Just to frame up the question briefly, let me quote the same passage Kyle did from Pius XII's 1950 encyclical Humani Generis, in which Pius addresses the question of the Church's understanding of human origins in light of modern (evolutionary) science. In summary, Pius sees no conflict between a Catholic understanding of humanity and evolutionary science, but he does lay out one possible area of conflict:
When, however, there is question of another conjectural opinion, namely polygenism, the children of the Church by no means enjoy such liberty. For the faithful cannot embrace that opinion which maintains that either after Adam there existed on this earth true men who did not take their origin through natural generation from him as from the first parent of all, or that Adam represents a certain number of first parents. Now it is in no way apparent how such an opinion can be reconciled with that which the sources of revealed truth and the documents of the Teaching Authority of the Church propose with regard to original sin, which proceeds from a sin actually committed by an individual Adam and which, through generation, is passed on to all and is in everyone as his own.So while Pius XII is quite comfortable with the evolutionary account of human origins so long as there is one clear ancestral couple who were first infused by God with a soul, and who are described in the Bible in the story of Adam and Eve, he expresses grave reservations as to whether we can accept a view of human history in which not all humans are descended from a single ancestral couple, who fell and thus bequethed us original sin. However, as Kyle points out, modern evolutionary science (sixty years further down the road from Pius XII's encyclical) suggests with near certainty that there was at any given point in time a population of humans from whom the subsequent generation was descended -- there never was a population bottleneck after which all subsequent humans were descended from one ancestral couple. (There are single ancestors, and doubtless single ancestral couples, whom all modern humans share as an ancestors, "Mitochondrial Eve" and "Y-Chromosomal Adam" for example, but in the generations immediately after these individuals there were many humans who were not related to them. It was only over tens of thousands of years of genetic mixing that we reached a point where all humans shared those single ancestors.) Further, there is very strong genetic evidence that on a few (rare) occasions, archaic human populations in various parts of the world interbred with the ancestral modern human population which spread out of Africa and which all humans share. Thus, those of European descent have a tiny genetic contribution which appears likely to have derived from Neandertals, but people who no European ancestry do not share this genetic heritage. Thus, mixing with Neandertals clearly came at some point after the otherwise common origin of all humans.
Let me see if I can step back to the basic question here (whether our understanding of original sin is modified if we accept a scientific understanding that we are descended not just from one unique pair of original humans, but rather from a population of original humans) and take a run at it, because this is something which has always seemed pretty straight-forward to me whereas many people find it rather worrying. (Whether this means I have any particular insight on the matter, or if it simply means I'm theologically tone deaf, you shall have to tell me. I hesitate to find little difficulty where a recent pope found much -- but perhaps there are some areas in which the passage of time is helpful.)
If I were to summarize the doctrine of Original Sin as I undertand it, leaving all questions of evolution aside, I would say: Original Sin is a stain, defect, or corruption which marks the soul of every human born since the fall. We are born with it, and it inclines us to sin. All humans (Mary aside) have been born with Original Sin since the sin of our first parents, Adam and Eve.
Now, let us bring into mind the apparent scientific truth that there was never a single "first" human couple (at least in the biological sense) from whom all modern humans are descended, but rather that there was a small population of humans who are the ancestors of all of us, some descendants of whom on a few subsequent rare occasions appear to have mixed with some regional archaic human populations elsewhere in the world as they spread out.
What of the above definition of original sin would we need to change in light of this? To think about it, I'd like to break the definition into two parts:
a) Original Sin is a stain, defect, or corruption which marks the soul of every human born since the fall. We are born with it, and it inclines us to sin. All humans (Mary aside) have been born with Original Sin
b) since the sin of our first parents, Adam and Eve.
First let us address a). It seems to me that within a Catholic understanding of God's revelation to us, we probably do not need to see any problem with a) as a result of accepting a scientific account of the history of humanity in which there was never a single original couple whose children made up all the rest of humanity.
On the face of it, one might ask, "But if our understanding of original sin is derived from thinking that the story of Adam and Eve was a basically historical account, doesn't that mean that with Adam and Eve removed, we must revise our understanding of what original sin is, or if it exists at all?"
I think, however, if we take a Catholic approach to scripture and to Church teaching, this is not the case. First, we understand that the Bible consists of a number of genres and that they contain several levels of meaning. I would propose that the opening chapters of genesis belong to the genre of mythology. This does not mean (as some people seem to take the word to mean) that they are nice stories to read to children under the age of ten but are essentially false and of no relation to "reality". Rather, mythology is a way of expressing deep truths about ourselves and the world through a narrative which may well not be historically true. However, myths are not "just a story", nor are they "false". They're simply not meant to be true in the same way that a history book or a newspaper story is meant to be true.
While many in the history of the Church may have assumed (for lack of any reason to think otherwise) that the story of Adam and Eve (and other Genesis stories such as the story of Cain and Able and the story of Noah) was historically true -- our understanding of what scripture is does not require that we believe so. Further, as Catholics we believe that Christ instituted the Church in order to safeguard His teachings, and sent the Holy Spirit to guide the Church and protect her from teaching error.
Now, if original sin were just some theological gloss which people had proposed in order to explain certain elements of the Genesis story, then I could see proposing that it needed to be revised or abandoned given a change in our understanding of the genre and historical accuracy of parts of Genesis. However, original sin is clearly a doctrine of the Church which has been taught authoritatively since the time of the Church Fathers. If we believe at all that the Holy Spirit prevents the Church from teaching error, then clearly we can accept the Church's basic account of original sin as correct -- even if it was in part arrived as through taking a mythological narrative to be more historically accurate than it now appears to have been.
Because of this, it seems to me that everything contained in a) can be taken as true, regardless of whether one takes the story of Adam and Eve literally or mythologically.
Now as to b), here it seems that we have several possible ways we can consider the story of Adam and Eve as presented in Genesis in light of what we currently believe we understand about the history of the human species due to the discoveries of modern science.
1) We could hold that at some point in the distant past, God chose a single pair of humans and made them like himself by infusing them with immortal, rational and moral souls. These first parents fell in some way which was best described to God's chosen people through the Genesis story. Their children all had souls, and at some points interbred with the rest of the early human population, with the result that at some point in the still quite distant past all humans had "Adam and Eve" as one of their ancestors and possessed a soul.
2) We could hold that at some point in time God infused the entire population of humans with souls, and one couple from among them were tested and fell. Given this eventuality, one could hold either that 2.a) as a result of the sin of the representative couple, all humans were stained with original sin at once or 2.b) only the descendants of this fallen couple had original sin, but through some sequence of events, all of us are direct descendants of them. (It strikes me that this leaves the most room for a really fascinating set of fantasy novel plots.)
3) One could hold that they may well never have been a single couple who went through a fall, but that this mythological story was inspired or guided in development by the Holy Spirit in order to describe to the Israelites (and eventually to us) the fallen nature of humanity and the nature of humanities relationship with God. In this way of thinking, we pretty much have to admit that while there was clearly some "fall" at some point after humans came to have souls and be able to have a moral consciousness and awareness of God, and after which humanity possessed original sin and all that that entails, we really have no idea what it was that happened other than that God chose to describe it and its results to us via the story of Adam and Eve.
To the extent that I have an opinion on the matter, I might lean towards 3), but honestly I'm a bit hesitant to even pick one. This is in part because, given the stance outlined by Pius XII above, I don't want to head off in directions which are in any way incompatible with our Church, but more so because I really don't think that it matters. What we do have in Genesis is the story that God chose to place (or allow to develop, depending on how you want to look at it) in the sacred writings of His chosen people. As such, I'm fairly confident that it tells us what we need to know about our nature and our relationship with Him. And given that we, at this remove, have no way of actually finding out "what really happened", I can't see that it's worth speculating much over or putting deep thought into. After all, the best we could do is build our own "just so" story, based on what we think most likely, and unlike God, we don't have the benefit of having been there.