, and water depth

The first column (node) will be the same for every line of data in the file. The oldest horizon is listed at the top of the file, and the youngest at the bottom, that is, in reverse stratigraphic order.

The second file for each node is given a name “name.node#.wd” and is simply a listing of water depths for the successive horizons, with the oldest horizon at the top, and the youngest at the bottom. These files are ready to be read into BIOSTRAT.

Sample occurrences…

This module reads an occurrence file (.occ), which lists occurrences as a function of time, and it reads a parsed STRATA file with the elevation and age of every horizon. It then samples the .occ file with respect to rock thickness, preventing samples from being collected closer than some minimum spacing, for which it asks a value. The module then writes a new occurrence file, in terms of rock thickness. This output file has two columns: species number and elevation

Cut horizons…

This module removes part of the top and bottom of an occurrence (with respect to thickness) file. It asks for the percentage of the top & bottom to be removed, and saves the middle part of the section to an occurrence file (with respect to thickness). This module is used to simulate an outcrop located somewhere within the basin, but without knowing how it correlates to other sections.

Find fads and lads…

This reads in an occurrence file (with respect to thickness) & finds the fad & lad of each species. It writes the fad and lad to a file with three columns: species number, fad, and lad

The complete sequence of events when using STRATA and BIOSTRAT should consist of the following:

  1. 1. Simulate a basin using STRATA
  2. 2. Parse the biostrat.dat file from STRATA, using the Strata…Make Depth Files routine in BIOSTRAT.
  3. 3. Generate a species database, using the Create Database…Species routine in BIOSTRAT.
  4. 4. Generate an occurrence database, using the Create Database…Occurrences routine in BIOSTRAT. Be sure to use the .spe species database from step 3 and the desired water depth history (.wd) from step 2.
  5. 5. Sample the occurrences from the occurrence database with regards to rock thickness to simulate the occurrence of fossils in an actual outcrop. To do this, use the Strata…Sample Occurrences routine in BIOSTRAT.
  6. 6. If desired, arbitrarily remove part of the top and the bottom of the section, using the Strata…Cut Horizons routine in BIOSTRAT. Use this routine on the file created in step 5.
  7. 7. If desired, find the fad and lad of each species with regards to rock thickness using the Strata…Find fads and lads routine in BIOSTRAT. Use the file generated in either step 5 or step 6. Note that these fads and lads will differ from what is listed in the modified species file (.mod) generated in step #4. The modified species file lists fads and lads in terms of time, assuming that all horizons are sampled. The fads and lads in the Strata… routine are in terms of rock thickness and only consider horizons that were actually sampled.

Known bugs in BIOSTRAT 1.7:

The cursor will look odd when outside of the main window; however, it still works normally.

An Introduction to Biostrat Files

Biostrat creates and uses many different kinds of files. The file handling system at this point is rather primitive and forces the user to name files carefully. All files must reside in the same folder as the program itself, or the program will not run. All files generated and used by the program are text (ASCII) files and can be opened by Word, Excel, TextEdit, etc. Suggested suffixes for the various types of files are indicated, but at present, the program has no way of enforcing this. If the wrong type of file is read in any module, the program will either exit, freeze, or produce erroneous results.

Water depth files (filename.wd)

Columns

Notes

Species database file (filename.spe)

Columns

  1. 1: species number (4 characters)
  2. 2: number of species' ancestor (4 characters)
  3. 3: time of origination of species (4 characters)
  4. 4: time of extinction of species (4 characters)
  5. 5: peak abundance of species (7 characters)
  6. 6: depth tolerance of species (7 characters)
  7. 7: preferred depth of species (7 characters)

Notes

Occurrence database file (filename.occ)

Columns

  1. 1: species number (4 characters)
  2. 2: horizon number at which species occurs (4 characters)

Notes

Modified species file (filename.mod)

Columns

  1. 1: species number (4 characters)
  2. 2: number of species' ancestor (4 characters)
  3. 3: time of origination of species (4 characters)
  4. 4: time of extinction of species (4 characters)
  5. 5: fad of species (4 characters)
  6. 6: lad of species (4 characters)
  7. 7: maximum abundance of species (7 characters)
  8. 8: depth tolerance of species (7 characters)
  9. 9: preferred depth of species (7 characters)

Notes

Horizon database file (filename.hor)

Columns

  1. 1: horizon number (4 characters)
  2. 2: number of FADs at horizon (4 characters)
  3. 3: number of LADs at horizon (4 characters)
  4. 4: number of originations at horizon (4 characters)
  5. 5: number of extinctions at horizon (4 characters)

Notes

Parsed STRATA output file (name.node#)

Columns

  1. 1. node number
  2. 2. age of horizon
  3. 3. elevation of horizon
  4. 4. water depth of horizon

Notes

STRATA water depth file (name.node#.wd)

Columns

  1. 1. water depth of horizon

Notes

Sampled occurrence file (name.node#.smp)

Columns

  1. 1. species number
  2. 2. elevation of horizon

Notes

Cut occurrence file (name.node#.cut)

Columns

  1. 1. species number
  2. 2. elevation of horizon

Notes

FAD/LAD file (name.node#.fad)

Columns

  1. 1. species number
  2. 2. elevation of fad
  3. 3. elevation of lad

Notes