Title pages and introduction
Page ii contains quotations by William Whewell and Francis Bacon on the theology of natural laws, harmonising science and religion in accordance with Isaac Newton's belief in a rational God who established a law-abiding cosmos. In the second edition, Darwin added an epigraph from Joseph Butler affirming that God could work through scientific laws as much as through miracles, in a nod to the religious concerns of his oldest friends. The Introduction establishes Darwin's credentials as a naturalist and author, then refers to John Herschel's letter suggesting that the origin of species "would be found to be a natural in contradistinction to a miraculous process":
WHEN on board HMS Beagle, as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me to throw some light on the origin of species—that mystery of mysteries, as it has been called by one of our greatest philosophers.
Darwin refers specifically to the distribution of the species rheas, and to that of the Galápagos tortoises and mockingbirds. He mentions his years of work on his theory, and the arrival of Wallace at the same conclusion, which led him to "publish this Abstract" of his incomplete work. He outlines his ideas, and sets out the essence of his theory:
As many more individuals of each species are born than can possibly survive; and as, consequently, there is a frequently recurring struggle for existence, it follows that any being, if it vary however slightly in any manner profitable to itself, under the complex and sometimes varying conditions of life, will have a better chance of surviving, and thus be naturally selected. From the strong principle of inheritance, any selected variety will tend to propagate its new and modified form.
Starting with the third edition, Darwin prefaced the introduction with a sketch of the historical development of evolutionary ideas. In that sketch he acknowledged that Patrick Matthew had, unknown to Wallace or himself, anticipated the concept of natural selection in an appendix to a book published in 1831; in the fourth edition he mentioned that William Charles Wells had done so as early as 1813.
Variation under domestication and under nature
Chapter I covers animal husbandry and plant breeding, going back to ancient Egypt. Darwin discusses contemporary opinions on the origins of different breeds under cultivation to argue that many have been produced from common ancestors by selective breeding. As an illustration of artificial selection, he describes fancy pigeon breeding, noting that "[t]he diversity of the breeds is something astonishing", yet all were descended from one species of rock pigeon. Darwin saw two distinct kinds of variation: (1) rare abrupt changes he called "sports" or "monstrosities" (example: ancon sheep with short legs), and (2) ubiquitous small differences (example: slightly shorter or longer bill of pigeons). Both types of hereditary changes can be used by breeders. However, for Darwin the small changes were most important in evolution.
In Chapter II, Darwin specifies that the distinction between species and varieties is arbitrary, with experts disagreeing and changing their decisions when new forms were found. He concludes that "a well-marked variety may be justly called an incipient species" and that "species are only strongly marked and permanent varieties". He argues for the ubiquity of variation in nature. Historians have noted that naturalists had long been aware that the individuals of a species differed from one another, but had generally considered such variations to be limited and unimportant deviations from the archetype of each species, that archetype being a fixed ideal in the mind of God. Darwin and Wallace made variation among individuals of the same species central to understanding the natural world.
Struggle for existence, natural selection, and divergence
In Chapter III, Darwin asks how varieties "which I have called incipient species" become distinct species, and in answer introduces the key concept he calls "natural selection"; in the fifth edition he adds, "But the expression often used by Mr. Herbert Spencer, of the Survival of the Fittest, is more accurate, and is sometimes equally convenient."
Owing to this struggle for life, any variation, however slight and from whatever cause proceeding, if it be in any degree profitable to an individual of any species, in its infinitely complex relations to other organic beings and to external nature, will tend to the preservation of that individual, and will generally be inherited by its offspring ... I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection, in order to mark its relation to man's power of selection.
He notes that both A. P. de Candolle and Charles Lyell had stated that all organisms are exposed to severe competition. Darwin emphasizes that he used the phrase "struggle for existence" in "a large and metaphorical sense, including dependence of one being on another"; he gives examples ranging from plants struggling against drought to plants competing for birds to eat their fruit and disseminate their seeds. He describes the struggle resulting from population growth: "It is the doctrine of Malthus applied with manifold force to the whole animal and vegetable kingdoms." He discusses checks to such increase including complex ecological interdependencies, and notes that competition is most severe between closely related forms "which fill nearly the same place in the economy of nature".
Chapter IV details natural selection under the "infinitely complex and close-fitting ... mutual relations of all organic beings to each other and to their physical conditions of life". Darwin takes as an example a country where a change in conditions led to extinction of some species, immigration of others and, where suitable variations occurred, descendants of some species became adapted to new conditions. He remarks that the artificial selection practised by animal breeders frequently produced sharp divergence in character between breeds, and suggests that natural selection might do the same, saying:
But how, it may be asked, can any analogous principle apply in nature? I believe it can and does apply most efficiently, from the simple circumstance that the more diversified the descendants from any one species become in structure, constitution, and habits, by so much will they be better enabled to seize on many and widely diversified places in the polity of nature, and so be enabled to increase in numbers.
Historians have remarked that here Darwin anticipated the modern concept of an ecological niche. He did not suggest that every favourable variation must be selected, nor that the favoured animals were better or higher, but merely more adapted to their surroundings.
Darwin proposes sexual selection, driven by competition between males for mates, to explain sexually dimorphic features such as lion manes, deer antlers, peacock tails, bird songs, and the bright plumage of some male birds. He analysed sexual selection more fully in The Descent of Man, and Selection in Relation to Sex (1871). Natural selection was expected to work very slowly in forming new species, but given the effectiveness of artificial selection, he could "see no limit to the amount of change, to the beauty and infinite complexity of the coadaptations between all organic beings, one with another and with their physical conditions of life, which may be effected in the long course of time by nature's power of selection". Using a tree diagram and calculations, he indicates the "divergence of character" from original species into new species and genera. He describes branches falling off as extinction occurred, while new branches formed in "the great Tree of life ... with its ever branching and beautiful ramifications".
Variation and heredity
In Darwin's time there was no agreed-upon model of heredity; in Chapter I Darwin admitted, "The laws governing inheritance are quite unknown." He accepted a version of the inheritance of acquired characteristics (which after Darwin's death came to be called Lamarckism), and Chapter V discusses what he called the effects of use and disuse; he wrote that he thought "there can be little doubt that use in our domestic animals strengthens and enlarges certain parts, and disuse diminishes them; and that such modifications are inherited", and that this also applied in nature. Darwin stated that some changes that were commonly attributed to use and disuse, such as the loss of functional wings in some island dwelling insects, might be produced by natural selection. In later editions of Origin, Darwin expanded the role attributed to the inheritance of acquired characteristics. Darwin also admitted ignorance of the source of inheritable variations, but speculated they might be produced by environmental factors. However, one thing was clear: whatever the exact nature and causes of new variations, Darwin knew from observation and experiment that breeders were able to select such variations and produce huge differences in many generations of selection. The observation that selection works in domestic animals is not destroyed by lack of understanding of the underlying hereditary mechanism.
Breeding of animals and plants showed related varieties varying in similar ways, or tending to revert to an ancestral form, and similar patterns of variation in distinct species were explained by Darwin as demonstrating common descent. He recounted how Lord Morton's mare apparently demonstrated telegony, offspring inheriting characteristics of a previous mate of the female parent, and accepted this process as increasing the variation available for natural selection.
More detail was given in Darwin's 1868 book on The Variation of Animals and Plants under Domestication, which tried to explain heredity through his hypothesis of pangenesis. Although Darwin had privately questioned blending inheritance, he struggled with the theoretical difficulty that novel individual variations would tend to blend into a population. However, inherited variation could be seen, and Darwin's concept of selection working on a population with a range of small variations was workable. It was not until the modern evolutionary synthesis in the 1930s and 1940s that a model of heredity became completely integrated with a model of variation. This modern evolutionary synthesis had been dubbed Neo Darwinian Evolution because it encompasses Charles Darwin's theories of evolution with Gregor Mendel's theories of genetic inheritance.
Difficulties for the theory
Chapter VI begins by saying the next three chapters will address possible objections to the theory, the first being that often no intermediate forms between closely related species are found, though the theory implies such forms must have existed. As Darwin noted, "Firstly, why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion, instead of the species being, as we see them, well defined?" Darwin attributed this to the competition between different forms, combined with the small number of individuals of intermediate forms, often leading to extinction of such forms. This difficulty can be referred to as the absence or rarity of transitional varieties in habitat space.
Another difficulty, related to the first one, is the absence or rarity of transitional varieties in time. Darwin commented that by the theory of natural selection "innumerable transitional forms must have existed," and wondered "why do we not find them embedded in countless numbers in the crust of the earth?"  (for further discussion of these difficulties, see Speciation#Darwin's Dilemma and Bernstein et al. and Michod)
The rest of the chapter deals with whether natural selection could produce complex specialised structures, and the behaviours to use them, when it would be difficult to imagine how intermediate forms could be functional. Darwin said:
Secondly, is it possible that an animal having, for instance, the structure and habits of a bat, could have been formed by the modification of some animal with wholly different habits? Can we believe that natural selection could produce, on the one hand, organs of trifling importance, such as the tail of a giraffe, which serves as a fly-flapper, and, on the other hand, organs of such wonderful structure, as the eye, of which we hardly as yet fully understand the inimitable perfection?
His answer was that in many cases animals exist with intermediate structures that are functional. He presented flying squirrels, and flying lemurs as examples of how bats might have evolved from non-flying ancestors. He discussed various simple eyes found in invertebrates, starting with nothing more than an optic nerve coated with pigment, as examples of how the vertebrate eye could have evolved. Darwin concludes: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case."
Chapter VII (of the first edition) addresses the evolution of instincts. His examples included two he had investigated experimentally: slave-making ants and the construction of hexagonal cells by honey bees. Darwin noted that some species of slave-making ants were more dependent on slaves than others, and he observed that many ant species will collect and store the pupae of other species as food. He thought it reasonable that species with an extreme dependency on slave workers had evolved in incremental steps. He suggested that bees that make hexagonal cells evolved in steps from bees that made round cells, under pressure from natural selection to economise wax. Darwin concluded:
Finally, it may not be a logical deduction, but to my imagination it is far more satisfactory to look at such instincts as the young cuckoo ejecting its foster-brothers, —ants making slaves, —the larvæ of ichneumonidæ feeding within the live bodies of caterpillars, —not as specially endowed or created instincts, but as small consequences of one general law, leading to the advancement of all organic beings, namely, multiply, vary, let the strongest live and the weakest die.
Chapter VIII addresses the idea that species had special characteristics that prevented hybrids from being fertile in order to preserve separately created species. Darwin said that, far from being constant, the difficulty in producing hybrids of related species, and the viability and fertility of the hybrids, varied greatly, especially among plants. Sometimes what were widely considered to be separate species produced fertile hybrid offspring freely, and in other cases what were considered to be mere varieties of the same species could only be crossed with difficulty. Darwin concluded: "Finally, then, the facts briefly given in this chapter do not seem to me opposed to, but even rather to support the view, that there is no fundamental distinction between species and varieties."
In the sixth edition Darwin inserted a new chapter VII (renumbering the subsequent chapters) to respond to criticisms of earlier editions, including the objection that many features of organisms were not adaptive and could not have been produced by natural selection. He said some such features could have been by-products of adaptive changes to other features, and that often features seemed non-adaptive because their function was unknown, as shown by his book on Fertilisation of Orchids that explained how their elaborate structures facilitated pollination by insects. Much of the chapter responds to George Jackson Mivart's criticisms, including his claim that features such as baleen filters in whales, flatfish with both eyes on one side and the camouflage of stick insects could not have evolved through natural selection because intermediate stages would not have been adaptive. Darwin proposed scenarios for the incremental evolution of each feature.
Chapter IX deals with the fact that the geologic record appears to show forms of life suddenly arising, without the innumerable transitional fossils expected from gradual changes. Darwin borrowed Charles Lyell's argument in Principles of Geology that the record is extremely imperfect as fossilisation is a very rare occurrence, spread over vast periods of time; since few areas had been geologically explored, there could only be fragmentary knowledge of geological formations, and fossil collections were very poor. Evolved local varieties which migrated into a wider area would seem to be the sudden appearance of a new species. Darwin did not expect to be able to reconstruct evolutionary history, but continuing discoveries gave him well founded hope that new finds would occasionally reveal transitional forms. To show that there had been enough time for natural selection to work slowly, he again cited Principles of Geology and other observations based on sedimentation and erosion, including an estimate that erosion of The Weald had taken 300 million years. The initial appearance of entire groups of well developed organisms in the oldest fossil-bearing layers, now known as the Cambrian explosion, posed a problem. Darwin had no doubt that earlier seas had swarmed with living creatures, but stated that he had no satisfactory explanation for the lack of fossils. Fossil evidence of pre-Cambrian life has since been found, extending the history of life back for billions of years.
Chapter X examines whether patterns in the fossil record are better explained by common descent and branching evolution through natural selection, than by the individual creation of fixed species. Darwin expected species to change slowly, but not at the same rate – some organisms such as Lingula were unchanged since the earliest fossils. The pace of natural selection would depend on variability and change in the environment. This distanced his theory from Lamarckian laws of inevitable progress. It has been argued that this anticipated the punctuated equilibrium hypothesis, but other scholars have preferred to emphasise Darwin's commitment to gradualism. He cited Richard Owen's findings that the earliest members of a class were a few simple and generalised species with characteristics intermediate between modern forms, and were followed by increasingly diverse and specialised forms, matching the branching of common descent from an ancestor. Patterns of extinction matched his theory, with related groups of species having a continued existence until extinction, then not reappearing. Recently extinct species were more similar to living species than those from earlier eras, and as he had seen in South America, and William Clift had shown in Australia, fossils from recent geological periods resembled species still living in the same area.
Chapter XI deals with evidence from biogeography, starting with the observation that differences in flora and fauna from separate regions cannot be explained by environmental differences alone; South America, Africa, and Australia all have regions with similar climates at similar latitudes, but those regions have very different plants and animals. The species found in one area of a continent are more closely allied with species found in other regions of that same continent than to species found on other continents. Darwin noted that barriers to migration played an important role in the differences between the species of different regions. The coastal sea life of the Atlantic and Pacific sides of Central America had almost no species in common even though the Isthmus of Panama was only a few miles wide. His explanation was a combination of migration and descent with modification. He went on to say: "On this principle of inheritance with modification, we can understand how it is that sections of genera, whole genera, and even families are confined to the same areas, as is so commonly and notoriously the case." Darwin explained how a volcanic island formed a few hundred miles from a continent might be colonised by a few species from that continent. These species would become modified over time, but would still be related to species found on the continent, and Darwin observed that this was a common pattern. Darwin discussed ways that species could be dispersed across oceans to colonise islands, many of which he had investigated experimentally.
Chapter XII continues the discussion of biogeography. After a brief discussion of freshwater species, it returns to oceanic islands and their peculiarities; for example on some islands roles played by mammals on continents were played by other animals such as flightless birds or reptiles. The summary of both chapters says:
... I think all the grand leading facts of geographical distribution are explicable on the theory of migration (generally of the more dominant forms of life), together with subsequent modification and the multiplication of new forms. We can thus understand the high importance of barriers, whether of land or water, which separate our several zoological and botanical provinces. We can thus understand the localisation of sub-genera, genera, and families; and how it is that under different latitudes, for instance in South America, the inhabitants of the plains and mountains, of the forests, marshes, and deserts, are in so mysterious a manner linked together by affinity, and are likewise linked to the extinct beings which formerly inhabited the same continent ... On these same principles, we can understand, as I have endeavoured to show, why oceanic islands should have few inhabitants, but of these a great number should be endemic or peculiar; ...
Classification, morphology, embryology, rudimentary organs
Chapter XIII starts by observing that classification depends on species being grouped together in a multilevel system of groups and sub groups based on varying degrees of resemblance. After discussing classification issues, Darwin concludes:
All the foregoing rules and aids and difficulties in classification are explained, if I do not greatly deceive myself, on the view that the natural system is founded on descent with modification; that the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, and, in so far, all true classification is genealogical; that community of descent is the hidden bond which naturalists have been unconsciously seeking, ...
Darwin discusses morphology, including the importance of homologous structures. He says, "What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include the same bones, in the same relative positions?" He notes that animals of the same class often have extremely similar embryos. Darwin discusses rudimentary organs, such as the wings of flightless birds and the rudiments of pelvis and leg bones found in some snakes. He remarks that some rudimentary organs, such as teeth in baleen whales, are found only in embryonic stages.
The final chapter reviews points from earlier chapters, and Darwin concludes by hoping that his theory might produce revolutionary changes in many fields of natural history. Although he avoids the controversial topic of human origins in the rest of the book so as not to prejudice readers against his theory, here he ventures a cautious hint that psychology would be put on a new foundation and that "Light will be thrown on the origin of man". Darwin ends with a passage that became well known and much quoted:
It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us ... Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.
As discussed under religious attitudes, Darwin added the phrase "by the Creator" from the 1860 second edition onwards, so that the ultimate sentence began "There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one".