Dating the radiation of birds using quartets

by Rod Page (r.page@bio.gla.ac.uk)

This exercise makes use of the method originally developed by Alan Cooper and David Penny to date the age of radiation of modern birds (Aves) using molecular data. The technique uses quartets, and has been implemented by Andrew Rambaut in the program Qdate .

Cooper and Penny argued that molecular sequence data for 12S rRNA and c-mos genes showed that modern birds were contemporaries of dinosaurs, and that 22 orders of birds survived the K-T boundary extinction event. This contrasts with Alan Feduccia's view that modern birds radiated after the K/T event. We will reanalyse Cooper and Penny's data using QDate, then test their results using another gene, RAG-1 .

Data files

References

Cooper, A. and D. Penny. 1997. Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence. Science 275: 1109-13.[http://intl.sciencemag.org/cgi/content/full/275/5303/1109]

Feduccia, A. 1995. Explosive Evolution in Tertiary Birds and Mammals. Science 267: 637-638.[HTML]

Groth, J. G. and G. F. Barrowclough. 1999. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Molecular Phylogenetics and Evolution 12: 115-23. doi:10.1006/mpev.1998.0603

Rambaut, A. and L. Bronham. 1998. Estimating divergence dates from molecular sequences. Molecular Biology and Evolution 15: 442-8. [http://mbe.oupjournals.org/cgi/content/abstract/15/4/442]

Fossil dates

The quartet method needs fossils for the two pairs of taxa in the quartet. Specifically, for each pair we want the date of the earliest occurrence of either member. One way to get this information is from the Fossil Record 2 database. This database lists the geological periods for many families of organisms. Below are some dates for bird orders. Because the dates are actually geological periods we get a lower and upper bound on the age of the oldest fossil. The column "age" is simply the average of these two dates:

The row for the Tinamiformes has intentionally been left blank. You can go to the Fossil Record web site to get this information.

1. Go to the Fossil Record Web site. Choose "manipulate data and plot graphs"
2. On the next Web page select "Families by chapter"
3. Choose Chapter 40 (Aves)
4. Click on Orders (47 records) to see a list of all bird orders in the database
5. Choose the desired order
6. Click on the button "Origination pattern"

If you get lost just go directly to the bird orders page.

This table lists the orders for the birds we will look at.

The combined c-mos and 12S rRNA data are in the file cmos12SrRNA.nex. Open this file in PAUP and build a phylogeny.

The program Qdate uses its own file format. The file cmos12SrRNA.qdate has the sequences, and a set of quartets. These are written like this:

3 
Tropicbird Gull 60 GuineaFowl Chicken 40 
Tropicbird Gull 60 Rhea Ostrich	   55 
GuineaFowl Chicken 40 Rhea Ostrich 55 

3 means there are 3 quartets, one per line. For each quartet the age of the oldest fossil for each pair is listed. In the above example, the oldest galliform fossil is about 40 Myr old, so this is the value for the GuineaFowl Chicken pair.

Run the program Qdate by clicking on the icon, and selecting the file cmos12SrRNA.qdate. Type "-mHKY" as the command line, and then click on the output file name button to specify an output file (we need this to save the results). Click on OK.

Open the output file in Microsoft Excel. You should see something like this (you may have to shift the column headings one cell to the right):

We want to plot a graph of age estimates for each quartet, together with upper and lower bounds. To do this:

• Select the values in the Date column and create and XY (scatter) chart using the Insert | Chart command.

• Create two additional columns in the spreadsheet for the lower- and upper-error bars. To get the lower error bar, select the first cell in the lower-bound column, type "=", then click on the value in date for row one, type "-", then click on the cell in low. The cell now contains the value will be use for the lower error bar. Copy and paste this cell into the cells below it to fill the column. Repeat these steps for the upper error bar, but remember that the formula here is High – Date. For the example above you should get some thing like this:

• Go to the chart and right-click on a data point. In the popup menu select Format Data Series. Click on the Y Error Bars tab. Select Custom and enter the ranges of the cells corresponding to the upper and lower error bars. The simplest way to do this is to click on the little box at the right of the + and – fields and select the corresponding range of cells.

You should now have a plot of the divergence times for each quartet, with the lower and upper error bars.

Part 2

We can test Cooper and Penny’s claim by using another gene. Groth and Barrowclough sequenced the RAG-1 gene in 14 birds. The file rag1.nex contains these sequences in NEXUS format, and the file rag1.qdate is in Qdate format.

Having seen how the technique works, build a tree for RAG-1, decide on some quartets, and add them to the file rag1.qdate. I’ve put one in the file already. Remember that you need two pairs of species such each member of the pair is more closely related to each other than to the other pair, and you need fossil dates for each pair. Plot your results as above.