Currently, Lync/Skype Connectivity is provided through the SIP Federation Providers and specifically MSN. Considering MSN is merging with Skype this makes sense. You will notice when you sign into Skype it will ask you to merge your Live ID account with Skype. This will allow you to log into Skype using your MS Live ID and will show you all your Skype contacts + Live contacts.
For now only Instant Messaging and Presence are available with Voice calls coming in June. The Office 365 Mediation servers will be leveraged to transcode the Skype Protocol in to RTA that the Lync client understands. For the full story checkout the Next Hop article.