The entire collection of your populations and turtles exists in a database file on the iPad. This file is backed up when you sync your iPad, or when you use the iTunes Backup feature. Either of these methods are quite adequate for making sure you have a backup of your database. For users who are more advanced, and would like to access the database file directly (not recommended for the average user), the database file can be accessed via the iTunes File Sharing feature. The file is named 'EvolvedArt.sqlite'. You should never replace this file or delete this file, unless you are an experienced database expert.
Despite the automated backup provided by the iTunes sync and backup mechanisms, iTunes does not make it easy to archive its backups other than using Time Machine. For this and other reasons, you may wish to backup population definitions individually. This also allows you to restore individual populations without having to replace the entire database. To backup a population, use the Export To iTunes action in the Population View, and save the population definition file to iTunes. Then open iTunes and use the file sharing feature to copy the population definition to a disk.
Individual turtles can also be backed up by exporting the turtle's definition file from the Turtle Details View. Use the Export Turtle action in the Turtle Details View, then use iTunes file sharing to save the turtle definition file to disk.
You can also use DropBox to backup population or turtle definition files offsite, which is an excellent way to ensure you never lose your turtles. You can use the Open Population In action in the Population View to open the population's definition file in the DropBox app, which will allow you to save the definition file to the DropBox server. Likewise, you can use the Open Turtle In action in the Turtle Details View to open a turtle's definition file in the DropBox app to save the definition file to the DropBox server. Once the definition files are stored on DropBox, you can use the DropBox app to open them using Evolved Art to import the population or turtle back into Evolved Art.
Finally, there is email. One of the oldest and most commonly used technologies of the Internet, email provides a very nice means of backing up your populations and turtles. I use Google Mail, which provides a nice feature for labeling email. By emailing populations and turtles to myself, then using Google's labeling mechanism, I am able to save and catalog populations and turtles in a nicely organized fashion.