One of the ironies of the history of biology is that Darwin did not really explain the origin of new species in The Origin of Species, because he didn’t know how to define a species. [Futuyma 1983: 152]
Comments like Futuyma's have been published in scores of textbooks and repeated ad nauseum. Similar criticisms go back to the 19th century, and in my view, they are totally wrong.
Charles Darwin was a student of some of the best geologists and naturalists in Britain at the time, when geology and natural history were regarded as being similar if not identical topics. When he set off on the Beagle, he had been taught by Henslow and others how to collect species and to describe them. So far as we know, he did not think much about these techniques or conventions. This changed during the voyage.
One of the ways museum taxonomists, like John Gould, who later described the famous finches, did their work on specimens returned to their museum by explorers like Darwin, was to employ traits that were distinctive. Many organisms were skinned and stuffed, and their skeletal remains used to identify special traits (note that "special" is the adjective of "species"; there's an interesting backstory to this in traditional logic I won't bore you with now).
However, these morphological traits didn't always line up with species. In his Journal of Researches (Darwin 1839), which is popularly known as the Voyage of the Beagle, Darwin noted that the main authority on the topic, Cuvier, had misdiagnosed two South American rabbit species from skeletons, when in fact, any gaucho knew they were the same.
In the Journal Darwin made few comments about species as such except to note, in the second edition of 1845 (Darwin 1845, Chapter VIII, p167), eight years after his thinking about transmutation began, that there are checks on the increases of populations. He also noted the difficulty of defining species in terms of morphology:
Of the latter [rabbit, a piebald hybrid of black and gray breeds] I now possess a specimen, and it is marked about the head differently from the French specific description. This circumstance shows how cautious naturalists should be in making species; for even Cuvier, on looking at the skull of one of these rabbits, thought it was probably distinct! [Chapter IX, p184]
Darwin reported that the Gauchos of South America were able to tell that these were one species because they shared the same territory and interbred, while Cuvier used only morphology. He noted in a footnote:
The distinction of the rabbit as a species, is taken from peculiarities in the fur, from the shape of the head, and from the shortness of the ears. I may here observe that the difference between the Irish and English hare rests upon nearly similar characters, only more strongly marked. [p184n]
From this we may conclude that Darwin was no naive morphologist, at any rate. He goes on to say
I was much struck with the marked difference between the vegetation of these eastern valleys and those on the Chilian side: yet the climate, as well as the kind of soil, is nearly the same, and the difference of longitude very trifling. The same remark holds good with the quadrupeds, and in a lesser degree with the birds and insects. I may instance the mice, of which I obtained thirteen species on the shores of the Atlantic, and five on the Pacific, and not one of them is identical. We must except all those species, which habitually or occasionally frequent elevated mountains; and certain birds, which range as far south as the Strait of Magellan. This fact is in perfect accordance with the geological history of the Andes; for these mountains have existed as a great barrier since the present races of animals have appeared; and therefore, unless we suppose the same species to have been created in two different places, we ought not to expect any closer similarity between the organic beings on the opposite sides of the Andes than on the opposite shores of the ocean. In both cases, we must leave out of the question those kinds which have been able to cross the barrier, whether of solid rock or salt-water.[5]
5 This is merely an illustration of the admirable laws, first laid down by Mr. Lyell, on the geographical distribution of animals, as influenced by geological changes. The whole reasoning, of course, is founded on the assumption of the immutability of species; otherwise the difference in the species in the two regions might be considered as superinduced during a length of time. [Chapter XV, p313]
Here he is undercutting the widely-held view that species are formed by climate or soil, the view that goes back to the medieval era (and which motivated Buffon’s view of deviation from the premiere souche, or "first stock" of each group, such as cats). Instead we have the beginnings of a biogeographic view of species as the result of geological isolation, which in his Notebooks was a focus of his thinking at this time. Ironically, geographic isolation dropped out of his thinking later as a cause of speciation, as natural and sexual selection took over in his theory. He later had a real battle with Moritz Wagner, who first proposed geographical isolation, and which is now the "standard" view.
Next, I'll cover his Notebook discussions.
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Hey, don't leave me hanging like that! Do tell.
Otherwise excellent, as always.