Coalescence

Simulates a coalescent history for 5 randomly-selected genes from among the 2*Ne genes in a random-mating population of size Ne. The MRCA is shown as a large, red-filled circle (if it is visible), but note that it will not be visible if it occurs at a time deeper than the 50 generations shown.

Use the drop-down control below the plot to change Ne The Refresh button regenerates the entire history (same as refreshing your browser except that Ne does not revert to its default value).

Keys that can be used:

• S Chooses a different random sample of 5 genes

Some experiments to try:

• Refresh 10 times with Ne = 5. How many times out of 10 did the MRCA occur within the 50 generations shown?
• Refresh 10 times with Ne = 15. How many times out of 10 did the MRCA occur within the 50 generations shown? Does the MRCA tend to occur nearer the present (top of the plot) or deeper into the past (bottom of the plot) when Ne is larger?
• Press the S key several times to choose a different sample of genes while keeping the population history the same. Does sampling different genes affect the position of the MRCA? Try the same exercise with several different population histories (hit the Refresh button to obtain a new population history as well as a new random sample of genes).

Acknowledgements

This applet makes use of the excellent d3js javascript library. Please see the GitHub site for details about licensing of other libraries that may have been used in the source code for this applet.

Licence

Creative Commons Attribution 4.0 International. License (CC BY 4.0). To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 559 Nathan Abbott Way, Stanford, California 94305, USA.