In both Commercial and Open Source environments GitHub Issues is replacing Jira.
Even Fortune 100 companies are begining to use Github Enterprise as their version control system. These teams then default to using Github Issues for issue tracking.
Previously, these teams would have chosen Jira without a second thought. Now someone really has to feel enough pain in GitHub Issues to justify moving to a 'separate' issue tracking system.
While this seems obvious, its not. Take a high profile open source project like TypeScript or Redis. In a pre-GitHub world, these projects would have beyond doubt used an open source Jira license. Now they use GitHub issues.
Even Spring Framework, which does use Jira for bug tracking, is being forced to use GitHub Issues for Spring Boot. It is the natural place where the Spring Boot users want to report their bugs.
Given the significance of above, it is surprising how little work GitHub is putting into GitHub Issues. They are in a unique position to significantly disrupt Atlassian.