Querying the Paleobiology Database

The Paleobiology database is a tremenous resource for explorations of the fossil record, as it contains geographic location as well as stratigraphic (geologic time) information of fossil occurrences. Such information is extraordinary useful for studying fossil diversity.

Let’s explore this with a brief tutorial. We will download a dataset on a rahter small group of fossil taxa to keep computation time managable, and visualize the geographic occurrence as well as diversity over time. Three new packages are required.

Let’s begin by downloading a dataset on ichthyosaurs from the Paleobiology database.

#load required packages
library(maps)
library(raster)
## Loading required package: sp
library(paleobioDB)

#here we are defining our taxon of interest
taxon<-"Ichthyopterygia"

#this step retrieves data from the Paleobiology Database, use help for more
taxon.data <- pbdb_occurrences(limit="all", vocab="pbdb", base_name=taxon, show=c("phylo", "coords", "ident"))

Plotting occurrence data

Now that we have some data on hour hands let’s first plot where fossils of ichthyosuars have been found. Such occurrence maps often reveal interesting patterns. When observing the maps below, think about what underlying mechanisms may explain the pattern for ichthyosaurs!

#let's first map occurences on a world map
pbdb_map (taxon.data)

Occurrences can also be represented as a “heat map”, highlighting areas with highest occurence densities.

pbdb_map_occur (taxon.data, res=5)

## class       : RasterLayer 
## dimensions  : 34, 74, 2516  (nrow, ncol, ncell)
## resolution  : 5, 5  (x, y)
## extent      : -180, 190, -86.40039, 83.59961  (xmin, xmax, ymin, ymax)
## coord. ref. : NA 
## data source : in memory
## names       : layer 
## values      : 1, 82  (min, max)

What are factors that influence occurrence patterns? Let’s discuss as a group.

Plotting diversity over time

After some initial explorations of the occurence maps above, let’s plot some taxon count data over time to begin understanding possible diversity patterns.

#plotting the number of genera over time
pbdb_richness (taxon.data, temporal_extent=c(65, 280), res=10, rank="genus")

##    temporal_intervals richness
## 1               65-75        1
## 2               75-85        1
## 3               85-95        3
## 4              95-105        5
## 5             105-115        7
## 6             115-125        5
## 7             125-135        8
## 8             135-145       15
## 9             145-155       14
## 10            155-165        9
## 11            165-175        8
## 12            175-185        9
## 13            185-195        5
## 14            195-205       11
## 15            205-215       12
## 16            215-225       15
## 17            225-235       17
## 18            235-245       23
## 19            245-255       20
## 20            255-265        0
## 21            265-275        0

We can also break this down into bar plots of the stratigraphic ranges of genera.

#plotting the stratigraphic ranges of genera
pbdb_temp_range (taxon.data, rank="genus", col="steel blue", names=FALSE)

##                          max    min
## Chonespondylus        252.17 201.30
## Cymbospondylus        252.17 201.30
## Grippia               252.17 201.30
## Shastasaurus          252.17 201.30
## Toretocnemus          252.17 201.30
## Omphalosaurus         252.17 237.00
## Chaohusaurus          251.30 247.20
## Gulosaurus            251.30 247.20
## Utatsusaurus          251.30 247.20
## Barracudasaurus       247.20 237.00
## Besanosaurus          247.20 237.00
## Contectopalatus       247.20 237.00
## Mikadocephalus        247.20 237.00
## Mixosaurus            247.20 237.00
## Phalarodon            247.20 237.00
## Wimanius              247.20 237.00
## Barracudasauroides    247.20 242.00
## Phantomosaurus        247.20 242.00
## Thalattoarchon        247.20 242.00
## Xinminosaurus         247.20 242.00
## Hudsonelpidia         237.00 201.30
## Callawayia            237.00 208.50
## Qianichthyosaurus     237.00 221.50
## Californosaurus       237.00 228.00
## Guanlingsaurus        237.00 228.00
## Guizhouichthyosaurus  237.00 228.00
## Shonisaurus           232.00 212.00
## Ghuizhouichthyosaurus 232.00 221.50
## Guanlingichthyosaurus 232.00 221.50
## Ichthyosaurus         228.00 112.03
## Macgowania            228.00 208.50
## Metashastasaurus      228.00 208.50
## Himalayasaurus        215.56 212.00
## Ophthalmosaurus       201.30 136.40
## Temnodontosaurus      201.30 174.10
## Leptonectes           201.30 175.60
## Excalibosaurus        199.30 190.80
## Stenopterygius        183.00 171.60
## Eurhinosaurus         183.00 182.00
## Hauffiopteryx         183.00 182.00
## Suevoleviathan        183.00 182.00
## Dearcmhara            182.70 168.40
## Chacaicosaurus        171.60 168.40
## Mollesaurus           171.60 168.40
## Baptanodon            168.30 155.70
## Arthropterygius       163.50 145.00
## Undorosaurus          163.50 145.00
## Apatodonosaurus       163.50 157.30
## Sphaerodontes         161.20 155.70
## Brachypterygius       157.30 145.00
## Nannopterygius        157.30 152.10
## Cryopterygius         152.10 145.00
## Janusaurus            152.10 145.00
## Macropterygius        152.10 145.00
## Palvennia             152.10 145.00
## Paraophthalmosaurus   152.10 145.00
## Platypterygius        150.80  66.00
## Aegirosaurus          150.80 136.40
## Caypullisaurus        150.80 139.80
## Malawania             136.40 125.00
## Acamptonectes         136.40 129.40
## Muiscasaurus          130.00 112.03
## Simbirskiasaurus      130.00 125.45
## Sveltonectes          130.00 125.45
## Leninia               125.45 122.46
## Sisteronia            113.00  93.50
## Maiaspondylus         113.00 100.50
## Athabascasaurus       112.03 109.00
## Cetarthrosaurus       105.30  99.60
## Pervushovisaurus       99.60  93.50

What is the ichthyosaur diversity pattern over time? Let’s disuss as a group.

After completing this tutorial, please repeat all steps with at least two groups of your choice (keep the group small…).