diff --git a/wp-admin/includes/upgrade.php b/wp-admin/includes/upgrade.php
index 090ef1a63..06c0ff894 100644
--- a/wp-admin/includes/upgrade.php
+++ b/wp-admin/includes/upgrade.php
@@ -346,6 +346,9 @@ function upgrade_all() {
 	if ( $wp_current_db_version < 10360 )
 		upgrade_280();
 
+	if ( $wp_current_db_version < 11958 )
+		upgrade_290();
+
 	maybe_disable_automattic_widgets();
 
 	update_option( 'db_version', $wp_db_version );
@@ -983,6 +986,23 @@ function upgrade_280() {
 		populate_roles_280();
 }
 
+/**
+ * Execute changes made in WordPress 2.9.
+ *
+ * @since 2.9.0
+ */
+function upgrade_290() {
+	global $wp_current_db_version;
+
+	if ( $wp_current_db_version < 11958 ) {
+		// Previously, setting depth to 1 would redundantly disable threading, but now 2 is the minimum depth to avoid confusion
+		if ( get_option( 'thread_comments_depth' ) == '1' ) {
+			update_option( 'thread_comments_depth', 2 );
+			update_option( 'thread_comments', 0 );
+		}
+	}
+}
+
 
 // The functions we use to actually do stuff
 
diff --git a/wp-admin/options-discussion.php b/wp-admin/options-discussion.php
index f6cc7747f..8093d1593 100644
--- a/wp-admin/options-discussion.php
+++ b/wp-admin/options-discussion.php
@@ -66,7 +66,7 @@ include('admin-header.php');
 $maxdeep = (int) apply_filters( 'thread_comments_depth_max', 10 );
 
 $thread_comments_depth = '</label><select name="thread_comments_depth" id="thread_comments_depth">';
-for ( $i = 1; $i <= $maxdeep; $i++ ) {
+for ( $i = 2; $i <= $maxdeep; $i++ ) {
 	$thread_comments_depth .= "<option value='" . esc_attr($i) . "'";
 	if ( get_option('thread_comments_depth') == $i ) $thread_comments_depth .= " selected='selected'";
 	$thread_comments_depth .= ">$i</option>";
diff --git a/wp-includes/version.php b/wp-includes/version.php
index a9bf4741f..6ade29abb 100644
--- a/wp-includes/version.php
+++ b/wp-includes/version.php
@@ -15,7 +15,7 @@ $wp_version = '2.9-rare';
  *
  * @global int $wp_db_version
  */
-$wp_db_version = 11943;
+$wp_db_version = 11958;
 
 /**
  * Holds the TinyMCE version