In recent months, we’ve shared our commitment to Yammer and have unveiled innovations that deepen Yammer’s integration with Office 365. As part of that journey, we are removing several features from Yammer that are now supported with more modern alternatives in Office 365.
In May of 2018, we will remove the following Yammer features, and encourage customers to explore the following alternatives in Office 365:
  • Yammer’s native org chart feature. Use the rich, interactive organization chart in Delve, Microsoft Teams, people search, and people cards that surface in many Office 365 experiences including Outlook, SharePoint, and OneDrive.
  • Recent Activity module on the home page. Activity from your connections can be seen in Delve, in the activity web part in SharePoint, and in people cards that surface in many Office 365 experiences including Outlook, SharePoint, and OneDrive.
  • Syncing contacts on the mobile apps. User profile data is automatically synced via Azure Active Directory, while Yammer uses the Microsoft Graph to recommend colleagues most relevant to you. 
  • The Yammer desktop notifier application. The new Yammer desktop application surfaces notifications and provides a fully-featured Yammer experience for desktop users.
We know that any change to our services may disappoint some customers, but we are confident that you will appreciate the investments we are making to ensure that Yammer is the most secure and capable platform for employee engagement and communications, integrated with best-of-breed experiences in Microsoft 365. 
We remain as committed as ever to Yammer, and look forward to sharing new capabilities of Yammer, including deeper integration with Office 365 groups and SharePoint, at the SharePoint Virtual Summit. Stay tuned for details!
Respected Contributor

What are the primary reasons for an organization to deploy the desktop app? this seems like just one more thing to keep track of and troubleshoot. 

Valued Contributor
As with the recent SharePoint Newsfeed deprecation, two things stand out for me.: the period to deprecation is short. The rationale may be strong but more notice is required. Secondly as indicated more integration for Yammer is planned to be announced at the SharePoint Conference in May. I would be inclined to announce then deprecate to reinforce the investment statement. Individually these changes may not be great but cumulatively across Office 365 change require communication, choice of an alternative product, rollout etc.. Sometimes ‘disappointment’ just doesn’t cover it.

The Yammer desktop app gives a fully functional, rich experience for Yammer.  Reasons to deploy it include:

  • An "always on" connection that makes it easy to get back to your conversations, without having to open a browser and navigate.
  • Integration with desktop notifications, so you can be alerted when a conversation needs your attention.

It's kind of similar reasons as why you might want the Teams app, or Outlook, as opposed to using the browser.  Like those apps, the choice of app vs. browser experience will depend on the user, their work preferences, and their use cases.