[Answer]-How do I populate the Django table MyApp_user_groups in a yaml fixture?

1👍

If you use Django >= 1.7 (with migrations) you could (and should) use Data Migrations.
https://docs.djangoproject.com/en/1.7/topics/migrations/#data-migrations

def create_group(apps, schema_editor):
    Group = apps.get_model("auth", "Group")
    g = Group.objects.create("Your group name")
    UserGroup = apps.get_model("MyApp", "User_Group")
    UserGroup.objects.create(user_id=2, group_id=g.id)


class Migration(migrations.Migration):

    dependencies = [
        ('MyApp', '0001_initial'),
        ('auth','0001_initial'),
    ]

    operations = [
        migrations.RunPython(create_group),
    ]

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