On SharePoint 2013 you can not add the Web Parts to the master page the same way of 2010.
Please use the Design Manager -> Snippet
Gallery.
In short:
You must wrap the Register tag
with: <!--SPM: register
tag -->
Like this:
<!--SPM:<%@Register Tagprefix="Publishing" Namespace="Microsoft.SharePoint.Publishing.WebControls" Assembly="Microsoft.SharePoint.Publishing, Version=15.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c"%>-->You should wrap the opening tag of your Web Part with: <!--MS: tag -->
And the closing tag with: <!--ME: tag -->
The Web Part would look like this:
<!--MS:<asp:SiteMapDataSource ShowStartingNode="True" SiteMapProvider="SPNavigationProvider" ID="topSiteMap" runat="server" StartingNodeUrl="sid:1002">-->
…
<!--ME:</asp:SiteMapDataSource>-->(Snippet Gallery will automatically create the tags in the right way and you can copy it to your master page.)