Yamnaya is sister group, not ancestor, to Corded Ware

Although the sampling is still smaller than we'd like, it seems almost certain that the Corded Ware Culture (CWC) people were a sister group, not a descendant of the Yamnaya people.  In fact, it may well have been the spread of the Yamnaya horizon that pushed the proto-CWC people to the north (or perhaps the migration of the CWC people left the western steppe open for the Yamnaya to expand.)  Given that most of the modern Indo-European languages, including all of the languages of northern and western Europe AND the Indo-Iranian branch can all be traced to the CWC rather than the Yamnaya, that puts some doubt on the Yamnaya as the source of late unified Proto-Indo-European.  Yamnaya MIGHT well have been the source of the Indo-European paleo-Balkan languages, and even the modern "Balkan" languages such as Greek, Albanian and Armenian (which originated in the Balkans even if they're not there now) as well as a number of extinct Indo-European languages like Phrygian, Cimmerian, etc.  We don't know enough about those languages to really say anyway.  Also, it might be the source of the Tocharian languages.

And certainly the interaction of westerly pushing late Yamnaya and lingering Corded Ware offshots as well as lingering Old European peoples created a complex melange of what developed later, like the Vučedol culture, for instance.

Another major vector of the spread of Indo-European is the Bell Beaker, which seems to show its closest genetic analogs; almost identical, really, to the Single Grave Culture, a Low Countries variant of the Corded Ware.  Contrary to Carlos Quiles and his Demic Diffusion and Uralic Substrate theories, the R1b clade of Y-DNA that is most strongly associated with the Beakerfolk is not part of the R1b clade most strongly associated with the Yamnaya, something that I didn't actually know until recently.  R1a-M417 is the haplogroup most strongly associated with the Corded Ware, but it isn't the only haplogroup, and R1b-L51, which is ancestral to R1b-P312 seems to have been with the CWC all along, and is present in some sampled areas of the Single Grave Culture.

The Yamnaya may well have been a flashy offshoot of the development of Indo-European, which is still more thoroughly nested within the Corded Ware Culture for almost all branches after all.  Not to suggest that CWC and Yamnaya weren't closely related, of course, but in the same way that your brother is closely related to you but has no role in marking your line of descent, the Yamnaya doesn't seem to have been as important as long thought in the development of most Indo-European branches after all.

But there's still a lot of questions driven by holes in the data about where and how certain lineages grew and expanded so quickly, and where exactly they came from.  The Corded Ware R1a--did it come from a northwestern branch of the steppe population (most likely, but there's only one sample so far that suggests that) and if so, from what population and when?  Late Sredni Stog II would be an obvious choice, and there are some archaeological hints that CWC can be found rooted in Sredni Stog, not Yamnaya, that have been out there for a long time already.  The Bell Beaker formation has a hypothesis rooted in the Single Grave culture, but much more data to make that assertion more sure would be appreciated.  And the formation and arrival of the Corded Ware is still somewhat mysterious.  How they got to where they are, especially if they come from the Sredi Stog II territory is a no-man's land when it comes to sampling, and we know that the non-Indo-European Globular Amphora Culture was laid across that exact same territory.  How the two of them interacted is also unknown.

This doesn't fundamentally challenge the steppe hypothesis, but it probably does require (or will require) some modification and tweaking to it.  And curiously, it means Carlos Quiles was right about one major aspect of his theory, at least, even if the other two big legs of his tripod are dead wrong.  Sredni Stog is almost certainly the most closely associated with the R1a haplogroup of the Corded Ware, and should be seen as its most likely direct ancestor.  But the Corded Ware people spoke an Indo-European language, quite clearly, and the Bell Beakers from Hungarian Yamnaya is not as likely as from within a Corded Ware group.  But that's some of the stuff that still isn't settled or sure, even if we can see the way it will likely develop.

Keep in mind that there could well be sampling bias in the samples we have, too.  The people who were buried in kurgans, for instance, were high status males, almost entirely.  The people who were found in bogs in Denmark were probably criminals or sacrifices (or both) and were, on the other hand, low status.

So, it is possible that as social status changed, suddenly we have the appearance of the explosion of a y-dna haplogroup from nowhere, but in reality it was there all along, just lacking in sufficient status to be buried in such a way that it would likely be found.

But again; the answer to all of these question is more sampling.