For some time now I have been convinced that Darwin’s original and most pressing problem was not adaptation. It was the existence of taxonomic diversity. I have thought that the debates over what was a natural classification amongst the unjustly derided Quinarians William Sharp Macleay and William Swainson were the jumping off point for Darwin’s theory of common descent. Michael Barton has pointed me to this recently added transcription at the Darwin Correspondence Project, of a note he wrote in February of 1841:
There is such disputes about affinity, linear, circular arrangement &c &c definition of species — that I cannot, as in geographical distribution & — as in relation of fossil to recent, or state my facts & deduce consequences, — but I must show,
howwhat light the conclusions deduced from other parts bear on those vexed questions — After showing what a ‘species’ is add remark that question about origin of all our dogs became less material — it is simply whether nature or man, has transported, exposed to different climates & selected the offspring from one common stock. — or whether these have been effected by natural or artificial means
The language here is clearly influenced by the discussions of the Quinarians, in particular Swainson’s Preliminary Discourse of 1834. At this time it was a widely held view that local geography caused the changes in varieties and local species from a common stock, a view proposed by Buffon in the previous century and to an extent revived by Geoffroy.
“Affinity” is a misunderstood term. Often it is read as meaning, as O’Hara 1991 put it, “a relationship based on some sort of essential similarity”. He rightly goes on to note a distinction with homology: “While the later and somewhat related concept of homology was rarely discussed in the purely systematic literature (homology was a relation that obtained among characters, in contrast to affinity which obtained among taxa), discussions of affinity pervaded that literature.” But affinity was simply a summary of the overall homological relations between taxa, and the idea that something was essential was never, to my knowledge, asserted at the time. In short, affinity is a kind of “parsimony analysis” of homological relations.
Darwin is motivated to explain these affinities. He does so by assuming that for all intents and purposes the taxonomic scheme that is current is a good approximation to the natural system, at least at some levels. And he explains these relations by appealing to shared ancestry. As I have written before, homology precedes ancestry. That is to say, we know the homological affinities of taxa before we explain them by appealing to shared ancestry; homology is not identical to shared ancestry. Darwin knew this.
O’Hara, Robert J. 1991. Representations of the natural system in the nineteenth century. Biology and Philosophy 6 (2):255–274.