Introduction to The Zoology of the Beagle

By Gordon Chancellor

Zoology of the Beagle is the most lavishly produced of all Charles Darwin's publications. It contains descriptions of the then new or previously little-known fossil and living vertebrates which he collected during the voyage of the Beagle (1831-1836), some of which were crucial to his conversion to a belief in the transmutation of species. Darwin Online has the most complete set of the work online (links below).

During the voyage Darwin made observations about the variation and geographical distribution of some of the mammals and birds, especially those on oceanic islands, which suggested that perhaps species were not always specially created to suit the environments in which they are found today. Also, the fossil bones of the mammals Darwin unearthed in South America seemed not to be very old and although they appeared to be of extinct forms they clearly bore some relationship to the living mammals he encountered there. As he put it in 1859 on the very first page of the Origin of species:

When on board H.M.S. '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. (p. 1)

Throughout the voyage Darwin, at his father's expense, sent his specimens to his mentor John Henslow  in Cambridge who had taken responsibility for sorting and storing them ready for his return (Porter 1985). The interest generated by some of Darwin's discoveries and specimens was so great that Henslow arranged to have some of the fossils displayed to the public as early as 1833 (see Herbert 2005, p. 304). He also published some extracts from Darwin's letters on geology so that by the end of the voyage Darwin's fame had preceded him. By 1837 when Darwin was back in England preparing to publish his results from the voyage, the 'certain facts' combined in his mind with the opinions of the experts who were describing his specimens for Zoology. This combination convinced him that species were not specially created but were the result of descent with modification from ancestral species (Hodge 2010).

Even though few modern readers seem to be aware of it, Zoology is therefore of considerable historical importance. Its publication stretched from 1838 to 1843, during which time Darwin also published his Journal of researches (1839), his groundbreaking monograph on Coral reefs (1842) and numerous shorter publications. Zoology is perhaps, however, his greatest testament to the scientific opportunities presented by the voyage. Over the same five years Darwin also prepared his book on Volcanic islands, served as Secretary to the Geological Society and Vice President of the Entomological Society and was elected a Fellow of the Royal Society. He also got married, moved to Down House, had four children and was at times a rather sick man. Although few knew it at the time, these were also the years when Darwin started his great project to find a theory to explain 'that mystery of mysteries' – the origin of species. He discovered natural selection in the autumn of 1838 and as Zoology neared completion in 1842 he drafted a private 35-page 'Sketch' of his theory of evolution. We are fortunate that Darwin was able to continue his research for a further seventeen years and finally publish his masterpiece, the Origin of species in 1859.

The Scottish zoologist  William MacLeay deserves credit for persuading Darwin to produce Zoology  which was eventually published under Darwin's editorship and superintendence by Smith, Elder & Co (note 1). It was originally issued in 19 fascicles or numbers. These were generally bound together into the five parts when the whole had been completed, making a total of 632 pages and 166 plates. It was mainly funded by £1,000 - approximately equivalent to £100,000 today - from the Treasury, although Darwin and the publisher seem to have covered the additional costs of about £200, some of which was presumably recouped from sales. When originally published Zoology retailed for around £9, which would be roughly £900 Today.

A summary of the five parts of Zoology  is as follows: 1. Fossil Mammalia by the comparative anatomist Richard Owen (1804-1892) has a preface, geological introduction and short appendix on the geological ages of the fossils based on mollusc identifications by the conchologist George Sowerby, all by Darwin (1838-1840); 2. Mammalia by the zoologist George Waterhouse (1810-1888) has a geographical introduction and 'a notice of their habits and ranges' which consists of extensive quotes from Darwin's notes on the animals (1838-1839); 3. Birds by the ornithologist and artist John Gould (1804-1881) and the zoologist George Gray (1808-1872) has an anatomical appendix by Darwin's friend Thomas Eyton (1809-1880) and an eight-page index of the species described, plus a brief introduction and 'a notice of their habits and ranges' by Darwin (1838-1841); 4. Fish by naturalist and clergyman Leonard Jenyns (1800-1893) includes Darwin's notes on the colours of the fishes and occasionally on their habits (1840-1842). The terms for the colours Darwin used in the field were those given in 1821 by the artist Patrick Syme in his Nomenclature of colours (see Gage 1999); 5. Reptiles by the dentist and zoologist Thomas Bell (1792-1880) has several references to Darwin's notes, especially concerning the iguanas of the Galápagos, but oddly does not mention the famous tortoises (1842-1843, see note 2).

All of the plates can be viewed here:

It is easy to assume that Zoology is not really a Darwin publication because others are listed as the authors. Several scholarly reviews of Darwin's oeuvre (e.g. Ghiselin 2009) more or less ignore Zoology even though Darwin's additions to it are in fact considerable. The false impression that Darwin only edited Zoology is strengthened by the fact that his contribution of only about fifteen pages to Fossil Mammalia is minor compared to the almost one hundred pages of Owen's fine anatomical descriptions. The other four parts are however suffused with Darwin's presence and rely sometimes heavily on quotes from his notes. The formal taxonomic descriptions were written by the specialists whose names appear on the by-line, but there are many, sometimes lengthy, insertions from Darwin's scientific notes from the voyage. The bulk of the Birds volume is actually by Darwin who wrote approximately 110 pages of the text, while Gould only wrote some 35 pages, with Eyton's appendix adding perhaps 20 pages (adjusted for the much smaller print size).

For Darwin readers today the title of Zoology is also misleading for two other reasons. Firstly, because it includes the fossil mammals which today would be regarded as palaeontology rather than zoology. In Darwin's time the title would not have seemed odd because vertebrate palaeontologists usually regarded themselves as zoologists, whereas fossil mollusc or plant specialists, say, would have been more likely to identify themselves as palaeontologists. The second reason that the title is misleading is that it deals only with the Beagle's vertebrate zoology. As explained by Richard Freeman in his excellent general introduction, Darwin had hoped to include a summary of the invertebrates as part of Zoology, but this plan was never realized. There never was a single publication which dealt with Darwin's Beagle plants or invertebrates but there were many separate papers and monographs by specialists on his living and fossil plants, fungi and invertebrate collections. (See Beagle specimens.) The invertebrate publications ranged across protozoans, sponges, bryozoans, brachiopods, corals, molluscs, echinoderms, arthropods such as insects and spiders, plus Darwin's own on barnacles and flatworms (note 3).

The most expensive element of the publication of Zoology was the lithographs and engravings, many of which were coloured (for background on Victorian natural history art see Smith 2006). Freeman lists the names of the artists whose signatures appear on the published versions but a February 1838 letter from Darwin to Gould (CCD2, p. 72) shows that others were involved and they all deserve credit for their skills. The Bavarian draughtsman George Scharf drew and lithographed the 32 plates of fossil mammals; George Waterhouse and C.M. Curtis drew and/or lithographed the 32 coloured plates of mammals in life poses while the drawings of teeth were engraved by J. Swaine, and Smith, Elder and Co's accounts imply that [William?] Dickes did the colouring; John Gould's wife Elizabeth (née Coxon) drew and lithographed some 50 of the birds in life poses but Gabriel Bayfield coloured them for five pence (one forty-eighth of a pound) each; the animal artist  Waterhouse Hawkins's 29 lithographed plates of the fish and 21 of the reptiles and amphibians, although they are referred to as engravings on the title pages, have exceptional beauty and realism. Darwin Online has two copies of Zoology, one set of the original parts from The Charles Darwin Trust and another from the Natural History Museum (the former scans are higher resolution).

In Mammalia it is the lovely illustrations and Darwin's notes on the animals' habits and ranges which make the whole monograph so charming. Some of the notes, especially those concerning the variation of rats and mice on islands and on the Falklands fox hint at Darwin's interest in descent with modification. Darwin's authorial presence is even stronger in Birds, in which the paintings of the species in life and Darwin's detailed discussions of their ranges and habits are far more impressive than the formal descriptions of Gould, Gray and Eyton. Of course, it is Darwin's discussions pointing to evolution in the Galápagos finches, mockingbirds and various other species which so excite modern readers.

In Fish and Reptiles Hawkins's illustrations are not coloured and it is Darwin's scattered comments on the live creatures' habits which enliven Jenyns's and Bell's descriptions. In places Jenyns paraphrases Darwin, effectively removing his voice, but the direct quotes such as 'when cooked, was good eating', 'bites very severely', or 'when first taken made a croaking noise' clearly reveal Darwin's careful observations as a naturalist. Reptiles is the shortest of the five parts and contains only a smattering of direct quotes from Darwin, mainly about the animals' behaviour while alive, although Bell does refer his readers to Darwin's accounts of the two Galápagos iguanas in Journal of researches. 

First editions of Zoology (Freeman numbers F8 and F9) are very rare on the antiquarian book market but it was reprinted a few times in the late twentieth and early twenty-first centuries. A reduced facsimile of Part 5, which we have not seen, was published in Kansas by the Society for the Study of Amphibians and Reptiles in 1975 (F9a) with an introduction by Roberto Donoso-Barros. There is also a brief but useful foreword by Charles Fleming to the 1980 full facsimile published by Nova Pacifica (F9b). This publication includes an essay by Roger Chapman on the general background to the voyage of the Beagle and a table of the dates of publication of the separate fascicles. Another facsimile was published from Darwin's own copy by CIS in 1994 (F1914). A Spanish translation of Birds and Mammals was published in 1981 (F2053), Birds was reprinted again in 2016 (F2864) and the whole series was republished between 2016-2021 (F2865-F2872).

Darwin's complex transactions during the six years of publication of Zoology and also his many other activities, projects and illnesses over that period, are covered in volume 2 of the Darwin correspondence (CCD2). This contains portraits by T.H. Maguire of all the main authors except Jenyns whose photo appears in Pearn (2009, p. 110); there is also a Maguire portrait of John Gray in CCD4. We are not aware of any other studies of Zoology, with the exception of the short introductions to the five parts in the Pickering Masters Works of Charles Darwin edited by Paul Barrett and Richard Freeman (1986). Daniel Pauly has also provided a short introduction to the Fish at


As was normal in Darwin's time, not all his collections were eventually described by the specialists he entrusted them to - see for example Chancellor et al. (1988) on Thomas Bell's failure to publish Darwin's crustacea and various other arthropods. Compared to many collectors, however, Darwin was actually served very well, no doubt because of his status as the official naturalist to an important surveying expedition, but also because by 1836 his collections and correspondence had already established his high reputation among the scientific community. Today Darwin's collections receive extraordinary levels of interest (see Rosen and Darrell 2010) and individual specimens have almost the aura of sacred relics for scientists. The chance find of a Beagle specimen, such as a bird's egg, today triggers international media interest and can be a real boost for a cash-strapped museum.

The key source for understanding the role of Darwin's collections in Zoology is Richard Keynes's (2000) fine edition of Darwin's Zoological Diary, which was essentially the chronological record of the zoological observations that Darwin kept throughout the voyage (note 4). Keynes also includes his transcriptions of Darwin's 'primary' biological specimen lists which are two series each of three notebooks, one series for dry specimens and another series for specimens preserved in spirits. These are the source lists from which Darwin's servant Syms Covington prepared his 'secondary' lists, each list for a particular type of organism prepared for the specialist who would be dealing with it. The names used by Darwin for the lists are practical rather than strictly accurate, for example 'Plants' includes fungi, 'Shells' generally means molluscs, 'Animals' means mammals, 'Reptiles' includes amphibians. The other lists are titled 'Insects', 'Birds' and 'Crustacea'. Some groups of organisms (for example spiders) were not assigned to any list. Keynes's introduction to the biological lists is comprehensive and gives details of which institutions Darwin sent his specimens and lists to and of where they are now. Despite careful searches, although the Crustacea list should be in Oxford it has not yet been found.

Several of the secondary lists have been published because they include lengthy additional notes on the species by Darwin, in some cases to the point that the term 'list' no longer does them justice. The most important of these for present purposes are the lists for Animals, Reptiles, Fish and Birds. The Animal list (or Animal Notes) has been transcribed by Richard Keynes at It is from this list that Waterhouse quoted Darwin extensively, in at least one case – probably by mistake - without acknowledgement. The Reptile list, which differs somewhat from the others in that it is held by the Natural History Museum rather than by Cambridge University Library and is bound with Bell's own notes on the specimens, has been transcribed by Christine Chua at The Fish list has been published by Jacqueline McGlade in Pauly (2004) but it is incomplete and the full version is at (note 5). The Bird list, generally known as the Ornithology Notes, includes Darwin's first recorded doubts about 'the stability of species'. It was published by Nora Barlow (1963) and is at

The major desideratum from Keynes (2000) is a transcription of Darwin's third series of primary specimen lists which were dedicated to rocks and fossils, in other words to the geological specimens. This series of four notebooks – identical to the biological series – is held at CUL but awaits conservation before it can be digitized or transcribed (see photo of the notebooks in Places of wonder CUP 2009). It is in this series of notebooks that Darwin first listed the fossils described in Fossil Mammalia.

There is a transcription of the rock descriptions but it does not include the fossils and we hope to be able to provide a full transcription before too long (see note 6). It is important to note that although the rocks and fossils are listed in this separate series of notebooks, their Darwin numbers are in the same sequence as his dry biological specimens. This means that where there is a gap in the dry biological specimen list (for example nos. 12-79) it is because those numbers are in the geological list.

PART 1: Fossil Mammalia

Darwin collected fossil herbivorous mammal bones and teeth, either by excavation or purchase, from three areas of Argentina and Uruguay, as summarized in his geological introduction to Fossil Mammalia and also in South America (chapter 11). From north to south the areas were, firstly, a huge tract of land bordering the Rio Plata; secondly, northern Patagonia along the coast around Bahia Blanca (see Quattrochio et al. 2009); thirdly, southern Patagonia on the coast at Port St. Julian.

In the first two areas he collected a range of genera whereas in the third area he only collected one genus, albeit a very important one. Most of the fossils in the first two areas were xenarthans (edentates) including Dasypus (the living armadillo), the extinct Megatherium, Glossotherium, Glyptodon, Hoplophorus, Mylodon and Scelidotherium. There was also what Darwin assumed was a 'giant rodent' but is now known to be the notoungulate Toxodon, the ungulate horse Equus and the rodents Hydrochoerus and Ctenomys. At Port St. Julian he found the greater part of a skeleton of what he assumed was a 'giant llama' and which Owen named Macrauchenia but is now known to have been a litoptern. In his discussion Owen rejected the idea that it was a close relative of the guanaco and pointed out that it had some resemblance to elephants and may have had a trunk (note 7).

Some idea of the relative importance of the fossils found by Darwin is given by the length of Owen's descriptions and discussions of their affinities. Macrauchenia and Scelidotherium come in top, mainly because Darwin's specimens although headless are excellent, at 23 pages with 10 plates and 26 pages with eight plates respectively. Toxodon is also important, receiving 19 pages with five plates. Mylodon with 11 pages and three plates, Megatherium with nine pages and three plates and Glossotherium with six pages and one plate are also significant. Mastodon and Megalonyx received less attention mainly because Darwin's were relatively poor specimens and those genera had already been reported from South America. The genera of which Darwin only found teeth, that is the horse and the rodents, together take up four pages and a quarter of one plate but are actually very important from the evolutionary perspective. Perhaps surprisingly, Owen was the only one of the five Zoology authors who diagnosed his genera and species in English; all the others used Latin.

What 'much struck' Darwin about his fossils was how they were so obviously of kinds no longer known to be living in South America and yet were found embedded with recent kinds of marine shells (note 8). Darwin wondered what had caused them all to become extinct when there was no clear evidence of any major environmental change as he had been led to expect from his reading, especially of Lyell's Principles of geology (1830-1833). Also, fossils with features such as bony armour or clawed feet suggested that some living South American animals which also had those features, such as the armadillo and the sloth, somehow 'represented' the fossil forms. Darwin was aware from Lyell (1833, vol. 3, p. 144) and other sources that 'representative species' had been reported from other countries without much explanation so as early as 1832 he was alerted to the possible wider significance of his specimens. Even the small bones and teeth of the 'cavy' which he found at Monte Hermoso in 1832 seemed to Darwin related to the agoutis with which he had become so familiar in South America (in fact Owen thought them more closely related to the tuco-tuco discussed in Mammalia). Eldredge (2009, p. 37) argues that because there was such a strong geographical link between these fossil 'cavy' teeth and the animals still living they were as important to Darwin as the Galápagos mockingbirds were to be in 1835.

Darwin's horse teeth were obviously related to the living Old World species, so why had these South American horses died out and were unknown to the Incas until Pizarro reintroduced them from Spain in 1524? As we read in the Origin (p. 318), Darwin was 'filled with astonishment' by finding a horse tooth embedded with and certainly of the same age as the extinct Megatherium. This and the other clear cases of extinction must have played on Darwin's mind as he unearthed the 'giant llama' in January 1834, again without finding any evidence for any catastrophic change of environment. He was very uncertain what sort of animal it was and opted for 'Mastodon' at least until he drew up a note a year later in which he tried to explain its extinction. In this note of February 1835 Darwin considered the possibility that species have life spans, an idea rejected by Lyell, so marking his first decisive break on 'the birth and death of species' with his geological mentor. The note, in which Darwin also suggests that the link between the fossil and living cavies may be telling us something about the 'birth' of species, is at Around March 1837 Darwin returned to the issue of the extinction of the 'llama' in a famous series of jottings on pp. 129-130 in his Red Notebook, discussed in detail by Herbert (1980).

In Fossil Mammalia Darwin shied away from revealing his growing theoretical speculations:

Having now briefly described the principal circumstances in the geology of the three districts, to which I at first alluded, I will conclude, by observing, that the fossil mammalia of La Plata, Bahia Blanca, and Port St. Julian, must all have lived during a very modern period in the geological history of the world. It is not the proper place in this work to enter on any speculations, concerning the cause of the extinction of so many gigantic animals. I will only here add, that there is the strongest evidence against admitting the theory of a period of overwhelming violence, by which the inhabitants of the land could have been swept away, and destroyed. On the contrary every thing indicates a former state of tranquillity, during which various deposits were accumulating near the then existing coasts, in the same manner, as we may suppose others are at this day in progress. The only physical change, which we know has taken place, since the existence of these ancient mammalia, has been a small and gradual rising of the continent; but it is difficult to believe, that this alone could have so greatly modified the climate, as to have been the cause of the utter extermination of so many animals. (pp. 11-12; emphasis added)

Darwin did not, however, hesitate to 'go public' with his thoughts on representative species in one of his earliest papers, presented to the Geological Society on 3 May 1837, just days before Victoria became Queen, and at length in his Journal of researches in which he referred to the 'law of the succession of types' (1839, p. 210). Of course, he discussed the full evolutionary implications of this law twenty years later in the Origin (p. 338-341). Taken together Darwin's finds were a huge step forward in our knowledge of the extinction of the South American megafauna, although even today it is still unclear how much the extinction was caused by the arrival of humans some 12,000 years ago (see Viscaino et al. 2009 and note 9). Owen himself summarized his high regard for the importance of Darwin's material for what he called oryctology (that is, palaeontology) at the end of his introduction:

… the abundance and variety of the osseous remains of extinct Mammalia in South America are amply attested by the materials for the following descriptions, collected by one individual, whose sphere of observation was limited to a comparatively small part of South America; and the future traveller may fairly hope for similar success, if he bring to the search the same zeal and tact which distinguish the gentleman to whom Oryctological Science is indebted for such novel and valuable accessions. (pp. 14-15)

Henslow had originally sent Darwin's fossil mammals to Owen at the Royal College of Surgeons in London (see Rupke 2009) but many specimens were destroyed when the Museum was bombed by the Luftwaffe on 11 May 1941. Almost all the remainder were then transferred to the Natural History Museum, where they are currently being scanned for publication (see A full list of Darwin's surviving fossil mammals with their accession numbers is provided by Fernicola et al. (2009) and they have also been summarized by Lister (2018). We do not know the whereabouts of any 'secondary' list of Darwin's fossil mammals which may have been sent to Owen with the specimens. We do, however, know the text of Darwin's notes on the Toxodon as this was quoted in Richard Owen's biography of his father (Owen 1894, pp. 119-120 indicating that such a list may be among Owen's papers in the Natural History Museum (note 10).

PART 2: Mammalia

Darwin only found fossil mammals in La Plata and Patagonia, but he collected living mammals in almost every part of South America he visited, including the Galápagos, and from the Ocean in the case of the dolphin. As he explained in his geographical introduction to Mammalia, his specimens went initially to the Zoological Society of London. They were transferred to the Natural History Museum in 1855, where we presume most if not all of them still reside.

In the following summary, for convenience, we follow the species names and the taxonomic order used by Waterhouse, although in some cases we point out where these have been altered by subsequent research (note 11).

The 65 species of living mammals described in Zoology were bats (four genera, five species), dogs, cats, a grison and otters (together four genera, 10 species), a dolphin, ungulates (two species, a camel and a deer), rodents (11 genera, 42 species), a hare, armadillos (one genus, two species) and opossums (one genus, four species). Most of the species were described from Darwin's specimens but in about 15 cases the account in the Mammalia has no description by Waterhouse and is quoted more or less verbatim from Darwin's Animal Notes. Some of the genera such as cavies and armadillos were also described in Fossil Mammalia.

The bats comprised Desmodus d'orbignyi, a vampire bat which Darwin's servant snatched from the flanks of his horse in Coquimbo and two Phyllostoma species from Brazil. The first was from a lime-kiln, the second from the room into which it had flown where Darwin says he 'scarcely ever saw an animal so tenacious of life'. There was also a Vespertilio from Chiloe given him by 2nd Lieut. Sulivan and a Dysopes which Darwin collected in La Plata and at Valparaiso.

The carnivores comprised four dog species, three cats, a grison and two otters. Some of these animals were seriously difficult to catch! The first dog was Canis antarcticus (now Dusicyon australis) a dangerous, wolf-like creature from the Falklands described from Captain FitzRoy's three specimens. This species is especially interesting as it was the only one Darwin encountered before the Galápagos in which examples from one island were thought to differ from those on a neighbouring island, although on examining the specimens in London 'Mr Gray' disputed this. Darwin was certain that through human persecution 'before the paper is decayed on which this animal has been figured, it will be ranked amongst those species which have perished from the face of the earth'. Sadly, Darwin's prediction was correct as the species was the first canid known to have gone extinct in historical times, in 1876.

The second dog was the fox C. megallanicus (now Lycalopex culpaeus) based on a bitch from Chile. Darwin recorded in his Copiapo Notebook (pp. 132-133) that it was a 'very heavy animal'. The third species was Darwin's Zorro, the C. fulvipes (now L. fulvipes) which he killed with his geological hammer on Chiloe and which he described in his Journal (p. 352) as 'more curious or more scientific, but less wise than the generality of his brethren'. The fourth species was the fox C. azarae based on specimens caught by dogs at La Plata. Darwin described it as 'not uncommon' and noted that boys were employed in Chile to keep them from eating the grape crop.

There were three cats: Felis yagouaroundi, F. pajeros and F. domestica (now Herpailurus yagouaroundi, Leopardus colocola and F. catus respectively). Darwin's specimen of the jaguarundi was given him by 'an old Portuguese priest' who caught it near Rio. Darwin initially accepted and was probably flattered by William Martin's view that the tail of this specimen differed sufficiently from previous specimens to justify the new species F. darwinii. Having later seen the variation of more specimens Darwin now regretted that the new species was no longer valid. He had two specimens of F. pajeros, the pampas cat - named for its habit of living in reeds – one of which hissed at him, both from Patagonia. He caught a presumed feral cat some distance from Maldonado and noted that it was much larger than any domestic cat he had seen and 'extremely fierce'.  This animal featured decades later in Darwin's Variation under domestication of 1868 where he recalled that he "shot one which seemed perfectly wild; it was certainly examined by Mr. Waterhouse, who found nothing remarkable in it, excepting its great size". (vol. 1, p. 47)

The Gallictis vittata was a grison which Darwin caught at Maldonado where it was known as 'the thief' for its habit of stealing eggs. The two otters were Lutra platensis, Darwin's specimen (the skull of which appears on plate 35) being killed by fishermen off Maldonado, and L. chilensis from Chonos,  although he encountered the species along a huge extent of the west coast. It loved to inhabit the kelp beds and ate a variety of sea food such as fish and crabs.

Delphinus fitzroyi was the only cetacean in Zoology. It was a single specimen 'harpooned out of a large troop' off the coast of Patagonia and although only the head was preserved it was measured accurately by Darwin and expertly painted by Captain FitzRoy (see Zoology Notes pp. 148-149). The species is today regarded as a dusky dolphin (Lagenorhynchus obscurus), a species described a decade earlier by John Gray, the naturalist brother of George who helped finish Birds. It is a highly gregarious, inquisitive and acrobatic species, as conveyed by Darwin's note that it was 'sporting round' the Beagle, and is widespread in the southern hemisphere.

There were two species of ungulates, the guanaco Auchenia llama and the deer Cervus campestris. Apart from a bezoar stone – a concretion bought from an Indian and probably from the stomach of this animal -  there was no specimen of the Patagonian guanaco and the charming account in Mammalia is entirely from Darwin's Animal Notes, pp. 28-30. The deer, closely related to the Old World red deer, was described on the basis of some skins and antlers from La Plata and northern Patagonia. The description was supplemented by Darwin's notes which included the following concerning the animal's objectionable smell, also printed in his Journal (p. 56):

The most curious fact, with respect to this animal, is the overpoweringly strong and offensive odour which proceeds from the buck. It is quite indescribable: several times, whilst skinning the specimen, which is now mounted at the Zoological Museum, I was almost overcome by nausea. I tied up the skin in a silk pocket-handkerchief, and so carried it home: this handkerchief, after being well washed, I continually used, and it was, of course, as repeatedly washed; yet every time, when first unfolded, for a space of one year and seven months, I distinctly perceived the odour...Frequently, when passing at the distance of half a mile to leeward of a herd, I have perceived the whole air tainted with the effluvium. I believe the smell from the buck is most powerful at the period when its horns are perfect, or free from the hairy skin. When in this state the meat is, of course, quite uneatable; but the Spaniards assert, that if buried for some time in fresh earth, the taint is removed. (pp. 30-31)

Reflecting the fact that about a third of all living mammal species are rodents, the tally of 42 species of rodents described in Mammalia is by far the largest of any order. There were 28 species of Mus, three of Reithrodon, one of Myopotamus (the coypu), one of Ctenomys (the tuco-tuco), one of Poephagomys, one of Octodon, two of Abrocoma, one of Lagostomus (the biscacha), one of Kerodon, two of Cavia and one of Hydrochoerus (the world's largest rodent, the capybara). For comparison, there were 10 species of carnivores and all the other orders total 15 species. Waterhouse divided the rodents into the murids (Mus and Reithroden), the 'Hystrichina' which includes the Myopotamus of uncertain family, the next four genera (Ctenomys, Poephagomys, Octodon and Abrocoma) which he assigned to the octodontids, Lagostomus to the chinchillids and Kerodon, Cavia and Hydrochoerus to the cavids.

We cannot discuss Darwin's every delightful note on the murids he caught or was given, but we do draw attention to his notes on the differences he observed in the obviously introduced common rat M. decumanus and mouse M. musculus across South America and beyond. His comment on M. jacobiae, named for James Island in the Galápagos where he believed it was introduced about 150 years previously and where he caught his specimen, is especially suggestive: "… if a very peculiar climate, a volcanic soil, and strange food, can together produce a race, or strongly marked variety, there is every probability of such change having taken place in this case." (p. 35). Darwin raised the same possibility two pages later for M. insularis from Ascension Island, a new species which Waterhouse thought might turn out to be a distinctive variety of the common rat. The new species Darwin found only on Chatham Island in the Galápagos and now known to be endemic was the rice rat M. galapagoensis, now referred to the genus Aegialomys.Waterhouse named one of the Mus species, from Coquimbo, after Darwin. Perhaps this was some compensation to Darwin for not having his name attached to a jaguarundi. The three species of the new genus Reithrodon were from Patagonia, La Plata and Tierra del Fuego respectively.

At the end of his description of the murid species Waterhouse appended a five-page summary of 'general observations' in which he seemed to stress the separation of the South American forms from those of the Old World. He focussed on a detailed discussion of their teeth (illustrated on plates 33 and 34) and shows their distribution in the form of a list arranged like a map with the Galápagos in the top left and the Falklands in the bottom right.

The account of the coypu followed and was quoted entirely from Darwin who seemed impressed by the animals' unusual ability to prosper in both fresh and sea water over a vast area of southern South America. Of the octodontids, the tuco-tuco from La Plata is likewise entirely described by Darwin over almost three pages taken from his Journal. As discussed in our introduction to that book at it was an exceptionally important account as it included Darwin's discussion of the tuco-tuco's habit of living in burrows and yet possessing eyes which are inadequately protected, frequently causing the animal's blindness. In the second (1845) edition of the Journal Darwin extended the discussion by comparison with other subterranean species and in a clearly evolutionary passage rather mocked Lamarck's explanation for a similar case. The tuco-tuco became a cornerstone for Darwin's discussion of use and disuse in the Origin (p. 137). The Poephagomys and Octodon species were again entirely by Darwin although the latter quote was not attributed to him. The new genus Abrocoma was named for two species, the first from Aconcagua high in the Andes, the second from Valparaiso.

The description of Lagostomus, the biscacha, was also by Darwin and referred to his own discussion in the Journal. He rather coyly remarked in Latin that, like dogs, after mating biscachas remain attached. In the Origin (p. 349) he remarked that, as with the Rhea, there were two species of Lagostomus, one found on the plains east of the Andes, the other 'replacing' it high in the mountains to the west. He also believed that the biscacha and the agouti filled similar niches to those occupied by the Old World hares and rabbits. Darwin again provided the entire account of the four species. He remarked of Kerodon that in Patagonia he had seen children dressed in cloaks of its fur. Of the Cavia patagonica he wondered – as he repeated in the Journal on p. 81 - what could have removed them from the Port St. Julian area where Captain John Wood of HMS Sweepstakes reported them as numerous in 1670? Perhaps Darwin had this in mind when he mentioned the fossil cavy in his 'February 1835' manuscript? Finally, Darwin remarked of the old female capybara he shot at Monte Video that 'she weighed 98 pounds'. 

The lagomorphs, the group which includes rabbits and which Waterhouse called Leporinae, was represented in Darwin's collections by Lepus, the hare. Darwin's interesting discussion of the variation in L. megallanicus from what he calls 'these islands' is slightly marred by his forgetting to say that he meant the Falklands.

As explained in note 11, the fact that the rest of the species described are not lagomorphs was omitted and had to be corrected by the only serious erratum to Zoology. Darwin's account again sufficed for the two species of armadillo, the animal which he knew to be an edentate and therefore related to several of the extinct animals which Owen had described. As Darwin mentioned in his Journal all these animals were intriguingly confined to South America:  "It is a most interesting fact thus to discover, that more than one gigantic animal in former ages was protected by a coat of mail, very similar to the kind now found on the numerous species of armadillo, and exclusively confined to that South-American genus." (pp. 181-182). The final species described in Mammalia were the four species of the marsupial Didelphis. D. azarae was barely mentioned but D. crassicaudata from La Plata, D. elegans from Valparaisoand D. brachyura from La Plata were all fully described by Waterhouse and beautifully illustrated. Darwin's brief but charming note on the last species is worth quoting, and it marks the end of Mammalia:

Was caught by some boys digging in a garden. Its intestines were full of the remains of insects, chiefly ants and others of the Hemipterous order.  (p. 97)

PART 3: Birds

Birds is the largest part of Zoology and as we have pointed out it contains the greatest proportion of accounts in the first person by Darwin himself. During the voyage Darwin collected approximately 500 bird specimens and made a significant contribution to South American ornithology, especially for the Galápagos. Birds also complemented the almost simultaneous publication on South American ornithology of the great French naturalist, Alcide d'Orbigny, whom Darwin often quoted in French in Zoology. It is unfortunate that the two men never met, although they collaborated on geology in the mid-1840s (see Legre-Zaidline 2004 and CCD3). Somewhat oddly, one of the lizards described in Reptiles (Proctotretis signifier) was collected by d'Orbigny and had nothing to do with the Beagle voyage.

Although during the voyage Darwin saw himself as a geologist rather than an ornithologist, he made valiant efforts to record as much information as he could about the birds he encountered (see Steinheimer 2004). While in the Galápagos in September 1835 he made the famous jotting in his Galapagos Notebook (p. 30b) about the tameness of the 'Thenca' which was 'certainly' a type of American mockingbird, a genus he already knew well. This was immediately followed by the question whether a botanist would also recognize America in the flora, proving that  Darwin was far more confident of his bird knowledge than of his botany.

The notebook entry indicates that Darwin either saw the birds as mainland species which had flown to the islands or had been derived from mainland species, in which case they would challenge the views of Lyell and others that species were created to suit particular environments. We also know that while in the Galápagos Darwin realized that the mockingbirds varied between the islands (see the quote from Birds, p. 64 below) and in the last months of the voyage, while compiling his Ornithology Notes, he made the famous entry about the Galápagos mockingbirds possibly providing evidence that 'would undermine the stability of species'.

On returning to England Darwin was delighted to secure John Gould's expert services to identify his bird specimens. As Taxidermist at the Zoological Society, Gould was the best person to deal with the Beagle birds which Darwin deposited there in January 1837. Darwin wanted especially to know whether the mockingbirds were new species or merely varieties of the already well-known mainland species (for discussions see Chancellor and van Wyhe 2009; Grant and Estes 2009; Hodge 2010; Kohn 2009). A few months later, Gould who was five years older than Darwin and already a highly respected ornithologist, confirmed that Darwin's mockingbirds were indeed among the approximately 22 new species he had collected from the Galápagos. This verdict convinced Darwin that species were indeed mutable, although he confined this theoretical breakthrough to his private notebooks. In November 1839, when the relevant fascicle of Birds appeared, Darwin restricted expression of his new beliefs to the following guarded statement:

It will be seen, that the three last species of the genus Mimus, were procured from the Galapagos Archipelago; and as there is a fact, connected with their geographical distribution, which appears to me of the highest interest, I have had these three figured. There are five large islands in this Archipelago, and several smaller ones. I fortunately happened to observe, that the specimens which I collected in the two first islands we visited, differed from each other, and this made me pay particular attention to their collection. I found that all in Charles Island belonged to M. trifasciatus; all in Albemarle Island to M. parvulus, and all in Chatham and James's Islands to M. melanotus. …The fact, that islands in sight of each other, should thus possess peculiar species, would be scarcely credible, if it were not supported by some others of an analogous nature, which I have mentioned in my Journal of the Voyage of the Beagle. I may observe, that as some naturalists may be inclined to attribute these differences to local varieties; that if birds so different as M. trifasciatus, and M. parvulus, can be considered as varieties of one species, then the experience of all the best ornithologists must be given up, and whole genera must be blended into one species. I cannot myself doubt that M. trifasciatus, and M. parvulus are as distinct species as any that can be named in one restricted genus. (pp. 63-64)

Exactly 20 years later Darwin stressed the momentous importance of the mockingbirds and the American character of the birds of the Galápagos in the Origin of species (pp. 398-402).

Gould also decided that all the small brown and black birds collected by Darwin and others from the Beagle on the Galápagos were 13 new species of finch (see Sulloway 1982 and Grant and Estes 2009). This was a complete surprise for Darwin, who had not even realized that all these birds were closely related. Ironically, after publication of the Origin, Gould did his best to resist Darwin's theories of natural and sexual selection at least in as far as they affected his portrayal of birds. As Queen Victoria's favourite ornithologist, Gould's wealthy subscribers expected him to portray birds as creatures created for their beauty, rather than as products manufactured by a blind natural process of trial and error (Smith 2009). One wonders what Gould thought of Darwin's abundant examples in the Descent of Man of spectacular bird plumage as weapons in the fight for reproductive success.

Once Darwin had deposited his specimens at the Zoological Society Gould lost no time in writing his formal descriptions (and Latin diagnoses) of Darwin's birds and in sketching them for his wife Elizabeth to draw on stone for lithographing and colouring. Before the Goulds had completed their work for Darwin in May 1838 they set off to study the birds of Australia, leaving George Gray of the British Museum to re-work Gould's manuscripts and help Darwin complete the last details of Birds. Gray made sure the synonymies were accurate and added a page of 'remarks and corrections' to the start of the volume, mainly listing 'new' combinations of taxon names with his own name attached. Although Darwin said he was indebted to Gray for these corrigenda, in 1842 he expressed his annoyance with Gray's egoism in a letter to Jenyns (see CCD2, p. 317). Another unfortunate consequence of the Goulds' departure was that Gray reassigned the genera of several species after the plates had already been engraved, presumably by Elizabeth Gould. Sadly, she died aged 37 in 1841, the year Birds was completed. She would have been amazed to see her work reproduced – often credited to her husband - on the covers of several books about Darwin (e.g. Ruse 2013).

There are entries in Birds for over 100 genera including 269 species, although many of these are simply notices by Darwin of where he obtained his specimens. All the new species have a formal description and most if not all of them have a coloured illustration, some of which are rather beautiful – for example the Tanagra darwinii (plate 34), a species based on one specimen which Gray said was merely the female of Aglaia striata, therefore invalidating Gould's new name after the plate had been engraved. Sometimes an anatomical description is also added in the appendix.

In many cases Darwin provided an engaging discussion of the birds' habits, behaviour and geographical range, often complementing the accounts in his Journal of researches. This is the case, for example, for the condor, several vultures such as the caracara, the various small birds he called 'Myothera' in his Beagle notes (note 12), the brood parasite Molothrus, the scissor-beak Rhychops and for many other species, especially the new ones. An interesting case is the great kiskadee (Birds, p. 43) which features in the Origin as an example of a species changing its habits: "I have often watched a tyrant flycatcher (Saurophagus sulphuratus) in South America, hovering over one spot and then proceeding to another, like a kestrel, and at other times standing stationary on the margin of water, and then dashing like a kingfisher at a fish." (p. 183)

It is almost impossible in the space we have here to convey the depth and perceptiveness of Darwin's descriptions of all these birds. Even for species well-known before the Beagle voyage, his remains the classic account of the birds' courtship, nest-building, egg-laying, flying, singing, feeding, in fact of all aspects of their behaviour, including their interactions with humans.

It is natural today that we read with the greatest interest Darwin's accounts of the birds which contributed so much to his conviction that 'species are not immutable', especially Darwin's rhea, Darwin's finches (note 13) and the Galápagos mockingbirds. It is also worth noting that there are some brief comments by Darwin on the relationships of other species, such as the group of genera including the spinetail Synallaxis (see p. 75), which make evolutionary sense for today's reader. Darwin's delightful accounts in Birds of all these species should, however, be read in their entirety and not just from a 'presentist' perspective.

PART 4: Fish

John Henslow, Darwin's tireless supporter in Cambridge throughout the Beagle voyage, processed all his consignments of specimens. Darwin sent the fishes to Henslow's brother-in-law the Rev. Leonard Jenyns at the Cambridge Philosophical Society for identification (see Pauly's introduction on Darwin Online and our notes 1 and 5). As can been seen from several letters to Jenyns in 1837, Darwin was delighted to have secured his friend's services (CCD2). Darwin was probably also rather pleased if he knew that Jenyns had been offered the position of naturalist on the Beagle before him but had turned it down.

Darwin's specimens had been mainly collected on the coasts of South America, but also at other locations including the Cape Verdes, Falklands, Galápagos, Tahiti, New Zealand, southwest Australia and the Keeling Islands. They had originally been preserved in spirits but as Jenyns explained in his thoughtful introduction 'a large proportion' were in too poor a condition for him to study. This was a grievous loss especially since the spoilt specimens were mainly from the most poorly-studied areas. Nevertheless, there were 137 species of which Hawkins illustrated 51. Jenyns believed at least half were new to science, with seven new genera. All the Galápagos species were new as were about half of those from South America, but fewer from the rest of the Pacific and Indian Oceans. Most of the specimens remain in spirits to this day, although some have been dried and mounted. An example is a globally-distributed jack species, the rainbow runner Seriola bipinnulatus, specimen no. 1423 from Keeling described in Fish, pp. 72-73 and which is photographed in Preece alongside Jenyns's notes on the species (2009, p. 111).

Following his introduction, Jenyns provided a detailed list of the described species which also stated where Darwin encountered them. Reflecting the taxonomic distribution of the world's 28,000 species of living fishes, almost all were bony fishes. Of these some 82 species were spiny-finned acanthopterygians (41 new; pp. 1-109), 39 soft-finned malacopterygians, including a flying fish and an anchovy (25 new – the highest proportion; pp. 110-146), 3 tuft-gilled lophobranchians (all new; pp. 147-149), 12 covered-gill plectognathians (5 new; pp. 150-158) and 1 new jawless and boneless cyclostome (hagfish; p. 150). There are no descriptions of cartilaginous fishes although Darwin certainly caught sharks and rays during the voyage (for example specimen 359). Interestingly, most of the 23 fresh-water malacopterygians – especially the cyprinids and salmonids - were new, as Cuvier would have predicted on the basis that such waters would be less well explored, but one suspects also reflecting Darwin's 'strong taste for angling' (see Pauly, pp. 6-7). Finally, there is an appendix of new descriptions and taxonomic revisions omitted from the main text for various reasons, plus a short errata list and a two-page index.

We have already quoted some of Darwin's contributions to the text, which although relatively minor in Fish added colour to a rather monochrome volume. Other examples were the grouper Plectropoma patagonica which '…when caught, vomited up small fish and a Pulimnus. Was tough for eating but good' (p. 12); the redlip blennie Salarius atlanticus which '…bites very severely, having driven its teeth through the finger of one of the officers in the ship's company [actually 2nd Lt Sulivan]. Its two very long sharp canine teeth at the back of the lower jaw are well calculated to inflict such a wound.' (p. 87); the hagfish Myxine australis which was '…very vivacious, and retained its life for a long time; that it had great powers of twisting itself, and could swim tail first. When irritated, it struck at any object with its teeth; and by protruding them, in its manner, much resembled an adder striking with its fangs. It vomited up a Sipunculus when caught.' (p. 159).

Other remarkable species were the wrasse Cheilio ramosus which was given to Darwin by the surgeon of a whaling-ship who believed it had been caught in Japan (p. 102); the fine-flounder Hippoglossus kingii described from a coloured drawing made by Midshipman Phillip King for Captain FitzRoy (p. 138, plate 26) and, finally, the burrfish Diodon antennatus which Darwin featured in the Journal of researches (pp. 13-14). He caught this fish in February 1832 and reported that it could suck air into its body and inflate itself so that it floated and swam upside-down! What impressed Darwin most was "that it emitted from the skin of its belly, when handled, a most beautiful carmine red and fibrous secretion, which permanently stained ivory and paper" (p. 151 and Pauly 2004, pp. 22-24).

PART 5: Reptiles

Darwin sent his reptiles and amphibians to the Natural History Department of the British Museum where Thomas Bell, Professor of Zoology at King's College London, agreed to deal with them (note 14). The snakes were sent to the French herpetologist Gabriel Bibron on the understanding that he would describe them, although in the event he was unable to do so, which was a great loss to science as Darwin had collected many specimens (see note 2).

Bell described 45 species in Reptiles, of which 'nearly thirty' were new. There were 24 species of true reptiles described on the first 30 pages and 15 plates (for some reason the numbers and therefore positions of plates 13 and 14 were in the wrong order). These were followed by 21 species of amphibians on the remaining 20 pages and six plates. All the plates were 'drawn from Nature' by Benjamin Waterhouse Hawkins and lithographed on stone using C[harles]. Hullmandel's Patent.

In his introduction Bell was especially interested in the toad Bofo chilensis which Darwin had found on both the east and west coasts of South America. He stressed that such a wide distribution was very rare in amphibians, which are normally prevented by their limited ability to cross mountain ranges or salt water. He was also intrigued by the opposite case of Proctotretus as an equally rare example of a reptile with many species (at least 14) which seemed to be confined to a limited area, namely the coasts of Chile and Argentina. Some of Darwin's frogs and toads ('anourous' amphibians, meaning tail-less) also highlighted Bell's dissatisfaction with their then current classification. He said that some of the species challenged the distinctions between them and used the quinarian term 'osculant' (see note 1) for the way in which two frog families seemed so close as to contact  each other via these intermediate species:

The close approximation of the Raniform and Hyliform groups of the Anourous Amphibia is strikingly illustrated by several new forms obtained by Mr. Darwin, which are so perfectly osculant between the two families, that it is difficult to assign them a decided location. (p. vi)

The reptiles were treated in the following order: Tropidurids (Proctotretus, Diplolaemus, Amblyrhynchus, Leiocephalus, Centrura); Geckotids (Gymnodactylus, Naultinus); Lacertids (Ameiva); Zonurids (Gerrhosaurus) and Scincids (Cyclodus).

Bell discussed the variation in Proctotretus species in great detail and for four species he illustrated this by figuring two forms. In his Santiago Notebook Darwin had himself commented on this variation in the following note in ink on 18 September 1834 made at Yaquil on his way to Valparaiso (he had been unwell for several days, probably from drinking some bad wine): Lizard above blackish tail very basking on stones in sun half of body brilliant greenish spot blue scales. — anterior greenish. — colors shade down till some individuals are simply brownish black with transverse black bars, & the [formostscale in head colored white (p. 37)

This was specimen in spirits 1063 and was identified by Bell as P. tenuis in Reptiles, pp. 7-8, plate 3. The notebook entry is highly significant as it marks the first date when Darwin started to include reflections as well as observations in his field notebooks (Chancellor and van Wyhe 2009, p. 372).

Bell moved on to describe two species of Diplolaemus, both from Port Desire, the first of which he named after Darwin, the second which had been supplied by Captain King from the Beagle's first voyage, after Gabriel Bibron . The next two genera of reptiles were among "the numerous interesting novelties obtained by Mr. Darwin in the Galapagos." (p. 25). Firstly, Bell used Darwin's specimen of the land iguana Amblyrhynchus demarlii as the model for its first illustration on plate 12. Secondly, he used Darwin's specimen of the marine iguana A. cristatus to correct the description he had made in 1825 on the basis of a poor specimen procured in Mexico. He then referred the reader to Darwin's 'interesting account' in the Journal of researches (pp. 466-472) of the creature's unique habits (note 15). Finally, Bell described the new species Leiocephalus grayii, 'one of the most beautiful in the whole order of Saurians' (p. 24), nowadays known as the Floreana lava lizard, Microlophus grayii.

Bell then described Darwin's specimen of Centrura flagellifer which had been in spirits for too long to show its full colours. He forgot to say where it came from and we have not been able to find the locality in the Reptile List, although specimens 1022, 1063 and 1171-1173 seem from the colour descriptions to be candidates and the species appears in the list at the bottom of p. 33. The published British Museum Catalogue gives the locality as Chili on p.226 (see

The gecko Gymnodactylus gaudichaudii from Port Desirefollowed, and for this species Bell quoted Darwin regarding its coloration:

Centre of the back yellowish brown, sometimes with a strong tinge of dark green; sides clouded with blackish brown; in very great numbers under stones; makes a grating noise when taken hold of; after death loses its darker colours. A specimen being kept for some days in a tin box, changed colour into an uniform grey, without the black cloudings. I thought I noticed some change after catching and bringing home these animals, but could observe no instantaneous change. (p. 27)

Finally, there was Naultinus grayii from New Zealand, Ameiva longicauda from Bahia Blanca, Gerrhosaurus sepiformis from the Cape of Good Hope and Cyclodes casuarinae from Tasmania.

The amphibians were treated in the following order: Ranids (Rana, Limnocharis, Cystignathus, Borborocoetes, Pleurodema, Leiuperus, Pyxicephalus, Alsodes, Litoria, Batrachyla, Hylorina, Hyla) and Bufonids (Rhinoderma, Phryniscus, Uperodon). Bufo chilensis was discussed under Rhinoderma.

Most of Darwin's specimens were from South America, but there was one from King George's Sound in Australia, one from Mauritius and one from the Cape of Good Hope. Bell's use of Darwin's notes in his descriptions was generally confined to clarification of the animals' colours when alive, as these were usually faded by the preserving spirits, but he made more extensive use in a few cases. Darwin had made the remarkable observation that Leiuperus salarius defied the general rule mentioned above that amphibians cannot tolerate salt water in that "it is bred in and inhabits water far too salt to drink." (p. 40) and he had written that Bufo chilensis is:

…exceedingly abundant all over the treeless damp mountains of granite, crawling about, and eating during the daytime, and making a noise similar to that which is commonly used in England to quicken horses. Many of them on being touched close their eyes, arch their back, and draw up their legs (as if the spinal marrow was divided), probably as an artifice. They are remarkable from their curious manner of running like the Natter Jack of England; they scarcely ever jump, neither do they crawl like a toad, but run very quickly. Their bright colours give them a very strange appearance. They abound at an elevation of 500 to 2500 feet. (p. 49)

Darwin had also thrown a Phryniscus nigricans into a pool of fresh-water, but found that it could hardly swim and if unassisted would soon have drowned. (p. 50)

Finally, and perhaps fittingly, the last species we have selected for comment is Rhinoderma darwinii which Bibron had named on the basis of Darwin's specimens before Zoology  appeared. This species has the distinction of having been the only vertebrate to have been first drawn by Darwin himself. On 3 December 1834 in his Port Desire Notebook (p. 91) he described and sketched this 'very pretty' frog and he recorded in his Zoology Notes that 'this species is excessively common in the forest of Valdivia' but that, sadly, 'all die soon in confinement.' (pp. 256-257)


1 William Sharp MacLeay (1792-1865) was a zoologist and diplomat who emigrated to Australia in 1839 (see Companion, p. 325). In a letter to Leonard Jenyns of 10 April 1837 Darwin explained that MacLeay had urged him to publish Zoology  'because it keeps together a series of observations made respecting animals inhabiting the same part of the world' (CCD2, pp. 15-17). "In his Horae entomologicae (MacLeay 1819-1821), he propounded the Quinary System of classification in which the five main animal groups are represented by 'circles of affinity'. To represent the continuity of forms the circles are arranged in a larger circle in which each is contiguous or 'inosculant' with two others." (CCD1, p. 282, note 8). Judging from a February 1832 mention of MacLeay in Darwin's first Beagle field notebook, he had probably been familiar with MacLeay's influential ideas since his student days. He referred to them frequently in his notes and seems to have been spurred on to find a better explanation for some of the affinities MacLeay was highlighting (see Ospovat 1981 and Winsor 2013 for detailed discussion). In the late 1830s Richard Owen, George Waterhouse and Thomas Bell followed at least partly the 'quinarian system'.

2 In the Reptiles (i.e. Zoology Part 3) there are some thirty pages on true reptiles and twenty pages on amphibians, but in Darwin's day the term 'reptiles' often included 'amphibians'. To avoid confusion between the title Reptiles and the today's meaning of 'reptiles' - which excludes amphibians – we use the term 'true reptiles'. Reptiles is incomplete, as the snakes (which in Darwin's day were often called ophidians) were reserved to be described by Gabriel Bibron as part of his monograph on that group. This is doubly unfortunate because some of Darwin's snakes (e.g. Bothrops alternatus) appear to have influenced his thinking on species (see Eldredge 2009). Some (especially Dromiscus biserialis from the Galápagos) were described by Albert Günther, while Bibron (with André Duméril) did describe some legless lizards and a frog. Unfortunately, Bibron died in 1848 so never completed his work. Bell did not mention the Galápagos tortoises even though Darwin himself donated a young one from James Island to the Natural History Museum (BMNH 1837.8.13.1).

As far as we are aware there were only a few of Darwin's other vertebrates which were described 'outside' Zoology. In 1837 William Martin also published on some of Darwin's cats, foxes and an armadillo and James Reid published a note on an opossum and a biscacha. See full list at

3 A partial list of the relevant publications appeared as an appendix to Paul Barrett's Collected papers of Charles Darwin in 1977 (supplemented in CCD 1, p. 548) and a complete list of these publications is at

4 As Porter (1985) pointed out, the Zoological Diary includes Darwin's notes on plants. The Geological Diary also includes several passages which might today be considered as ecology rather than geology (see our introduction to the Geological Diary).

5 There are two other lists for the extant fish specimens, those at the Cambridge Zoological Museum and those at the Natural History Museum, where the majority were transferred in 1917. Both have been published by Daniel Pauly (2004). Jenyns's own notes on Darwin's fishes are held at the Cambridge Zoological Museum and excellent photographs of the specimens and notes appear in Richard Preece's account in Pearn (2009, pp. 40, 90-91 and 110-112 respectively).

6 Nearly all Darwin's rock specimens are now held at the Sedgwick Museum where Alfred Harker prepared a separate specimen list which is now available at (see also Lyall Anderson in Pearn 2009, p. 68). [Since transcribed by Christine Chua]

7 We here generally use the Owen's Latin names of the various genera to make reference easy although in some cases the names may have changed. Buckland (1837, p. 603) published a short note on Darwin's fossils in his Geology and Mineralogy (see Porter 1985).

8 Herbert (1980, p. 112) has photos of the right forefoot of Darwin's Macrauchenia specimen. In an erratum on p. 56 Owen pointed out that this forefoot had been misdescribed on pp. 35-36 as from the left rather than the right hand side of the animal.

Gardiner (2004, p. 19) has photos of the horse's teeth. See also Allmon (2015), Brinkmann (2009), Herbert and Norman (2009) and Norman (2009). Van Wyhe (2008-9) has photos of the fossil horse tooth, the Macrauchenia forefoot and the Toxodon skull. Bartolomé and Glickman (2007) and Lister (2018) also have many fine photos of a wide range of the fossil and living animals described in Zoology.

9 Today it is recognized that several factors may be involved in the megafauna extinction. Firstly, the 'great American biotic interchange (GABI)' whereby many North and South American forms which had evolved separately crossed over when the Isthmus of Panama started to form a land bridge about 2.7Ma, thus greatly altering the fauna of each continent. This major zoogeographic event was first discussed by Alfred Russel Wallace in 1876. Secondly, the arrival in the Americas of Palaeolithic hunter-gatherer people from Asia across the Bering Straits (Beringia) when sea level was low during the Ice Age. People arrived in Patagonia at least 12,000 years ago and almost certainly hunted the large mammals or damaged their environment, a process which probably accelerated as technology improved, such as the invention of the bow and arrow. Some of the large mammals, such as the Mylodon, were still living only a few thousand years ago and possibly into historical times, as appears to have happened in isolated areas of Europe with the woolly mammoth. Thirdly, the more direct effects of climate change since the last glacial maximum, on a similar timescale, cannot be disregarded, although any such direct effect should have caused mass extinction across the globe. For further discussion see Defler (2018).

10 We have deduced from various secondary sources that some of the Punta Alta fossils were numbered by Darwin 727-744, 807-808 and 821-822 and the fossils from Port St. Julian include numbers 1406, 1719 and 1796.

11 An illustration of the importance of errata (i.e. corrections added after the main body of the text has been printed) is the note added opposite p. i, just before Darwin's introduction. By some oversight the name of the order to which the armadillo belongs (i.e. edentata) had been omitted above the name Dasypus on p. 92. Also, the order to which the opossum belongs (i.e. marsupalia) had been omitted above the name Didelphis on p. 93. Without the errata these omissions would have given the completely false impression that Waterhouse was classifying the armadillo and the opossum as lagomorphs – the order which includes Lepus the hare. Today, marsupials - which retain their young in a pouch - are classified as a separate infraclass from all the other mammals described by Waterhouse which are placentals! As Freeman observes in his introduction, the editing was excellent and with the possible exception of the mistake by Owen mentioned in note 8 this is the only significant error in Zoology.

12 We discuss the importance of Darwin's 'Myothera' in our introduction to the Journal of researches.

13 John van Wyhe (2012) has demonstrated where the myth that 'Darwin's finches' were the most important evidence for evolution gathered or used by Darwin originates from. They featured strongly in the second (1845) edition of the Journal of researches, but they were not even mentioned in the Origin of species (see also Davis 2013).

14 Richard Owen became Superintendent of the Natural History Department of the British Museum in 1856. He was the driving force behind the opening in 1881 of the what is now the Natural History Museum in South Kensington, of which he was the first Director. The Museum was designed by Alfred Waterhouse (1830-1905), no relation to George Waterhouse.

15 For some reason which we have not discovered, in the Zoology Bell always misspelled the genus name Amblyrhynchus by omitting the first 'h'. This is rather strange because he created the name himself in the Zoological Journal in 1825 and there used the first 'h' and he certainly knew his Greek.


Allmon, Warren D. 2015. Darwin and palaeontology: a re-evaluation of his interpretation of the fossil record. Historical Biology 28: 680-706.

Anderson, Lyall 2009. The Sedgwick Museum: Darwin's geological specimens. Pp. 67-71 In Pearn, Alison. A voyage round the world. CUP

Barlow, Nora 1963. Darwin's ornithological notes. Bulletin of the British Museum (Natural History) Historical Series 2: 201-278.

Bartolomé, Gerardo and Glickman, Barry 2007. Patagonia con los oyos de Darwin. Zagier and Urruty Publications.

Brinkmann, Paul D. 2009. Charles Darwin's Beagle voyage, fossil vertebrate succession, and the "gradual birth and death of species". JHB 43: 363-399.

Chancellor, Gordon, DiMauro, Angelo, Ingle, Ray and King, Gillian. 1988: Charles Darwin's Beagle collections in the Oxford University Museum. Archives of Natural History 15: 197-231. Text PDF F1838

Chancellor, Gordon and van Wyhe, John 2009. Charles Darwin's notebooks from the voyage of the 'Beagle'. CUP.

Davis, Frederick Rowe 2013. Darwin and the finches. In Ruse, Michael (ed.): The Cambridge encyclopedia of Darwin and evolutionary thought: 368-374. CUP.

Defler, T. 2018. History of terrestrial mammals in South America. Springer.

D'Orbigny, Alcide 1835-1847. Voyage dans l'Amérique Meridionale.

Eldredge, Niles. 2009. Experimenting with transmutation: Darwin, the Beagle and evolution. Evolution: Education and Outreach 2: 35-54.

Fernicola, Juan Carlos, Vizcaíno, Sergio F. and De Iuliis, Gerardo. 2009. Historical review of the fossil mammals collected by Charles Darwin in South America during his travels on board the HMS Beagle. Revista de la Asociación Geológica Argentina 64 (1): 147-159.

Gage, John 1999. Colour and meaning. Thames and Hudson.

Gardiner, Brian 2004. Darwin and South American fossils. The Linnean 20: 16-22.

Ghiselin, Michael 2009. Darwin: a reader's guide. Occasional papers of the Californian Academy of Science. No. 55. Text PDF A622

Grant, K. Thalia and Estes, Gregory B. 2009. Darwin in Galápagos. Princeton UP.

Herbert, Sandra 1980. The red notebook of Charles Darwin. Bulletin of the British Museum (Natural History), Historical Series 7: 1-164. Text   PDF F1583e

Herbert, Sandra 2005. Charles Darwin, geologist. Cornell UP.

Herbert, Sandra and Norman, D. 2009. Darwin's geology and perspective on the fossil record. In Ruse, Michael and Richards, Robert (eds). The Cambridge companion to the 'Origin of Species': 129-152.

Hodge, Jonathan 2010. Darwin, the Galápagos and his changing thoughts about species origins: 1835-1837. Proceedings of the California Academy of Sciences 61, supplement II, no. 7:89-106.

Keynes, Richard 2000. Charles Darwin's zoology notes and specimen lists from H.M.S. Beagle. CUP.

Kohn, David 2009. Silent species: South American Beagle collections and the origins of Darwin's species theory. In Pearn, A. M. (ed.) A voyage round the world: 95-100. CUP.

Legre-Zaidline, Francoise 2004. Alcide Dessalines d'Orbigny (1802-1857).

Lister, Adrian 2018. Darwin's fossils. Natural History Museum.

Norman, David 2009. South American fossils: Darwin's palaeontology. In Pearn, Alison M. (ed.) A voyage round the world: 62-65. CUP.

Ospovat, Dov 1981. The development of Darwin's theory. CUP.

Pauly, Daniel 2004. Darwin's Fishes: an encyclopedia of ichthyology, ecology and evolution. CUP.

Pearn, Alison (ed.) 2009. A voyage around the world. CUP.

Porter, Duncan M. 1985. The Beagle collector and his collections. in D. Kohn (ed.) The Darwinian Heritage: 973-1019. Princeton UP.

Preece, Richard C. 2009. Leonard Jenyns and fish identification. Pp. 110-112 In Pearn, A, A voyage round the world. CUP.

Quattrocchio, M.E., Deschamps, C.M., Zavala, C.A., Grill, C.S. and Borromei, A.M. 2009. Geology of the area of Bahía Blanca, Darwin's view and the present knowledge: a story of 10 million years. Revista de la Asociación Geológica Argentina 64 (1): 137-146.

Rosen, Brian R. and Darrell, Jill G. 2011.  A generalised historical trajectory for Charles Darwin's specimen collections, with a case study of his Coral Reef Specimen List in the Natural History Museum, London. In Stoppa, F. & Veraldi, R. eds, Darwin tra scienza, storia e società: 150° anniversario della publicazione di Origine delle Specie. Rome: Edizionei Universitarie Romane.

Rupke, Nicolaas 2009. Richard Owen, evolution before Darwin. Chicago UP.

Ruse, Michael (ed.). The Cambridge encyclopedia of Darwin and evolutionary thought. CUP.

Smith, Jonathan 2006. Charles Darwin and Victorian visual culture. CUP.

Steinheimer, F. D. 2004. Charles Darwin's bird collection and ornithological knowledge during the voyage of H.M.S. Beagle, 1831-1836. Journal of Ornithology 145(4): 300-320, (appendix [pp. 1-40]).

Sulloway, Frank J. 1982. Darwin and his finches: the evolution of a legend. JHB 15: 1-54.

Van Wyhe 2009. Darwin. Andre Deutsch.

Van Wyhe 2012. Where did Darwin's finches come from? Evolutionary Review 3: 185-195. Text PDF A932

Vizcaíno, S.F., Fernicola, J.C. and Fariña, R.A., 2009. Young Darwin and the ecology of South American fossil mammals. Revista de la Asociación Geológica Argentina 64 (1): 160-169.

Winsor, Mary Pickard 2013 Darwin and taxonomy. In Ruse, Michael (ed.). The Cambridge encyclopedia of Darwin and evolutionary thought: 72-79. CUP.


1838-1843. The zoology of the voyage of H.M.S. Beagle. Edited and superintended by Charles Darwin. London: Colburn.

Part 1 Fossil Mammalia by R. Owen. By Darwin: Preface & Geological introduction. Text Image PDF F9.1
Original numbers issued: 1. Text Image 2. Text Image 3. Text Image 4. Text Image

Part 2 Mammalia by G. R. Waterhouse. By Darwin: Geographical introduction & A notice of their habits and ranges. Text Image PDF F9.2
Original numbers issued: 1. Text Image 2. Text Image 3. Text Image 4. Text Image

Part 3 Birds by J. Gould [& G. R. Gray]. Text Image PDF F9.3
Original numbers issued: 1. Text Image 2. Text Image 3. Text Image 4. Text Image 5. Text Image

Part 4 Fish by L. Jenyns. Text Image PDF F9.4 Introduction
Original numbers issued: 1. Text Image 2. Text Image 3. Text Image 4. Text Image

Part 5 Reptiles [& Amphibia] by T. Bell. Text Image PDF F9.5
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Edited by John van Wyhe


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