“Looking not to any one time, but to all time, if my theory be true, numberless intermediate varieties, linking most closely all the species of the same group together, must assuredly have existed; but the very process of natural selection constantly tends, as has been so often remarked, to exterminate the parent forms and the intermediate links. Consequently evidence of their former existence could be found only amongst fossil remains”

You Can Lead an Atheist to Evidence, But You Can't Make Him Think (2009)

Source: Evolution: A Theory in Crisis (1986), p. 77

Source: On the Origin of Species (1859), chapter X: "On the Geological Succession of Organic Beings", pages 341-343 http://darwin-online.org.uk/content/frameset?pageseq=359&itemID=F373&viewtype=side
Context: p>I have attempted to show that the geological record is extremely imperfect; that only a small portion of the globe has been geologically explored with care; that only certain classes of organic beings have been largely preserved in a fossil state; that the number both of specimens and of species, preserved in our museums, is absolutely as nothing compared with the incalculable number of generations which must have passed away even during a single formation; that, owing to subsidence being necessary for the accumulation of fossiliferous deposits thick enough to resist future degradation, enormous intervals of time have elapsed between the successive formations; that there has probably been more extinction during the periods of subsidence, and more variation during the periods of elevation, and during the latter the record will have been least perfectly kept; that each single formation has not been continuously deposited; that the duration of each formation is, perhaps, short compared with the average duration of specific forms; that migration has played an important part in the first appearance of new forms in any one area and formation; that widely ranging species are those which have varied most, and have oftenest given rise to new species; and that varieties have at first often been local (emphasis not Darwin's). All these causes taken conjointly, must have tended to make the geological record extremely imperfect, and will to a large extent explain why we do not find interminable varieties, connecting together all the extinct and existing forms of life by the finest graduated steps. He who rejects these views on the nature of the geological record, will rightly reject my whole theory. For he may ask in vain where are the numberless transitional links which must formerly have connected the closely allied or representative species, found in the several stages of the same great formation. He may disbelieve in the enormous intervals of time which have elapsed between our consecutive formations; he may overlook how important a part migration must have played, when the formations of any one great region alone, as that of Europe, are considered; he may urge the apparent, but often falsely apparent, sudden coming in of whole groups of species. He may ask where are the remains of those infinitely numerous organisms which must have existed long before the first bed of the Silurian system was deposited: I can answer this latter question only hypothetically, by saying that as far as we can see, where our oceans now extend they have for an enormous period extended, and where our oscillating continents now stand they have stood ever since the Silurian epoch; but that long before that period, the world may have presented a wholly different aspect; and that the older continents, formed of formations older than any known to us, may now all be in a metamorphosed condition, or may lie buried under the ocean.</p

Source: The Theory of Evolution (1958), p. xv.

Source: Vestiges of the Natural History of Creation (1844), p. 60

Source: Mendel's Principles of Heredity (1913), p. 3

"Introduction", page 5 http://darwin-online.org.uk/content/frameset?pageseq=20&itemID=F373&viewtype=image
On the Origin of Species (1859)

First Congress of the International Association of Shell Structures (now IASS), Madrid (1959) discussion following presentation of his paper paper ‘New Shapes for Shells’, as quoted by John Chilton, "39 etc… : Heinz Isler’s infinite spectrum of new shapes for shells" (2009) Proceedings of the International Association for Shell and Spatial Structures (IASS) Symposium 2009, Valencia, Evolution and Trends in Design, Analysis and Construction of Shell and Spatial Structures, 28 September – 2 October 2009, Universidad Politecnica de Valencia, Spain, eds. Alberto Domingo, Carlos Lazaro.

"On the Law which has Regulated the Introduction of New Species" (1855).